Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers

Organic matter decomposition in the globally widespread coniferous forests has an important role in the carbon cycle, and cellulose decomposition is especially important in this respect because cellulose is the most abundant polysaccharide in plant litter. Cellulose decomposition was 10 times faster in the fungi-dominated litter of Picea abies forest than in the bacteria-dominated soil. In the soil, the added (13)C-labelled cellulose was the main source of microbial respiration and was preferentially accumulated in the fungal biomass and cellulose induced fungal proliferation. In contrast, in the litter, bacterial biomass showed higher labelling after (13)C-cellulose addition and bacterial biomass increased. While 80% of the total community was represented by 104-106 bacterial and 33-59 fungal operational taxonomic units (OTUs), 80% of the cellulolytic communities of bacteria and fungi were only composed of 8-18 highly abundant OTUs. Both the total and (13)C-labelled communities differed substantially between the litter and soil. Cellulolytic bacteria in the acidic topsoil included Betaproteobacteria, Bacteroidetes and Acidobacteria, whereas these typically found in neutral soils were absent. Most fungal cellulose decomposers belonged to Ascomycota; cellulolytic Basidiomycota were mainly represented by the yeasts Trichosporon and Cryptococcus. Several bacteria and fungi demonstrated here to derive their carbon from cellulose were previously not recognized as cellulolytic.     

Microbial decomposition of reed (Phragmites communis) leaves in a saline lake

Microbial colonization and its relation to the decomposition of reed (Phragmites communis) leaf litter were studied in the littoral area of a saline lake from autumn to summer using litter bag method. There was considerable fungal population on the leaves at the beginning of submergence. These fungi were probably terrestrial in origin. The fungal population rapidly disappeared few days after submergence, when bacteria, including cellulolytic and xylanolytic types, proliferated. Associated with this rapid colonization of bacteria, decomposition rates of cellulose and xylan increased. The rates declined from day 39 to day 100 with decreasing water temperature, though cellulolytic and xylanolytic bacteria maintained a sizeable population until day 150. A community of cellulolytic and xylanolytic fungi increased steeply after day 150. It coincided with a second increase in decomposition rate. These results suggest that the principal decomposers of reed leaf litter were bacteria in the initial phase and fungi in the later phase of the experiment.     

Studies on soil fungi III. Seasonal variation and distribution of microfungi in some soils of Andhra Pradesh (India)

The seasonal variation and distribution of microfungi in four soil types collected from two districts of Andhra Pradesh (India) were studied.Besides soil type and surface vegetation, it appears from the present study that soil moisture, organic matter, potassium, calcium, iron and phosphorus contents also may affect the fungal numbers favourably, while chlorides, total soluble salts, total nitrogen and manganese contents may have an adverse effect.Even alkaline soils harbour greater numbers of fungi, but small fluctuations in the pH seem to influence the fungal numbers in soils inversely.A total of 101 species representing 43 genera were isolated. These included 18 Phycomycetes, 5 Ascomycetes, 72 Fungi Imperfecti, 5 Mycelia Sterilia and a single Myxomycete. The order of occurrence of the chief genera of fungi isolated wasAspergillus, Penicillium, Fusarium, Pythium, Curvularia, Phoma, Cunninghamella, Rhizopus, Alternaria andTrichoderma.A large number of genera and species were found common to the forest, maize field, garden and uncultivated soils; and the fungal flora was also not very much different from those recorded from various parts of the world.     

Colonization ofRetama raetam seeds by fungi and their significance in seed germination

Examination by scanning electron microscopy and incubation on potato-dextrose agar medium showed that dry seeds ofRetama raetam were externally free of fungi. When planted in sandy loam soil, the seeds become colonized with eleven soil-borne fungal species. The fungi were isolated on cellulose agar, pectin agar and lignin agar media.Aspergillus flavus, A. niger, A. fumigatus, Penicillium capsolatum andFusarium oxysporum had broad occurrence and were recovered on all the three media. The production of hydrolytic enzymes by the isolated fungi depends on the substrate and species.Penicillium capsolatum, P. spinulosum andA. niger had wide enzymatic amplitude and they were able to produce cellulolytic, pectolytic and lignolytic activities on corresponding substrates as well as on seed-coat-containing media. The lignolytic activities of the isolated species exceptChaetomium bostrychodes andTrichoderma viride were enhanced by applying the seed-coat materials as C- source rather than lignin. SoakingR. raetam seeds in culture filtrates of most of the fungi grown on seed-coat-supplemented media induced a pronounced and distinct stimulating effect on seed germination. The most effective filtrates were those ofP. capsolatum, P. spinulosum andSporotrichum pulverulentum.     

N concentration controls decomposition rates of different strains of ectomycorrhizal fungi

The decomposition of soil organic matter in forest ecosystems is important in two ways. First, soil organic matter is the largest pool of C in terrestrial ecosystems, so understanding global carbon cycling requires an appreciation of the factors that control the size of that pool and the fluxes through it. Among these factors are those that control the rate of organic matter decomposition. Second, organic matter decomposition is the major process controlling the supply of nutrients to plants. In some ecosystems ectomycorrhizal fungi comprise a surprisingly large fraction of soil organic matter. However, little is known of the rates of decomposition of ectomycorrhizal fungi, or of the factors that control those rates. Therefore, we set out to examine the relationship between N concentrations and decomposition rates of ectomycorrhizal fungi using a wide variety of strains isolated from a Pinus resinosa plantation. We found that substantial variation among strains existed in decomposition rate, and that decomposition rate was highly correlated with tissue N concentration. We conclude, therefore, that the structures of ectomycorrhizal fungal communities may be ecologically important in terms of ecosystem C and N dynamics.     

Decomposition rate of organic substrates in relation to the species diversity of soil saprophytic fungi

Despite the great interest concerning the relationship between species diversity and ecosystem functioning, there is virtually no knowledge as to how the diversity of decomposer microbes influences the decomposition rate of soil organic matter. We established a microcosm study in which the number of soil fungi was investigated in relation to the systems ability to (i) degrade raw coniferous forest humus, and (ii) use resources that were either added to the systems or released into the soils after a disturbance (drought). With the exception of the most diverse treatment, in each of the six replicates of each of the six diversity treatments (1, 3, 6, 12, 24 or 43 taxa), fungal taxa were randomly chosen from a pool of 43 commonly isolated fungal species of raw humus. Two months after initiation of the study CO₂ production increased as fungal diversity increased, but in the species-poor end of the diversity gradient only. Addition of various energy resources to the microcosms generally increased the level of soil respiration but did not affect the shape of the diversity-CO₂-production curve. Rewetting the soil after severe drought resulted in a rapid flush of CO₂, particularly in the most diverse communities. The biomass of the fungi in the non-disturbed soils, and soil NH₄-N concentration and soil pH in both disturbed and non-disturbed systems were slightly but significantly higher in the diverse than in the simple systems. Fungal species richness had no influence on the organic matter content of the humus at the end of the experiment. The results suggest that the functional efficiency of fungal communities can increase with the number of fungal taxa. This diversity effect was, however, significant at the species-poor end of the diversity gradient only, which implies considerable functional equivalency (redundancy) among the decomposer fungi.     

Effectiveness of Hirsutella minnesotensis and H. rhossiliensis in control of the soybean cyst nematode in four soils with various pH,texture, and organic matter

The parasitism of soybean cyst nematode, Heterodera glycines, by the fungi Hirsutella rhossiliensis and Hirsutella minnesotensis and their biocontrol effectiveness against the nematode were investigated in four soils with various pH, texture, and organic matter. Fungal parasitism was assayed in the soils in 25 mL vials. As expected, percentage of H. glycines second-stage juveniles (J2) parasitized by either fungus increased with increasing number of fungus-colonized J2 initially added into the soils. Parasitism of J2 by the fungi was negatively related with soil pH. Both positive and negative relationships with fungal parasitism were observed for soil sandiness and organic matter. In greenhouse study, both fungi at 0.2–0.8 g fresh mycelium of liquid culture per 0.3 L pot and 1% corn-grits culture effectively reduced nematode population density. The relationship between biocontrol effectiveness and the soil factors depended on fungal species and inoculation levels. In general, percentage reduction of egg population density in the soil was negatively correlated with soil pH and positively correlated with sandiness. There was no or weak correlation between egg reduction and organic matter. The percentage of J2 parasitized by the fungi 2 months after planting did not correlate with the soil factors. Plant growth was better in the two soils with intermediate pH and sand than the soil with high pH and low sand or with low pH and high sand. It appeared that soil pH and/or texture are important in influencing biocontrol effectiveness, but further studies are needed to determine the effect of individual factors because they are correlated.     

Fungal succession and decomposition of <Emphasis Type="Italic">Camellia japonica</Emphasis> leaf litter

Decomposition processes of Camellia japonica leaf litter were investigated over an 18-month period with reference to the role of fungal succession in the decomposition of lignin and holocellulose. Decomposition and fungal succession were studied in bleached and nonbleached portions of litter, which were precolonized by ligninolytic and cellulolytic fungi, respectively. Coccomyces nipponicum and Lophodermium sp. (Rhytismataceae), which can attack lignin selectively, caused mass loss of lignin and were responsible for bleaching during the first 4 months (stage I), whereas cellulolytic fungi caused mass loss of holocellulose in adjacent nonbleached portions. Soluble carbohydrates and polyphenols also decreased rapidly during this stage. Pestalotiopsis guepini, coelomycete sp.1, and the Nigrospora state of Khuskia oryzae caused mass loss of holocellulose between 4 and 14 months (stage II) and Xylaria sp. caused mass loss of both lignin and holocellulose from 14–18 months (stage III). In stages II and III, decomposition was more rapid in bleached portions than in nonbleached portions probably due to the prior delignification of lignified holocellulose in bleached portions. Frequencies of these fungi showed different responses among species to the pattern of changes in lignin and holocellulose contents during decomposition. Total hyphal length increased in both portions over the study period, but mycelia of basidiomycetes accounted for about 2% of total hyphal length, suggesting that their role in fungal succession and decomposition was low. Lignin and nitrogen contents were consistently lower and holocellulose content was higher in bleached portions than in nonbleached portions during decomposition. The succession of ligninolytic and cellulolytic fungi was a major driving factor that promoted decomposition and precolonization by ligninolytic fungi enhanced decomposition.     

Isolation of Cellulolytic Fungi from Waste of Castor (<Emphasis Type="Italic">Ricinus communis</Emphasis> L.)

This is the first report of isolation of fungi present in fatty and defatted castor bean meal as well as the first of crop’s selection to test the cellulolytic potential, in order to verify the diversity and potential of cellulolytic fungi in castor bean waste (Ricinus communis L.). For the screening on solid medium, it was used carboxymethylcellulose (CMC) as the sole carbon source. The microcrystalline cellulose (Avicel) was used as a substrate for submerged fermentation for production of cellobiohydrolase (FPase) and the CMC to produce endoglucanases (CMCase) and β-glycosidases (BG). 189 cultures of fungi were isolated, including 40 species of filamentous fungi and three yeasts. The Aspergillus was the most frequent found genus. Regarding the distribution of isolated species from defatted castor bean meal, the A. niger was the most frequent one; and within the fatty castor bean meal, the Emericela variecolor prevailed among other species. Among the 67 fungal cultures tested in the initial screening on solid media to assess the cellulolytic potential, 54 disclosed Cellulolytic Index (CI) ranging from 1.04 to 6.00 mm. The isolates were selected for enzyme production in liquid medium with values above 2.0 CI. They were obtained with A. japonicus URM5620 FPase activity (4.99 U/ml) and BG (0.05 U/ml), and Rhodotorula glutinis URM5724 activity of CMCase 3.58 U/ml. These cases occurred after 168 h of submersion for both species of fungi. In our study, we could conclude that the castor bean is a promising source of fungi capable of producing cellulolytic enzymes.     

Studies on microbial antagonism in the establishment of clover pasture

Summary Fungi inhabiting soil recently cleared of the native vegetation have been isolated and compared with those isolated from under established clover pastures, Three methods of isolation of the fungi were used in each situation, and profoundly influenced the population obtained.In newly cleared soils the composite fungal population pattern deduced all three isolation methods comprised species of Mortierella, Phoma, Trichoderma, Penicillium, Fusarium, Sclerotium and non-sporing mycelia. In soil supporting established clover pastures the main rhizosphere fungi were species of Fusarium, Aspergillus, Phoma, Curvularia, Macrophomina, Sclerotium and one Ascomycete.Fusarium oxysporum was the most frequently isolated fungus.Conventional plating techniques suggested that the dominant fungi in the rhizosphere of clover wereFusarium oxysporum andAspergillus versicolor, whereas isolation of fungi from hyphae adhering to the clover roots indicated that species of Macrophomina, Curvularia and an Ascomycete were the most abundantly occurring organisms. In the case of the root residues of the native vegetation in newly cleared soils plating techniques resulted in species of the freely sporing Mortierella, Trichoderma, Aspergillus, Fusarium and Penicillium occurring most frequently, whereas the isolation of fungi from hyphal strands on the residues gave a population pattern dominated by species of Mortierella, Phoma, Sclerotium, and non-sporing mycelia.The study indicated a marked succession of fungal species during the decomposition of the root debris in newly cleared soils, and also that some early members of this changing population might exert an adverse effect on the establishment of clover.     

Isolation of keratinolytic fungi from a coal mine dump

During the study of fungal succesion in the coal mine dump in Brzezinka (Poland), soil samples were examined for keratinolytic fungi. These micro-organisms were rather poorly represented in the area studied. Out of 300 soil samples examined, only 48 (16%) were positive for keratinolytic fungi.Trichophyton ajelloi andArthroderma curreyi were the prevailing species. These species occurred practically at two locations, i.e. on the naked carbon rocks inhabited by algae crops (chiefly byCyanophyta) and in the pine litter. It can be supposed that the occurrence of keratinolytic fungi was more dependent on the favourable general conditions such as increasing organic matter content, microflora, and humidity than on the presence of keratin remains in the soil. Because of the lack of potentially pathogenic fungi, the coal mine dump examined cannot be considered as an important source of fungal infection.     

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance.     

Eisenia fetida (Oligochaeta, Lumbricidae) Activates Fungal Growth, Triggering Cellulose Decomposition During Vermicomposting

Cellulose is the most abundant polymer in nature and constitutes a large pool of carbon for microorganisms, the main agents responsible for soil organic matter decomposition. Cellulolysis occurs as the result of the combined action of fungi and bacteria with different requirements. Earthworms influence decomposition indirectly by affecting microbial population structure and dynamics and also directly because the guts of some species possess cellulolytic activity. Here we assess whether the earthworm Eisenia fetida (Savigny 1826) digests cellulose directly (i.e., with its associated gut microbiota) and also whether the effects of E. fetida on microbial biomass and activity lead to a change in the equilibrium between fungi and bacteria. By enhancing fungal communities, E. fetida would presumably trigger more efficient cellulose decomposition. To evaluate the role of E. fetida in cellulose decomposition, we carried out an experiment in which pig slurry, a microbial-rich substrate, was treated in small-scale vermireactors with and without earthworms. The presence of earthworms in vermireactors significantly increased the rate of cellulose decomposition (0.43 and 0.26% cellulose loss day⁻¹, with and without earthworms, respectively). However, the direct contribution of E. fetida to degradation of cellulose was not significant, although its presence increased microbial biomass (C_mic) and enzyme activity (cellulase and β-glucosidase). Surprisingly, as fungi may be part of the diet of earthworms, the activity of E. fetida triggered fungal growth during vermicomposting. We suggest that this activation is a key step leading to more intense and efficient cellulolysis during vermicomposting of organic wastes.     

Nitrogen availability affects saprotrophic basidiomycetes decomposing pine needles in a long term laboratory study

Fungi, especially basidiomycetous litter decomposers, are pivotal to the turnover of soil organic matter in forest soils. Many litter decomposing fungi have a well-developed capacity to translocate resources in their mycelia, a feature that may significantly affect carbon (C) and nitrogen (N) dynamics in decomposing litter. In an eight-month long laboratory study we investigated how the external availability of N affected the decomposition of Scots pine needles, fungal biomass production, N retention and N-mineralization by two litter decomposing fungi – Marasmius androsaceus and Mycena epipterygia. Glycine additions had a general, positive effect on fungal biomass production and increased accumulated needle mass loss after 8 months, suggesting that low N availability may limit fungal growth and activity in decomposing pine litter. Changes in the needle N pool reflected the dynamics of the fungal mycelium. During late decomposition stages, redistribution of mycelium and N out from the decomposed needles was observed for M. epipterygia, suggesting autophagous self degradation.     

Aquatic Actinomycete-Fungal Interactions and Their Effects on Organic Matter Decomposition: A Microcosm Study

The role of fungi in the decomposition of organic matter in streams has been well examined, although the role of bacterial antagonists in such processes has gained little attention. To examine bacterial-fungal interactions, experiments involving pairwise combinations of four actinomycete isolates (A1+ and A2+ could remove chitin from chitin-containing media, and A1? and A2? could not) and two fungal isolates (F+ a true fungus, F? an oomycote) were conducted. For each bacterial-fungal combination, 250-ml microcosms were sampled at 8 day intervals for 32 days. Microbial biomass and organic matter, as well as the activities of five extracellular enzymes, were measured. Each experiment consisted of a control group and four treatment groups. Controls comprised sterilized stream water and macrophytes. The first treatment was inoculated with only actinomycetes (~103 cells ml-1), the second treatment was inoculated with only fungi (~102 cells ml-1), the third group was inoculated simultaneously with actinomycetes and fungi, and the fourth group was inoculated with actinomycetes 2 days after fungal establishment. For all combinations, the lowest rates of organic matter decomposition were expected in the controls, as a result of only physical degradation. In contrast, the greatest rates of organic matter decomposition were predicted in treatments inoculated with F+ 2 days prior to A1? or A2?. Greater than 50% of the organic matter was decomposed in each of the fungal treatments. Fungal-actinomycete interactions resulted in reduced fungal biomass relative to the fungal-only treatments. However, when inoculated 2 days apart, combinations of F? and actinomycetes resulted in enhanced rates of organic matter decomposition, as well as greater levels of extracellular enzyme activities. These results demonstrate that actinomycete-fungal interactions and their colonization dynamics affect the accumulation of biomass, extracellular enzyme activities, and rates of organic matter decomposition.     

Microbial mineralization of organic phosphate in soil

Summary Phosphate-dissolving microorganisms were isolated from non-rhizosphere and rhizosphere of plants. These isolates included bacteria, fungi and actinomycetes. In broth cultures, Gram-negative short rod,Bacillus andStreptomyces species were found to be more active in solubilizing phosphate thanAspergillus, Penicillium, Proteus, Serratia, Pseudomonas andMicrococcus spp. The sterile soils mixed with isolated pure culture showed slower mineralization of organic phosphate than that of non-sterile soil samples at all incubation periods. Maximum amount of phosphate mineralization by isolated microorganisms were obtained at the 60th and the 75th day of incubation in sterile and non-sterile soils respectively. The mixed cultures were most effective in mineralizing organic phosphate and individuallyBacillus sp. could be ranked next to mixed cultures. Species ofPseudomonas andMicrococcus were almost the same as that of the control under both sterile and non-sterile conditions.     

Fibrinolytic activity of some fungi isolated from self-heated composted fertilizer

Mesophilic fungi isolated from organic fertilizer compost samples accounted for 70.94% of the total fungal count, while thermophilic and thermotolerant fungi constituted 29.05% of that count. Eight mesophilic fungal species, namelyAspergillus niger, Monilia sitophila, Paecilomyces divaricata, Penicillium chrysogenum, P. fellutanum, Scopulariopsis brevicaulis, S. brumptii andZygorhynchus japonicus; two thermophilic fungiHumicola grisea andOidiodendron flavum and three thermotolerant speciesAspergillus fumigatus, Thermomyces lanuginosus andZygorhynchus vuilleminii were isolated during the study. Most of the tested fungi showed a proteolytic activity and liquified gelatin in the test tube method and in cup plates. The thermophilic fungusO. flavum was the most potent proteolytic fungus. The comparative fibrinolytic assay revealed the following sequence in the ability of the tested fungi to hydrolyse fibrin:O. fiavum>S. brevicaulis>H. grisea>A. fumigatus>T. lanuginosus.     

Influence of soil organic matter decomposition on arbuscular mycorrhizal fungi in terms of asymbiotic hyphal growth and root colonization

Soil organic matter is known to influence arbuscular mycorrhizal (AM) fungi, but limited information is available on the chemical components in the organic matter causing these effects. We studied the influence of decomposing organic matter (pure cellulose and alfalfa shoot and root material) on AM fungi after 30, 100, and 300 days of decomposition in nonsterile soil with and without addition of mineral N and P. Decomposing organic matter affected maize root length colonized by the AM fungus Glomus claroideum in a similar manner as other plant growth parameters. Colonized root length was slightly increased by both nitrogen and phosphorus application and plant materials, but not by application of cellulose. In vitro hyphal growth of Glomus intraradices was increased by soil extracts from the treatments with all types of organic materials independently of mineral N and P application. Pyrolysis of soil samples from the different decomposition treatments revealed in total 266 recognizable organic compounds and in vitro hyphal growth of G. intraradices in soil extract positively correlated with 33 of these compounds. The strongest correlation was found with 3,4,5-trimethoxybenzoic acid methyl ester. This compound is a typical product of pyrolysis of phenolic compounds produced by angiosperm woody plants, but in our experiment, it was produced mainly from cellulose by some components of the soil microflora. In conclusion, our results indicate that mycelia of AM fungi are influenced by organic matter decomposition both via compounds released during the decomposition process and also by secondary metabolites produced by microorganisms involved in organic matter decomposition.     

Continuous single cell protein production fromCellulomonas sp. andCandida utilis grown in mixture on barley straw

Summary Continuous fermentations with mixed cultures of the cellulolytic bacteriaCellulomonas sp. and the yeastCandida utilis were examined. Fermentations were carried out in an aerated 5-l fermenter with different preparations of wet disintegrated barley straw as the cellulose source (3.6–4.2%). The straw was pretreated with NaOH (3.2–8.5 kg NaOH/100 kg dry straw) under high pressure and temperature in a feedstuff pellet press. The quantity of dry cell mass produced and the breakdown of the straw were measured. Crude protein and ash content in cell dry matter and residual fiber were determined. The experiments showed thatCellulomonas sp. andCandida utilis may be grown together in a continuous culture (dilution rate D=0.12–0.14 h^–1) for at least 3 days without washing out one of the organisms. Highest productivity was 1.39 g cell dry matter/l/h when using straw pretreated with 5.7% NaOH. The dry cell product contained 58–66% crude protein and up to 51% of the organic fiber dry matter was solubilized. The yield constants were 0.32–0.61 g cell dry matter per g solubilized organic fibers.