Saprotrophic Fungal Biomass Research Articles

Long term effects of tillage and fertilization upon microbiota of a Romanian Chernozem under maize monoculture

The effects of agricultural practices upon soil microbiota were assessed in case of a long-term (42 years) tillage and fertilization experiment run on Chernozem soil under maize monoculture, as well as by comparing the experimental field with a grassland located nearby. We measured overall microbial biomass carbon (Cmic) as an indicator for total community size and ergosterol as a proxy for saprotrophic fungal biomass. We interpreted ergosterol: Cmic ratio as an indicator for community structure. Our findings showed that no till is characterized by a significantly increase in Cmic compared to chisel and mouldboard plough (+31% and + 16%, respectively). We further found that Cmic of the grassland was more than double the microbial biomass of experimental plots. Ergosterol concentration manifested the same tendency as overall microbial biomass across tillage treatments, however the impact was statistically significant only between zero tillage and chisel plough (+51%). Although ergosterol to Cmic ratio was higher in case of no till (+6% and + 17% compared to conventional tillage and chisel plough, respectively), the impact was not statistically significant. Similarly, moderate nitrogen fertilization (60 kg/ha) induced no significant effect whatsoever, a consequence that is attributed to the rather low dose applied.

Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings.

SummarySaprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose‐rich materials. Here, we examined if sawdust‐stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust‐amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2‐pulse‐labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA‐SIP) and nucleic acids (DNA‐SIP). Sawdust‐stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α‐Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate‐consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root‐associated microbiomes.

Site fertility and soil water-table level affect fungal biomass production and community composition in boreal peatland forests.

A substantial amount of below-ground carbon (C) is suggested to be associated with fungi, which may significantly affect the soil C balance in forested ecosystems. Ergosterol from in-growth mesh bags and litterbags was used to estimate fungal biomass production and community composition in drained peatland forests with differing fertility. Extramatrical mycelia (EMM) biomass production was generally higher in the nutrient-poor site, increased with deeper water table level and decreased along the length of the recovery time. EMM biomass production was of the same magnitude as in mineral-soil forests. Saprotrophic fungal biomass production was higher in the nutrient-rich site. Both ectomycorrhizal (ECM) and saprotrophic fungal community composition changed according to site fertility and water table level. ECM fungal community composition with different exploration types may explain the differences in fungal biomass production between peatland forests. Melanin-rich Hyaloscypha may indicate decreased turnover of biomass in nutrient-rich young peatland forest. Genera Lactarius and Laccaria may be important in nutrient rich and Piloderma in the nutrient-poor conditions, respectively. Furthermore, Paxillus involutus and Cortinarius sp. may be important generalists in all sites and responsible for EMM biomass production during the first summer months. Saprotrophs showed a functionally more diverse fungal community in the nutrient-rich site.

The hidden potential of saprotrophic fungi in arable soil: Patterns of short-term stimulation by organic amendments

Saprotrophic fungi are abundant in soils of (semi-)natural ecosystems, where they play a major role in ecosystem functioning. On the contrary, saprotrophic fungal biomass is remarkably low in intensively managed soils and this can have a negative impact on soil functioning. Nevertheless, arable soils harbour a diverse pool of fungi, which can be stimulated by organic amendments. Management targeted towards increasing soil organic matter often coincides with an increase of fungal biomass, but it can take years before effects are seen. However, a rapid stimulation of fungal biomass at the start of the growing season could immediately benefit crop production, by improving nutrient availability, soil structure and suppression of soil-borne diseases. The objective of this study is to realize a rapid increase of saprotrophic fungal biomass with organic amendments. In controlled pot experiments, dried and milled organic materials of different quality were added to an arable sandy soil. Ergosterol-based fungal biomass and ITS2-based fungal community structure were measured over a period of two months. Wood sawdust of deciduous tree species and paper pulp resulted in a high and lasting increase of fungal biomass, as opposed to transient effects given by cover crops and other non-woody plant materials. Little or no stimulation of fungi was seen for coniferous wood sawdust and agro-industrial by-products. Nitrogen immobilization induced by sawdust and paper pulp was compensated by supplementing mineral nitrogen, which enhanced the stimulation of saprotrophic fungi. The composition of the stimulated fungi was influenced by the quality of organic amendments. In particular, deciduous wood sawdust and paper pulp favoured saprotrophic ascomycete fungi (mainly Sordariomycetes), with no increment in potential plant-pathogenic fungi. Overall, our results point at a good perspective to use woody materials as sustainable soil improver via stimulation of saprotrophic fungi.

Water availability regulates negative effects of species mixture on soil microbial biomass in boreal forests

Soil microorganisms are critical for the maintenance of terrestrial biodiversity and ecosystem functions. Both plant diversity and water availability are individually known to influence soil microorganisms; however, their interactive effects remain largely unknown. Here, we investigated whether the effects of tree species mixtures on microbial biomass and composition were altered by water availability. This was accomplished by sampling soils in the growing season from stands that were dominated by Populus tremuloides and Pinus banksiana, respectively, and their relatively even mixtures under reduced (−25% throughfall), ambient, and added (+25% throughfall) water. Microbial community biomass and composition were determined by phospholipid fatty acid analysis. We found that water addition increased soil total microbial biomass and by individual groups, whereas water reduction had no effect. Under ambient water conditions, soil total microbial biomass, arbuscular mycorrhizal fungal, bacterial, gram-positive (GP) bacterial, and gram-negative (GN) bacterial biomass were significantly lower in mixtures than from those of constituent monocultures, but saprotrophic fungal biomass and the ratios of fungal/bacterial and GP/GN bacteria were not significantly affected by tree species mixtures. Water reduction increased species mixture effects on total and individual group microbial biomass from negative to neutral, while water addition only increased mixture effects on arbuscular mycorrhizal fungal and GP bacterial biomass. Across all water treatments, soil total and individual group microbial biomass significantly increased with the abundance of broadleaved trees, but only weakly with species richness. Further, microbial community compositions differed significantly with both overstory type and water treatment. Microbial community compositions exhibited strong associations with tree species richness, soil moisture, soil pH, and litterfall production, whereas microbial biomass did not. Our results suggest that higher species diversity is not always of benefit for soil microorganisms; however, mixed tree species have the potential to regulate ecosystem responses to climate change.

Spatio-temporal heterogeneity in extracellular enzyme activities tracks variation in saprotrophic fungal biomass in a temperate hardwood forest

Saprotrophic fungi are the dominant producers of organic matter-degrading extracellular enzymes in forest soils, but the extent to which they drive spatio-temporal variation in enzyme activities is unclear. We quantified the relationships between saprotrophic fungal biomass and enzyme activities in a mature temperate hardwood forest by placing soil-filled ingrowth bags inside trenches. Trenches were located in replicate stands (n = 7) dominated by either arbuscular mycorrhizal (AM)- or ectomycorrhizal (ECM)-associated tree species, which reflect differences in soil substrate quality and nutrient availability. Additionally, we assessed the extent to which the relationships between saprotrophic fungal biomass and enzyme activities varied across seasons and were altered by experimental nitrogen (N) addition. Overall, both fungal production and enzyme activities differed between mycorrhizal types and across seasons, but were unaffected by N addition. Additionally, enzyme activities exhibited strong, positive relationships with saprotrophic fungal biomass. However, the relative production of carbon (C)-degrading enzymes was greater in stands dominated by AM-associated trees in the late growing season, and the relative production of N-degrading enzymes was greater in the late growing season across both AM- and ECM-dominated forest stands. These patterns reflected tree- and season-driven changes in microbial C and N limitation. As such, while the common assumption that microbial biomass and enzyme activities are positively correlated is robust for saprotrophic fungi, enzyme produced per unit biomass may not be consistent among stands and across seasons.

Ectomycorrhizal and saprotrophic soil fungal biomass are driven by different factors and vary among broadleaf and coniferous temperate forests

Functionally, ectomycorrhizal (ECM) and saprotrophic (SAP) fungi belong to different guilds, and they play contrasting roles in forest ecosystem C-cycling. SAP fungi acquire C by degrading the soil organic material, which precipitates massive CO2 release, whereas, as plant symbionts, ECM fungi receive C from plants representing a channel of recently assimilated C to the soil. In this study, we aim to measure the amounts and identify the drivers of ECM and SAP fungal biomass in temperate forest topsoil. To this end, we measured ECM and SAP fungal biomass in mineral topsoils (0–12 cm depth) of different forest types (pure European beech, pure conifers, and mixed European beech with other broadleaf trees or conifers) in a range of about 800 km across Germany; moreover, we conducted multi-model inference analyses using variables for forest and vegetation, nutritive resources from soil and roots, and soil conditions as potential drivers of fungal biomass. Total fungal biomass ranged from 2.4 ± 0.3 mg g−1 (soil dry weight) in pure European beech to 5.2 ± 0.8 mg g−1 in pure conifer forests. Forest type, particularly the conifer presence, had a strong effect on SAP biomass, which ranged from a mean value of 1.5 ± 0.1 mg g−1 in broadleaf to 3.3 ± 0.6 mg g−1 in conifer forests. The European beech forests had the lowest ECM fungal biomass (1.1 ± 0.3 mg g−1), but in mixtures with other broadleaf species, ECM biomass had the highest value (2.3 ± 0.2 mg g−1) among other forest types. Resources from soil and roots such as N and C concentrations or C:N ratios were the most influential variables for both SAP and ECM biomass. Furthermore, SAP biomass were driven by factors related to forest structure and vegetation, whereas ECM biomass was mainly influenced by factors related to soil conditions, such as soil temperature, moisture, and pH. Our results show that we need to consider a complex of factors differentially affecting biomass of soil fungal functional groups and highlight the potential of forest management to control forest C-storage and the consequences of changes in soil fungal biomass.

Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization

Cattle farmyard manure application is an important tool for maintaining soil fertility in organic agriculture, especially in biodynamic systems. The first objective was to investigate whether application of biodynamic preparations (CMBD treatment) causes positive effects additional to those of composted cattle farmyard manure fertilization (CM treatment). The second objective was to investigate the response of microbial cell-wall and cell-membrane biomarkers to the CM and CMBD treatments in comparison with inorganic fertilization plus straw return (MIN treatment). The third objective was to re-assess conversion values from the phospho-lipid fatty acid (PLFA) 16:1ω5 to arbuscular mycorrhizal fungal (AMF) biomass as well as those from ergosterol and the PLFA 18:2ω6,9 to saprotrophic fungal biomass. Application of biodynamic preparations did not cause any positive effects additional to those of composted farmyard manure fertilization. In the CM and CMBD treatments, bacterial PLFA content was 33% higher than in the MIN treatment, whereas bacterial muramic acid (MurN) content was 55% higher. The AMF indicator PLFA 16:1ω5 as well as neutral lipid fatty acid (NLFA) 16:1ω5 were both increased by roughly 80%, as the NLFA/PLFA ratio of 16:1ω5 varied only in a small range around 3.8. This indicates negligible interference from bacteria, suggesting that PLFA 16:1ω5 is a suitable marker for AMF biomass in soil. The indicators for saprotrophic fungi, the ergosterol content and the contribution of 18:2ω6,9 to total PLFA (mol%) were 40 and 60% higher, respectively, in the CM and CMBD than in the MIN treatments. In contrast, fungal GlcN was not affected by the fertilizer treatments. An increased ergosterol/fungal GlcN ratio indicates a shift in fungal community from AMF towards saprotrophic fungi in arable soils.

Belowground carbon allocation by trees, understory vegetation and soil type alter microbial community composition and nutrient cycling in tropical Eucalyptus plantations

We studied the influence of plant functional groups on soil microbial community composition and nutrient cycling in a tropical Eucalyptus forest ecosystem with different plantation age and soil types by means of stem girdling (SG) and understory removal (UR). Fungal and bacterial communities were characterized using phospholipid fatty acids, and ectomycorrhizal fungi (EMF) colonisation was estimated visually. Total bacterial and saprotrophic fungal biomass was highest in soils treated with SG, followed by UR, through modification of plant belowground C allocation and N supply. EMF root colonisation, biomass of EMF, arbuscular mycorrhizal fungi (AMF) and the fungal-to-bacterial ratio were lowest in these soils. We found that EMF, AMF and the fungal-to-bacterial ratio were highest in sandy loam soils with a high C/N ratio and low pH. The fungal-to-bacterial ratio was higher in 5-year-old than in 15-year-old plantation. We propose that girdling of trees and removal of understory plants are important ecological components, due to their modification of plant belowground C allocation and N supply as key determinants of microbial community composition. Our results highlight the fact that soil abiotic factors play an important role in shaping the microbial community and nutrient cycling in tropical forest ecosystems.

Soil disturbance alters plant community composition and decreases mycorrhizal carbon allocation in a sandy grassland

We have studied how disturbance by ploughing and rotavation affects the carbon (C) flow to arbuscular mycorrhizal (AM) fungi in a dry, semi-natural grassland. AM fungal biomass was estimated using the indicator neutral lipid fatty acid (NLFA) 16:1ω5, and saprotrophic fungal biomass using NLFA 18:2ω6,9. We labeled vegetation plots with (13)CO(2) and studied the C flow to the signature fatty acids as well as uptake and allocation in plants. We found that AM fungal biomass in roots and soil decreased with disturbance, while saprotrophic fungal biomass in soil was not influenced by disturbance. Rotavation decreased the (13)C enrichment in NLFA 16:1ω5 in soil, but (13)C enrichment in the AM fungal indicator NLFA 16:1ω5 in roots or soil was not influenced by any other disturbance. In roots, (13)C enrichment was consistently higher in NLFA 16:1ω5 than in crude root material. Grasses (mainly Festuca brevipila) decreased as a result of disturbance, while non-mycorrhizal annual forbs increased. This decreases the potential for mycorrhizal C sequestration and may have been the main reason for the reduced mycorrhizal C allocation found in disturbed plots. Disturbance decreased the soil ammonium content but did not change the pH, nitrate or phosphate availability. The overall effect of disturbance on C allocation was that more of the C in AM fungal mycelium was directed to the external phase. Furthermore, the functional identity of the plants seemed to play a minor role in the C cycle as no differences were seen between different groups, although annuals contained less AM fungi than the other groups.

Long-term effects of organic farming on fungal and bacterial residues in relation to microbial energy metabolism

Samples from the bio-dynamic, bio-organic, and conventional trial, Therwil, Switzerland, were analyzed with the aim of determining the effects of organic land use management on the energy metabolism of the soil microbial biomass and on the fraction of microbial residues. The contents of adenylates, adenosine triphosphate (ATP), glucosamine, muramic acid, and galactosamine were significantly largest in the biodynamic organic farming (BYODIN) treatment and significantly lowest in the conventional farming treatment with inorganic fertilization (CONMIN). In contrast, the ergosterol-to-ATP ratio and fungal C-to-bacterial C ratios were significantly lowest in the BYODIN treatment and significantly largest in the CONMIN treatment. No clear treatment effects were observed for the ergosterol content and the adenylate energy charge (AEC), the ATP-to-microbial biomass C ratio and the ergosterol-to-fungal C ratio. Ergosterol, an indicator for saprotrophic fungal biomass, and fungal residues were significantly correlated. The microbial biomass carbon-to-nitrogen ratio showed a negative relationship with the AEC and strong positive relationships with the ratios ergosterol-to-microbial biomass C, ergosterol-to-ATP and fungal C-to-bacterial C. In conclusion, the long-term application of farmyard manure in combination with organic farming practices led to an increased accumulation of bacterial residues.

Measuring external mycelia production of ectomycorrhizal fungi in the field: the soil matrix matters

Assessing mycorrhizal fungi production in field settings has been hindered by the inability to measure external mycelia. Recently, external mycelia production was measured in the field using a novel in-growth core technique with acid-washed sand as the in-growth matrix. Here, we tested the assumption that external mycelia production in acid-washed sand is representative of that in native soil. External mycelia production was estimated as the difference in fungal growth between closed (allowing only saprotrophic fungal production) and open (allowing mycorrhizal and saprotrophic fungal production) cores using a factorial design of soil matrices (acid-washed sand vs native) and fertilization treatments (control vs nitrogen (N)) in a longleaf pine (Pinus palustris) plantation. In native soils, the ectomycorrhizal to saprotrophic fungal biomass signal was strong and consistent facilitating the assessment of external mycelia production, which was 300% higher than corresponding rates in acid-washed sand and inversely correlated with soil N. These results demonstrate the efficacy and importance of using native soil as the in-growth matrix to measure ectomycorrhizal fungi external mycelia production in field settings.

Using lipid analysis and hyphal length to quantify AM and saprotrophic fungal abundance along a soil chronosequence

We evaluate the use of signature fatty acids and direct hyphal counts as tools to detect and quantify arbuscular mycorrhizal (AM) and saprotrophic fungal (SF) biomass in three Hawaiian soils along a natural soil fertility gradient. Phospholipids16:1ω5c and 18:2ω6,9c were used as an index of AM and saprotrophic fungal biomass, respectively. Both phospholipid analysis and hyphal length indicated that the biomass of AMF was greatest at the highest fertility site, and lowest where phosphorus limits plant growth. Saprotrophic fungal biomass did not vary. Hyphal length counts appeared to under-estimate SF abundance, while the phospholipid AMF:SF ratio was in line with expectations. This study indicates that phospholipids may be a valuable and reliable tool for studying the abundance, distribution, and interactions between AM and saprotrophic fungi in soil.