5.11: Interacting with Water - Biology

5.11: Interacting with Water - Biology

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We can get an idea of the hydrophilic, hydrophobic/hydroapathetic, and amphipathic nature of molecules through their behaviors when we try to dissolve them in water. In liquid water the H-bond-type electrostatic interactions between the molecules break and form rapidly.

To insert a molecule A, known as a solute, into this network you have to break some of the H-bond-type electrostatic interactions between the water molecules, known as the solvent. If the A molecules can make H-bond-type electrostatic interactions with water molecules, that is, if it is hydrophilic, then there is little net effect on the free energy of the system. Such a molecule is soluble in water. So what determines how soluble the solute is. As a first order estimate, each solute molecule will need to have at least one layer of water molecules around it, otherwise it will be forced to interact with other solute molecules. If the number of these interacting solute molecules is large enough, the solute will no longer be in solution. In some cases, aggregates of solute molecule can, because they are small enough, remain suspended in the solution. This is a situation known as a colloid. While a solution consists of individual solute molecules surrounded by solvent molecules, a colloid consists of aggregates of solute molecules in a solvent. We might predict that all other things being equal (a unrealistic assumption), the larger the solute molecule the lower its solubility. You might be able to generate a similar rule for the size of particles in a colloid.

Now we can turn to a conceptually trickier situation, the behavior of a hydrophobic solute molecule in water. Such a molecule cannot make H-bond-type electrostatic interactions with water, so when it is inserted into water the total number of H-bond-type electrostatic interactions in the system decreases - the energy of the system increases (remember, bond forming lowers potential energy). However, it turns out that much of this “enthalpy” change, conventionally indicated as ΔH, is compensated for by van der Waals interactions (that is, non-H-bond-type electrostatic interactions) between the molecules. Generally, the net enthalpic effect is minimal. Something else must be going on to explain the insolubility of such molecules.

Turning to entropy: In a liquid water molecules will typically be found in a state that maximizes the number of H-bond-type electrostatic interactions present. And because these interactions have a distinct, roughly tetragonal geometry, their presence constrains the possible orientations of molecules with respect to one another. This constraint is captured when water freezes; it is the basis for ice crystal formation, why the density of water increases before freezing, and why ice floats in liquid water164. In the absence of the hydrophobic solute molecule there are many many equivalent ways that liquid water molecules can interact to produce these geometrically specified orientations. But the presence of a solute molecule that cannot form H-bond-type electrostatic interactions restricts this number to a much smaller number of configurations that result in maximizing H-bond formation between water molecules. The end result is that the water molecules become arranged in a limited number of ways around each solute molecule; they are in a more ordered, that is, a more improbable state, than they would be in the absence of solute. The end result is that there will be a decrease in entropy (indicated as ΔS), themeasure of the probability of a state. ΔS will be negative compared to arrangement of water molecules in the absence of the solute.

How does this influence whether dissolving a molecule into water is thermodynamically favorable or unfavorable. It turns out that the interaction energy (ΔH) of placing most solutes into the solvent is near 0, so that it is the ΔS that makes the difference. Keeping in mind that ΔG = ΔH - TΔS, if ΔS is negative, then -T ΔS will be positive. The ΔG of a thermodynamically favorable reaction is, by definition, negative. This implies that the reaction:

[ ext{water} + ext{solute} ightleftharpoons ext{solution (water + solute)}]

will be thermodynamically unfavorable; the reaction will move to the left. That is, if we start with a solution, it will separate so that the solute is removed from the water. How does this happen? The solute molecules aggregate with one another. This reduces their effects on water, and so the ΔS for aggregation is positive. If the solute is oil, and we mix it into water, the oil will separate from the water, driven by the increase in entropy associated with minimizing solute-water interactions. This same basic process plays a critical influence on macromolecular structures.

Questions to answer & to ponder:

  • Given what you know about water, why is ice less dense than liquid water?
  • Make of model relating the solubility of a molecule with a hydrophilic surface to the volume of the molecule?
  • Use your model to predict the effect on solubility if your molecule with a hydrophilic surface had a hydrophobic interior.
  • Under what conditions might entropic effects influence the interactions between two solute molecules?


The porbeagle (Lamna nasus) is a species of mackerel shark in the family Lamnidae, distributed widely in the cold and temperate marine waters of the North Atlantic and Southern Hemisphere. In the North Pacific, its ecological equivalent is the closely related salmon shark (L. ditropis). It typically reaches 2.5 m (8.2 ft) in length and a weight of 135 kg (298 lb) North Atlantic sharks grow larger than Southern Hemisphere sharks and differ in coloration and aspects of life history. Gray above and white below, the porbeagle has a very stout midsection that tapers towards the long, pointed snout and the narrow base of the tail. It has large pectoral and first dorsal fins, tiny pelvic, second dorsal, and anal fins, and a crescent-shaped caudal fin. The most distinctive features of this species are its three-cusped teeth, the white blotch at the aft base of its first dorsal fin, and the two pairs of lateral keels on its tail.

Lamna philippii Perez Canto, 1886
Lamna punctata Storer, 1839
Lamna whitleyi Phillipps, 1935
Oxyrhina daekayi Gill, 1861
Selanonius walkeri Fleming, 1828
Squalus cornubicus Gmelin, 1789
Squalus cornubiensis Pennant, 1812
Squalus monensis Shaw, 1804
Squalus nasus Bonnaterre, 1788
Squalus pennanti Walbaum, 1792
Squalus selanonus Leach, 1818

The porbeagle is an opportunistic hunter that preys mainly on bony fishes and cephalopods throughout the water column, including the bottom. Most commonly found over food-rich banks on the outer continental shelf, it makes occasional forays both close to shore and into the open ocean to a depth of 1,360 m (4,460 ft). It also conducts long-distance seasonal migrations, generally shifting between shallower and deeper water. The porbeagle is fast and highly active, with physiological adaptations that enable it to maintain a higher body temperature than the surrounding water. It can be solitary or gregarious, and has been known to perform seemingly playful behavior. This shark is aplacental viviparous with oophagy, developing embryos being retained within the mother's uterus and subsisting on non-viable eggs. Females typically bear four pups every year.

Only a few shark attacks of uncertain provenance have been attributed to the porbeagle. It is well regarded as a game fish by recreational anglers. The meat and fins of the porbeagle are highly valued, which has led to a long history of intense human exploitation. However, this species cannot sustain heavy fishing pressure due to its low reproductive capacity. Direct commercial fishing for the porbeagle, principally by Norwegian longliners, led to stock collapses in the eastern North Atlantic in the 1950s, and the western North Atlantic in the 1960s. The porbeagle continues to be caught throughout its range, both intentionally and as bycatch, with varying degrees of monitoring and management. The International Union for Conservation of Nature (IUCN) has assessed the porbeagle as vulnerable worldwide, and as either endangered or critically endangered in different parts of its northern range.


The term geobiology was coined by Lourens Baas Becking in 1934. In his words, geobiology "is an attempt to describe the relationship between organisms and the Earth," for "the organism is part of the Earth and its lot is interwoven with that of the Earth." Baas Becking's definition of geobiology was born of a desire to unify environmental biology with laboratory biology. The way he practiced it aligns closely with modern environmental microbial ecology, though his definition remains applicable to all of geobiology. In his book, Geobiology, Bass Becking stated that he had no intention of inventing a new field of study. [4] Baas Becking's understanding of geobiology was heavily influenced by his predecessors, including Martinus Beyerinck, his teacher from the Dutch School of Microbiology. Others included Vladimir Vernadsky, who argued that life changes the surface environment of Earth in The Biosphere, his 1926 book, [5] and Sergei Vinogradsky, famous for discovering lithotrophic bacteria. [6]

The first laboratory officially dedicated to the study of geobiology was the Baas Becking Geobiological Laboratory in Australia, which opened its doors in 1965. [4] However, it took another 40 or so years for geobiology to become a firmly rooted scientific discipline, thanks in part to advances in geochemistry and genetics that enabled scientists to begin to synthesize the study of life and planet.

In the 1930s, Alfred Treibs discovered chlorophyll-like porphyrins in petroleum, confirming its biological origin, [7] thereby founding organic geochemistry and establishing the notion of biomarkers, a critical aspect of geobiology. But several decades passed before the tools were available to begin to search in earnest for chemical marks of life in the rocks. In the 1970s and '80s, scientists like Geoffrey Eglington and Roger Summons began to find lipid biomarkers in the rock record using equipment like GCMS. [8]

On the biology side of things, in 1977, Carl Woese and George Fox published a phylogeny of life on Earth, including a new domain - the Archaea. [9] And in the 1990s, genetics and genomics studies became possible, broadening the scope of investigation of the interaction of life and planet.

Today, geobiology has its own journals, such as Geobiology, established in 2003, [10] and Biogeosciences, established in 2004, [11] as well as recognition at major scientific conferences. It got its own Gordon Research Conference in 2011, [12] a number of geobiology textbooks have been published, [3] [13] and many universities around the world offer degree programs in geobiology (see External links).

Perhaps the most profound geobiological event is the introduction of oxygen into the atmosphere by photosynthetic bacteria. This oxygenation of Earth's primordial atmosphere (the so-called oxygen catastrophe or Great Oxygenation Event) and the oxygenation of the oceans altered surface biogeochemical cycles and the types of organisms that have been evolutionarily selected for.

A subsequent major change was the advent of multicellularity. The presence of oxygen allowed eukaryotes and, later, multicellular life to evolve.

More anthropocentric geobiologic events include the origin of animals and the establishment of terrestrial plant life, which affected continental erosion and nutrient cycling, and likely changed the types of rivers observed, allowing channelization of what were previously predominantly braided rivers.

More subtle geobiological events include the role of termites in overturning sediments, coral reefs in depositing calcium carbonate and breaking waves, sponges in absorbing dissolved marine silica, the role of dinosaurs in breaching river levees and promoting flooding, and the role of large mammal dung in distributing nutrients. [15] [16]

Geobiology is founded upon a few core concepts that unite the study of Earth and life. While there are many aspects of studying past and present interactions between life and Earth that are unclear, several important ideas and concepts provide a basis of knowledge in geobiology that serve as a platform for posing researchable questions, including the evolution of life and planet and the co-evolution of the two, genetics - from both a historical and functional standpoint, the metabolic diversity of all life, the sedimentological preservation of past life, and the origin of life.

Co-evolution of life and Earth Edit

A core concept in geobiology is that life changes over time through evolution. The theory of evolution postulates that unique populations of organisms or species arose from genetic modifications in the ancestral population which were passed down by drift and natural selection. [17]

Along with standard biological evolution, life and planet co-evolve. Since the best adaptations are those that suit the ecological niche that the organism lives in, the physical and chemical characteristics of the environment drive the evolution of life by natural selection, but the opposite can also be true: with every advent of evolution, the environment changes.

A classic example of co-evolution is the evolution of oxygen-producing photosynthetic cyanobacteria which oxygenated Earth's Archean atmosphere. The ancestors of cyanobacteria began using water as an electron source to harness the energy of the sun and expelling oxygen before or during the early Paleoproterozoic. During this time, around 2.4 to 2.1 billion years ago, [18] geologic data suggests that atmospheric oxygen began to rise in what is termed the Great Oxygenation Event (GOE). [19] [20] It is unclear for how long cyanobacteria had been doing oxygenic photosynthesis before the GOE. Some evidence suggests there were geochemical "buffers" or sinks suppressing the rise of oxygen such as volcanism [21] though cyanobacteria may have been around producing it before the GOE. [22] Other evidence indicates that the rise of oxygenic photosynthesis was coincident with the GOE. [23]

The presence of oxygen on Earth from its first production by cyanobacteria to the GOE and through today has drastically impacted the course of evolution of life and planet. [19] It may have triggered the formation of oxidized minerals [24] and the disappearance of oxidizable minerals like pyrite from ancient stream beds. [25] The presence of banded-iron formations (BIFs) have been interpreted as a clue for the rise of oxygen since small amounts of oxygen could have reacted with reduced ferrous iron (Fe(II)) in the oceans, resulting in the deposition of sediments containing Fe(III) oxide in places like Western Australia. [26] However, any oxidizing environment, including that provided by microbes such as the iron-oxidizing photoautotroph Rhodopseudomonas palustris, [27] can trigger iron oxide formation and thus BIF deposition. [28] [29] [30] Other mechanisms include oxidation by UV light. [31] Indeed, BIFs occur across large swaths of Earth's history and may not correlate with only one event. [30]

Other changes correlated with the rise of oxygen include the appearance of rust-red ancient paleosols, [19] different isotope fractionation of elements such as sulfur, [32] and global glaciations and Snowball Earth events, [33] perhaps caused by the oxidation of methane by oxygen, not to mention an overhaul of the types of organisms and metabolisms on Earth. Whereas organisms prior to the rise of oxygen were likely poisoned by oxygen gas as many anaerobes are today, [34] those that evolved ways to harness the electron-accepting and energy-giving power of oxygen were poised to thrive and colonize the aerobic environment.

The Earth has changed Edit

Earth has not remained the same since its planetary formation 4.5 billion years ago. [35] [36] Continents have formed, broken up, and collided, offering new opportunities for and barriers to the dispersal of life. The redox state of the atmosphere and the oceans has changed, as indicated by isotope data. Fluctuating quantities of inorganic compounds such as carbon dioxide, nitrogen, methane, and oxygen have been driven by life evolving new biological metabolisms to make these chemicals and have driven the evolution of new metabolisms to use those chemicals. Earth acquired a magnetic field about 3.4 Ga [37] that has undergone a series of geomagnetic reversals on the order of millions of years. [38] The surface temperature is in constant fluctuation, falling in glaciations and Snowball Earth events due to ice–albedo feedback, [39] rising and melting due to volcanic outgassing, and stabilizing due to silicate weathering feedback. [40]

And the Earth is not the only one that changed - the luminosity of the sun has increased over time. Because rocks record a history of relatively constant temperatures since Earth's beginnings, there must have been more greenhouse gasses to keep the temperatures up in the Archean when the sun was younger and fainter. [41] All these major differences in the environment of the Earth placed very different constraints on the evolution of life throughout our planet's history. Moreover, more subtle changes in the habitat of life are always occurring, shaping the organisms and traces that we observe today and in the rock record.

Genes encode geobiological function and history Edit

The genetic code is key to observing the history of evolution and understanding the capabilities of organisms. Genes are the basic unit of inheritance and function and, as such, they are the basic unit of evolution and the means behind metabolism. [42]

Phylogeny predicts evolutionary history Edit

Phylogeny takes genetic sequences from living organisms and compares them to each other to reveal evolutionary relationships, much like a family tree reveals how individuals are connected to their distant cousins. [43] It allows us to decipher modern relationships and infer how evolution happened in the past.

Phylogeny can give some sense of history when combined with a little bit more information. Each difference in the DNA indicates divergence between one species and another. [43] This divergence, whether via drift or natural selection, is representative of some lapse of time. [43] Comparing DNA sequences alone gives a record of the history of evolution with an arbitrary measure of phylogenetic distance “dating” that last common ancestor. However, if information about the rate of genetic mutation is available or geologic markers are present to calibrate evolutionary divergence (i.e. fossils), we have a timeline of evolution. [44] From there, with an idea about other contemporaneous changes in life and environment, we can begin to speculate why certain evolutionary paths might have been selected for. [45]

Genes encode metabolism Edit

Molecular biology allows scientists to understand a gene's function using microbial culturing and mutagenesis. Searching for similar genes in other organisms and in metagenomic and metatranscriptomic data allows us to understand what processes could be relevant and important in a given ecosystem, providing insight into the biogeochemical cycles in that environment.

For example, an intriguing problem in geobiology is the role of organisms in the global cycling of methane. Genetics has revealed that the methane monooxygenase gene (pmo) is used for oxidizing methane and is present in all aerobic methane-oxidizers, or methanotrophs. [46] The presence of DNA sequences of the pmo gene in the environment can be used as a proxy for methanotrophy. [47] [48] A more generalizable tool is the 16S ribosomal RNA gene, which is found in bacteria and archaea. This gene evolves very slowly over time and is not usually horizontally transferred, and so it is often used to distinguish different taxonomic units of organisms in the environment. [9] [49] In this way, genes are clues to organismal metabolism and identity. Genetics enables us to ask 'who is there?' and 'what are they doing?' This approach is called metagenomics. [49]

Metabolic diversity influences the environment Edit

Life harnesses chemical reactions to generate energy, perform biosynthesis, and eliminate waste. [52] Different organisms use very different metabolic approaches to meet these basic needs. [53] While animals such as ourselves are limited to aerobic respiration, other organisms can "breathe" sulfate (SO42-), nitrate (NO3-), ferric iron (Fe(III)), and uranium (U(VI)), or live off energy from fermentation. [53] Some organisms, like plants, are autotrophs, meaning that they can fix carbon dioxide for biosynthesis. Plants are photoautotrophs, in that they use the energy of light to fix carbon. Microorganisms employ oxygenic and anoxygenic photoautotrophy, as well as chemoautotrophy. Microbial communities can coordinate in syntrophic metabolisms to shift reaction kinetics in their favor. Many organisms can perform multiple metabolisms to achieve the same end goal these are called mixotrophs. [53]

Biotic metabolism is directly tied to the global cycling of elements and compounds on Earth. The geochemical environment fuels life, which then produces different molecules that go into the external environment. (This is directly relevant to biogeochemistry.) In addition, biochemical reactions are catalyzed by enzymes which sometimes prefer one isotope over others. For example, oxygenic photosynthesis is catalyzed by RuBisCO, which prefers carbon-12 over carbon-13, resulting in carbon isotope fractionation in the rock record. [54]

Sedimentary rocks tell a story Edit

Sedimentary rocks preserve remnants of the history of life on Earth in the form of fossils, biomarkers, isotopes, and other traces. The rock record is far from perfect, and the preservation of biosignatures is a rare occurrence. Understanding what factors determine the extent of preservation and the meaning behind what is preserved are important components to detangling the ancient history of the co-evolution of life and Earth. [8] The sedimentary record allows scientists to observe changes in life and Earth in composition over time and sometimes even date major transitions, like extinction events.

Some classic examples of geobiology in the sedimentary record include stromatolites and banded-iron formations. The role of life in the origin of both of these is a heavily debated topic. [19]

Life is fundamentally chemistry Edit

The first life arose from abiotic chemical reactions. When this happened, how it happened, and even what planet it happened on are uncertain. However, life follows the rules of and arose from lifeless chemistry and physics. It is constrained by principles such as thermodynamics. This is an important concept in the field because it is represents the epitome of the interconnectedness, if not sameness, of life and Earth. [55]

While often delegated to the field of astrobiology, attempts to understand how and when life arose are relevant to geobiology as well. [56] The first major strides towards understanding the “how” came with the Miller-Urey experiment, when amino acids formed out of a simulated “primordial soup”. Another theory is that life originated in a system much like the hydrothermal vents at mid-oceanic spreading centers. In the Fischer-Tropsch synthesis, a variety of hydrocarbons form under vent-like conditions. Other ideas include the “RNA World” hypothesis, which postulates that the first biologic molecule was RNA and the idea that life originated elsewhere in the solar system and was brought to Earth, perhaps via a meteorite. [55]

While geobiology is a diverse and varied field, encompassing ideas and techniques from a wide range of disciplines, there are a number of important methods that are key to the study of the interaction of life and Earth that are highlighted here. [3]

  1. Laboratory culturing of microbes is used to characterize the metabolism and lifestyle of organisms of interest.
  2. Gene sequencing allows scientists to study the relationships between extant organisms using phylogenetics.
  3. Experimental genetic manipulation or mutagenesis is used to determine the function of genes in living organisms.
  4. Microscopy is used to visualize the microbial world. Microscope work ranges from environmental observation to quantitative studies with DNA probes to high-definition visualization of the microbe-mineral interface by electron microscope (EM).
  5. Isotope tracers can be used to track biochemical reactions to understand microbial metabolism.
  6. Isotope natural abundance in rocks can be measured to look for isotopic fractionation that is consistent with biologic origin.
  7. Detailed environmental characterization is important to understanding what about a habitat might be driving life's evolution and, in turn, how life might be changing that niche. It includes and is not limited to, temperature, light, pH, salinity, concentration of specific molecules like oxygen, and the biologic community.
  8. Sedimentology and stratigraphy are used to read the rocks. The rock record stores a history of geobiologic processes in sediments which can be unearthed through an understanding of deposition, sedimentation, compaction, diagenesis, and deformation.
  9. The search for and study of fossils, while often delegated to the separate field of paleontology, is important in geobiology, though the scale of fossils is typically smaller (micropaleontology).
  10. The biochemical analysis of biomarkers, which are fossilized or modern molecules that are indicative of the presence of a certain group of organisms or metabolism, is used to answer the evidence for life and metabolic diversity questions. [8]
  11. Paleomagnetics is the study of the planet's ancient magnetic field. It is significant to understanding magnetofossils, biomineralization, and global ecosystem changes.

As its name suggests, geobiology is closely related to many other fields of study, and does not have clearly defined boundaries or perfect agreement on what exactly they comprise. Some practitioners take a very broad view of its boundaries, encompassing many older, more established fields such as biogeochemistry, paleontology, and microbial ecology. Others take a more narrow view, assigning it to emerging research that falls between these existing fields, such as with geomicrobiology. The following list includes both those that are clearly a part of geobiology, e.g. geomicrobiology, as well as those that share scientific interests but have not historically been considered a sub-discipline of geobiology, e.g. paleontology.

Astrobiology Edit

Astrobiology is an interdisciplinary field that uses a combination of geobiological and planetary science data to establish a context for the search for life on other planets. The origin of life from non-living chemistry and geology, or abiogenesis, is a major topic in astrobiology. Even though it is fundamentally an earth-bound concern, and therefore of great geobiological interest, getting at the origin of life necessitates considering what life requires, what, if anything, is special about Earth, what might have changed to allow life to blossom, what constitutes evidence for life, and even what constitutes life itself. These are the same questions that scientists might ask when searching for alien life. In addition, astrobiologists research the possibility of life based on other metabolisms and elements, the survivability of Earth's organisms on other planets or spacecraft, planetary and solar system evolution, and space geochemistry. [57]

Biogeochemistry Edit

Biogeochemistry is a systems science that synthesizes the study of biological, geological, and chemical processes to understand the reactions and composition of the natural environment. It is concerned primarily with global elemental cycles, such as that of nitrogen and carbon. The father of biogeochemistry was James Lovelock, whose “Gaia hypothesis” proposed that Earth's biological, chemical, and geologic systems interact to stabilize the conditions on Earth that support life. [58]

Geobiochemistry Edit

Geobiochemistry is similar to biogeochemistry, but differs by placing emphasis on the effects of geology on the development of life's biochemical processes, as distinct from the role of life on Earth's cycles. Its primary goal is to link biological changes, encompassing evolutionary modifications of genes and changes in the expression of genes and proteins, to changes in the temperature, pressure, and composition of geochemical processes to understand when and how metabolism evolved. Geobiochemistry is founded on the notion that life is a planetary response because metabolic catalysis enables the release of energy trapped by a cooling planet. [59]

Environmental microbiology Edit

Microbiology is a broad scientific discipline pertaining to the study of that life which is best viewed under a microscope. It encompasses several fields that are of direct relevance to geobiology, and the tools of microbiology all pertain to geobiology. Environmental microbiology is especially entangled in geobiology since it seeks an understanding of the actual organisms and processes that are relevant in nature, as opposed to the traditional lab-based approach to microbiology. Microbial ecology is similar, but tend to focus more on lab studies and the relationships between organisms within a community, as well as within the ecosystem of their chemical and geological physical environment. Both rely on techniques such as sample collection from diverse environments, metagenomics, DNA sequencing, and statistics.

Geomicrobiology and microbial geochemistry Edit

Geomicrobiology traditionally studies the interactions between microbes and minerals. While it is generally reliant on the tools of microbiology, microbial geochemistry uses geological and chemical methods to approach the same topic from the perspective of the rocks. Geomicrobiology and microbial geochemistry (GMG) is a relatively new interdisciplinary field that more broadly takes on the relationship between microbes, Earth, and environmental systems. Billed as a subset of both geobiology and geochemistry, GMG seeks to understand elemental biogeochemical cycles and the evolution of life on Earth. Specifically, it asks questions about where microbes live, their local and global abundance, their structural and functional biochemistry, how they have evolved, biomineralization, and their preservation potential and presence in the rock record. In many ways, GMG appears to be equivalent to geobiology, but differs in scope: geobiology focuses on the role of all life, while GMG is strictly microbial. Regardless, it is these tiniest creatures that dominated to history of life integrated over time and seem to have had the most far-reaching effects. [60]

Molecular geomicrobiology Edit

Molecular geomicrobiology takes a mechanistic approach to understanding biological processes that are geologically relevant. It can be at the level of DNA, protein, lipids, or any metabolite. One example of Molecular geomicrobiology research is studying how recently created lava fields are colonized by microbes. The University of Helskinki is currently conducting research to determine what specific microbial traits are necessary for successful initial colonization, and how waves of microbial succession can transform the volcanic rock into fertile soil. [61]

Organic geochemistry Edit

Organic geochemistry is the study of organic molecules that appear in the fossil record in sedimentary rocks. Research in this field concerns molecular fossils that are often lipid biomarkers. Molecules like sterols and hopanoids, membrane lipids found in eukaryotes and bacteria, respectively, can be preserved in the rock record on billion-year timescales. Following the death of the organism they came from and sedimentation, they undergo a process called diagenesis whereby many of the specific functional groups from the lipids are lost, but the hydrocarbon skeleton remains intact. These fossilized lipids are called steranes and hopanes, respectively. [62] There are also other types of molecular fossils, like porphyrins, the discovery of which in petroleum by Alfred E. Treibs actually led to the invention of the field. [8] Other aspects of geochemistry that are also pertinent to geobiology include isotope geochemistry, in which scientists search for isotope fractionation in the rock record, and the chemical analysis of biominerals, such as magnetite or microbially-precipitated gold.

Paleontology Edit

Perhaps the oldest of the bunch, paleontology is the study of fossils. It involves the discovery, excavation, dating, and paleoecological understanding of any type of fossil, microbial or dinosaur, trace or body fossil. Micropaleontology is particularly relevant to geobiology. Putative bacterial microfossils and ancient stromatolites are used as evidence for the rise of metabolisms such as oxygenic photosynthesis. [63] The search for molecular fossils, such as lipid biomarkers like steranes and hopanes, has also played an important role in geobiology and organic geochemistry. [8] Relevant sub-disciples include paleoecology and paleobiogeoraphy.

Biogeography Edit

Biogeography is the study of the geographic distribution of life through time. It can look at the present distribution of organisms across continents or between microniches, or the distribution of organisms through time, or in the past, which is called paleobiogeography.

Evolutionary biology Edit

Evolutionary biology is the study of the evolutionary processes that have shaped the diversity of life on Earth. It incorporates genetics, ecology, biogeography, and paleontology to analyze topics including natural selection, variance, adaptation, divergence, genetic drift, and speciation.

Ecohydrology Edit

Ecohydrology is an interdisciplinary field studying the interactions between water and ecosystems. Stable isotopes of water are sometimes used as tracers of water sources and flow paths between the physical environment and the biosphere. [64] [65]


The hydrologic cycle describes the continuous movement of water above, on, and below the surface of the Earth. The water on the Earth's surface--surface water--occurs as streams, lakes, and wetlands, as well as bays and oceans. Surface water also includes the solid forms of water-- snow and ice. The water below the surface of the Earth primarily is ground water, but it also includes soil water.

The hydrologic cycle commonly is portrayed by a very simplified diagram that shows only major transfers of water between continents and oceans, as in Figure 1. However, for understanding hydrologic processes and managing water resources, the hydrologic cycle needs to be viewed at a wide range of scales and as having a great deal of variability in time and space. Precipitation, which is the source of virtually all freshwater in the hydrologic cycle, falls nearly everywhere, but its distribution is highly variable. Similarly, evaporation and transpiration return water to the atmosphere nearly everywhere, but evaporation and transpiration rates vary considerably according to climatic conditions. As a result, much of the precipitation never reaches the oceans as surface and subsurface runoff before the water is returned to the atmosphere. The relative magnitudes of the individual components of the hydrologic cycle, such as evapotranspiration, may differ significantly even at small scales, as between an agricultural field and a nearby woodland.

Figure 1. Ground water is the second smallest of the four main pools of water on Earth, and river flow to the oceans is one of the smallest fluxes, yet ground water and surface water are the components of the hydrologic system that humans use most. (Modified from Schelesinger, W.H., 1991, Biogeochemistry-An analysis of global change: Academic Press, San Diego, California.) (Used with permission.)

To present the concepts and many facets of the interaction of ground water and surface water in a unified way, a conceptual landscape is used (Figure 2). The conceptual landscape shows in a very general and simplified way the interaction of ground water with all types of surface water, such as streams, lakes, and wetlands, in many different terrains from the mountains to the oceans. The intent of Figure 2 is to emphasize that ground water and surface water interact at many places throughout the landscape.

Figure 2. Ground water and surface water interact throughout all landscapes from the mountains to the oceans, as depicted in this diagram of a conceptual landscape. M, mountainous K, karst G, glacial R, riverine (small) V, riverine (large) C, coastal.

Haze over Appalachian Mountains in North Carolina. (Photograph courtesy of North Carolina Department of Travel and Tourism.)

Movement of water in the atmosphere and on the land surface is relatively easy to visualize, but the movement of ground water is not. Concepts related to ground water and the movement of ground water are introduced in Box A. As illustrated in Figure 3, ground water moves along flow paths of varying lengths from areas of recharge to areas of discharge. The generalized flow paths in Figure 3 start at the water table, continue through the ground-water system, and terminate at the stream or at the pumped well. The source of water to the water table (ground-water recharge) is infiltration of precipitation through the unsaturated zone. In the uppermost, unconfined aquifer, flow paths near the stream can be tens to hundreds of feet in length and have corresponding traveltimes of days to a few years. The longest and deepest flow paths in Figure 3 may be thousands of feet to tens of miles in length, and traveltimes may range from decades to millennia. In general, shallow ground water is more susceptible to contamination from human sources and activities because of its close proximity to the land surface. Therefore, shallow, local patterns of ground-water flow near surface water are emphasized in this Circular.

(Box A)

Ground water moves along flow paths of varying lengths in transmitting water from areas of recharge to areas of discharge"

Small-scale geologic features in beds of surface-water bodies affect seepage patterns at scales too small to be shown in Figure 3. For example, the size, shape, and orientation of the sediment grains in surface-water beds affect seepage patterns. If a surface-water bed consists of one sediment type, such as sand, inflow seepage is greatest at the shoreline, and it decreases in a nonlinear pattern away from the shoreline (Figure 4). Geologic units having different permeabilities also affect seepage distribution in surface-water beds. For example, a highly permeable sand layer within a surface-water bed consisting largely of silt will transmit water preferentially into the surface water as a spring (Figure 5).

Subaqueous spring in Nebraska. (Photograph by Charels Flowerday.)

Figure 3. Ground-water flow paths vary greatly in length, depth, and traveltime from points of recharge to points of discharge in the ground-water system.

Figure 4. Ground-water seepage into surface water usually is greatest near shore. In flow diagrams such as that shown here, the quantity of discharge is equal between any two flow lines therefore, the closer flow lines indicate greater discharge per unit of bottom area.

Figure 5. Subaqueous springs can result from preferred paths of ground-water flow through highly permeable sediments.

Changing meteorological conditions also strongly affect seepage patterns in surface-water beds, especially near the shoreline. The water table commonly intersects land surface at the shoreline, resulting in no unsaturated zone at this point. Infiltrating precipitation passes rapidly through a thin unsaturated zone adjacent to the shoreline, which causes water-table mounds to form quickly adjacent to the surface water (Figure 6). This process, termed focused recharge, can result in increased ground-water inflow to surface-water bodies, or it can cause inflow to surface-water bodies that normally have seepage to ground water. Each precipitation event has the potential to cause this highly transient flow condition near shorelines as well as at depressions in uplands (Figure 6).

Figure 6. Ground-water recharge commonly is focused initially where the unsaturated zone is relatively thin at the edges of surface-water bodies and beneath depressions in the land surface.

Transpiration by nearshore plants has the opposite effect of focused recharge. Again, because the water table is near land surface at edges of surface-water bodies, plant roots can penetrate into the saturated zone, allowing the plants to transpire water directly from the ground-water system (Figure 7). Transpiration of ground water commonly results in a drawdown of the water table much like the effect of a pumped well. This highly variable daily and seasonal transpiration of ground water may significantly reduce ground-water discharge to a surface-water body or even cause movement of surface water into the subsurface. In many places it is possible to measure diurnal changes in the direction of flow during seasons of active plant growth that is, ground water moves into the surface water during the night, and surface water moves into shallow ground water during the day.

Figure 7. Where the depth to the water table is small adjacent to surface-water bodies, transpiration directly from ground water can cause cones of depression similar to those caused by pumping wells. This sometimes draws water directly from the surface water into the subsurface.

These periodic changes in the direction of flow also take place on longer time scales: focused recharge from precipitation predominates during wet periods and drawdown by transpiration predominates during dry periods. As a result, the two processes, together with the geologic controls on seepage distribution, can cause flow conditions at the edges of surface-water bodies to be extremely variable. These "edge effects" probably affect small surface-water bodies more than large surface-water bodies because the ratio of edge length to total volume is greater for small water bodies than it is for large ones.

Phreatophytes along the Rio Grande in Texas. (Photograph by Michael Collier.)

Interaction of Ground Water and Streams

Streams interact with ground water in all types of landscapes (see Box B). The interaction takes place in three basic ways: streams gain water from inflow of ground water through the streambed (gaining stream, Figure 8A), they lose water to ground water by outflow through the streambed (losing stream, Figure 9A), or they do both, gaining in some reaches and losing in other reaches. For ground water to discharge into a stream channel, the altitude of the water table in the vicinity of the stream must be higher than the altitude of the stream-water surface. Conversely, for surface water to seep to ground water, the altitude of the water table in the vicinity of the stream must be lower than the altitude of the stream-water surface. Contours of water-table elevation indicate gaining streams by pointing in an upstream direction (Figure 8B), and they indicate losing streams by pointing in a downstream direction (Figure 9B) in the immediate vicinity of the stream.

(Box B)

Figure 8. Gaining streams receive water from the ground-water system (A). This can be determined from water-table contour maps because the contour lines point in the upstream direction where they cross the stream (B).

Figure 9. Losing streams lose water to the ground-water system (A). This can be determined from water-table contour maps because the contour lines point in the downstream direction where they cross the stream (B).

Losing streams can be connected to the ground-water system by a continuous saturated zone (Figure 9A) or can be disconnected from the ground-water system by an unsaturated zone. Where the stream is disconnected from the ground-water system by an unsaturated zone, the water table may have a discernible mound below the stream (Figure 10) if the rate of recharge through the streambed and unsaturated zone is greater than the rate of lateral ground-water flow away from the water-table mound. An important feature of streams that are disconnected from ground water is that pumping of shallow ground water near the stream does not affect the flow of the stream near the pumped wells.

Figure 10. Disconnected streams are separated from the ground-water system by an unsaturated zone.

In some environments, streamflow gain or loss can persist that is, a stream might always gain water from ground water, or it might always lose water to ground water. However, in other environments, flow direction can vary a great deal along a stream some reaches receive ground water, and other reaches lose water to ground water. Furthermore, flow direction can change in very short timeframes as a result of individual storms causing focused recharge near the streambank, temporary flood peaks moving down the channel, or transpiration of ground water by streamside vegetation.

A type of interaction between ground water and streams that takes place in nearly all streams at one time or another is a rapid rise in stream stage that causes water to move from the stream into the streambanks. This process, termed bank storage (Figures 11 and 12B), usually is caused by storm precipitation, rapid snowmelt, or release of water from a reservoir upstream. As long as the rise in stage does not overtop the streambanks, most of the volume of stream water that enters the streambanks returns to the stream within a few days or weeks. The loss of stream water to bank storage and return of this water to the stream in a period of days or weeks tends to reduce flood peaks and later supplement stream flows. If the rise in stream stage is sufficient to overtop the banks and flood large areas of the land surface, widespread recharge to the water table can take place throughout the flooded area (Figure 12C). In this case, the time it takes for the recharged floodwater to return to the stream by ground-water flow may be weeks, months, or years because the lengths of the ground-water flow paths are much longer than those resulting from local bank storage. Depending on the frequency, magnitude, and intensity of storms and on the related magnitude of increases in stream stage, some streams and adjacent shallow aquifers may be in a continuous readjustment from interactions related to bank storage and overbank flooding.

Figure 11. If stream levels rise higher than adjacent ground-water levels, stream water moves into the streambanks as bank storage.

Streams interact with ground water in three basic ways: streams gain water from inflow of ground water through the streambed (gaining stream), they lose water to ground water by outflow through the streambed (losing stream), or they do both, gaining in some reaches and losing in other reaches"

Figure 12. If stream levels rise higher than their streambanks (C), the floodwaters recharge ground water throughout the flooded areas.

In addition to bank storage, other processes may affect the local exchange of water between streams and adjacent shallow aquifers. Changes in streamflow between gaining and losing conditions can also be caused by pumping ground water near streams (see Box C). Pumping can intercept ground water that would otherwise have discharged to a gaining stream, or at higher pumping rates it can induce flow from the stream to the aquifer.

(Box C)

Flooding at the confluence of the Missouri and Mississippi Rivers. (Photograph by Robert Meade.)

Where streamflow is generated in head-waters areas, the changes in streamflow between gaining and losing conditions may be particularly variable (Figure 13). The headwaters segment of streams can be completely dry except during storm events or during certain seasons of the year when snowmelt or precipitation is sufficient to maintain continuous flow for days or weeks. During these times, the stream will lose water to the unsaturated zone beneath its bed. However, as the water table rises through recharge in the headwaters area, the losing reach may become a gaining reach as the water table rises above the level of the stream. Under these conditions, the point where ground water first contributes to the stream gradually moves upstream.

Figure 13. The location where perennial streamflow begins in a channel can vary depending on the distribution of recharge in headwaters areas. Following dry periods (A), the start of streamflow will move up-channel during wet periods as the ground-water system becomes more saturated (B).

Some gaining streams have reaches that lose water to the aquifer under normal conditions of streamflow. The direction of seepage through the bed of these streams commonly is related to abrupt changes in the slope of the streambed (Figure 14A) or to meanders in the stream channel (Figure 14B). For example, a losing stream reach usually is located at the downstream end of pools in pool and riffle streams (Figure 14A), or upstream from channel bends in meandering streams (Figure 14B). The subsurface zone where stream water flows through short segments of its adjacent bed and banks is referred to as the hyporheic zone. The size and geometry of hyporheic zones surrounding streams vary greatly in time and space. Because of mixing between ground water and surface water in the hyporheic zone, the chemical and biological character of the hyporheic zone may differ markedly from adjacent surface water and ground water.

Figure 14. Surface-water exchange with ground water in the hyporheic zone is associated with abrupt changes in streambed slope (A) and with stream meanders (B).

Pool and riffle stream in Colorado. (Photograph by Robert Broshears.)

Ground-water systems that discharge to streams can underlie extensive areas of the land surface (Figure 15). As a result, environmental conditions at the interface between ground water and surface water reflect changes in the broader landscape. For example, the types and numbers of organisms in a given reach of streambed result, in part, from interactions between water in the hyporheic zone and ground water from distant sources.

Figure 15. Streambeds and banks are unique environments because they are where ground water that drains much of the subsurface of landscapes interacts with surface water that drains much of the surface of landscapes.


Lakes interact with ground water in three basic ways: some receive ground-water inflow throughout their entire bed some have seepage loss to ground water throughout their entire bed but perhaps most lakes receive ground-water inflow through part of their bed and have seepage loss to ground water through other parts (Figure 16). Although these basic interactions are the same for lakes as they are for streams, the interactions differ in several ways.

Figure 16. Lakes can receive ground-water inflow (A), lose water as seepage to ground water (B), or both (C).

The water level of natural lakes, that is, those not controlled by dams, generally does not change as rapidly as the water level of streams therefore, bank storage is of lesser importance in lakes than it is in streams. Evaporation generally has a greater effect on lake levels than on stream levels because the surface area of lakes is generally larger and less shaded than many reaches of streams, and because lake water is not replenished as readily as a reach of a stream. Lakes can be present in many different parts of the landscape and can have complex ground-water flow systems associated with them. This is especially true for lakes in glacial and dune terrain, as is discussed in a later section of this Circular. Furthermore, lake sediments commonly have greater volumes of organic deposits than streams. These poorly permeable organic deposits can affect the distribution of seepage and biogeochemical exchanges of water and solutes more in lakes than in streams.

Lake country in northern Wisconsin. (Photograph by David Krabbenhoft.)

Reservoirs are human-made lakes that are designed primarily to control the flow and distribution of surface water. Most reservoirs are constructed in stream valleys therefore, they have some characteristics both of streams and lakes. Like streams, reservoirs can have widely fluctuating levels, bank storage can be significant, and they commonly have a continuous flushing of water through them. Like lakes, reservoirs can have significant loss of water by evaporation, significant cycling of chemical and biological materials within their waters, and extensive biogeochemical exchanges of solutes with organic sediments.

" Lakes and wetlands can receive ground-water inflow throughout their entire bed, have outflow throughout their entire bed, or have both inflow and outflow at different localities"


Wetlands are present in climates and landscapes that cause ground water to discharge to land surface or that prevent rapid drainage of water from the land surface. Similar to streams and lakes, wetlands can receive ground-water inflow, recharge ground water, or do both. Those wetlands that occupy depressions in the land surface have interactions with ground water similar to lakes and streams. Unlike streams and lakes, however, wetlands do not always occupy low points and depressions in the landscape (Figure 17A) they also can be present on slopes (such as fens) or even on drainage divides (such as some types of bogs). Fens are wetlands that commonly receive ground-water discharge (Figure 17B) therefore, they receive a continuous supply of chemical constituents dissolved in the ground water. Bogs are wetlands that occupy uplands (Figure 17D) or extensive flat areas, and they receive much of their water and chemical constituents from precipitation. The distribution of major wetland areas in the United States is shown in Figure 18.

Upland bog Labrador, Canada. (Photograph by Lehn Franke.)

In areas of steep land slopes, the water table sometimes intersects the land surface, resulting in ground-water discharge directly to the land surface. The constant source of water at these seepage faces (Figure 17B) permits the growth of wetland plants. A constant source of ground water to wetland plants is also provided to parts of the landscape that are downgradient from breaks in slope of the water table (Figure 17B), and where subsurface discontinuities in geologic units cause upward movement of ground water (Figure 17A). Many wetlands are present along streams, especially slow-moving streams. Although these riverine wetlands (Figure 17C) commonly receive ground-water discharge, they are dependent primarily on the stream for their water supply.

Figure 17. The source of water to wetlands can be from ground-water discharge where the land surface is underlain by complex ground-water flow fields (A), from ground-water discharge at seepage faces and at breaks in slope of the water table (B), from streams (C), and from precipitation in cases where wetlands have no stream inflow and ground-water gradients slope away from the wetland (D).

Figure 18. Wetlands are present throughout the Nation, but they cover the largest areas in the glacial terrain of the north-central United States, coastal terrain along the Atlantic and gulf coasts, and riverine terrain in the lower Mississippi River Valley.

Wetlands in riverine and coastal areas have especially complex hydrological interactions because they are subject to periodic water-level changes. Some wetlands in coastal areas are affected by very predictable tidal cycles. Other coastal wetlands and riverine wetlands are more affected by seasonal water-level changes and by flooding. The combined effects of precipitation, evapotranspiration, and interaction with surface water and ground water result in a pattern of water depths in wetlands that is distinctive.

Hydroperiod is a term commonly used in wetland science that refers to the amplitude and frequency of water-level fluctuations. Hydroperiod affects all wetland characteristics, including the type of vegetation, nutrient cycling, and the types of invertebrates, fish, and bird species present.

Seepage face in Zion National Park, Utah. (Photograph by Robert Shedlock.)

A major difference between lakes and wetlands, with respect to their interaction with ground water, is the ease with which water moves through their beds. Lakes commonly are shallow around their perimeter where waves can remove fine-grained sediments, permitting the surface water and ground water to interact freely. In wetlands, on the other hand, if fine-grained and highly decomposed organic sediments are present near the wetland edge, the transfer of water and solutes between ground water and surface water is likely to be much slower.

Another difference in the interaction between ground water and surface water in wetlands compared to lakes is determined by rooted vegetation in wetlands. The fibrous root mat in wetland soils is highly conductive to water flow therefore, water uptake by roots of emergent plants results in significant interchange between surface water and pore water of wetland sediments. The water exchanges in this upper soil zone even if exchange between surface water and ground water is restricted at the base of the wetland sediments.

Chemical Interactions of Ground Water and Surface Water


Two of the fundamental controls on water chemistry in drainage basins are the type of geologic materials that are present and the length of time that water is in contact with those materials. Chemical reactions that affect the biological and geochemical characteristics of a basin include (1) acid-base reactions, (2) precipitation and dissolution of minerals, (3) sorption and ion exchange, (4) oxidation-reduction reactions, (5) biodegradation, and (6) dissolution and exsolution of gases (see Box D). When water first infiltrates the land surface, microorganisms in the soil have a significant effect on the evolution of water chemistry. Organic matter in soils is degraded by microbes, producing high concentrations of dissolved carbon dioxide (CO 2 ). This process lowers the pH by increasing the carbonic acid (H 2 CO 3 ) concentration in the soil water. The production of carbonic acid starts a number of mineral-weathering reactions, which result in bicarbonate (HCO 3 - ) commonly being the most abundant anion in the water. Where contact times between water and minerals in shallow ground-water flow paths are short, the dissolved-solids concentration in the water generally is low. In such settings, limited chemical changes take place before ground water is discharged to surface water.

(Box D)

" Two of the fundamental controls on water chemistry in drainage basins are the type of geologic materials that are present and the length of time that water is in contact with those materials"

In deeper ground-water flow systems, the contact time between water and minerals is much longer than it is in shallow flow systems. As a result, the initial importance of reactions relating to microbes in the soil zone may be superseded over time by chemical reactions between minerals and water (geochemical weathering). As weathering progresses, the concentration of dissolved solids increases. Depending on the chemical composition of the minerals that are weathered, the relative abundance of the major inorganic chemicals dissolved in the water changes (see Box E).

(Box E)

Surface water in streams, lakes, and wetlands can repeatedly interchange with nearby ground water. Thus, the length of time water is in contact with mineral surfaces in its drainage basin can continue after the water first enters a stream, lake, or wetland. An important consequence of these continued interchanges between surface water and ground water is their potential to further increase the contact time between water and chemically reactive geologic materials.


Ground-water chemistry and surface-water chemistry cannot be dealt with separately where surface and subsurface flow systems interact. The movement of water between ground water and surface water provides a major pathway for chemical transfer between terrestrial and aquatic systems (see Box F). This transfer of chemicals affects the supply of carbon, oxygen, nutrients such as nitrogen and phosphorus, and other chemical constituents that enhance biogeochemical processes on both sides of the interface. This transfer can ultimately affect the biological and chemical characteristics of aquatic systems downstream.

(Box F)

" The movement of water between ground water and surface water provides a major pathway for chemical transfer between terrestrial and aquatic systems"

Many streams are contaminated. Therefore, the need to determine the extent of the chemical reactions that take place in the hyporheic zone is widespread because of the concern that the contaminated stream water will contaminate shallow ground water (see Box G). Streams offer good examples of how interconnections between ground water and surface water affect chemical processes. Rough channel bottoms cause stream water to enter the streambed and to mix with ground water in the hyporheic zone. This mixing establishes sharp changes in chemical concentrations in the hyporheic zone.A zone of enhanced biogeochemical activity usually develops in shallow ground water as a result of the flow of oxygen-rich surface water into the subsurface environment, where bacteria and geochemically active sediment coatings are abundant (Figure 19). This input of oxygen to the streambed stimulates a high level of activity by aerobic (oxygen-using) microorganisms if dissolved oxygen is readily available. It is not uncommon for dissolved oxygen to be completely used up in hyporheic flow paths at some distance into the streambed, where anaerobic microorganisms dominate microbial activity. Anaerobic bacteria can use nitrate, sulfate, or other solutes in place of oxygen for metabolism. The result of these processes is that many solutes are highly reactive in shallow ground water in the vicinity of streambeds.

(Box G)

Figure 19. Microbial activity and chemical transformations commonly are enhanced in the hyporheic zone compared to those that take place in ground water and surface water. This diagram illustrates some of the processes and chemical transformations that may take place in the hyporheic zone. Actual chemical interactions depend on numerous factors including aquifer mineralogy, shape of the aquifer, types of organic matter in surface water and ground water, and nearby land use.

The movement of nutrients and other chemical constituents, including contaminants, between ground water and surface water is affected by biogeochemical processes in the hyporheic zone. For example, the rate at which organic contaminants biodegrade in the hyporheic zone can exceed rates in stream water or in ground water away from the stream. Another example is the removal of dissolved metals in the hyporheic zone. As water passes through the hyporheic zone, dissolved metals are removed by precipitation of metal oxide coatings on the sediments.

Lakes and wetlands also have distinctive biogeochemical characteristics with respect to their interaction with ground water. The chemistry of ground water and the direction and magnitude of exchange with surface water significantly affect the input of dissolved chemicals to lakes and wetlands. In general, if lakes and wetlands have little interaction with streams or with ground water, input of dissolved chemicals is mostly from precipitation therefore, the input of chemicals is minimal. Lakes and wetlands that have a considerable amount of ground-water inflow generally have large inputs of dissolved chemicals. In cases where the input of dissolved nutrients such as phosphorus and nitrogen exceeds the output, primary production by algae and wetland plants is large. When this large amount of plant material dies, oxygen is used in the process of decomposition. In some cases the loss of oxygen from lake water can be large enough to kill fish and other aquatic organisms.

The magnitude of surface-water inflow and outflow also affects the retention of nutrients in wetlands. If lakes or wetlands have no stream outflow, retention of chemicals is high. The tendency to retain nutrients usually is less in wetlands that are flushed substantially by throughflow of surface water. In general, as surface-water inputs increase, wetlands vary from those that strongly retain nutrients to those that both import and export large amounts of nutrients. Furthermore, wetlands commonly have a significant role in altering the chemical form of dissolved constituents. For example, wetlands that have throughflow of surface water tend to retain the chemically oxidized forms and release the chemically reduced forms of metals and nutrients.

Eutrophic lake in Saskatchewan, Canada. (Photograph by James LaBaugh.)

" The chemistry of ground water and the direction and magnitude of exchange with surface water significantly affect the input of dissolved chemicals to lakes and wetlands"

Interaction of Ground Water and Surface Water in Different Landscapes

Ground water is present in virtually all landscapes. The interaction of ground water with surface water depends on the physiographic and climatic setting of the landscape. For example, a stream in a wet climate might receive ground-water inflow, but a stream in an identical physiographic setting in an arid climate might lose water to ground water. To provide a broad and unified perspective of the interaction of ground water and surface water in different landscapes, a conceptual landscape (Figure 2) is used as a reference. Some common features of the interaction for various parts of the conceptual landscape are described below. The five general types of terrain discussed are mountainous, riverine, coastal, glacial and dune, and karst.


The hydrology of mountainous terrain (area M of the conceptual landscape, Figure 2) is characterized by highly variable precipitation and water movement over and through steep land slopes. On mountain slopes, macropores created by burrowing organisms and by decay of plant roots have the capacity to transmit subsurface flow downslope quickly. In addition, some rock types underlying soils may be highly weathered or fractured and may transmit significant additional amounts of flow through the subsurface. In some settings this rapid flow of water results in hillside springs.

A general concept of water flow in mountainous terrain includes several pathways by which precipitation moves through the hillside to a stream (Figure 20). Between storm and snowmelt periods, streamflow is sustained by discharge from the ground-water system (Figure 20A). During intense storms, most water reaches streams very rapidly by partially saturating and flowing through the highly conductive soils. On the lower parts of hillslopes, the water table sometimes rises to the land surface during storms, resulting in overland flow (Figure 20B). When this occurs, precipitation on the saturated area adds to the quantity of overland flow. When storms or snowmelt persist in mountainous areas, near-stream saturated areas can expand outward from streams to include areas higher on the hillslope. In some settings, especially in arid regions, overland flow can be generated when the rate of rainfall exceeds the infiltration capacity of the soil (Figure 20C).

Figure 20. Water from precipitation moves to mountain streams along several pathways. Between storms and snowmelt periods, most inflow to streams commonly is from ground water (A). During storms and snowmelt periods, much of the water inflow to streams is from shallow flow in saturated macropores in the soil zone. If infiltration to the water table is large enough, the water table will rise to the land surface and flow to the stream is from ground water, soil water, and overland runoff (B). In arid areas where soils are very dry and plants are sparse, infiltration is impeded and runoff from precipitation can occur as overland flow (C). (Modified from Dunne, T., and Leopold, L.B., 1978, Water in environmental planning: San Francisco, W.H. Freeman.) (Used with permission.)

Near the base of some mountainsides, the water table intersects the steep valley wall some distance up from the base of the slope (Figure 21, left side of valley). This results in perennial discharge of ground water and, in many cases, the presence of wetlands. A more common hydrologic process that results in the presence of wetlands in some mountain valleys is the upward discharge of ground water caused by the change in slope of the water table from being steep on the valley side to being relatively flat in the alluvial valley (Figure 21, right side of valley). Where both of these water-table conditions exist, wetlands fed by ground water, which commonly are referred to as fens, can be present.

Figure 21. In mountainous terrain, ground water can discharge at the base of steep slopes (left side of valley), at the edges of flood plains (right side of valley), and to the stream.

Another dynamic aspect of the interaction of ground water and surface water in mountain settings is caused by the marked longitudinal component of flow in mountain valleys. The high gradient of mountain streams, coupled with the coarse texture of streambed sediments, results in a strong down-valley component of flow accompanied by frequent exchange of stream water with water in the hyporheic zone (Figure 14) (see Box H). The driving force for water exchange between a stream and its hyporheic zone is created by the surface water flowing over rough streambeds, through pools and riffles, over cascades, and around boulders and logs. Typically, the stream enters the hyporheic zone at the downstream end of pools and then flows beneath steep sections of the stream (called riffles), returning to the stream at the upstream end of the next pool (Figure 14A). Stream water also may enter the hyporheic zone upstream from channel meanders, causing stream water to flow through a gravel bar before reentering the channel downstream (Figure 14B).

(Box H)

Mountain stream in Oregon. (Photograph by Dennis Wentz.)

Alluvial fan in Alaska. (Photograph by Earl Brabb.)

Streams flowing from mountainous terrain commonly flow across alluvial fans at the edges of the valleys. Most streams in this type of setting lose water to ground water as they traverse the highly permeable alluvial fans. This process has long been recognized in arid western regions, but it also has been documented in humid regions, such as the Appalachian Mountains. In arid and semiarid regions, seepage of water from the stream can be the principal source of aquifer recharge. Despite its importance, ground-water recharge from losing streams remains a highly uncertain part of the water balance of aquifers in these regions. Promising new methods of estimating ground-water recharge, at least locally, along mountain fronts are being developed-these methods include use of environmental tracers, measuring vertical temperature profiles in streambeds, measuring hydraulic characteristics of streambeds, and measuring the difference in hydraulic head between the stream and the underlying aquifer.

The most common natural lakes in mountainous terrain are those that are dammed by rock sills or glacial deposits high in the mountains. Termed cirque lakes, they receive much of their water from snowmelt. However, they interact with ground water much like the processes shown in Figure 21, and they can be maintained by ground water throughout the snow-free season.

The geochemical environment of mountains is quite diverse because of the effects of highly variable climate and many different rock and soil types on the evolution of water chemistry. Geologic materials can include crystalline, volcanic, and sedimentary rocks and glacial deposits. Sediments can vary from those having well-developed soil horizons to stream alluvium that has no soil development. During heavy precipitation, much water flows through shallow flow paths, where it interacts with microbes and soil gases. In the deeper flow through fractured bedrock, longer term geochemical interactions of ground water with minerals determine the chemistry of water that eventually discharges to streams. Base flow of streams in mountainous terrain is derived by drainage from saturated alluvium in valley bottoms and from drainage of bedrock fractures. Mixing of these chemically different water types results in geochemical reactions that affect the chemistry of water in streams. During downstream transport in the channel, stream water mixes with ground water in the hyporheic zone. In some mountain streams, the volume of water in the hyporheic zone is considerably larger than that in the stream channel. Chemical reactions in hyporheic zones can, in some cases, substantially alter the water chemistry of streams (Figure 19).


In some landscapes, stream valleys are small and they commonly do not have well-developed flood plains (area R of the conceptual landscape, Figure 2) (see Box I). However, major rivers (area V of the reference landscape, Figure 2) have valleys that usually become increasingly wider downstream. Terraces, natural levees, and abandoned river meanders are common landscape features in major river valleys, and wetlands and lakes commonly are associated with these features.

(Box I)

The interaction of ground water and surface water in river valleys is affected by the interchange of local and regional ground-water flow systems with the rivers and by flooding and evapotranspiration. Small streams receive ground-water inflow primarily from local flow systems, which usually have limited extent and are highly variable seasonally. Therefore, it is not unusual for small streams to have gaining or losing reaches that change seasonally.

Alluvial valley of the Mississippi River. (Photograph by Robert Meade.)

For larger rivers that flow in alluvial valleys, the interaction of ground water and surface water usually is more spatially diverse than it is for smaller streams. Ground water from regional flow systems discharges to the river as well as at various places across the flood plain (Figure 22). If terraces are present in the alluvial valley, local ground-water flow systems may be associated with each terrace, and lakes and wetlands may be formed because of this source of ground water. At some locations, such as at the valley wall and at the river, local and regional ground-water flow systems may discharge in close proximity. Furthermore, in large alluvial valleys, significant down-valley components of flow in the streambed and in the shallow alluvium also may be present (see Box I).

Figure 22. In broad river valleys, small local ground-water flow systems associated with terraces overlie more regional ground-water flow systems. Recharge from flood waters superimposed on these ground-water flow systems further complicates the hydrology of river valleys.

Added to this distribution of ground-water discharge from different flow systems to different parts of the valley is the effect of flooding. At times of high river flows, water moves into the ground-water system as bank storage (Figure 11). The flow paths can be as lateral flow through the riverbank (Figure 12B) or, during flooding, as vertical seepage over the flood plain (Figure 12C). As flood waters rise, they cause bank storage to move into higher and higher terraces.

The water table generally is not far below the land surface in alluvial valleys. Therefore, vegetation on flood plains, as well as at the base of some terraces, commonly has root systems deep enough so that the plants can transpire water directly from ground water. Because of the relatively stable source of ground water, particularly in areas of ground-water discharge, the vegetation can transpire water near the maximum potential transpiration rate, resulting in the same effect as if the water were being pumped by a well (see Figure 7). This large loss of water can result in drawdown of the water table such that the plants intercept some of the water that would otherwise flow to the river, wetland, or lake. Furthermore, in some settings it is not uncommon during the growing season for the pumping effect of transpiration to be significant enough that surface water moves into the subsurface to replenish the transpired ground water.

Riverine alluvial deposits range in size from clay to boulders, but in many alluvial valleys, sand and gravel are the predominant deposits. Chemical reactions involving dissolution or precipitation of minerals (see Box D) commonly do not have a significant effect on water chemistry in sand and gravel alluvial aquifers because the rate of water movement is relatively fast compared to weathering rates. Instead, sorption and desorption reactions and oxidation/reduction reactions related to the activity of microorganisms probably have a greater effect on water chemistry in these systems. As in small streams, biogeochemical processes in the hyporheic zone may have a significant effect on the chemistry of ground water and surface water in larger riverine systems. Movement of oxygen-rich surface water into the subsurface, where chemically reactive sediment coatings are abundant, causes increased chemical reactions related to activity of microorganisms. Sharp gradients in concentration of some chemical constituents in water, which delimit this zone of increased biogeochemical activity, are common near the boundary between ground water and surface water. In addition, chemical reactions in the hyporheic zone can cause precipitation of some reactive solutes and contaminants, thereby affecting water quality.


Coastal terrain, such as that along the east-central and southern coasts of the United States, extends from inland scarps and terraces to the ocean (area C of the conceptual landscape, Figure 2). This terrain is characterized by (1) low scarps and terraces that were formed when the ocean was higher than at present (2) streams, estuaries, and lagoons that are affected by tides (3) ponds that are commonly associated with coastal sand dunes and (4) barrier islands. Wetlands cover extensive areas in some coastal terrains (see Figure 18).

The interaction of ground water and surface water in coastal terrain is affected by discharge of ground water from regional flow systems and from local flow systems associated with scarps and terraces (Figure 23), evapotranspiration, and tidal flooding. The local flow systems associated with scarps and terraces are caused by the configuration of the water table near these features (see Box J). Where the water table has a downward break in slope near the top of scarps and terraces, downward components of ground-water flow are present where the water table has an upward break in slope near the base of these features, upward components of ground-water flow are present.

(Box J)

Figure 23. In coastal terrain, small local ground-water flow cells associated with terraces overlie more regional ground-water flow systems. In the tidal zone, saline and brackish surface water mixes with fresh ground water from local and regional flow systems.

Evapotranspiration directly from ground water is widespread in coastal terrain. The land surface is flat and the water table generally is close to land surface therefore, many plants have root systems deep enough to transpire ground water at nearly the maximum potential rate. The result is that evapotranspiration causes a significant water loss, which affects the configuration of ground-water flow systems as well as how ground water interacts with surface water.

Coastal terrain in Maryland. (Photograph by Robert Shedlock.)

In the parts of coastal landscapes that are affected by tidal flooding, the interaction of ground water and surface water is similar to that in alluvial valleys affected by flooding. The principal difference between the two is that tidal flooding is more predictable in both timing and magnitude than river flooding. The other significant difference is in water chemistry. The water that moves into bank storage from rivers is generally fresh, but the water that moves into bank storage from tides generally is brackish or saline.

Tidal mangrove wetland in Florida. (Photograph by Virginia Carter.)

Estuaries are a highly dynamic interface between the continents and the ocean, where discharge of freshwater from large rivers mixes with saline water from the ocean. In addition, ground water discharges to estuaries and the ocean, delivering nutrients and contaminants directly to coastal waters. However, few estimates of the location and magnitude of ground-water discharge to coasts have been made.

In some estuaries, sulfate-rich regional ground water mixes with carbonate-rich local ground water and with chloride-rich seawater, creating sharp boundaries that separate plant and wildlife communities. Biological communities associated with these sharp boundaries are adapted to different hydrochemical conditions, and they undergo periodic stresses that result from inputs of water having different chemistry. The balance between river inflow and tides causes estuaries to retain much of the particulate and dissolved matter that is transported in surface and subsurface flows, including contaminants.

" Ground water discharges to estuaries and the ocean, delivering nutrients and contaminants directly to coastal waters"


Glacial and dune terrain (area G of the conceptual landscape, Figure 2) is characterized by a landscape of hills and depressions. Although stream networks drain parts of these landscapes, many areas of glacial and dune terrain do not contribute runoff to an integrated surface drainage network. Instead, surface runoff from precipitation falling on the landscape accumulates in the depressions, commonly resulting in the presence of lakes and wetlands. Because of the lack of stream outlets, the water balance of these "closed" types of lakes and wetlands is controlled largely by exchange of water with the atmosphere (precipitation and evapotranspiration) and with ground water (see Box K).

(Box K)

Glacial terrain in Minnesota. (Photograph by Robert Karls.)

Lakes and wetlands in glacial and dune terrain can have inflow from ground water, outflow to ground water, or both (Figure 16). The interaction between lakes and wetlands and ground water is determined to a large extent by their position with respect to local and regional ground-water flow systems. A common conception is that lakes and wetlands that are present in topographically high areas recharge ground water, and that lakes and wetlands that are present in low areas receive discharge from ground water. However, lakes and wetlands underlain by deposits having low permeability can receive discharge from local ground-water flow systems even if they are located in a regional ground-water recharge area. Conversely, they can lose water to local ground-water flow systems even if they are located in a regional ground-water discharge area (Figure 24).

Figure 24. In glacial and dune terrain, local, intermediate, and regional ground-water flow systems interact with lakes and wetlands. It is not uncommon for wetlands that recharge local ground-water flow systems to be present in lowlands and for wetlands that receive discharge from local ground water to be present in uplands.

Lakes and wetlands in glacial and dune terrain underlain by highly permeable deposits commonly have ground-water seepage into one side and seepage to ground water on the other side. This relation is relatively stable because the water-table gradient between surface-water bodies in this type of setting is relatively constant. However, the boundary between inflow to the lake or wetland and outflow from it, termed the hinge line, can move up and down along the shoreline. Movement of the hinge line between inflow and outflow is a result of the changing slope of the water table in response to changes in ground-water recharge in the adjacent uplands.

Dune terrain in Nebraska. (Photograph by James Swinehart.)

Transpiration directly from ground water has a significant effect on the interaction of lakes and wetlands with ground water in glacial and dune terrain. Transpiration from ground water (Figure 7) has perhaps a greater effect on lakes and wetlands underlain by low-permeability deposits than in any other landscape. The lateral movement of ground water in low-permeability deposits may not be fast enough to supply the quantity of water at the rate it is removed by transpiration, resulting in deep and steep-sided cones of depression. These cones of depression commonly are present around the perimeter of the lakes and wetlands (Figure 7 and Box K).

In the north-central United States, cycles in the balance between precipitation and evapotranspiration that range from 5 to 30 years can result in large changes in water levels, chemical concentrations, and major-ion water type of individual wetlands. In some settings, repeated cycling of water between the surface and subsurface in the same locale results in evaporative concentration of solutes and eventually in mineral precipitation in the subsurface. In addition, these dynamic hydrological and chemical conditions can cause significant changes in the types, number, and distribution of wetland plants and invertebrate animals within wetlands. These changing hydrological conditions that range from seasons to decades are an essential process for rejuvenating wetlands that provide ideal habitat and feeding conditions for migratory waterfowl.

" The hydrological and chemical characteristics of lakes and wetlands in glacial and dune terrain are determined to a large extent by their position with respect to local and regional ground-water flow systems"


Karst may be broadly defined as all landforms that are produced primarily by the dissolution of rocks, mainly limestone and dolomite. Karst terrains (area K of the conceptual landscape, Figure 2) are characterized by (1) closed surface depressions of various sizes and shapes known as sinkholes, (2) an underground drainage network that consists of solution openings that range in size from enlarged cracks in the rock to large caves, and (3) highly disrupted surface drainage systems, which relate directly to the unique character of the underground drainage system.

Big Spring, Missouri. (Photograph by James Barks.)

Dissolution of limestone and dolomite guides the initial development of fractures into solution holes that are diagnostic of karst terrain. Perhaps nowhere else is the complex interplay between hydrology and chemistry so important to changes in landform. Limestone and dolomite weather quickly, producing calcium and magnesium carbonate waters that are relatively high in ionic strength. The increasing size of solution holes allows higher ground-water flow rates across a greater surface area of exposed minerals, which stimulates the dissolution process further, eventually leading to development of caves. Development of karst terrain also involves biological processes. Microbial production of carbon dioxide in the soil affects the carbonate equilibrium of water as it recharges ground water, which then affects how much mineral dissolution will take place before solute equilibrium is reached.

Ground-water recharge is very efficient in karst terrain because precipitation readily infiltrates through the rock openings that intersect the land surface. Water moves at greatly different rates through karst aquifers it moves slowly through fine fractures and pores and rapidly through solution-enlarged fractures and conduits. As a result, the water discharging from many springs in karst terrain may be a combination of relatively slow-moving water draining from pores and rapidly moving storm-derived water. The slow-moving component tends to reflect the chemistry of the aquifer materials, and the more rapidly moving water associated with recent rainfall tends to reflect the chemical characteristics of precipitation and surface runoff.

Water movement in karst terrain is especially unpredictable because of the many paths ground water takes through the maze of fractures and solution openings in the rock (see Box L). Because of the large size of interconnected openings in well-developed karst systems, karst terrain can have true underground streams. These underground streams can have high rates of flow, in some places as great as rates of flow in surface streams. Furthermore, it is not unusual for medium-sized streams to disappear into the rock openings, thereby completely disrupting the surface drainage system, and to reappear at the surface at another place. Seeps and springs of all sizes are characteristic features of karst terrains. Springs having sufficiently large ground-water recharge areas commonly are the source of small- to medium-sized streams and constitute a large part of tributary flow to larger streams. In addition, the location where the streams emerge can change, depending on the spatial distribution of ground-water recharge in relation to individual precipitation events. Large spring inflows to streams in karst terrain contrast sharply with the generally more diffuse ground-water inflow characteristic of streams flowing across sand and gravel aquifers.

(Box L)

Stream disappearing into sinkhole in karst terrain in Texas. (Photograph by Jon Gilhousen.)

Because of the complex patterns of surface-water and ground-water flow in karst terrain, many studies have shown that surface-water drainage divides and ground-water drainage divides do not coincide. An extreme example is a stream that disappears in one surface-water basin and reappears in another basin. This situation complicates the identification of source areas for water and associated dissolved constituents, including contaminants, in karst terrain.

Water chemistry is widely used for studying the hydrology of karst aquifers. Extensive tracer studies (see Box G) and field mapping to locate points of recharge and discharge have been used to estimate the recharge areas of springs, rates of ground-water movement, and the water balance of aquifers. Variations in parameters such as temperature, hardness, calcium/magnesium ratios, and other chemical characteristics have been used to identify areas of ground-water recharge, differentiate rapid- and slow-moving ground-water flow paths, and compare springflow characteristics in different regions. Rapid transport of contaminants within karst aquifers and to springs has been documented in many locations. Because of the rapid movement of water in karst aquifers, water-quality problems that might be localized in other aquifer systems can become regional problems in karst systems.

Some landscapes considered to be karst terrain do not have carbonate rocks at the land surface. For example, in some areas of the southeastern United States, surficial deposits overlie carbonate rocks, resulting in a "mantled" karst terrain. Lakes and wetlands in mantled karst terrain interact with shallow ground water in a manner similar to that in sandy glacial and dune terrains. The difference between how lakes and wetlands interact with ground water in sandy glacial and dune terrain and how they interact in the mantled karst is related to the buried carbonate rocks. If dissolution of the buried carbonate rocks causes slumpage of an overlying confining bed, such that water can move freely through the confining bed, the lakes and wetlands also can be affected by changing hydraulic heads in the aquifers underlying the confining bed (see Box L).

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5.11: Interacting with Water - Biology

H 2 O - The Mystery, Art, and Science of Water

Structure Means Function

Indeed! Water is one of our most plentiful chemicals. Its chemical formula, H 2 0 , is probably the most well known of all chemical formulas.

What does the chemical formula tell us?

The formula H 2 0 tells us that one molecule of water is comprised of 2 atoms of hydrogen and one atom of oxygen bonded together. The bonds which hold the hydrogen and oxygen together are called covalent bonds - they are very strong.

Let's look at a picture of a molecule of water: In this picture the two hydrogens are represented by white spheres and the oxygen by a red sphere.

IMAGE SOURCE: "Chemistry and Life", 4th Edition, John W. Hill, Dorothy M. Feigl, and Stuart J. Baum, Macmillan Publishing Company, New York, 1993

In this second picture, the hydrogens are shown as white spheres, the oygen as a red sphere. The 'sticks' holding the hydrogens to the oxygen represent covalent bonds.

Why does the water molecule look bent?

The water molecule maintains a bent shape (bent at 107.5 degrees actually) because of two considerations. First the tetrahedral arrangment around the oxygen and Second the presence of lone pair electrons on the oxygen.

What are Lone Pair Electrons?

These are the electrons that are not involved in the covalent bonds. The pairs of electrons are left alone. In our picture they are represented by the double dots. These lone pairs are very negative - containing two negative electrons each - and want to stay away from each other as much as possible. These repulsive forces act to push the hydrogens closer together

Did you say "Tetrahedral" - What does that mean?

Tetrahedral means "four-sided". In chemistry we interpret this in our imaginations. Draw the central atom in an imaginary space. Next put the atoms attached to the central atom around it such that the distance between them is maximized. The arrangement you'll adopt will be the form of a regular tetrahedron. This molecular shape is shown below. It has regular bond angles of 109.5

IMAGE SOURCE: "Chemistry and Life", 4th Edition, John W. Hill, Dorothy M. Feigl, and Stuart J. Baum, Macmillan Publishing Company, New York, 1993

If we do a similar arrangement of water, putting oxygen in the center, and using the two hydrogens and two lone pairs at the corners, we also come up with a tetrahedral arrangement. However, there is one important difference - the bond angles for water are not 109.5. Because of the presence of the very negative lone pair electrons, the two hydrogens are squeezed together as the two lone pairs try to get away from each other as far as possible. The resulting angle gives water a 104.5 bond angle. Because we don't "see" the electrons, the resulting tetrahedron "looks" BENT!

IMAGE SOURCE: "Chemistry and Life", 4th Edition, John W. Hill, Dorothy M. Feigl, and Stuart J. Baum, Macmillan Publishing Company, New York, 1993

Like many things in the chemical world, the shape and structure of a molecule is an important determinant of its function. The importance of the bent structure of water is that it provides water with two distinct "sides": One side of the water molecule has two negative lone pairs, while the other side presents the two hydrogens. Let's take another look:

[ fig of electron density map of water ]

Does this make water unusual?

YES! But it's not just that the molecule is bent that makes it special. Water is also highly polar - the two sides of water have very different charge.

The lone pairs are negative - Are the Hydrogens positive?

The hydrogens are slightly positive. They get this way because of the "electronegativity" of oxygen. Electronegativity is a measure of how much one atom wants to have electrons, and oxygen wants to have electrons more than hydrogen does. Oxygen has a higher electronegativity. Because of this difference in electronegativity, the electrons in the covalent bonds between oxygen and hydrogen get pulled slightly toward the oxygen. This leaves the hydrogens a little bit electron-deficient and thus slightly positive. We can draw this polarization like this:

IMAGE SOURCE: "Chemistry in Context" Wm C Brown Publishers, Dubuque Iowa, 2nd edition, A project of the American Chemical Society, ed: A. Truman Schwartz et al., 1997, Chapter 5 "The Wonder of Water"

Or looking at it from a "net polarization" perspective, like this:

IMAGE SOURCE: "Chemistry and Life", 4th Edition, John W. Hill, Dorothy M. Feigl, and Stuart J. Baum, Macmillan Publishing Company, New York, 1993

What does the polarization have to do with the properties of water?

Everything! Because water has a slightly negative end and a slightly positive end, it can interact with itself and form a highly organized 'inter-molecular' network. The positive hydrogen end of one molecule can interact favorably with the negative lone pair of another water molecule. This interaction is call "Hydrogen Bonding". It is a type of weak electrostatic attraction (positive to negative). Because each and every one of the water molecules can form four Hydrogen Bonds, an elaborate network of molecules is formed.

IMAGE SOURCE: "Chemistry in Context" Wm C Brown Publishers, Dubuque Iowa, 2nd edition, A project of the American Chemical Society, ed: A. Truman Schwartz et al., 1997, Chapter 5 "The Wonder of Water"

But if the Hydrogen Bonds are weak, how can they be important?

Think of how many there are! There is strength in numbers!

The polarity also allows water interact with an electric field:

And to interact with other polar molecules - which is how substances become dissolved in water.

IMAGE SOURCE: "Chemistry in Context" Wm C Brown Publishers, Dubuque Iowa, 2nd edition, A project of the American Chemical Society, ed: A. Truman Schwartz et al., 1997, Chapter 5 "The Wonder of Water"

Water Is Polar

The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape seen in Figure 2. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats (Figure 1). These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.

Figure 2. Hydrogen bonds form between slightly positive (δ+) and slightly negative (δ–) charges of polar covalent molecules, such as water.


The concept of trophic level was developed by Raymond Lindeman (1942), based on the terminology of August Thienemann (1926): "producers", "consumers" and "reducers" (modified to "decomposers" by Lindeman). [2] [3]

The three basic ways in which organisms get food are as producers, consumers, and decomposers.

  • Producers (autotrophs) are typically plants or algae. Plants and algae do not usually eat other organisms, but pull nutrients from the soil or the ocean and manufacture their own food using photosynthesis. For this reason, they are called primary producers. In this way, it is energy from the sun that usually powers the base of the food chain. [4] An exception occurs in deep-sea hydrothermal ecosystems, where there is no sunlight. Here primary producers manufacture food through a process called chemosynthesis. [5] (heterotrophs) are species that cannot manufacture their own food and need to consume other organisms. Animals that eat primary producers (like plants) are called herbivores. Animals that eat other animals are called carnivores, and animals that eat both plants and other animals are called omnivores. (detritivores) break down dead plant and animal material and wastes and release it again as energy and nutrients into the ecosystem for recycling. Decomposers, such as bacteria and fungi (mushrooms), feed on waste and dead matter, converting it into inorganic chemicals that can be recycled as mineral nutrients for plants to use again.

Trophic levels can be represented by numbers, starting at level 1 with plants. Further trophic levels are numbered subsequently according to how far the organism is along the food chain.

  • Level 1: Plants and algae make their own food and are called producers.
  • Level 2: Herbivores eat plants and are called primary consumers.
  • Level 3: Carnivores that eat herbivores are called secondary consumers.
  • Level 4: Carnivores that eat other carnivores are called tertiary consumers. by definition have no predators and are at the top of their food web.

In real-world ecosystems, there is more than one food chain for most organisms, since most organisms eat more than one kind of food or are eaten by more than one type of predator. A diagram that sets out the intricate network of intersecting and overlapping food chains for an ecosystem is called its food web. [6] Decomposers are often left off food webs, but if included, they mark the end of a food chain. [6] Thus food chains start with primary producers and end with decay and decomposers. Since decomposers recycle nutrients, leaving them so they can be reused by primary producers, they are sometimes regarded as occupying their own trophic level. [7] [8]

The trophic level of a species may vary if it has a choice of diet. Virtually all plants and phytoplankton are purely phototrophic and are at exactly level 1.0. Many worms are at around 2.1 insects 2.2 jellyfish 3.0 birds 3.6. [9] A 2013 study estimates the average trophic level of human beings at 2.21, similar to pigs or anchovies. [10] This is only an average, and plainly both modern and ancient human eating habits are complex and vary greatly. For example, a traditional Eskimo living on a diet consisting primarily of seals would have a trophic level of nearly 5. [11]

In general, each trophic level relates to the one below it by absorbing some of the energy it consumes, and in this way can be regarded as resting on, or supported by, the next lower trophic level. Food chains can be diagrammed to illustrate the amount of energy that moves from one feeding level to the next in a food chain. This is called an energy pyramid. The energy transferred between levels can also be thought of as approximating to a transfer in biomass, so energy pyramids can also be viewed as biomass pyramids, picturing the amount of biomass that results at higher levels from biomass consumed at lower levels. However, when primary producers grow rapidly and are consumed rapidly, the biomass at any one moment may be low for example, phytoplankton (producer) biomass can be low compared to the zooplankton (consumer) biomass in the same area of ocean. [12]

The efficiency with which energy or biomass is transferred from one trophic level to the next is called the ecological efficiency. Consumers at each level convert on average only about 10% of the chemical energy in their food to their own organic tissue (the ten-percent law). For this reason, food chains rarely extend for more than 5 or 6 levels. At the lowest trophic level (the bottom of the food chain), plants convert about 1% of the sunlight they receive into chemical energy. It follows from this that the total energy originally present in the incident sunlight that is finally embodied in a tertiary consumer is about 0.001% [7]

Both the number of trophic levels and the complexity of relationships between them evolve as life diversifies through time, the exception being intermittent mass extinction events. [13]

Food webs largely define ecosystems, and the trophic levels define the position of organisms within the webs. But these trophic levels are not always simple integers, because organisms often feed at more than one trophic level. [14] [15] For example, some carnivores also eat plants, and some plants are carnivores. A large carnivore may eat both smaller carnivores and herbivores the bobcat eats rabbits, but the mountain lion eats both bobcats and rabbits. Animals can also eat each other the bullfrog eats crayfish and crayfish eat young bullfrogs. The feeding habits of a juvenile animal, and, as a consequence, its trophic level, can change as it grows up.

The fisheries scientist Daniel Pauly sets the values of trophic levels to one in plants and detritus, two in herbivores and detritivores (primary consumers), three in secondary consumers, and so on. The definition of the trophic level, TL, for any consumer species is: [8]

In the case of marine ecosystems, the trophic level of most fish and other marine consumers takes a value between 2.0 and 5.0. The upper value, 5.0, is unusual, even for large fish, [16] though it occurs in apex predators of marine mammals, such as polar bears and killer whales. [17]

In addition to observational studies of animal behavior, and quantification of animal stomach contents, trophic level can be quantified through stable isotope analysis of animal tissues such as muscle, skin, hair, bone collagen. This is because there is a consistent increase in the nitrogen isotopic composition at each trophic level caused by fractionations that occur with the synthesis of biomolecules the magnitude of this increase in nitrogen isotopic composition is approximately 3–4‰. [18] [19]

In fisheries, the mean trophic level for the fisheries catch across an entire area or ecosystem is calculated for year y as:

Fish at higher trophic levels usually have a higher economic value, which can result in overfishing at the higher trophic levels. Earlier reports found precipitous declines in mean trophic level of fisheries catch, in a process known as fishing down the food web. [20] However, more recent work finds no relation between economic value and trophic level [21] and that mean trophic levels in catches, surveys and stock assessments have not in fact declined, suggesting that fishing down the food web is not a global phenomenon. [22] However Pauly et al. note that trophic levels peaked at 3.4 in 1970 in the northwest and west-central Atlantic, followed by a subsequent decline to 2.9 in 1994. They report a shift away from long-lived, piscivorous, high-trophic-level bottom fishes, such as cod and haddock, to short-lived, planktivorous, low-trophic-level invertebrates (e.g., shrimps) and small, pelagic fish (e.g., herrings). This shift from high-trophic-level fishes to low-trophic-level invertebrates and fishes is a response to changes in the relative abundance of the preferred catch. They argue this is part of the global fishery collapse. [17] [23]

Humans have a mean trophic level of about 2.21, about the same as a pig or an anchovy. [24] [25]

Since biomass transfer efficiencies are only about 10%, it follows that the rate of biological production is much greater at lower trophic levels than it is at higher levels. Fisheries catch, at least, to begin with, will tend to increase as the trophic level declines. At this point the fisheries will target species lower in the food web. [23] In 2000, this led Pauly and others to construct a "Fisheries in Balance" index, usually called the FiB index. [26] The FiB index is defined, for any year y, by [8]

The FiB index is stable (zero) over periods of time when changes in trophic levels are matched by appropriate changes in the catch in the opposite direction. The index increases if catches increase for any reason, e.g. higher fish biomass, or geographic expansion. [8] Such decreases explain the "backward-bending" plots of trophic level versus catch originally observed by Pauly and others in 1998. [23]

One aspect of trophic levels is called tritrophic interaction. Ecologists often restrict their research to two trophic levels as a way of simplifying the analysis however, this can be misleading if tritrophic interactions (such as plant–herbivore–predator) are not easily understood by simply adding pairwise interactions (plant-herbivore plus herbivore–predator, for example). Significant interactions can occur between the first trophic level (plant) and the third trophic level (a predator) in determining herbivore population growth, for example. Simple genetic changes may yield morphological variants in plants that then differ in their resistance to herbivores because of the effects of the plant architecture on enemies of the herbivore. [27] Plants can also develop defenses against herbivores such as chemical defenses. [28]

5.11: Interacting with Water - Biology

Water is a "polar" molecule, meaning that there is an uneven distribution of electron density. Water has a partial negative charge () near the oxygen atom due the unshared pairs of electrons, and partial positive charges () near the hydrogen atoms.

An electrostatic attraction between the partial positive charge near the hydrogen atoms and the partial negative charge near the oxygen results in the formation of a hydrogen bond as shown in the illustration.

The ability of ions and other molecules to dissolve in water is due to polarity. For example, in the illustration below sodium chloride is shown in its crystalline form and dissolved in water.

Many other unique properties of water are due to the hydrogen bonds. For example, ice floats because hydrogen bonds hold water molecules further apart in a solid than in a liquid, where there is one less hydrogen bond per molecule. The unique physical properties, including a high heat of vaporization, strong surface tension, high specific heat, and nearly universal solvent properties of water are also due to hydrogen bonding. The hydrophobic effect, or the exclusion of compounds containing carbon and hydrogen (nonpolar compounds) is another unique property of water caused by the hydrogen bonds. The hydrophobic effect is particularly important in the formation of cell membranes. The best description is to say that water "squeezes" nonpolar molecules together.


Crosslinking is the general term for the process of forming covalent bonds or relatively short sequences of chemical bonds to join two polymer chains together. The term curing refers to the crosslinking of thermosetting resins, such as unsaturated polyester and epoxy resin, and the term vulcanization is characteristically used for rubbers. [2] When polymer chains are crosslinked, the material becomes more rigid.

In polymer chemistry, when a synthetic polymer is said to be "cross-linked", it usually means that the entire bulk of the polymer has been exposed to the cross-linking method. The resulting modification of mechanical properties depends strongly on the cross-link density. Low cross-link densities increase the viscosities of polymer melts. Intermediate cross-link densities transform gummy polymers into materials that have elastomeric properties and potentially high strengths. Very high cross-link densities can cause materials to become very rigid or glassy, such as phenol-formaldehyde materials. [3]

Formation Edit

Cross-links can be formed by chemical reactions that are initiated by heat, pressure, change in pH, or irradiation. For example, mixing of an unpolymerized or partially polymerized resin with specific chemicals called crosslinking reagents results in a chemical reaction that forms cross-links. Cross-linking can also be induced in materials that are normally thermoplastic through exposure to a radiation source, such as electron beam exposure, [5] gamma radiation, or UV light. For example, electron beam processing is used to cross-link the C type of cross-linked polyethylene. Other types of cross-linked polyethylene are made by addition of peroxide during extruding (type A) or by addition of a cross-linking agent (e.g. vinylsilane) and a catalyst during extruding and then performing a post-extrusion curing.

The chemical process of vulcanization is a type of cross-linking that changes rubber to the hard, durable material associated with car and bike tires. This process is often called sulfur curing the term vulcanization comes from Vulcan, the Roman god of fire. This is, however, a slower process. A typical car tire is cured for 15 minutes at 150 °C. However, the time can be reduced by the addition of accelerators such as 2-benzothiazolethiol or tetramethylthiuram disulfide. Both of these contain a sulfur atom in the molecule that initiates the reaction of the sulfur chains with the rubber. Accelerators increase the rate of cure by catalysing the addition of sulfur chains to the rubber molecules.

Cross-links are the characteristic property of thermosetting plastic materials. In most cases, cross-linking is irreversible, and the resulting thermosetting material will degrade or burn if heated, without melting. Especially in the case of commercially used plastics, once a substance is cross-linked, the product is very hard or impossible to recycle. In some cases, though, if the cross-link bonds are sufficiently different, chemically, from the bonds forming the polymers, the process can be reversed. Permanent wave solutions, for example, break and re-form naturally occurring cross-links (disulfide bonds) between protein chains in hair.

Physical cross-links Edit

Where chemical cross-links are covalent bonds, physical cross-links are formed by weak interactions. For example, sodium alginate gels upon exposure to calcium ion, which allows it to form ionic bonds that bridge between alginate chains. [6] Polyvinyl alcohol gels upon the addition of borax through hydrogen bonding between boric acid and the polymer's alcohol groups. [7] [8] Other examples of materials which form physically cross-linked gels include gelatin, collagen, agarose, and agar agar.

Chemical covalent cross-links are stable mechanically and thermally, so once formed are difficult to break. Therefore, cross-linked products like car tires cannot be recycled easily. A class of polymers known as thermoplastic elastomers rely on physical cross-links in their microstructure to achieve stability, and are widely used in non-tire applications, such as snowmobile tracks, and catheters for medical use. They offer a much wider range of properties than conventional cross-linked elastomers because the domains that act as cross-links are reversible, so can be reformed by heat. The stabilizing domains may be non-crystalline (as in styrene-butadiene block copolymers) or crystalline as in thermoplastic copolyesters.

Note: A rubber which cannot be reformed by heat or chemical treatment is called a thermoset elastomer. On the other hand, a thermoplastic elastomer can be molded and recycled by heat.

Oxidative cross-links Edit

Many polymers undergo oxidative cross-linking, typically when exposed to atmospheric oxygen. In some cases this is undesirable and thus polymerization reactions may involve the use of an antioxidant to slow the formation of oxidative cross-links. In other cases, when formation of cross-links by oxidation is desirable, an oxidizer such as hydrogen peroxide may be used to speed up the process.

The aforementioned process of applying a permanent wave to hair is one example of oxidative cross-linking. In that process the disulfide bonds are reduced, typically using a mercaptan such as ammonium thioglycolate. Following this, the hair is curled and then "neutralized". The neutralizer is typically an acidic solution of hydrogen peroxide, which causes new disulfide bonds to form under conditions of oxidation, thus permanently fixing the hair into its new configuration.

Proteins naturally present in the body can contain crosslinks generated by enzyme-catalyzed or spontaneous reactions. Such crosslinks are important in generating mechanically stable structures such as hair, skin, and cartilage. Disulfide bond formation is one of the most common crosslinks, but isopeptide bond formation is also common. Proteins can also be cross-linked artificially using small-molecule crosslinkers. Compromised collagen in the cornea, a condition known as keratoconus, can be treated with clinical crosslinking. [9]

In biological context crosslinking could play a role in Atherosclerosis through advanced glycation end-products which have been implicated to induce crosslinking of collagen which may lead to vascular stiffening. [10]

Use in protein study Edit

The interactions or mere proximity of proteins can be studied by the clever use of crosslinking agents. For example, protein A and protein B may be very close to each other in a cell, and a chemical crosslinker [11] could be used to probe the protein–protein interaction between these two proteins by linking them together, disrupting the cell, and looking for the crosslinked proteins. [12]

A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions, and various parameters of protein function by using differing crosslinkers, often with diverse spacer arm lengths. [13] Subunit structure is deduced, since crosslinkers bind only surface residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be stabilized, captured, and analyzed.

Examples of some common crosslinkers are the imidoester crosslinker dimethyl suberimidate, the N-Hydroxysuccinimide-ester crosslinker BS3 and formaldehyde. Each of these crosslinkers induces nucleophilic attack of the amino group of lysine and subsequent covalent bonding via the crosslinker. The zero-length carbodiimide crosslinker EDC functions by converting carboxyls into amine-reactive isourea intermediates that bind to lysine residues or other available primary amines. SMCC or its water-soluble analog, Sulfo-SMCC, is commonly used to prepare antibody-hapten conjugates for antibody development.

In-vitro cross-linking method, termed PICUP (photo-induced cross-linking of unmodified proteins), was developed in 1999. [14] They devised a process in which ammonium persulfate (APS), which acts as an electron acceptor, and [[tris(bipyridine)ruthenium(II) chloride|tris-bipyridylruthenium (II) cation ( [Ru(bpy)
3 ] 2+
) are added to the protein of interest and irradiated with UV light. [14] PICUP is more expeditious and high yielding compared to previous chemical cross-linking methods. [14]

In-vivo crosslinking of protein complexes using photo-reactive amino acid analogs was introduced in 2005 by researchers from the Max Planck Institute of Molecular Cell Biology and Genetics. [15] In this method, cells are grown with photoreactive diazirine analogs to leucine and methionine, which are incorporated into proteins. Upon exposure to ultraviolet light, the diazirines are activated and bind to interacting proteins that are within a few ångströms of the photo-reactive amino acid analog (UV cross-linking).

Synthetically crosslinked polymers have many uses, including those in the biological sciences, such as applications in forming polyacrylamide gels for gel electrophoresis. Synthetic rubber used for tires is made by crosslinking rubber through the process of vulcanization. This crosslinking makes them more elastic. Hard-shell kayaks are also often manufactured with crosslinked polymers.

Other examples of polymers that can be crosslinked are ethylene-vinyl acetate–as used in solar panel manufacturing [16] – and polyethylene. [17] [18] [19]

Alkyd enamels, the dominant type of commercial oil-based paint, cure by oxidative crosslinking after exposure to air. [ citation needed ]

In many hydraulic fracturing treatments, a delayed gel-cross-linker fluid is used to carry out fracture treatment of the rock. [ citation needed ]

The earliest examples of crosslinking, linking long chains of polymers together to increase strength and mass, involved tires. Rubber was vulcanized with sulfur under heat, which created a link between latex models. [20]

Novel uses for crosslinking can be found in regenerative medicine, where bio-scaffolds are crosslinked to improve their mechanical properties. [21] More specifically increasing the resistance to dissolution in water based solutions.

Crosslinking is often measured by swelling tests. The crosslinked sample is placed into a good solvent at a specific temperature, and either the change in mass or the change in volume is measured. The more crosslinking, the less swelling is attainable. Based on the degree of swelling, the Flory Interaction Parameter (which relates the solvent interaction with the sample), and the density of the solvent, the theoretical degree of crosslinking can be calculated according to Flory's Network Theory. [22] Two ASTM standards are commonly used to describe the degree of crosslinking in thermoplastics. In ASTM D2765, the sample is weighed, then placed in a solvent for 24 hours, weighed again while swollen, then dried and weighed a final time. [23] The degree of swelling and the soluble portion can be calculated. In another ASTM standard, F2214, the sample is placed in an instrument that measures the height change in the sample, allowing the user to measure the volume change. [24] The crosslink density can then be calculated.

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