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8.17C: Fungi Habitat, Decomposition, and Recycling - Biology

8.17C: Fungi Habitat, Decomposition, and Recycling - Biology


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Fungi are the major decomposers of nature; they break down organic matter which would otherwise not be recycled.

Learning Objectives

  • Explain the roles played by fungi in decomposition and recycling

Key Points

  • Aiding the survival of species from other kingdoms through the supply of nutrients, fungi play a major role as decomposers and recyclers in the wide variety of habitats in which they exist.
  • Fungi provide a vital role in releasing scarce, yet biologically-essential elements, such as nitrogen and phosphorus, from decaying matter.
  • Their mode of nutrition, which involves digestion before ingestion, allows fungi to degrade many large and insoluble molecules that would otherwise remain trapped in a habitat.

Key Terms

  • decomposer: any organism that feeds off decomposing organic material, especially bacterium or fungi
  • exoenzyme: any enzyme, generated by a cell, that functions outside of that cell
  • saprobe: an organism that lives off of dead or decaying organic material

Fungi & Their Roles as Decomposers and Recyclers

Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on earth, preferring dark, moist conditions. They can thrive in seemingly-hostile environments, such as the tundra. However, most members of the Kingdom Fungi grow on the forest floor where the dark and damp environment is rich in decaying debris from plants and animals. In these environments, fungi play a major role as decomposers and recyclers, making it possible for members of the other kingdoms to be supplied with nutrients and to live.

The food web would be incomplete without organisms that decompose organic matter. Some elements, such as nitrogen and phosphorus, are required in large quantities by biological systems; yet, they are not abundant in the environment. The action of fungi releases these elements from decaying matter, making them available to other living organisms. Trace elements present in low amounts in many habitats are essential for growth, but would remain tied up in rotting organic matter if fungi and bacteria did not return them to the environment via their metabolic activity.

The ability of fungi to degrade many large and insoluble molecules is due to their mode of nutrition. As seen earlier, digestion precedes ingestion. Fungi produce a variety of exoenzymes to digest nutrients. These enzymes are either released into the substrate or remain bound to the outside of the fungal cell wall. Large molecules are broken down into small molecules, which are transported into the cell by a system of protein carriers embedded in the cell membrane. Because the movement of small molecules and enzymes is dependent on the presence of water, active growth depends on a relatively-high percentage of moisture in the environment.

As saprobes, fungi help maintain a sustainable ecosystem for the animals and plants that share the same habitat. In addition to replenishing the environment with nutrients, fungi interact directly with other organisms in beneficial, but sometimes damaging, ways.


The Fungi

The fungi are one of the great groups of living organisms, comparable in numbers of species, diversity and ecological significance with animals, plants, protists and bacteria. This textbook deals with all fundamental and applied aspects of mycology, illustrated by reference to well studied species from major fungal groups. Since the publication of the first edition of The Fungi, there have been many important advances in the field of mycology. This second up-to-date edition has been revised and substantially expanded, and incorporates the application of methods of molecular biology, especially DNA technology to mycology.

The fungi are one of the great groups of living organisms, comparable in numbers of species, diversity and ecological significance with animals, plants, protists and bacteria. This textbook deals with all fundamental and applied aspects of mycology, illustrated by reference to well studied species from major fungal groups. Since the publication of the first edition of The Fungi, there have been many important advances in the field of mycology. This second up-to-date edition has been revised and substantially expanded, and incorporates the application of methods of molecular biology, especially DNA technology to mycology.


Reproduction

Fungi reproduce sexually and/or asexually. Perfect fungi reproduce both sexually and asexually, while imperfect fungi reproduce only asexually (by mitosis).

In both sexual and asexual reproduction, fungi produce spores that disperse from the parent organism by either floating on the wind or hitching a ride on an animal. Fungal spores are smaller and lighter than plant seeds. The giant puffball mushroom bursts open and releases trillions of spores. The huge number of spores released increases the likelihood of landing in an environment that will support growth .


8.17C: Fungi Habitat, Decomposition, and Recycling - Biology

Introduction to Biology of Fungi
OUTLINE

I. Brief Introduction to the Kingdom Fungi

II. Generalized Life Cycle of Fungi

III. Human-fungus Interactions


BRIEF INTRODUCTION TO THE KINGDOM FUNGI

The Kingdom Fungi is an ensemble of diverse species. Current evidence suggests that all fungal species are not derived from a single common ancestor, consequently the Fungi are polyphyletic (multiple genealogies or lineages).


I. COMMON CHARACTERISTICS OF FUNGI

1. Heterotrophy - 'other food'. There are three major categories of heterotrophs, which include the saprophytes, symbionts, and parasites. Saprophytes (feed on dead tissues or organic waste) symbionts (mutually beneficial relationship between a fungus and another organism) parasites (feeding on living tissue of a host). Parasites that cause disease are called pathogens. Some parasites are obligate parasites (require a living host to survive), while others are facultative or nonobligate parasites (do not require a living host in order to survive).

Below: The sclerotium of Wolfiporia cocos or "tuckahoe" - the sclerotium is broken in two parts with a diameter of about 6 inches. Dug up from a flower bed near Jonesboro, AR. Photograph by M. Huss.

3. Fungus is often hidden from view. It grows through its food source (substratum), excretes extracellular digestive enzymes, and absorbs dissolved food.

5. Spores - asexual (product of mitosis) or sexual (product of meiosis) in origin.

(a) Allows the fungus to move to new food source.
(b) Resistant stage - allows fungus to survive periods of adversity.
(c) Means of introducing new genetic combinations into a population.

6. Vegetative phase of fungus is generally sedentary.

7. Cell wall present, composed of cellulose and/or chitin.

8. Food storage - generally in the form of lipids and glycogen.

9. Eukaryotes - true nucleus and other organelles present.

10. All fungi require water and oxygen (no obligate anaerobes).

11. Fungi grow in almost every habitat imaginable, as long as there is some type of organic matter present and the environment is not too extreme.

12. Diverse group, number of described species is about 69,000 (estimated 1.5 million species total).


II. LIFE CYCLE OF A 'TYPICAL' FUNGUS

Generalized Life Cycle of Fungi

REFER TO DIAGRAM FROM CLASS NOTES OR TO THE FOLLOWING:

Also visit the following links for additional information:

Some fungi produce spores or other modified cells to reproduce sexually (perfect stage or the teleomorph), others to reproduce asexually (imperfect state or the anamorp), and some species are capable of reproducing both ways (holomorph).


Symbiosis

Some species of fungi form symbiotic relationships with plants. Mycorrhizal fungi are associated with plant roots. This relationship is mutually beneficial because fungi facilitate the transfer of nutrients from the soil into plant roots, and in turn receive carbon from the plant. Carbon is stored by fungi in the soil and therefore is not released as carbon dioxide. It was once thought that plants were the only source of carbon for mycorrhizal fungi. However, an article published in the May 2008 issue of “Functional Ecology” reveals that mycorrhizal fungi can actively decompose organic carbon, and therefore play a greater role in carbon loss and input from soil than previously thought. Lichens are another type of fungi that form a symbiotic relationship, but they do so with cyanobacteria. Lichens provide shelter for the bacteria, which in turn make energy and carbon for lichens via photosynthesis.


Zygomycota: The Conjugated Fungi

Zygomycota, a small group in the fungi kingdom, can reproduce asexually or sexually, in a process called conjugation.

Learning Objectives

Describe the ecology and reproduction of Zygomycetes

Key Takeaways

Key Points

  • Most zygomycota are saprobes, while a few species are parasites.
  • Zygomycota usually reproduce asexually by producing sporangiospores.
  • Zygomycota reproduce sexually when environmental conditions become unfavorable.
  • To reproduce sexually, two opposing mating strains must fuse or conjugate, thereby, sharing genetic content and creating zygospores.
  • The resulting diploid zygospores remain dormant and protected by thick coats until environmental conditions have improved.
  • When conditions become favorable, zygospores undergo meiosis to produce haploid spores, which will eventually grow into a new organism.

Key Terms

  • zygomycete: an organism of the phylum Zygomycota
  • karyogamy: the fusion of two nuclei within a cell
  • zygospore: a spore formed by the union of several zoospores
  • conjugation: the temporary fusion of organisms, especially as part of sexual reproduction

Zygomycota: The Conjugated Fungi

The zygomycetes are a relatively small group in the fungi kingdom and belong to the Phylum Zygomycota. They include the familiar bread mold, Rhizopus stolonifer, which rapidly propagates on the surfaces of breads, fruits, and vegetables. They are mostly terrestrial in habitat, living in soil or on plants and animals. Most species are saprobes meaning they live off decaying organic material. Some are parasites of plants, insects, and small animals, while others form symbiotic relationships with plants. Zygomycetes play a considerable commercial role. The metabolic products of other species of Rhizopus are intermediates in the synthesis of semi-synthetic steroid hormones.

Zygomycetes have a thallus of coenocytic hyphae in which the nuclei are haploid when the organism is in the vegetative stage. The fungi usually reproduce asexually by producing sporangiospores. The black tips of bread mold, Rhizopus stolonifer, are the swollen sporangia packed with black spores. When spores land on a suitable substrate, they germinate and produce a new mycelium.

Sporangia of bread mold: Sporangia grow at the end of stalks, which appear as (a) white fuzz seen on this bread mold, Rhizopus stolonifer. The (b) tips of bread mold are the spore-containing sporangia.

Zygomycete life cycle: Zygomycetes have asexual and sexual life cycles. In the sexual life cycle, plus and minus mating types conjugate to form a zygosporangium.

Sexual reproduction starts when conditions become unfavorable. Two opposing mating strains (type + and type –) must be in close proximity for gametangia (singular: gametangium) from the hyphae to be produced and fuse, leading to karyogamy. The developing diploid zygospores have thick coats that protect them from desiccation and other hazards. They may remain dormant until environmental conditions become favorable. When the zygospore germinates, it undergoes meiosis and produces haploid spores, which will, in turn, grow into a new organism. This form of sexual reproduction in fungi is called conjugation (although it differs markedly from conjugation in bacteria and protists), giving rise to the name “conjugated fungi”.


Decomposition and decay

The former is mainly associated with things that are rotten, have a bad smell and are generally symptomatic of death. The latter is similarly viewed as undesirable. Examples include urban decay, or, on a more personal level, tooth decay. However, decomposition and decay are vital processes in nature. They play an essential role in the breakdown of organic matter, recycling it and making it available again for new organisms to utilise.

Decomposition and decay are the yin to the yang of growth. Together they form two halves of the whole that is the closed-loop cycle of natural ecosystems. Everything dies, and without decomposition and decay the world would overflow with plant and animal remains. It would also experience a decline in new growth, due to a shortage of nutrients that would be locked up and unavailable in the dead forms.

What is decomposition?

Decomposition is the first stage in the recycling of nutrients that have been used by an organism (plant or animal) to build its body.

It is the process whereby the dead tissues break down and are converted into simpler organic forms. These are the food source for many of the species at the base of ecosystems. The species that carry out the process of decomposition are known as detritivores. Detritivore means literally ‘feeders on dead or decaying organic matter’. Many of these decomposer species function in tandem or parallel with one another. Each is responsible for a specific part of the decomposition process. Collectively they are known as the detritivore community.

Nature’s unsung heroes of recycling

A wide range of organisms takes part in the decomposition process. Most of them are inconspicuous and unglamorous. From a conventional human perspective, they are even undesirable. The detritivore community includes insects such as beetles and their larvae as well as flies and maggots (fly larvae). It also includes woodlice, fungi, slime moulds, bacteria, slugs and snails, millipedes, springtails and earthworms. Most of them work out of sight, and their handiwork isn’t immediately obvious, but they are the forest’s unsung heroes of recycling. Almost all of them are tiny, and their function happens gradually in most cases, over months or years. But together they convert dead plants and animals into forms that are useable either by themselves or other organisms.

Decomposition in plants

The primary decomposers of most dead plant material are fungi. Dead leaves fall from trees and herbaceous plants collapse to the ground after they have produced seeds. These form a layer of litter on the soil surface. The litter layer can be quite substantial in volume. The litter fall in a Scots pine is around 1-1.5 tonnes per hectare per year, while that in temperate deciduous forests is over 3 tonnes per hectare per year. The litter is quickly invaded by the hyphae of fungi. Hyphae are the white thread-like filaments that are the main body of a fungus. (The mushrooms that appear on the forest floor, are merely the fruiting bodies of the fungus.) The hyphae draw nourishment from the litter. This enables the fungi to grow and spread, while breaking down the structure of the dead plant material. Bacteria also play a part in this process, as do various invertebrates, including slugs, snails and springtails. As the decay becomes more advanced, earthworms begin their work.

This decomposition process is usually odourless. It is aerobic, meaning that it takes place in the presence of air (oxygen in particular). On the forest floor it is spread out in both space and time. When people make compost heaps in their garden, they are utilising the same process. It is concentrated and accelerated by piling the dead material together in a heap, and the heat that is generated speeds up the process of decay.

Fungi that feed on dead plant material are called saprotrophic fungi. Common examples include the horsehair parachute fungus, which can be seen growing out of dead grass stems, leaves or pine needles. Another is the sulphur tuft fungus, which fruits on logs that are at an advanced state of decomposition.

In a forest, the rate of decomposition depends on what the dead plant material is. Leaves of deciduous trees and the stems and foliage of non-woody plants generally break down quickly. They are usually gone within a year of falling to the forest floor. Some plant material, such as the fibrous dead fronds of bracken, takes longer. But even these will still be decomposed within three years. The needles of conifers, such as Scots pine, are much tougher. It can take up to seven years for them to be completely broken down and recycled. The rate of decay is also determined by how wet the material is, and in general the wetter it is the faster it breaks down. In dry periods or dry climates, the organic matter becomes dessicated. Many detritivores, such as fungi and slugs, are inactive so the decomposition process becomes prolonged.

Decomposition of woody material – the rot sets in

In contrast to the softer tissues of herbaceous plants, the fibres of trees and other woody plants are much tougher and take a longer time to break down. Fungi are still, for the most part, the first agents of decay, and there are many species that grow in dead wood. The common names of species such as the wet rot fungus and the jelly rot fungus indicate their role in helping wood to decompose. The growth of the fungal hyphae within the wood helps other detritivores, such as bacteria and beetle larvae, to gain access. The fungi feed on the cellulose and lignin, converting those into their softer tissues. These in turn begin to decompose when the fungal fruiting bodies die. Many species of slime mould also grow inside dead logs and play a role in decomposition. Like fungi, they are generally only visible when they are ready to reproduce and their fruiting bodies appear.

Some decomposers are highly-specialised. For example, the earpick fungus grows out of decaying Scots pine cones that are partially or wholly buried in the soil. Another fungus known as Cyclaneusma minus grows on the fallen needles of Scots pine.

As the wood becomes more penetrated and open, through, for example, the galleries produced by beetle larvae, it becomes wetter. Being wet facilitates the next phase of decomposition. Invertebrates such as woodlice and millipedes feed on the decaying wood. Predators and parasites, such as robber flies and ichneumon wasps, will also arrive, to feed on beetles and other invertebrates. For trees such as birch the wood becomes very wet and rotten, and falls apart quite easily after a few years. Earthworms and springtails are often seen at this stage, when the decomposing wood will soon become assimilated into the soil. They can reach high densities – there can be 1 tonne or earthworms in a single hectare of broadleaved European forest! The wood of Scots pine, however, has a high resin content. This makes it much more resistant to decay, and it can take several decades for a pine log to decompose fully.

It’s a fungus eat fungus world

Most fungi are soft-bodied and having a high water content. This means they often disintegrate and disappear within a few days or weeks of fruiting. The tougher, more woody fungi, such as the tinder fungus, can persist for several years. Even so, they often have specialist decomposers at work on them. The tinder fungus, for example, is the host for the larvae of the black tinder fungus beetle and the forked fungus beetle. These feed on the fungal fruiting body, helping to break down its woody structure

Another bracket fungus that grows on dead birch trees, is the birch polypore. This fungus is itself colonised by the ochre cushion fungus, which feeds on and breaks down the polypore’s brackets. The bolete mould fungus is another species that grows on fungi, in this case members of the bolete group. (Boletes have pores on the underside of their caps and include edible species such as the cep.) The silky piggyback fungus and the powdery piggyback fungus fruit on the caps of brittlegill fungi. They speed up the process of breakdown and decay in them. Slime moulds, although not fungi, are somewhat fungus-like when they are in the fruiting stage of their life cycle. The fruiting bodies of a species called Trichia decipiens are susceptible to fungal mould growing on them. This in turn accelerates their decomposition.

Decomposition in the animal kingdom

Fungi play a key role in breaking down plants, but this isn’t the case then it comes to dead animal matter. The vast majority of the decomposers in this case are other animals and bacteria. Animal decomposers include scavengers and carrion feeders. These consume parts of an animal carcass, using it as an energy source. They also convert it into the tissues of their own bodies and the dung they excrete. These animals range from foxes and badgers to birds such as the hooded crow. They also include invertebrates such as carrion flies, blow-flies and various beetles. Their dung in turn is eaten by other organisms, particularly dung beetles and burying beetles. Some fungi, including the dung roundhead grow out of dung, helping to break it down.

Not all animal carcasses are immediately consumed by large scavengers. In these cases there are five main stages in the decomposition process. The first of these is when the corpse is still fresh. At this stage carrion flies and blow-flies arrive and lay their eggs around the openings, such as the nose, mouth and ears. In the second stage, the action of bacteria inside the corpse causes putrefaction. These bacteria produce gasses which make the carcass to swell. This is anaerobic decomposition, or decay in the absence of air. It is characterised by its bad smell, in contrast to the odourless nature of aerobic decomposition.

The next stage commences when the skin of the corpse is ruptured. The gases escape and the carcass deflates again. In this decay stage, the larvae or maggots of flies proliferate and consume much of the soft tissue. Predators such as wasps, ants and beetles also arrive, to feed on the fly larvae. In the following stage, only cartilage, skin and bones remain. At this point different groups of flies and beetles, along with their parasites, take over the decomposition process. Finally, only bones and hair remain, and they can persist for several years or more. Eventually even these are consumed – for example, mice and voles will gnaw on old bones, to obtain the calcium they contain. Clothes moths help break down hair or feathers. The progression through these stages depends to some extent on the time of year when death occurs. But typically it takes several months from beginning to end.

One example of a fungus that helps break down animal matter is the scarlet caterpillar club fungus. This species grows out of the living pupa or larva of a moth or butterfly. It converts the body of its host into a fruiting body, which is club-shaped and orange, with a pimply surface.

Decomposition feeds new growth

Decomposition and decay may appear to be unpleasant processes from our human perspective. However they are vital for the functioning of ecosystems. Just like compost in a garden, they provide essential nutrients for the growth of new organisms. They are a key aspect of the cyclical processes that maintain all life on Earth. A renewed appreciation of their importance will help humans to protect and sustain ecosystems. This appreciation may even provide inspiration for alternatives to the unsustainable unlimited growth model that drives human culture today.


Materials and Methods

Site description

The study was conducted in the Reichraminger Hintergebirge, a mountain range located in the Austrian Calcareous Alps (47°49′08″N, 14°23′34″E). The forest stand is dominated by European beech (Fagus sylvatica L.) with a stand age of c. 146 yr in 2015. The site is southeast exposed with a slope inclination of 35° at an elevation of 1000 to 1100 m above sea level (asl) (Supporting Information Fig. S1). The parent bedrock is limestone, the dominant soil types are Rendzic Leptosol and Chromic Cambisol. Average annual air temperature and precipitation are 7.8°C and 1645 mm, respectively (Kobler et al., 2015 ). Sixteen plots (c. 25 m × 25 m) were selected along a natural fertility gradient (extent c. 700 m Fig. S1), characterised by a change in topography, soil type and depth, and hydrology. The fertility gradient followed the contour line, with less fertile plots featuring a convex topography, shallower, stony soils and more fertile plots holding deeper, loamy soils and a concave topography (Fig. 1a).

Stand inventory, vegetation survey, microclimatic measurements and litter fall collection

In May 2015, diameter at breast height and height of trees were measured at each plot allometric functions were applied to calculate above-ground woody biomass of trees (Wutzler et al., 2008 ). For each plot, the identity and dominance of plant species in the herbal layer was determined at four subplots species dominance was visually estimated and expressed in percentage soil cover. Subplots were defined as triangular areas between three beech trees each. Plant species were assigned Ellenberg indicator values (Table S1) and cover-weighted mean indicator values were calculated per plot (Ellenberg et al., 1992 ). Measurements of soil temperature (5 cm depth) and moisture (0–7 cm depth) were conducted six times between May and August 2015 using a handheld thermometer and a TDR moisture meter (Spectrum Technologies, Aurora, IL, USA) plot-wise means of the six measurement campaigns were used for further analyses. In total, 20 litter traps (d: 52 cm, h: 70 cm) were installed along the gradient in September 2015. Traps were installed in close vicinity to the established plots (Fig. S1). Until October 2016, litter traps were emptied regularly and collected litter was dried (105°C) and weighed (± 0.01 g) litter fall was subsequently summed up for each trap and is given in g m −2 yr −1 . Depending on the location along the gradient, litter traps were grouped into three levels of fertility for further analyses (low, medium, high fertility Fig. S1).

Organic layer and mineral soil sampling and processing

In June 2015, organic layer samples were taken at 12 selected plots along the gradient (Fig. S1, dotted line rectangles). Litter (OLF) and humus horizons (OH, if present) were sampled separately with a large corer (d: 19 cm). Four replicates were taken per plot. Samples were pooled per plot and horizon, and roots and stones were removed. Total mass of litter and humus samples was determined by weighing (± 0.01 g) and subsequent multiplication with weight-conversion factors determined for subsamples (105°C, 48 h).

In August 2015, mineral soil samples were taken at each plot along the gradient (Fig. S1, solid line rectangles). Samples were taken from the mineral topsoil (0–10 cm, c. 1 l soil volume) using a shovel. Four replicates were taken per plot. Due to the high stone content (up to 80% of soil volume), sampling deeper than c. 10 cm was hardly feasible at many locations. Topsoil was, however, the largest pool for organic C and N (see Methods S1 Table S2). Soil samples were immediately sieved (2 mm) in the field. For fungal community analysis, 0.5 g of homogenised mineral soil was weighed into 1.5 ml LifeGuard Soil Preservation Solution (MO BIO, Carlsbad, CA, USA). Mineral soil for enzyme analyses was frozen at −20°C on the same day, and soil for other analyses was kept at 4°C until further processing.

To determine mineral soil bulk density, stone content and root biomass, three small soil pits (c. 15 cm × 15 cm surface area) were dug down to 10 cm mineral soil depth per plot. After the organic layer was removed, the mineral soil was sampled the sampled soil volume was estimated by refilling the pit with quartz sand and measuring the volume sand used. In the laboratory, samples were weighed roots and stones were picked per hand and rinsed clean. Fine roots (d ≤ 2 mm), coarse roots (d > 2 mm), stones, and subsamples (c. 10 g) of sieved (2 mm) soil were dried (105°C, 24 h) and weighed (± 0.0001 g). Root biomass volume (g m −2 ) and stone content (vol%) were determined using dry weight and specific densities. Fine soil dry mass (g m −2 ) and fine soil bulk density (g cm −3 ) was subsequently calculated for each plot. Coarse roots were not used for statistical analysis.

Organic layer and mineral soil analyses

Total C and N concentration (%) of organic layer and mineral soil samples was analysed on a 300 mg subsample using a TruSpec CHN analyser (Leco, St Joseph, MI, USA) subsamples were dried (105°C, 24 h) and ground before analysis (Pulverisette 5 Fritsch, Germany). Carbon and N stocks of the organic layer were subsequently calculated by multiplying the total dry mass of the horizon by C and N concentrations. Inorganic C concentration of mineral soil subsamples was determined using the Scheibler method (ÖNORM L 1084, 1999 ). Organic soil C concentration of mineral soil layers was calculated as the difference in inorganic and total C concentrations. Mineral soil organic C and N stocks (0–10 cm g m −2 ) were calculated from respective organic C and N concentrations multiplied by dry weight of mineral soil.

The mean residence time of the organic layer was calculated per plot (Berger et al., 2009 ). For that, the organic layer dry mass was divided by the average annual litter fall rate of the closest litter traps (Fig. S1). This approach assumes root litter input into the organic layer to be negligible.

Soil CO2 efflux from microbial respiration was measured on fresh mineral soil (equivalent to c. 25 g oven-dried soil) within a few days after sampling. For respiration measurements, soil was sieved to 2 mm and filled in 200 cm 3 steel cylinders at field bulk density (Reichstein et al., 2000 Schindlbacher et al., 2015 ). After c. 3 d of equilibration at 4°C, cylinders were placed into 2 l plastic containers connected to an infrared gas analyser unit (SBA-4 PP Systems International, Amesbury, MA, USA). In brief, microbial respiration of each sample was determined as ΔCO2 within closed containers for Δ6 min. Microbial respiration was determined at a standardised temperature of 15°C. Respiration rates are expressed in mg C g −1 Cd −1 , and in mg C m −2 d −1 using total dry mass of mineral soil for conversion. Details on the measurement system and protocol can be found elsewhere (Mayer et al., 2017a , b ).

Potential activities of hydrolytic soil enzymes were measured fluorometrically according to Marx et al. ( 2001 ) and German et al. ( 2011 ). Briefly, 0.5 g of mineral soil was suspended in 50 ml of a 100 mM Tris buffer, pH 7.5, and homogenised for 1 min in a sonication bath (48 kHz, 50 W). Aliquots of 200 μl were pipetted under constant stirring (on a magnetic plate) into black 96-well microplates, with four technical replicates for each sample. Optimal substrate concentrations and incubation times for leucine aminopeptidase (1 mM), N-acetyl-β- d -glucosaminidase (1 mM), β-glucosidase (0.5 mM), acid phosphatase (2 mM), β-xylosidase (1 mM) and cellobiohydrolase (0.3 mM) were evaluated in advance to avoid potential substrate inhibition. Next, 50 µl of substrate (dissolved in deionised water) were added to each well and the plate shaken horizontally for 30 s for mixing. The microplates were incubated at 20°C in the dark for 120 min (acid phosphatase) or 180 min (for all other enzymes). Fluorescence was measured using a multiplate reader with an excitation of 365 nm and an emission of 450 nm, at 20 and 100 flashes (EnSpire Perkin Elmer, Waltham, MA, USA). Standard curves were prepared in buffer solution using four standard solutions with concentrations between 10 µM and 250 μM, for substrates based on 4-methylumbelliferone (all enzymes except leucine aminopeptidase) and two standard curves with concentrations of 20 μM and 50 μM, for substrates based on 7-amino-4-methylcoumarin (leucine aminopeptidase). Corresponding sets of standard curves were prepared in soil slurry to account for quenching. To measure potential phenol oxidase activity, 3,4-dihydroxy- l -phenylalanine (DOPA) was used as substrate. Here, 900 µl of soil suspension (or 900 µl of buffer solution for blank wells) were mixed with an equivalent amount of a 10 mM DOPA solution (prepared in 100 mM TRIS buffer), shaken horizontally for 10 min and centrifuged at c. 1500 g force for 5 min. Then, 250 µl of this suspension was transferred into a clear 96-well plate with three-fold repetition. Absorption was measured immediately (time 0), and after c. 6 h of incubation in the dark (20°C), at 450 nm using a multiplate reader (as above). Potential phenol oxidase activity was calculated as the difference between absorption at time 0 and after incubation. Potential activities of hydrolytic and oxidative enzymes are expressed in mmol or mol g −1 Ch −1 and in mmol or mol m −2 h −1 using total dry mass of mineral soil for conversion.

Soil fungal community analysis

For DNA isolation from mineral soil samples, half of the suspension in LifeGuard Soil Preservation Solution (see above) was transferred to the wells of a Bead Plate from the PowerSoil-htp 96 Well Soil DNA Isolation Kit (Mo Bio, Carlsbad, CA, USA). After centrifugation and removal of the supernatant, the combined vacuum and centrifugation protocol of the manufacturer was followed. Cell lysis was carried out in a FastPrep-96 bead beater (MP Biomedicals, Santa Ana, CA, USA) twice at 6 m s −1 for 45 s with a 1 min break before the second lysis. To increase recovery of DNA from soil (Feinstein et al., 2009 ), new Bead Solution and Solution C1 were added to the soil pellet after the first extraction and the full extraction was repeated. Library preparation and Illumina MiSeq sequencing of fungal amplicons was conducted as described in Keiblinger et al. ( 2018 ). In brief, the fungal ITS2 region was amplified with the primer pair of ITS3Mix_NeXTf and ITS4Mix_NeXTr. Forward and reverse primers were equimolar mixes of modified versions of original primers published by White et al. ( 1990 ) as suggested by Tedersoo et al. ( 2015 ). Nextera XT adapters were attached to the 5′-end of the fungal-specific primers for subsequent indexing and high-throughput sequencing. Illumina MiSeq PE250 sequencing was performed at the NGS Unit of the Vienna Biocenter Core Facility GmbH (Vienna, Austria). Quantification of total fungal DNA was carried out using qPCR with FungiQuant primers targeting the SSU region (Liu et al., 2012 ) and following the protocol described in Unterwurzacher et al. ( 2018 ) with a modified assay volume of 10 µl. The qPCR standard was prepared by mixing equal amounts of genomic DNAs from Penicillium canescens NG_p02, Trichoderma harzianum NG_p29, and Tritirachium sp. gab0401. Total fungal DNA is expressed in µg DNA m −2 using total dry mass of mineral soil for conversion. Primers for sequencing and qPCR targeted different regions (ITS2 and SSU, respectively) in the rRNA gene cluster due to different requirements for specificity and sequence variability. Both regions are present in the same copy number per genome.

Sequence data analysis followed the steps outlined in Unterwurzacher et al. ( 2018 ) and Gorfer et al. ( 2021 ). Usearch scripts were used for chimaera detection and filtering of underrepresented sequences (< 10 reads in the full dataset). Vsearch (Rognes et al., 2016 ) was used for clustering and counting sequences per cluster given a 97% sequence similarity, which compensated for an artificial inflation of operational taxonomic units (OTU) numbers. Taxonomic affiliation of OTUs was carried out with the Utax script against the UNITE database (Kõljalg et al., 2013 ), while manual editing of the data increased phylogenetic accuracy (Hofstetter et al., 2019 ). When no accurate classification at the genus level was possible, the closest taxonomic level, to which a clear affiliation was possible, was used instead. Nonfungal sequences were excluded from further analyses. Fungal OTUs were affiliated to ecological lifestyles/guilds (Deltedesco et al., 2020 Gorfer et al., 2021 ) the lifestyles/guilds are: ectomycorrhizal fungi, other symbiotic fungi (e.g. species with unspecific mycorrhizal lifestyle or forming arbuscular mycorrhizas), saprotrophic ascomycetes, saprotrophic basidiomycetes, other saprotrophic fungi (e.g. Mortierella, Rhizophydiales, Mucor), pathogenic fungi, and those of unknown lifestyle (Table S3). For statistical community analysis (see below), fungal OTUs were taxonomically grouped at genus level or closest higher taxonomic level (e.g. family). Ratios between relative abundances of ectomycorrhizal fungi and saprotrophic fungal guilds were calculated for each plot.

Statistical analysis

All variables were averaged per plot before analyses. To assess soil fertility continuously, vascular plant’s Ellenberg indicator values for nutrients, soil reaction (a proxy for soil pH), and moisture were used. In brief, the indicator variables were analysed by means of principal component analysis (PCA Fig. S2). The scores of the first PCA axis, integrating the availability of soil resources to plants, were used to represent a ‘fertility index’. See Methods S2 for a detailed description of the calculated fertility index.

Variables were related to each other using linear regression models. Models were extended by a variogram correlation structure when residuals were spatially autocorrelated (Zuur et al., 2009 ). Differences in annual litter fall among fertility levels (Fig. S1) was tested by means of analysis of variance (ANOVA) to meet the criteria of ANOVA, data were log transformed before analysis.

Detrended correspondence analysis (DCA) was used to determine patterns among the fungal community in mineral soil (Paliy & Shankar, 2016 ). To study the effect of fertility on the fungal community, the fertility index was correlated to the DCA scores. To explore the role of fungi in SOM decomposition in greater detail, potential soil enzyme activities, microbial respiration, and mineral soil C : N ratios were additionally correlated to DCA scores. Canonical correspondence analysis (CCA) was used to investigate how much of the total variation was explained by the individual variables. The significances of the variables were tested by means of Monte Carlo permutation tests (n = 999). DCA and CCA were based on relative abundance of 352 taxonomic groups that occurred on ≥ 3 plots.

Level of significance was set at P < 0.05. Statistical analysis and plotting was conducted in R (R Core Team, 2017 ) using packages nlme (Pinheiro et al., 2014 ) and vegan (Oksanen et al., 2016 ).


8.17C: Fungi Habitat, Decomposition, and Recycling - Biology

Introduction to Biology of Fungi
OUTLINE

I. Brief Introduction to the Kingdom Fungi

II. Generalized Life Cycle of Fungi

III. Human-fungus Interactions


BRIEF INTRODUCTION TO THE KINGDOM FUNGI

The Kingdom Fungi is an ensemble of diverse species. Current evidence suggests that all fungal species are not derived from a single common ancestor, consequently the Fungi are polyphyletic (multiple genealogies or lineages).


I. COMMON CHARACTERISTICS OF FUNGI

1. Heterotrophy - 'other food'. There are three major categories of heterotrophs, which include the saprophytes, symbionts, and parasites. Saprophytes (feed on dead tissues or organic waste) symbionts (mutually beneficial relationship between a fungus and another organism) parasites (feeding on living tissue of a host). arasites that cause disease are called pathogens. Some parasites are obligate parasites (require a living host to survive), while others are facultative or nonobligate parasites (do not require a living host in order to survive).

Below: The sclerotium of Wolfiporia cocos or "tuckahoe" - the sclerotium is broken in two parts with a diameter of about 6 inches. Dug up from a flower bed near Jonesboro, AR. Photograph by M. Huss.

3. Fungus is often hidden from view. It grows through its food source (substratum), excretes extracellular digestive enzymes, and absorbs dissolved food.

4. Indeterminate clonal growth.

5. Spores - asexual (product of mitosis) or sexual (product of meiosis) in origin.

(a) Allows the fungus to move to new food source.
(b) Resistant stage - allows fungus to survive periods of adversity.
(c) Means of introducing new genetic combinations into a population.

6. Vegetative phase of fungus is generally sedentary.

7. Cell wall present, composed of cellulose and/or chitin.

8. Food storage - generally in the form of lipids and glycogen.

9. Eukaryotes - true nucleus and other organelles present.

10. All fungi require water and oxygen (no obligate anaerobes).

11. Fungi grow in almost every habitat imaginable, as long as there is some type of organic matter present and the environment is not too extreme.

12. Diverse group, number of described species is about 69,000 (estimated 1.5 million species total).


II. LIFE CYCLE OF A 'TYPICAL' FUNGUS

Generalized Life Cycle of Fungi

REFER TO DIAGRAM FROM CLASS NOTES or Figure 1-9 in the textbook.

Some fungi produce spores or other modified cells to reproduce sexually (perfect stage or the teleomorph), others to reproduce asexually (imperfect state or the anamorp), and some species are capable of reproducing both ways (holomorph).


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