Shifts In Fungal Community Composition Research Articles

Shift in fungal communities associated with Pinus sylvestris stands affected by root rot

Introduction
 Scots pine (Pinus sylvestris) covers large areas in European regions with significant economic importance to Ukrainian forest industry. Root rot caused by the wood-decay fungus Heterobasidion annosum damages both below- and above-ground parts of Scots pines. The disease progress is likely to be affected by reshaping in the forest such as soil properties, vegetation composition, and tree age. These changes are apparently followed up by paralleled shifts in fungal community composition on forest soil with potential feedback on ecosystem functioning.
 The objective of the study was to screen fungal groups associated with the root system of P. sylvestris in stands affected by H.annosum s.s. to better understand the pathogenesis and development of root rot infection, as well as to recognize whether root size and disease severity affect diversity of fungi of the root system in the forest-steppe conditions of Ukraine. The additional object was to study other resident microflora of P. sylvestris root infested by H.annosum s.s. to find out whether the H. annosum s.s. impacts the overall diversity of other fungi.
 Materials and Methods
 The field study was carried out in 2018–2020. Field study sites were pure pine forest stands located in Kharkiv region (compartment 126, subcompartment 7, tract Bugri, Kharkiv Forest Research Station). Wood core and root samples from P. sylvestris were collected from the five infected (50–100 m apart from each other) and five non-infected trees (up to 500 m apart from the infested area and 50–100 m apart from each other). Wood and root samples were used for fungal culturing and direct sequencing using ITS1F and ITS4 primers.
 Results
 In the present study, we tried to evaluate fungal communities across diseased Pinus sylvestris stands and investigated correlations between taxonomic composition and forest health. Not surprisingly, root rot infestation had a significant effect on root-associated fungal abundance and diversity. During disease development, the root-associated fungal community shifted in composition from dominance by saprotrophic fungi to ectomycorrhizal and pathogenic fungal species. Our results suggested that maintenance of functional diversity in the root-associated fungal community may sustain long-term forest health or even root rot resistance to some extent by retaining a capacity for symbiosis-driven recycling of organic nutrients; however, this hypothesis is necessary to carefully examine and prove further.
 Conclusions
 Fungal culturing from 10 surface-sterilized wood cores resulted in 21 fungal cultures, 2.1 per wood segment. Direct sequencing from 40 surface-sterilized segments of lateral roots resulted in 247 fungal sequences or 6.2 per root segment on average. The most dominant fungi from the infested trees of Pinus sylvestris were Dactylonectria macrodidyma (4.98%), Acremonium sp (4.52%), Cladosporium cladosporioides (4.07%) from Ascomycota and Heterobasidion annosum s.s. (4.07%) from Basidiomycota, while for non-infested group Unidentified Ascomycota175244 (13.19%), Penicillium spinulosum (9.89%), Acremonium sp. (8.79%), Bionectriaceae sp. (8.79%) were the most common.
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Correction for Miao et al., "Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness".

Correction for Miao et al., "Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness".

Vinasse and straw retention decrease fungal diversity and pathogenicity in sugarcane soil / Aplicação de vinhaça e retenção de palha diminuem a diversidade e patogenicidade de fungos em solo canavieiro

This study focused on the effects of vinasse (V), a by-product of the sugar-ethanol industry, combined with mineral nitrogen fertilizer (N) and straw retention on the fungal community diversity, composition, and structure in a sugarcane-cultivated soil. The experiment consisted of a combination of V, mineral N and sugarcane-straw blanket. Soil samples were collected at 7, 157, and 217 days after planting, corresponding to maximum carbon dioxide emissions from soil after three repeated applications of fertilizers into the soil. Across 57 soil metagenomics datasets, it was revealed that the application the V in combination with N fertilizer and straw retention decreased the diversity, evenness and richness of fungi at the community level in soil. Analysis of the soil fungal community composition based on the 20 genera most abundant revealed decrease for Blastomyces, Melampsora, and Penicillium after the third application of V in combination with N fertilizer and straw blanket. An opposite response was revealed for Amauroascus, Cantharellus, Chrysosporium, Clavaria, Morchella, Puccinia, and Tuber in soil under this treatment. Shifts in fungal community composition were followed by increases in mycorrhizal and decomposers soil-borne fungi and decrease in potentially pathogenic fungi, but not by changes in community structure. Based on these results, it is possible to attest that repeated applications of V in combination with N fertilizer and sugarcane-straw blankets affect ecological aspects of the soil fungal community composition and potential functions played by fungi in sugarcane soil, which are essentials to ecosystem function and sustainable management of agricultural ecosystems.

Evidence of micro and macroplastic toxicity along a stream detrital food-chain

Freshwater ecosystems are subjected to plastic extensive pollution because they are the direct link between plastic wastes and marine ecosystems. The aim of this study was to assess the impacts of different sizes of polyethylene plastics (micro: µPs and macroplastics: PBs) on freshwater decomposers of plant litter. We exposed leaf associated microbial assemblages to µPs (0.5 or 1.5 g L-1) and discs of PBs as follows: green plastic bags (PB-G) alone or in mixtures with transparent plastic bags (PB-Mix). Then, we conducted a feeding preference experiment with the invertebrate shredder Limnephilus sp. to assess their capacity to distinguish leaf discs from PB discs of the same size (12 mm). Leaf decomposition, activities of fungal enzymes and sporulation were inhibited by µPs and PB-Mix, and shifts in fungal community composition were observed. The invertebrate shredders preferred to feed on leaves treated with µPs avoiding those exposed to PB-G/PB-Mix. Our results demonstrated that plastics can have a direct effect on stream-dwelling microbial decomposers and an indirect effect on higher trophic levels (shredders), highlighting that trophic transfer is a route of plastic exposure. The plastic properties (size, concentration, colour) appear to influence plastic toxicity to microbes and shredders, indicating the importance of considering physicochemical properties when assessing their risks to freshwater ecosystems.

Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness.

ABSTRACTCellulose is the most abundant polysaccharide in plant biomass and an important precursor of soil organic matter formation. Fungi play a key role in carbon cycling dynamics because they tend to decompose recalcitrant materials. Here, we applied [12C]cellulose and [13C]cellulose to distinguish the effects of application of compost, nitrogen-phosphorus-potassium (NPK) fertilizer, and no fertilizer (control) for 27 years upon cellulose decomposition via RNA-based stable isotope probing (RNA-SIP). The loss ratio of added cellulose C in compost soil was 67.6 to 106.7% higher than in NPK and control soils during their 20-day incubation. Dothideomycetes (mainly members of the genus Cryptococcus) dominated cellulose utilization in compost soil, whereas the copiotrophic Sordariomycetes were more abundant in NPK and unfertilized soils. Compared with NPK and control soils, compost application increased the diversity of 13C-assimilating fungi. The 13C-labeled fungal communities in compost soil were more phylogenetically clustered and exhibited greater species relatedness than those in NPK and control soils, perhaps because of stringent filtering of narrow-spectrum organic resources and biological invasion originating from added compost. These changes led to an augmented decomposition capacity of fungal species for cellulose-rich substrates and reduced cellulose C sequestration efficiency. The RNA-SIP technique is more sensitive to responses of fungi to altered soil resource availability than DNA-SIP. Overall, long-term compost application modified fungal community composition and promoted fungal diversity and phylogenetic relatedness, accelerating the decomposition of substrate cellulose in soil. This work also highlights the RNA-SIP technique’s value for comprehensively assessing the contributions of active fungi to the substrate decomposition process.

Dysbiosis of nail microbiome in patients with psoriasis.

Shifts in skin microbiome are considered to be involved in the pathogenesis of psoriasis. However, data on the microbial dysbiosis of nail psoriasis are scarce. In this study, we aim to investigate and characterize the nail bacterial and fungal microbiome in patients with psoriasis. Nail samples were collected prospectively from 36 subjects with nail psoriasis, 24 psoriatic subjects without nail involvement and 32 healthy controls. Amplicon sequencing was performed to evaluate the bacterial and fungal community compositions. Significant alterations in the bacterial microbiome were found in the nail samples of psoriatic patients. The unaffected nails in psoriatic patients were associated with higher bacterial diversity, and a higher relative abundance of Enhydrobacter, whereas nail psoriasis was correlated with a decreased relative abundance of Anaerococcus. Shifts in fungal community composition were reflected by a higher proportion of Malassezia in the unaffected nails of psoriatic patients and an increased proportion of Candida in psoriatic nails. Shifts in the nail microbiome in psoriasis suggest a potential role of microbes in the development of nail psoriasis. Future researches focusing on these microorganisms may help to explain the pathogenesis of psoriasis.

Forest and Plantation Soil Microbiomes Differ in Their Capacity to Suppress Feedback Between Geosmithia morbida and Rhizosphere Pathogens of Juglans nigra Seedlings

Thousand cankers disease (TCD) is hypothesized to have a greater impact on eastern black walnut (Juglans nigra) in urban forests and plantations compared with natural forest stands. Along with other factors such as resource availability, the phytobiome could partly account for observed differences in disease severity across management regimes. We investigated the extent to which J. nigra-associated soil microbiomes from plantations and natural forests modulate (i) the amount of necrosis caused by Geosmithia morbida in 1-year-old seedlings, and (ii) relative abundance of rhizosphere endophytes and opportunistic pathogens Fusarium and Rhizoctonia in response to aboveground inoculation with G. morbida. Our results suggest that the microbiome from natural forest soil in central Indiana suppresses Fusarium spp. and is indirectly suppressive of G. morbida. Natural forest soil had a greater ability to reduce the size of necrotic area caused by G. morbida compared with steam-treated soil. Inoculating stems of seedlings with G. morbida induced a shift in fungal community composition in the rhizosphere, including Fusarium and Rhizoctonia spp.; however, the direction and magnitude of the shift depended on whether seedlings were amended with forest, plantation, or steam-treated soil. In a companion experiment, necrotic area in G. morbida-inoculated seedlings was twice as high in seedlings grown from seeds that were treated with Fusarium solani relative to those grown from seed treated with water. Our findings support the hypothesis that TCD severity can be modulated by host-mediated feedback between above- and belowground pathogens, as well as by microbial interactions in the rhizosphere.

Nutrient and stress tolerance traits linked to fungal responses to global change

In this case study analysis, we identified fungal traits that were associated with the responses of taxa to 4 global change factors: elevated CO2, warming and drying, increased precipitation, and nitrogen (N) enrichment. We developed a trait-based framework predicting that as global change increases limitation of a given nutrient, fungal taxa with traits that target that nutrient will represent a larger proportion of the community (and vice versa). In addition, we expected that warming and drying and N enrichment would generate environmental stress for fungi and may select for stress tolerance traits. We tested the framework by analyzing fungal community data from previously published field manipulations and linking taxa to functional gene traits from the MycoCosm Fungal Portal. Altogether, fungal genera tended to respond similarly to 3 elements of global change: increased precipitation, N enrichment, and warming and drying. The genera that proliferated under these changes also tended to possess functional genes for stress tolerance, which suggests that these global changes—even increases in precipitation—could have caused environmental stress that selected for certain taxa. In addition, these genera did not exhibit a strong capacity for C breakdown or P acquisition, so soil C turnover may slow down or remain unchanged following shifts in fungal community composition under global change. Since we did not find strong evidence that changes in nutrient limitation select for taxa with traits that target the more limiting nutrient, we revised our trait-based framework. The new framework sorts fungal taxa into Stress Tolerating versus C and P Targeting groups, with the global change elements of increased precipitation, warming and drying, and N enrichment selecting for the stress tolerators.

Steering the soil microbiome by repeated litter addition

AbstractMicrobial communities drive plant litter breakdown. Litters originating from different plant species are often associated with specialised microbiomes that accelerate the breakdown of that litter, known as home‐field advantage. Yet, how and how fast microbial communities specialise towards litter inputs is not known.Here we study effects of repeated litter additions on soil microbial community structure and functioning. We set up a 9‐month, full‐factorial, reciprocal litter transplant experiment with soils and litters from six plant species (three grasses and three trees). We measured fungal and bacterial community composition, litter mass loss and home‐field effects.We found that repeated litter additions resulted in convergence in fungal community composition driven by litter functional group (trees vs. grasses). Grasses enriched Sordariomycetes, while Tremellomycetes, Eurotiomycetes and Leotiomycetes were favoured by tree litter. Bacterial community composition, litter mass loss and home‐field effects were not affected by litter incubation, but there was a relationship between fungal community composition and mass loss.We conclude that repeated litter incubations can result in directional shifts in fungal community composition, while 9 months of litter addition did not change bacterial community composition and the functioning and specialisation of microbial communities.Testing further how repeated litter inputs affect microbial functioning is essential for steering decomposer communities for optimal soil carbon and nutrient cycling.

Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland.

Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), -glucosidase (BG), -xylosidase (BX), and N-acetyl---glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.

Soil fungal communities across land use types

Abstract: Land use change is one of the major causes of biodiversity loss, mostly due to habitat change and fragmentation. Belowground fungal diversity is very important in terrestrial ecosystems, however, the effect of land use change on soil fungal community is poorly understood. In this review, a total of 190 studies worldwide were analyzed. To monitor the effect of land use change, different fungal parameters such as richness, diversity, community composition, root colonization by arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi, spore density, ergosterol, and phospholipid fatty acid (PLFA) content and AM fungal glomalin related soil protein (GRSP) were studied. In general, results from analyzed studies often showed a negative response of fungal quantitative parameters after land use change from less-intensive site management to intensive site management. Land use change mostly showed significant shifts in fungal community composition. Considering land use change types, only 18 out of 91 land use change types were included in more than 10 studies, conversion of primary and secondary forest to various, more intensive land use was most often represented. All these 18 types of land use change influenced fungal community composition, however, the effects on quantitative parameters were mostly inconsistent. Current knowledge is not sufficient to conclude general land use impacts on soil fungi as the reviewed studies are fragmented and limited by the local context of land use change. Unification of the methodology, detailed descriptions of environmental factors, more reference sequences in public databases, and especially data on ecology and quantitative parameters of key fungal species would significantly improve the understanding of this issue.

Tight coupling of fungal community composition with soil quality in a Chinese fir plantation chronosequence

AbstractPredicting changes in carbon and nutrient cycles in plantations requires a mechanistic understanding of the effects of stand age on soil quality and microbial communities. Here, we evaluated soil quality by using an integrated soil quality index (SQI) and traced the parallel shifts in fungal community composition using high‐throughput sequencing in a chronosequence of Chinese fir (Cunninghamia lanceolata) plantations (stand age of 3, 16, 25, 32, >80 years). Soil properties showed pronounced changes with stand age in the topsoil. Soil organic carbon (SOC), total nitrogen (TN) and available phosphorus (AP) were 2.1, 1.9 and 2.2 times higher, respectively, in the oldest stands than in the youngest stands. SQI of the top 5 cm increased logarithmically with stand age. Mycorrhizal fungi initially increased in younger stands, but then they were gradually replaced by saprotrophs in older stands due to larger litterfall. Strong positive correlations between saprotrophic fungi and key soil quality indicators, such as TN, AP and NH4+, confirmed that abundance of decomposers is tightly linked with higher soil quality. Mycorrhizal orders Thelephorales, Sebacinales and Russulales increased in abundance and raised the activity of acid phosphatase to mobilise limiting phosphorus from organic matter. Consequently, mycorrhizal fungi are especially relevant in younger stands to acquire nutrients to sustain tree productivity. In developed stands, however, saprotrophic fungi are crucial in recycling nutrients from the litter. Collectively, the increase of topsoil quality during the life cycle of Chinese fir plantations is closely linked with the observed transition of fungal communities from mycorrhizae to saprotrophs.

Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.

In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.

Saprotrophic and Ectomycorrhizal Fungi Contribute Differentially to Organic P Mobilization in Beech-Dominated Forest Ecosystems

Phosphorus (P) is an essential nutrient, but European forest ecosystems are experiencing widespread declines in soil P concentrations. To clarify the roles of ectomycorrhizal (EM) and saprotrophic (SAP) fungi in P cycling in forest soils that differ in inorganic and organic P availability, we conducted an ingrowth tube (IGT) experiment over 18 months of exposure in five beech (Fagus sylvatica L.) forests in Germany. To separate the contributions of both fungal guilds in situ, two different types of IGTs were used: (i) open IGTs with micromesh windows to allow EM fungi to regrow into the tubes, and (ii) closed IGTs (without mesh windows) in which recolonization by EM hyphae was restricted. We then measured phosphatase and oxidase activities in EM (open IGTs) and SAP (closed IGTs) dominated fungal assemblages. Our results show that shifts in fungal assemblages occurred over time, but that the speed and extent of those shifts differed. In three forest sites fungal community composition shifted towards greater dominance of EM fungi in open IGTs after a period of 18 months, but these changes were not apparent in two other sites. Although shifts in fungal community composition were noticeable between treatments, we found no effect on phosphomonoesterase activity. Since phosphomonoesterase is present in both fungal guilds, this indicates functional redundancy. Phosphodiesterase activity was slightly reduced in SAP dominated IGTs, indicating that SAP fungi contribute to phosphodiesterase activity to a lesser extent than do EM fungi. P cycling enzymes did not appear to have been influenced by the total P stocks of the forest sites but may have been affected by additional abiotic factors. Contrary to our expectation, phenoloxidase activity was unaffected by fungal community composition, and only peroxidase activity was higher in SAP dominated IGTs, indicating that the contribution of EM fungi to degradation of complex organic material is driven by the need to obtain nutrients in addition to C. Overall, the results of this study contribute to a better understanding of the roles of EM and SAP fungi in P cycling in forest soils.

Soil Properties Control Microbial Carbon Assimilation and Its Mean Residence Time

Microbial assimilation and stabilization of soil organic carbon (SOC) is an important process in global carbon cycling. For an improved understanding of climate-induced changes in ecosystem C dynamics, it is important to know the group-specific turnover of microbial C. Consequently, we wanted to answer the questions if fungi store newly assimilated C longer than bacteria and if climatic and edaphic properties of different regions affect microbial C assimilation and its subsequent release. This study presents results from a 112-day long field experiment where endogenous soil microorganisms were labelled with 13C labelled glucose to follow the dynamics of newly assimilated C in two study regions (Kraichgau and Swabian Alb). Whereas microbial assimilation of newly added C was higher in Kraichgau than in Swabian Alb, the opposite result was obtained for the mean residence time (MRT) of microbial biomass C (76 days in Kraichgau and 93 days in Swabian Alb). The accelerated turnover rates of microbial C in the warmer soils of Kraichgau with lower clay content might be an important mechanism explaining the differences in SOC content between both regions. Gram-positive bacteria assimilated more 13C-glucose into their biomass than fungi and the MRT of C was higher in bacteria as compared to fungi in both regions. Beside these dynamic substrate utilization strategies, we could proof cross feeding by gram-negative bacteria. Carbon MRT in fungi was region specific and was best represented by a two-pool model; the initial MRT ranged between 5 to 39 days and was, in the end, higher than 4 years. This provides evidence of a possible shift in fungal community composition; fast growing fungi dominant in the early phase and internal redistribution of C in the second phase of decomposition. Our study identified microbial group and region specific MRT of freshly assimilated C as an important parameter, which might help to explain the commonly found variation in soil respiration and SOC stabilization.

Interactive effects of nitrogen fertilizer and altered precipitation on fungal communities in arid grasslands of northern China

Fungi play an essential role in regulating the functioning of terrestrial ecosystems and are sensitive to climate change factors. Climate change incidents, such as N deposition and altered precipitation, create abiotic stress regarding the water use efficiency of soil and nutrient limitation impacting the activity of soil fungi. This study aimed to examine the combined effects of N fertilization and altered precipitation on soil fungal diversity and composition in the desert steppe. In the present study, we carried out a field experiment to assess the soil fungal diversity and composition of the desert steppe in response to N fertilizer (0 or 35 kg N ha−1 year−1) and precipitation changes (control, − 50% precipitation, or + 50% precipitation) in the desert steppe. The study was initiated in 2012, and plant and soil samples were collected after 5 years (August, 2017) of field treatments. High-throughput sequencing was applied to estimate the fungal diversity and composition. The soil fungal communities were dominated by Ascomycota (87.85% ± 1.26%), which primarily drove the fungal community composition. Decreased precipitation promoted strong shifts in fungal community composition under both N fertilizer levels. Increased precipitation significantly reduced Shannon-Wiener indices by 9.96%. The increasing relative abundances of fungal functional groups (lichenized saprotroph, animaland plant pathogens) resulted in a marked shift in fungal community composition from decreased precipitation to increased precipitation, which is attributed to the important role of the Ascomycota phylum in fungal communities. Structural equation modeling (SEM) indicated that C4 biomass was the predominant factor determining the Shannon-Wiener index for these fungi. Direct altered precipitation, indirect soil pH, and C4 biomass together controlled soil fungal community composition, with altered precipitation as the main driver. The interactive effects of N fertilizer and altered precipitation on grassland plant density, biomass, and soil properties may play an essential role in determining fungal diversity and community composition. Precipitation is a primary limiting factor that influences fungal community composition. Effects of N fertilizer on soil fungal community composition are highly dependent on changes in precipitation.

Divergence in fungal abundance and community structure between soils under long-term mineral and organic fertilization

Fertilization maintains soil fertility and maximizes crop productivity, but changes soil microbial community structure and functions. However, little is known about the effects of long-term mineral and/or organic fertilization on fungal communities which regulate nutrient cycling and crop growth. The responses of fungal abundance and community structure to 29-year mineral and/or organic fertilization were investigated in Ultisol using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (Illumina Mi-Seq). Compared to the control, mineral N fertilization decreased fungal abundance by 44%, but showed little effect on crop yield and fungal diversity. The NPK fertilization increased crop yield by 4.5 times and fungal diversity by 1.4 times, but had little effect on fungal abundance relative to the control. Manure application increased crop yield by 8.4 times, fungal abundance by 1.8 times and fungal diversity by 1.5 times relative to the control. Application of manure plus NPK increased crop yield by 9.5 times, fungal abundance by 1.9 times and fungal diversity by 1.6 times relative to the control. Long-term fertilization led to dramatic shifts in fungal community composition. Compared to the control, mineral and organic fertilization decreased the relative abundance of Ascomycota and Basidiomycota, respectively. The fungal community composition diverged between soils with mineral and organic fertilization. Changes in soil organic carbon (SOC) and nutrient contents primarily shifted fungal abundance and community structure. Manure application resulted in higher SOC and nutrient contents, and thus affected fungal abundance and community structure more strongly than mineral fertilization. Manure application rather than mineral fertilization increased the relative abundance of certain favorable fungal taxa (e.g., Pseudaleuria and Hypocreales) which suppress crop pathogens. Overall, long-term manure application explained patterns in soil fertility, crop productivity, fungal abundance, diversity and community composition better than mineral fertilization.

Plant-driven changes in soil microbial communities influence seed germination through negative feedbacks.

Plant–soil feedbacks (PSFs) drive plant community diversity via interactions between plants and soil microbes. However, we know little about how frequently PSFs affect plants at the seed stage, and the compositional shifts in fungi that accompany PSFs on germination.We conducted a pairwise PSF experiment to test whether seed germination was differentially impacted by conspecific versus heterospecific soils for seven grassland species. We used metagenomics to characterize shifts in fungal community composition in soils conditioned by each plant species. To investigate whether changes in the abundance of certain fungal taxa were associated with multiple PSFs, we assigned taxonomy to soil fungi and identified putative pathogens that were significantly more abundant in soils conditioned by plant species that experienced negative or positive PSFs.We observed negative, positive, and neutral PSFs on seed germination. Although conspecific and heterospecific soils for pairs with significant PSFs contained host‐specialized soil fungal communities, soils with specialized microbial communities did not always lead to PSFs. The identity of host‐specialized pathogens, that is, taxa uniquely present or significantly more abundant in soils conditioned by plant species experiencing negative PSFs, overlapped among plant species, while putative pathogens within a single host plant species differed depending on the identity of the heterospecific plant partner. Finally, the magnitude of feedback on germination was not related to the degree of fungal community differentiation between species pairs involved in negative PSFs. Synthesis. Our findings reveal the potential importance of PSFs at the seed stage. Although plant species developed specialized fungal communities in rhizosphere soil, pathogens were not strictly host‐specific and varied not just between plant species, but according to the identity of plant partner. These results illustrate the complexity of microbe‐mediated interactions between plants at different life stages that next‐generation sequencing can begin to unravel.

Warming alters fungal communities and litter chemistry with implications for soil carbon stocks

Rates of leaf litter decay are generally expected to accelerate with increasing temperature. However, chronic temperature elevation may cause changes in the quality of litter residues or in the composition of decomposer communities that result in unexpected decay responses. We performed a 23-month litter decomposition study at a long-term soil warming experiment to determine how soil warming affects litter decay rate, litter chemistry, extracellular enzyme activities, and fungal community composition. Experimental soil warming did not affect litter mass loss, but did result in a 23% increase in the relative abundance of lignin; a concomitant shift in enzyme activity wherein lignin-decomposing enzymes had higher activity in the heated treatment while cellulose-decomposing enzymes were suppressed; and a shift in the composition of the active fungal community. In particular, ectomycorrhizal fungi were three times more abundant in the heated treatment than the control, and shifts in fungal community composition were significantly correlated with the observed changes in extracellular enzyme activities. Our results suggest that warming altered the trajectory of decay resulting in litter residues enriched in lignin compounds and that were populated by a higher relative abundance of ectomycorrhizal fungi. These shifts may have altered the temperature sensitivity of litter decay by reducing the quality of litter residues and changing fungal community function.

Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities

Fungi are important members of soil microbial communities in row-crop and grassland soils, provide essential ecosystem services such as nutrient cycling, organic matter decomposition, and soil structure, but fungi are also more sensitive to physical disturbance than other microorganisms. Adoption of conservation management practices such as no-till and cover cropping shape the structure and function of soil fungal communities. No-till eliminates or greatly reduces the physical disturbance that re-distributes organisms and nutrients in the soil profile and disrupts fungal hyphal networks, while cover crops provide additional types and greater abundance of organic carbon sources. In a long-term, row crop field experiment in California's Central Valley we hypothesized that a more diverse and plant symbiont-enriched fungal soil community would develop in soil managed with reduced tillage practices and/or cover crops compared to standard tillage and no cover crops. We measured the interacting effects of tillage and cover cropping on fungal communities based on fungal ITS sequence assigned to ecological guilds. Functional groups within fungal communities were most sensitive to long-term tillage practices, with 45% of guild-assigned taxa responding to tillage, and a higher proportion of symbiotroph taxa under no-till. In contrast, diversity measures reflected greater sensitivity to cover crops, with higher phylogenetic diversity observed in soils managed with cover crops, though only 10% of guild-assigned taxa responded to cover crops. The relative abundance of pathotrophs did not vary across the management treatments. Cover cropping increased species diversity, while no-till shifted the symbiotroph:saprotroph ratio to favor symbiotrophs. These management-induced shifts in fungal community composition could lead to greater ecosystem resilience and provide greater access of crops to limiting resources.