Micromycetes in podzolic and bog-podzolic soils in the middle taiga subzone of northeastern European Russia

The qualitative and quantitative characteristics of the mycobiota in podzolic and bog-podzolic soils were studied in the middle taiga subzone (the Republic of Komi). The complex of micromycetes was found to include 73 species of 18 genera from the Zygomycota and Ascomycota orders and from the formal class of anamorphic fungi. The latter has the following specific features: many forms of sterile mycelium, the predominance of Penicillium species (25), the constant presence of Mucor and Trichoderma species, and single Aspergillus species. With increasing moisture in the sequence of the podzolic, surface-gleyic podzolic, peaty podzolic-gleyic, and peat podzolic-gley soils, the dominant soil fungi are preserved, but the species composition of the micromycete complexes becomes poorer due to the removal of rare species. In the podzolic and bog-podzolic soils, fungi absolutely predominate in the microbial biomass. They accounted for more than 99% of the total biomass, 1–6% of the latter is the biomass of spores, and more than 94% falls on mycelium. In these soils, the reserves of bacterial biomass, as compared to those of fungi, are lower by two orders of magnitude.     

Fraxinus-Glomus-Pisolithus symbiosis: Plant growth and soil aggregation effects

It has been established that arbuscular mycorrhizal (AM) fungi are involved in the conservation of soil structure. However, the effect of ectomycorrhizal (EM) fungi alone or in interaction with AM fungi in soil structure has been much less studied. This experiment evaluated EM and AM fungi effects on soil aggregation and plant growth. Ash plants (Fraxinus uhdei) were grown in pots, and were inoculated with Glomus intraradices and Pisolithus tinctorius separately but also in combination. Our results showed that F. uhdei established a symbiotic association with EM and AM fungi, and that these organisms, when interacting, showed synergistic and additive effects on plant growth compared to singly inoculated treatments. EM and AM fungi prompted changes in root morphology and increased water-stable aggregates. AM fungi affect mainly small-sized macroaggregates, while EM and EM-AM fungi interaction mainly affected aggregates bigger than 0.5 mm diameter. These results suggest that ectomyccorrhizal as well as arbuscular mycorrhizal fungi should be considered in restoration programs with Fraxinus plants.     

Co-remediation of DDT-contaminated soil using white rot fungi and laccase extract from white rot fungi

Purpose

2,2-Bis(p-chlorophenyl)-1,1,1-trichloroethane (DDT), one of the most widely used organochlorine pesticides in soil, was banned in the 1970s for agricultural use because of its detrimental impacts on wildlife and harmful effects on human health via the food chain. However, high levels of DDT are frequently detected in agricultural soils in China. Considering this situation, this study investigated the use of white rot fungi and laccase derived from white rot fungi to co-remediate DDT-contaminated soil.

Materials and methods

A culture of white rot fungi was used to inoculate soil samples and also to extract laccase from. Soil was contaminated with four components of DDT (p,p′-DDE, o,p′-DDT, p,p′-DDD, and p,p′-DDT). Individual DDT components and the sum of the DDT components (p,p′-DDE, o,p′-DDT, p,p′-DDD, and p,p′-DDT—collectively referred to as DDTs) were both analyzed by GC at various stages during the incubation period. The efficacy of co-remediating DDT-contaminated soil using white rot fungi and laccase was tested by investigating how degradation varied with varying amounts of white rot fungi, sterilizing soil, temperature, soil pH, concentrations of DDT, and concentration of the heavy metal ion Cd²⁺.

Results and discussion

“”It was concluded that the reduction of DDTs in soil using white rot fungi and laccase was higher than reduction using only white rot fungi or laccase by nearly 14 and 16 %, respectively. Five milliliters fungi per 15 g soil and 6 U laccase per gram soil were the optimal application rates for remediation, as shown by a reduction in DDTs of 66.82 %. The difference in the reduction of individual DDT components and DDTs between natural and sterilized soils was insignificant. The optimal temperature and pH in the study were 28 °C and 4.5, respectively. In addition, reduction of individual DDT components and DDTs increased with increasing concentrations of DDT and decreased with increasing concentrations of Cd²⁺.

Conclusions

Compared with the remediation of DDT using only white rot fungi or laccase, the co-remediation of DDT using white rot fungi and laccase degraded DDT in soil more rapidly and efficiently; the highest reduction of DDTs was 66.82 %.     

Interaction between earthworms and arbuscular mycorrhizal fungi on the degradation of oxytetracycline in soils

The interactive impact of earthworms (Eisenia fetida) and arbuscular mycorrhizal fungi (Rhizophagus intraradices, AM fungi) on the degradation of oxytetracycline (OTC) in soils was studied under greenhouse conditions. Treatments included maize plants inoculated vs. not inoculated with AM fungi and treated with or without earthworms at low (1 mg kg⁻¹ soil DM) or high (100 mg kg⁻¹ soil DM) OTC rates. The root colonization rate, the hyphal density of mycorrhizae, the residual OTC concentration in soils, catalase, dehydrogenase, urease, soil microbial biomass C, Shannon–Wiener index (H) for microbial communities from T-RFLP profiles were measured at harvest. The results indicated that earthworms and AM fungi would individually or interactively enhance OTC decomposition and significantly decreased the residual OTC concentration at both high and low OTC rates. Both earthworms and AM fungi could promote the degradation of OTC by increasing soil microbial biomass C at both high and low OTC rates. The effect of soil enzyme activity and soil microbial diversity on OTC decomposition was different between high and low OTC rates. Hyphomicrobium and Bacillus cereus were dominant bacteria, and Thielavia and Chaetomium were dominant phyla of fungi at all occasions. Earthworm activity stimulated the growth of Hyphomicrobium and Thielavia, while AM fungi may stimulate B. cereus, Thielavia and Chaetomium, resulting in greater OTC decomposition. The interaction between earthworms and AM fungi in affecting the degradation of OTC may be attributed to different mechanisms, depending on soil microbial biomass, function (enzyme activity) and communities (the abundance of Hyphomicrobium, B. cereus, Thielavia and Chaetomium) in the soil.     

The combined effects of earthworms and arbuscular mycorrhizal fungi on microbial biomass and enzyme activities in a calcareous soil spiked with cadmium

Earthworms and arbuscular mycorrhizal fungi (AMF) are known to independently affect soil microbial and biochemical properties, in particular soil microbial biomass (SMB) and enzymes. However, less information is available about their interactive effects, particularly in soils contaminated with heavy metals such as cadmium (Cd). The amount of soil microbial biomass C (MBC), the rate of soil respiration (SRR) and the activities of urease and alkaline phosphatase (ALP) were measured in a calcareous soil artificially spiked with Cd (10 and 20 mg Cd kg⁻¹), inoculated with earthworm (Lumbricus rubellus L.), and AMF (Glomus intraradices and Glomus mosseae species) under maize (Zea mays L.) crop for 60 days. Results showed that the quantity of MBC, SRR and enzyme activities decreased with increasing Cd levels as a result of the elevated exchangeable Cd concentration. Earthworm addition increased soil exchangeable Cd levels, while AMF and their interaction with earthworms had no influence on this fraction of Cd. Earthworm activity resulted in no change in soil MBC, while inoculation with both AMF species significantly enhanced soil MBC contents. However, the presence of earthworms lowered soil MBC when inoculated with G. mosseae fungi, showing an interaction between the two organisms. Soil enzyme activities and SRR values tended to increase considerably with the inoculation of both earthworms and AMF. Nevertheless, earthworm activity did not affect ALP activity when inoculated with G. mosseae fungi, while the presence of earthworm enhanced urease activity only with G. intraradices species. The increases in enzyme activities and SRR were better ascribed to changes in soil organic carbon (OC), MBC and dissolved organic carbon (DOC) contents. In summary, results demonstrated that the influence of earthworms alone on Cd availability is more important than that of AMF in Cd-polluted soils; and that the interaction effects between these organisms on soil microorganism are much more important than on Cd availability. Thus, the presence of both earthworms and AMF could alleviate Cd effects on soil microbial life.     

Changes in the structure of fungal communities of soil treated with sewage sludge

The influence of a single addition of sewage sludges to soils on the composition of fungal communities, soil pH (physical factor) and presence of Eschericha coli (sanitary factor) during 1 year was studied. Only the pH of soil treated with limed sewage sludge increased significantly from 7.01 to 7.58 after 3 months. E. coli was still present in soil 1 year after application of sewage sludge. Fungal numbers increased in the sewage-sludge-treated soil up to 6 months after application (maximum value was 7.5 times that of the control) and then decreased to reach values comparable to those of the control. Treated soils showed different fungal communities to the control with presence of keratinolytic fungi (Sporothrix schenckii, Microsporum sp.), yeasts (Geotrichum candidum, Candida sp., Rhodotorula sp. Cryptococcus sp.), and other potential pathogenic fungi (Aspergillus niger, Fusarium solani). The results indicate that fungi belonging to the genus Candida could be used as specific indicator organisms of the sanitary condition of soils treated with sewage sludge.     

Soil microorganisms antagonistic towards Rhizobium japonicum

Success in introducing Rhizobium japonicum strains into soil is related to their interaction with native microorganisms including some that are antagonistic. Actinomycetes, bacteria, fungi and rhizobiophages antagonistic towards strains of R. japonicum were counted directly using soil samples from field plots under different crop and soil management systems. The antagonistic actinomycete population varied from 1.3 × 10³ to 4.5 × 10⁵ g^?1 dry soil and ranged up to 90% of total actinomycetes. Soybean rhizosphere soil samples included antagonistic actinomycetes ranging up to 70% of total actinomycetes. The antagonistic bacterial population was less than 10% of total bacteria and the proportion did not vary significantly with crop or soil management practices. Antagonistic fungi were observed for many of the soils examined but they could not be counted. There were few rhizobiophages and they were found most frequently in soybean rhizospheres. Occasional bacterial and actinomycete colonies that stimulated growth of R. japonicum were randomly observed among the soil samples tested.     

Wheat straw and its biochar had contrasting effects on soil C and N cycling two growing seasons after addition to a Black Chernozemic soil planted to barley

Application of crop residues and its biochar produced through slow pyrolysis can potentially increase carbon (C) sequestration in agricultural production systems. The impact of crop residue and its biochar addition on greenhouse gas emission rates and the associated changes of soil gross N transformation rates in agricultural soils are poorly understood. We evaluated the effect of wheat straw and its biochar applied to a Black Chernozemic soil planted to barley, two growing seasons or 15 months (at the full-bloom stage of barley in the second growing season) after their field application, on CO₂ and N₂O emission rates, soil inorganic N and soil gross N transformation rates in a laboratory incubation experiment. Gross N transformation rates were studied using the ¹⁵N isotope pool dilution method. The field experiment included four treatments: control, addition of wheat straw (30 t ha^?1), addition of biochar pyrolyzed from wheat straw (20 t ha^?1), and addition of wheat straw plus its biochar (30 t ha^?1 wheat straw + 20 t ha^?1 biochar). Fifteen months after their application, wheat straw and its biochar addition increased soil total organic C concentrations (p?=?0.039 and <0.001, respectively) but did not affect soil dissolved organic C, total N and NH₄ ⁺-N concentrations, and soil pH. Biochar addition increased soil NO₃ ^?-N concentrations (p?=?0.004). Soil CO₂ and N₂O emission rates were increased by 40 (p?p?=?0.03), respectively, after wheat straw addition, but were not affected by biochar application. Straw and its biochar addition did not affect gross and net N mineralization rates or net nitrification rates. However, biochar addition doubled gross nitrification rates relative to the control (p?2 and N₂O emissions and enhance soil C sequestration. However, the implications of the increased soil gross nitrification rate and NO₃ ^?-N in the biochar addition treatment for long-term NO₃ ^?-N dynamics and N₂O emissions need to be further studied.     

Suppression of other soil microorganisms by mycelium of arbuscular mycorrhizal fungi in root-free soil

The influence of mycelium of two arbuscular mycorrhizal (AM) fungi, Glomus intraradices and Glomus mosseae, on other soil microorganisms, was examined in root-free soil with and without organic substrate amendment in terms of cellulose. The AM fungi were grown in symbiosis with cucumber in a compartmented growth system, which allowed AM fungal external mycelium to grow into root-free compartments. The fungicide Benomyl was applied to the root-free compartments to create an alternative non-mycorrhizal control treatment. Whole cell biomarker fatty acids were employed to quantify different groups of soil microorganisms including the two AM fungi. Abundance of most microbial groups were reduced by external mycelium of both AM fungi, though differential effects on the microbial community composition were observed between the two AM fungi as revealed from principal component analysis. Inhibition of other soil microorganisms was more pronounced in root-free soil with mycelium of G. mosseae than with mycelium of G. intraradices. In general, cellulose increased the amount of biomarker fatty acids of most groups of soil microorganisms, but cellulose did not affect the influence of AM fungi on other soil microorganisms. Benomyl suppressed growth of the external mycelium of the two AM fungi and had limited non-target effects on other microbial groups. In conclusion, our results show differential effects of external mycelium of AM fungi on other soil microbial communities, though both AM fungi included in the study overall inhibited most microbial groups as examined using whole cell biomarker fatty acids.     

Soil temperature,mycorrhizal infection and nodulation of Medicago truncatula and Trifolium subterraneum

Establishment of vesicular-arbuscular mycorrhizal fungi in plant roots involves a pre-infection phase of propagule germination, hyphal growth and appressorium formation, followed by growth of the fungus within the root. The effect of soil temperature on the pre-infection stage was examined by counting the numbers of fungal “entry-points” on the main roots of Medicago truncatula and Trifolium subterraneum, grown at soil temperatures of 12°, 16°, 20° and 25°C for periods up to 12 days. Increased root temperature was positively associated with increased numbers of “entry-points”. This effect was more marked between 12° and 16°C than at higher temperatures, as shown by comparing plants at the same stage of development (emergence of spade leaf) and by calculating the results as entry points per cm root.The first root nodules appeared sooner at higher temperatures (20° and 25°), but subsequent development of nodules (measured as nodule number and aggregate volume of nodules per plant, up to 21 days) was best at 16°C for both host Rhizobium combinations in non-sterile and autoclaved soil. There was no evidence that competition between mycorrhizal fungi and Rhizobium for infection sites occurred.A method of obtaining numbers of infective propagules of vesicular-arbuscular mycorrhizal fungi in soil is described.     

Arbuscular mycorrhizal fungal community structure and diversity in response to 3-year conservation tillage management in a sandy loam soil in North China

Purpose

Modern agricultural science has greatly reduced the use of tillage. Monitoring conservation versus conventional tillage effects on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to investigate the effects of conservation tillage on the spore community structure and the diversity of soil arbuscular mycorrhizal (AM) fungi and to find out the main factors that influence these parameters.

Materials and methods

A long-term field experiment established in a sandy loam soil in Northern China has received continuous tillage management treatments for 3?years, including conventional tillage (CT), no tillage (NT), and alternating tillage (AT). Topsoil samples (0?C15?cm) from four individual plots per treatment were collected for the analysis of chemical properties and fungal parameters. AM fungal spores were isolated using the wet-sieving method and identified to species level based on morphology by light microscopy. The community structure and the diversity of AM fungi were evaluated using the following parameters: spore density, relative abundance, species richness, Shannon?CWiener index (H??), evenness (E), and Simpson's index (D). Jaccard index (J) of similarity was calculated to compare AM fungal species composition under different treatments.

Results and discussion

Twenty-eight species of AM fungi within four genera, Glomus, Acaulospora, Scutellospora, and Entrophospora, were recovered from the 12 plots within the three tillage management treatments. Higher spore density, species richness, and species diversity (H??, E, and D) of AM fungi were observed in the two conservation tillage treatments, and the redundancy analysis showed that the species richness significantly correlated to soil organic carbon content (P?<?0.05). The positive effects of NT and AT on the species richness were very close, while the AT had relatively greater beneficial impacts on the spore density and the evenness of AM fungi compared to the NT. The lowest Jaccard index (J) of similarity in species composition was also observed between the AT and CT treatments.

Conclusions

Soil organic carbon, the spore density, and species richness and diversity of AM fungi increased in the two conservation tillage treatments. The species richness of AM fungi significantly correlated to soil organic carbon content (P?<?0.05). Compared with the CT treatment, the AT rather than the NT significantly increased the spore density and the evenness of AM fungi (P?<?0.05). Thus, alternating tillage practice may be more beneficial to agroecosystem in this region.     

Arbuscular mycorrhizal fungi and collembola non-additively increase soil aggregation

Soil aggregation is a principal ecosystem process mediated by soil biota. Collembola and arbuscular mycorrhizal (AM) fungi are important groups in the soil, and can interact in various ways. Few studies have examined collembola effects on soil aggregation, while many have quantified AM effects. Here, we asked if collembola have any effect on soil aggregation, and if they alter AM fungi-mediated effects on soil aggregation.We carried out a factorial greenhouse study, manipulating the presence of both collembola and AM fungi, using two different plant species, Sorghum vulgare and Daucus carota. We measured root length and biomass, AMF (and non-AMF) soil hyphal length, root colonization, and collembolan populations, and quantified water stable soil aggregates (WSA) in four size classes.Soil exposed to growth of AMF hyphae and collembola individually had higher WSA than control treatments. Moreover, the interaction effects between AMF and collembola were significant, with non-additive increases in the combined application compared to the single treatments.Our findings show that collembola can play a crucial role in maintaining ecological sustainability through promoting soil aggregation, and point to the importance of considering organism interactions in understanding formation of soil structure.     

Interactions of the microflora from nodulation problem and non-problem soils towards Rhizobium spp on agar culture

Microorganisms (348 fungi, 388 actinomycetes and 319 bacteria) were isolated from a nodulation problem soil, a non-problem virgin soil, a cultivated problem soil and the rhizosphere of clover plants grown in the problem soil. Rhizobium trifolii TA 1 which failed to establish in problem soils was inhibited on laboratory media by a greater number of these soil microorganisms than the better soil colonizing R. trifolii (WU95 and WU290) and R. lupini (WU425). R. lupini was not inhibited or stimulated on agar by many soil or rhizosphere isolates. R. meliloti showed greater stimulation than either R. trifolii or R. lupini and was inhibited by relatively few soil microorganisms so that its poor soil survival was thought to be due to chemical or physical soil conditions rather than to biotic factors. The greatest incidence of rhizobial inhibitors, mainly associated with TA 1, was found among the isolates from the clover rhizosphere. There was a reduction in the relative numbers of rhizobial inhibitors isolated from the cultivated soil compared with the virgin problem soils, a result possibly due to the changed soil environment changing with cultivation, altered vegetation and the addition of superphosphate. Inhibitors of rhizobia were more frequent amongst the bacteria than fungi or actinomycetes. Strong stimulation was more commonly shown by fungi than by actinomycetes or bacteria. The interaction on agar between rhizobia and the soil microflora is related to soil colonization and persistence.     

Effect of Continuous Monocropping of Tomato on Soil Microorganism and Microbial Biomass Carbon

Soil microorganisms play an important role in recycling and transformation of nutrients. Soil microbiological parameters and microbial biomass carbon (MBC) have been suggested as possible indicators of soil quality. Soil microorganisms and MBC in different continuous cropping soils were investigated. Results showed that bacterial population was the highest, followed by actinomycetes, and fungi were the lowest at 0–30 cm soil depth. The amount of soil microorganisms decreased with increasing soil depth (0–10 > 10–20 > 20–30 cm). Soil microbial ratios at different depths proved to be responsive to time (year) variations in continuous monocropping tomato, except those at 0–10 to 10–20 cm depth for fungi and 10–20 to 20–30 cm depth for bacteria. Soil MBC for 12 years of continuous cropping was significantly lower than those for 5, 8, and 10 years (P < 0.05). Continuous cropping years, soil depth, and the interaction of these two parameters significantly influenced soil fungal, bacterial, and actinomycetes populations and MBC. Bacterial population at the 0–10 cm soil layer was a sensitive indicator of continuous cropping of tomato. Soil fungal count increased with increasing monocropping time within 5–8 years.     

Interactions between arbuscular mycorrhizal fungi and fungivorous nematodes on the growth and arsenic uptake of tobacco in arsenic-contaminated soils

The effects of inoculation with two AM fungi (M1, Glomus caledonium; M2, Glomus spp. and Acaulospora spp.) and a fungivorous nematode Aphelenchoides sp. on growth and arsenic (As) uptake of Nicotiana tabacum L. were investigated in soils contaminated with a range of As. The reproduction of Aphelenchoides sp. was triggered by the co-inoculation of AM fungi regardless of AM fungal isolates and As levels. Stimulative effects of Aphelenchoides sp. on the development of mycorrhiza, slightly different between two AM fungi, were found particularly at the lowest As level. Irrespective of mycorrhizal inoculi, increasing soil As level decreased plant growth, but increased plant As uptake. Co-inoculation of AM fungi and Aphelenchoides sp. led plants to achieving further growth and greater As accumulation at the lowest As level. Results showed that the interactions between AM fungi and fungivorous nematodes were important in plant As tolerance and phytoextraction at low level As-polluted soil.     

Effects of straw amendment and moisture on microbial communities in Chinese fluvo-aquic soil

Purpose

Returning crop straw into fields is a typical agricultural practice to resolve an oversupply of straw and improve soil fertility. Soil microorganisms, especially eukaryotic microorganisms, play a critical role in straw decomposition. To date, microbial communities in response to straw amendment at different moisture levels in Chinese fluvo-aquic soil are poorly understood. The aim of this study was to explore the effects of straw amendment and moisture on microbial communities in Chinese fluvo-aquic soil.

Materials and methods

Two soils (one was applied with organic manure, and the other was not applied with any fertilizer) from a long-term field experiment in the North China Plain were collected. Soils with and without straw amendment at 25 and 55 % of the average water-holding capacities of the two soils were incubated at 25 °C for 80 days. All treatments were sampled 20 and 80 days after the start of incubation. Microbial biomass and community structure were analyzed by phospholipid fatty acids (PLFA) assay, and the eukaryotic diversity and community composition were assessed via barcoded pyrosequencing of the 18S ribosomal RNA (rRNA) gene amplicons.

Results and discussion

PLFA analysis showed that straw amendment increased the biomass of Gram-positive bacteria, Gram-negative bacteria, actinobacteria, and fungi and shifted microbial community structure. The varied straw availability resulted in a large variation in microbial community structure. In the presence of straw, actinobacterial and fungal biomass both decreased under high moisture content. 18S rRNA gene pyrosequencing indicated that straw amendment decreased eukaryotic diversity and richness and probably restructured the eukaryotic community. Under identical moisture content, long-term organic manure-fertilized soil had higher eukaryotic diversity and richness than the unfertilized soil. In the amended soils under high moisture content, the relative abundance of dominant fungal taxa (Dikarya subkingdom, Ascomycota phylum, and Pezizomycotina subphylum) decreased.

Conclusions

Straw amendment increases microbial biomass, shifts microbial community structure, and decreases eukaryotic diversity and richness. High moisture content probably has a negative effect on fungal growth in the amended soils. In conclusion, microbial communities in Chinese fluvo-aquic soil are significantly affected by straw amendment at different moisture levels.     

Studies on soil fumigation—IV: Effects on fungi

The effect of soil fumigation with a chloropicrin-methyl bromide mixture(1:1) at 440 kg·ha^?1 on the fungal flora of a wheat-field has been investigated. Recolonization of fumigated soil and the occurrence of fungi on roots of wheat growing in fumigated and untreated soil were also followed. Very few fungi survived in fumigated soil that had been covered with polythene sheeting, but in uncovered fumigated soil some fungi survived especially at or near the soil surface.Study of recolonization of covered fumigated soil showed that some fungi, notably species of Chaetomium and Mortierella, appeared to survive fumigation and then increase in number, but many of the fungi recolonizing surface soil (2.5 cm), Alternaria, Stemphylium, Mucor, Cladosporium, Epicoccum), appeared to have come from the air. Recolonization of surface soil was not uniform; high counts were often due to the spores of one or a few fungi and samples collected a few cm apart might show different fungi in high number. In subsurface soil (5–22.5 cm) recolonization was much slower and even 117 days after fumigation the number of colonies and species of fungi was low compared with untreated soil.The common fungi on roots of plants grown in uncovered fumigated or untreated soil were very similar though initially there were fewer fungi on roots from fumigated soil. The main differences recorded were that Chaetomium species were more frequent on roots from fumigated soil and that. in general, Cylindrocarpon destruetans, Embellisia chlamydospora, species of Pythium and Rhizoctonia, and Gaeumannomyces graminis were more common on roots in untreated soil.     

Diversity and vertical distribution of indigenous arbuscular mycorrhizal fungi under two soybean rotational systems

To evaluate the importance of arbuscular mycorrhizal fungi (AMF) to crop production, it is imperative to move beyond the plow layer to include the full soil profile impacted by plant roots. To illustrate this, we investigated the vertical distribution of AMF biomass and community structure within the top 100 cm of soil in soybean (Glycine max (L.) Merr., cv: Enrei) rotational systems cropped to wheat (Triticuma estivum L. cv: Bandowase) or left fallow using fatty acid methyl ester (FAME) biomarkers and molecular analysis, respectively. AMF biomass, as measured by concentration of C16:1cis11, declined during fallow and with increasing soil depth. Greater than 50 % of the stored AMF biomass was found at depths below 35 cm. Phylogenetic analysis revealed 16 AMF phylotypes, including nine Glomus, two Gigaspora, two Scutellospora, and one each of Diversispora, Paraglomus, and an unknown glomeromycete, at different sampling depths in this study. Cluster analysis based on the number and abundance of each AMF phylotype formed two distinct clusters separating wheat from fallow rotations. There was no distinct relationship with soil depth beyond clustering AMF communities above and below 20 cm under wheat. Redundancy analysis (RDA) and hierarchical cluster analysis demonstrated that AMF communities by soil depth within each rotation were not significantly different. However, AMF communities were clearly influenced by crop rotation, where the distribution of specific AMF phylotypes responded to the presence of the wheat crop.     

Microbial populations involved in the suppression of Rhizoctonia solani AG1-1B by lignin incorporation in soil

Rhizoctonia solani causes worldwide losses in numerous crops. Sclerotia of R. solani remain viable for several years in soil and are an important source of primary infection. In this study the effect of soil incorporation of Kraft pine lignin, a side product of the paper industry, on viability of R. solani AG1-1B sclerotia was investigated. The efficacy of lignin was assessed in a sandy loam (Oppuurs) and a silt loam soil (Leest) collected from commercial fields in Belgium. Evaluating sclerotial viability after 4 weeks incubation in the two soils amended with 1% (w/w) Kraft pine lignin demonstrated a soil-dependent effect. In Leest soil the addition of lignin resulted in a significantly reduced sclerotial viability, together with an increased mycoparasitism by Trichoderma spp.; in Oppuurs soil, on the other hand, only a slight and insignificant reduction in sclerotial viability was observed. Based on phospholipid fatty acid analysis, different changes in microbial community structure upon lignin amendment were detected in the two soils. Both amended soils showed a significant increase in Gram negative bacteria. In Leest soil this increase was accompanied with a significantly higher increase in fungi and actinomycetes compared with Oppuurs soil. In addition, Kraft pine lignin resulted in both soils in a small but significant increase in manganese peroxidase activity and this increase tended to be higher in Leest soil. Manganese peroxidase produced by lignin-degrading basidiomycetes has previously been shown to degrade melanin, which protects the sclerotia against biotic and abiotic stress. We hypothesize that lignin-degrading fungi increased the susceptibility of the sclerotia to sclerotial antagonists such as Trichoderma, Gram negative bacteria and actinomycetes. Clearly, the effect observed here did not rely on the stimulation of one microbial group, but is the result of an interaction of different groups.     

Indirect host effect on ectomycorrhizal fungi: Leaf fall and litter quality explain changes in fungal communities on the roots of co-occurring Mediterranean oaks

Host trees can modify their soil abiotic conditions through their leaf fall quality which in turn may influence the ectomycorrhizal (ECM) fungal community composition. We investigated this indirect interaction using a causal modelling approach. We identified ECM fungi on the roots of two coexisting oak species growing in two forests in southern Spain - Quercus suber (evergreen) and Quercus canariensis (winter deciduous)-using a PCR-based molecular method. We also analysed the leaf fall, litter and soil sampled beneath the tree canopies to determine the concentrations of key nutrients. The total mycorrhizal pool was comprised of 69 operational taxonomic units (OTUs). Tomentella and Russula were the most species-rich, frequent and abundant genera. ECM fungi with epigeous and resupinate fruiting bodies were found in 60% and 34% of the identified mycorrhizas, respectively. The calcium content of litter, which was significantly higher beneath the winter-deciduous oak species due to differences in leaf fall quality, was the most important variable for explaining ECM species distribution. The evaluation of alternative causal models by the d-sep method revealed that only those considering indirect leaf fall-mediated host effects statistically matched the observed covariation patterns between host, environment (litter, topsoil, subsoil) and fungal community variables.