Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats

BACKGROUND

Biting midges (Culicoides spp.) are important vectors of diverse microbes such as viruses, protozoa, and nematodes that cause diseases in wild and domestic animals. However, little is known about the role of microbial communities in midge larval habitat utilization in the wild. In this study, we characterized microbial communities (bacterial, protistan, fungal and metazoan) in soils from disturbed (bison and cattle grazed) and undisturbed (non-grazed) pond and spring potential midge larval habitats. We evaluated the influence of habitat and grazing disturbance and their interaction on microbial communities, diversity, presence of midges, and soil properties.

RESULTS

Bacterial, protistan, fungal and metazoan community compositions were significantly influenced by habitat and grazing type. Irrespective of habitat and grazing type, soil communities were dominated by phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria (Bacteria); Apicomplexa, Cercozoa, Ciliophora, Ochrophyta (Protists); Chytridiomycota, Cryptomycota (Fungi) and Nematoda, Arthropoda (Metazoa). The relative abundance of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia (Bacteria); Apicomplexa, Lobosa (Protists); Ascomycota, Blastomycotina, Cryptomycota (Fungi); and Platyhelminthes (Metazoa) were significantly affected by grazing type. Of note, midge prevalence was higher in grazed sites (67-100%) than non-grazed (25%). Presence of midges in the soil was negatively correlated with bacterial, protistan, fungal and metazoan beta diversities and metazoan species richness but positively correlated with protistan and fungal species richness. Moreover, total carbon (TC), nitrogen (TN) and organic matter (OM) were negatively correlated with the presence of midges and relative abundances of unclassified Solirubrobacterales (Bacteria) and Chlamydomonadales (Protists) but positively with Proteobacteria and unclassified Burkholderiales (Bacteria).

CONCLUSIONS

Habitat and grazing type shaped the soil bacterial, protistan, fungal and metazoan communities, their compositions and diversities, as well as presence of midges. Soil properties (TN, TC, OM) also influenced soil microbial communities, diversities and the presence of midges. Prevalence of midges mainly in grazed sites indicates that midges prefer to breed and shelter in a habitat with abundant hosts, probably due to greater accessibility of food (blood meals). These results provide a first glimpse into the microbial communities, soil properties and prevalence of midges in suspected midge larval habitats at a protected natural prairie site.

Soil Depth Significantly Shifted Microbial Community Structures and Functions in a Semiarid Prairie Agroecosystem

The North American Great Plains cover a large area of the Nearctic ecozone, and an important part of this biome is semiarid. The sustainable intensification of agriculture that is necessary to produce food for an ever-increasing world population requires knowledge of the taxonomic and functional structure of the soil microbial community. In this study, we investigated the influence of soil depth on the composition and functions of the microbial communities hosted in agricultural soils of a semiarid agroecosystem, using metagenomic profiling, and compared them to changes in soil chemical and physical properties. Shotgun sequencing was used to determine the composition and functions of the soil microbial community of 45 soil samples from three soil depths (0-15 cm, 15-30 cm, and 30-60 cm) under different agricultural land use types (native prairie, seeded prairie, and cropland) in southwest Saskatchewan. Analysis of community composition revealed the declining abundance of phyla Verrucomicrobia, Bacteroidetes, Chlorophyta, Bacillariophyta, and Acidobacteria with soil depth, whereas the abundance of phyla Ascomycota, Nitrospirae, Planctomycetes, and Cyanobacteria increased with soil depth. Soil functional genes related to nucleosides and nucleotides, phosphorus (P) metabolism, cell division and cell cycle, amino acids and derivatives, membrane transport, and fatty acids were particularly abundant at 30-60 cm. In contrast, functional genes related to DNA and RNA metabolism, metabolism of nitrogen, sulfur and carbohydrates, and stress response were more abundant in the top soil depth. The RDA analysis of functional genes and soil physico-chemical properties revealed a positive correlation between phages and soil organic P concentrations. In the rooting zone of this semiarid agroecosystem, soil microbes express variable structural patterns of taxonomic and functional diversity at different soil depths. This study shows that the soil microbial community is structured by soil depth and physicochemical properties, with the middle soil depth being an intermediate transition zone with a higher taxonomic diversity. Our results suggest the co-existence of various microbial phyla adapted to upper and lower soil depths in an intermediate-depth transition zone.

Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts

The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.

Trends in Microbial Community Composition and Function by Soil Depth

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

The genus Calonectria includes pathogens of various agricultural, horticultural, and forestry crops. Species of Calonectria are commonly collected from soils, fruits, leaves, stems, and roots. Some species of Calonectria isolated from soils are considered as important plant pathogens. Understanding the species diversity and distribution characteristics of Calonectria species in different soil layers will help us to clarify their long-term potential harm to plants and their patterns of dissemination. To our knowledge, no systematic research has been conducted concerning the species diversity and distribution characteristics of Calonectria in different soil layers. In this study, 1000 soil samples were collected from five soil layers (0-20, 20-40, 40-60, 60-80, and 80-100 cm) at 100 sampling points in one 15-year-old Eucalyptus urophylla hybrid plantation in southern China. A total of 1037 isolates of Calonectria present in all five soil layers were obtained from 93 of 100 sampling points. The 1037 isolates were identified based on DNA sequence comparisons of the translation elongation factor 1-alpha (tef1), β-tubulin (tub2), calmodulin (cmdA), and histone H3 (his3) gene regions, as well as the combination of morphological characteristics. These isolates were identified as C. hongkongensis (665 isolates; 64.1%), C. aconidialis (250 isolates; 24.1%), C. kyotensis (58 isolates; 5.6%), C. ilicicola (47 isolates; 4.5%), C. chinensis (2 isolates; 0.2%), and C. orientalis (15 isolates; 1.5%). With the exception of C. orientalis, which resides in the C. brassicae species complex, the other five species belonged to the C. kyotensis species complex. The results showed that the number of sampling points that yielded Calonectria and the number (and percentage) of Calonectria isolates obtained decreased with increasing depth of the soil. More than 84% of the isolates were obtained from the 0-20 and 20-40 cm soil layers. The deeper soil layers had comparatively lower numbers but still harbored a considerable number of Calonectria. The diversity of five species in the C. kyotensis species complex decreased with increasing soil depth. The genotypes of isolates in each Calonectria species were determined by tef1 and tub2 gene sequences. For each species in the C. kyotensis species complex, in most cases, the number of genotypes decreased with increasing soil depth. The 0-20 cm soil layer contained all of the genotypes of each species. To our knowledge, this study presents the first report of C. orientalis isolated in China. This species was isolated from the 40-60 and 60-80 cm soil layers at only one sampling point, and only one genotype was present. This study has enhanced our understanding of the species diversity and distribution characteristics of Calonectria in different soil layers.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Temporal turnover of the soil microbiome composition is guild-specific

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.

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.

How Tillage and Crop Rotation Change the Distribution Pattern of Fungi

Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.

Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils

Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.

Straw retention efficiently improves fungal communities and functions in the fallow ecosystem

BACKGROUND

Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields.

RESULT

The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity.

CONCLUSIONS

Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.

Community structure of soil fungi in a novel perennial crop monoculture, annual agriculture, and native prairie reconstruction

The use of perennial crop species in agricultural systems may increase ecosystem services and sustainability. Because soil microbial communities play a major role in many processes on which ecosystem services and sustainability depend, characterization of soil community structure in novel perennial crop systems is necessary to understand potential shifts in function and crop responses. Here, we characterized soil fungal community composition at two depths (0–10 and 10–30 cm) in replicated, long-term plots containing one of three different cropping systems: a tilled three-crop rotation of annual crops, a novel perennial crop monoculture (Intermediate wheatgrass, which produces the grain Kernza^®), and a native prairie reconstruction. The overall fungal community was similar under the perennial monoculture and native vegetation, but both were distinct from those in annual agriculture. The mutualist and saprotrophic community subsets mirrored differences of the overall community, but pathogens were similar among cropping systems. Depth structured overall communities as well as each functional group subset. These results reinforce studies showing strong effects of tillage and sampling depth on soil community structure and suggest plant species diversity may play a weaker role. Similarities in the overall and functional fungal communities between the perennial monoculture and native vegetation suggest Kernza^® cropping systems have the potential to mimic reconstructed natural systems.

Mycobiome diversity: high-throughput sequencing and identification of fungi

Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.

Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area

Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community's metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.IMPORTANCE Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a significant impact on the structure and function of soil microbial communities, including shifts in expression of specific metabolic pathways, such as those leading toward production of osmoprotectant compounds. This study demonstrates the application of an untargeted multi-omics approach to decipher details of the soil microbial community's metaphenotypic response to environmental perturbations and should be applicable to studies of other complex microbial systems as well.

Fungal community composition and diversity vary with soil depth and landscape position in a no-till wheat-based cropping system

Soil edaphic characteristics are major drivers of fungal communities, but there is a lack of information on how communities vary with soil depth and landscape position in no-till cropping systems. Eastern Washington is dominated by dryland wheat grown on a highly variable landscape with steep, rolling hills. High-throughput sequencing of fungal ITS1 amplicons was used to characterize fungal communities across soil depth profiles (0 to 100 cm from the soil surface) among distinct landscape positions and aspects across a no-till wheat field. Fungal communities were highly stratified with soil depth, where deeper depths harbored distinct fungal taxa and more variable, less diverse fungal communities. Fungal communities from deep soils harbored a greater portion of taxa inferred to have pathotrophic or symbiotrophic in addition to saprotrophic lifestyles. Co-occurrence networks of fungal taxa became smaller and denser as soil depth increased. In contrast, differences between fungal communities from north-facing and south-facing slopes were relatively minor, suggesting that plant host, tillage, and fertilizer may be stronger drivers of fungal communities than landscape position.

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity

There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a 'black box' in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.

Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

Changes in frequency and amplitude of rain events, that is, precipitation patterns, result in different water conditions with soil depth, and likely affect plant growth and shape plant and soil microbial activity. Here, we used ¹⁸O stable isotope probing (SIP) to investigate bacterial and fungal communities that actively grew or not upon rewetting, at three different depths in soil mesocosms previously subjected to frequent or infrequent watering for 12 weeks (equal total water input). Phylogenetic marker genes for bacteria and fungi were sequenced after rewetting, and plant-soil microbial coupling documented by plant ¹³C-CO₂ labeling. Soil depth, rather than precipitation pattern, was most influential in shaping microbial response to rewetting, and had differential effects on active and inactive bacterial and fungal communities. After rewetting, active bacterial communities were less rich, more even and phylogenetically related than the inactive, and reactivated throughout the soil profile. Active fungal communities after rewetting were less abundant and rich than the inactive. The coupling between plants and soil microbes decreased under infrequent watering in the top soil layer. We suggest that differences in fungal and bacterial abundance and relative activity could result in large effects on subsequent soil biogeochemical cycling.

Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity

Future increases in temperature and cloud cover will alter plant growth and decomposition of the large carbon pools stored in Arctic soils. A better understanding of interactions between above- and belowground processes and communities of plants and microorganisms is essential for predicting Arctic ecosystem responses to climate change. We measured ecosystem CO2 fluxes during the growing season for seven years in a dwarf-shrub tundra in West Greenland manipulated with warming and shading and experiencing a natural larvae outbreak. Vegetation composition, soil fungal community composition, microbial activity, and nutrient availability were analyzed after six years of treatment. Warming and shading altered the plant community, reduced plant CO2 uptake, and changed fungal community composition. Ecosystem carbon accumulation decreased during the growing season by 61% in shaded plots and 51% in warmed plots. Also, plant recovery was reduced in both manipulations following the larvae outbreak during the fifth treatment year. The reduced plant recovery in manipulated plots following the larvae outbreak suggests that climate change may increase tundra ecosystem sensitivity to disturbances. Also, plant community changes mediated via reduced light and reduced water availability due to increased temperature can strongly lower the carbon sink strength of tundra ecosystems.

Microbial diversity in solar greenhouse soils in Round-Bohai Bay-Region, China: The influence of cultivation year and environmental condition

Round-Bohai Bay (RBB)-Region is an important crop production area in China, where vegetables are mainly produced in solar greenhouses. However, excessive fertilization and monoculture have caused serious deterioration of soil quality in this region. Soil microbial communities play pivotal roles in many ecosystem processes and are recognized as integrative components of soil quality. Therefore, in this study, we investigated bacterial and fungal diversity in solar greenhouse soils covering a wide range of cultivation year (CY) and sampling site (SS), by using pyrosequencing technology. Surprisingly, CY and SS had little influence on bacterial and fungal relative abundance and diversity. However, environmental factors (EF) and soil available potassium (K) in particular made a significant contribution to the variation of soil bacterial and fungal communities. Specifically, K showed significant (P < 0.05) correlations with dominant bacterial phyla Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes and fungal phyla Ascomycota and Basidiomycota. These results suggested that soil EF appeared more important than CY and SS in shaping the compositions of bacterial and fungal communities. In addition, since fertilizer K has been in the long-term abused in RBB-Region, future vegetable production should pay more attention to K input to reduce the negative effect on soil microbial communities.

Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass

The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.

Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence

The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.

The relative importance of vertical soil nutrient heterogeneity, and mean and depth-specific soil nutrient availabilities for tree species richness in tropical forests and woodlands

The relative importance of resource heterogeneity and quantity on plant diversity is an ongoing debate among ecologists, but we have limited knowledge on relationships between tree diversity and heterogeneity in soil nutrient availability in tropical forests. We expected tree species richness to be: (1) positively related to vertical soil nutrient heterogeneity; (2) negatively related to mean soil nutrient availability; and (3) more influenced by nutrient availability in the upper than lower soil horizons. Using a data set from 60, 20 × 40-m plots in a moist forest, and 126 plots in miombo woodlands in Tanzania, we regressed tree species richness against vertical soil nutrient heterogeneity, both depth-specific (0-15, 15-30, and 30-60 cm) and mean soil nutrient availability, and soil physical properties, with elevation and measures of anthropogenic disturbance as co-variables. Overall, vertical soil nutrient heterogeneity was the best predictor of tree species richness in miombo but, contrary to our prediction, the relationships between tree species richness and soil nutrient heterogeneity were negative. In the moist forest, mean soil nutrient availability explained considerable variations in tree species richness, and in line with our expectations, these relationships were mainly negative. Soil nutrient availability in the top soil layer explained more of the variation in tree species richness than that in the middle and lower layers in both vegetation types. Our study shows that vertical soil nutrient heterogeneity and mean availability can influence tree species richness at different magnitudes in intensively utilized tropical vegetation types.

Spatial Distribution of Fungal Communities in an Arable Soil

Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0–10 cm, b) rooted soil in 40–50 cm, c) root-free soil in 60–70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment.

Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence.

Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad

Understanding how community structure of Bacteria, Archaea, and Fungi varies as a function of edaphic characteristics is key to elucidating associations between soil ecosystem function and the microbiome that sustains it. In this study, non-managed tropical soils were examined that represented a range of edaphic characteristics, and a comprehensive soil microbiome analysis was done by Illumina sequencing of amplicon libraries that targeted Bacteria (universal prokaryotic 16S rRNA gene primers), Archaea (primers selective for archaeal 16S rRNA genes), or Fungi (internal transcribed spacer region). Microbiome diversity decreased in the order: Bacteria > Archaea > Fungi. Bacterial community composition had a strong relationship to edaphic factors while that of Archaea and Fungi was comparatively weak. Bacterial communities were 70–80% alike, while communities of Fungi and Archaea had 40–50% similarity. While each of the three component communities differed in species turnover patterns, soils having relatively similar bacterial communities also housed similar archaeal communities. In contrast, the composition of fungal communities had no correlation to bacterial or archaeal communities. Bacterial and archaeal diversity had significant (negative) correlations to pH, whereas fungal diversity was not correlated to pH. Edaphic characteristics that best explained variation between soils in bacterial community structure were: total carbon, sodium, magnesium, and zinc. For fungi, the best variables were: sodium, magnesium, phosphorus, boron, and C/N. Archaeal communities had two sets of edaphic factors of equal strength, one contained sulfur, sodium, and ammonium-N and the other was composed of clay, potassium, ammonium-N, and nitrate-N. Collectively, the data indicate that Bacteria, Archaea, and Fungi did not closely parallel one another in community structure development, and thus microbiomes in each soil acquired unique identities. This divergence could in part reflect the finding that unknown factor(s) were stronger than edaphic characteristics in shaping fungal and archaeal communities.

Nutrient input influences fungal community composition and size and can stimulate manganese (II) oxidation in caves

Little is known about the fungal role in biogeochemical cycling in oligotrophic ecosystems. This study compared fungal communities and assessed the role of exogenous carbon on microbial community structure and function in two southern Appalachian caves: an anthropogenically impacted cave and a near-pristine cave. Due to carbon input from shallow soils, the anthropogenically impacted cave had an order of magnitude greater fungal and bacterial quantitative-polymerase chain reaction (qPCR) gene copy numbers, had significantly greater community diversity, and was dominated by ascomycotal phylotypes common in early phase, labile organic matter decomposition. Fungal assemblages in the near-pristine cave samples were dominated by Basidiomycota typically found in deeper soils (and/or in late phase, recalcitrant organic matter decomposition), suggesting more oligotrophic conditions. In situ carbon and manganese (II) [Mn(II)] addition over 10 weeks resulted in growth of fungal mycelia followed by increased Mn(II) oxidation. A before/after comparison of the fungal communities indicated that this enrichment increased the quantity of fungal and bacterial cells, yet decreased overall fungal diversity. Anthropogenic carbon sources can therefore dramatically influence the diversity and quantity of fungi, impact microbial community function, and stimulate Mn(II) oxidation, resulting in a cascade of changes that can strongly influence nutrient and trace element biogeochemical cycles in karst aquifers.

Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles

Soil fungi play an essential role in the decomposition of plant-derived organic material entering soils. The quality and quantity of organic compounds vary seasonally as well as with soil depth. To elucidate how these resources affect fungal communities in an arable soil, a field experiment was set up with two plant species, maize and wheat. Resource availability was experimentally manipulated by maize litter input on one half of these maize and wheat plots after harvest in autumn. Fungal biomass was determined by ergosterol quantification, and community structure was investigated by fungal automated ribosomal intergenic spacer analysis (F-ARISA). An annual cycle was assessed across a depth gradient, distinguishing three soil habitats: the plough layer, rooted soil below the plough layer, and deeper root-free soil. Fungal communities appeared highly dynamic and varied according to soil depth and plant resources. In the plough layer, the availability of litter played a dominant role in shaping fungal communities, whereas in the rooted layer below, community structure and biomass mainly differed between plant species. This plant effect was also extended into the root-free soil at a depth of 70 cm. In winter, the availability of litter also affected fungal communities in deeper soil layers, suggesting vertical transport processes under fallow conditions. These distinct resource effects indicate diverse ecological niches along the soil profile, comprising specific fungal metacommunities. The recorded responses to both living plants and litter point to a central role of fungi in connecting primary production and decomposition within the plant-soil system.

Soil fungal communities respond to grassland plant community richness and soil edaphics

Fungal communities in soil have significant influences on terrestrial ecosystem dynamics, yet our understanding of the drivers of fungal diversity and community structure in soil is limited. Fungal communities associated with the rhizosphere of four native perennial grassland plant species, two legumes and two grasses, grown in monoculture and polyculture in a long-term field experiment were characterized. Reference databases were developed for, and amplicon libraries sequenced from, multiple-copy rRNA and single-copy protein-coding loci. Clustering and alignment-based pipelines were utilized to evaluate differences in fungal community structure and diversity in response to plant host, plant community richness, and soil edaphics. Fungal diversity increased in the rhizosphere of plants growing in polyculture plant communities as compared to monoculture plant communities. Fungal community structure was differentiated between legumes and grasses growing in monoculture but not in polyculture. To specifically monitor fungi in the genus Fusarium in the soil, the protein-coding locus was used to increase phylogenetic resolution and enrich for this taxon. These data show that fungal community richness and structure are strongly linked with plant community dynamics and associated soil edaphic characteristics in these grassland soils.

Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing

Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semi-arid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semi-arid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1940 Operational Taxonomic Units (OTUs) were identified from 362 332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows.

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi

Knowledge of spatiotemporal patterns in species distribution is fundamental to understanding the ecological and evolutionary processes shaping communities. The emergence of DNA-based tools has expanded the geographic and taxonomic scope of studies examining spatial and temporal distribution of mycorrhizal fungi. However, the nature of spatiotemporal patterns documented and subsequent interpretation of ecological processes can vary significantly from study to study. In order to look for general patterns we synthesize the available data across different sampling scales and mycorrhizal types. The results of this analysis shed light on the relative importance of space, time and vertical soil structure on community variability across different mycorrhizal types. Although we found no significant trend in spatiotemporal variation amongmycorrhizal types, the vertical community variation was distinctly greater than the spatial and temporal variability in mycorrhizal fungal communities. Both spatial and temporal variability of communities was greater in topsoil compared with lower horizons, suggesting that greater environmental heterogeneity drives community variation on a fine scale. This further emphasizes the importance of both niche differentiation and environmental filtering in maintaining diverse fungal communities.

Fungal communities respond to long-term CO2 elevation by community reassembly

Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO2 (eCO2), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO2, and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO2 for 12 years. Long-term eCO2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ∼27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO2, especially with increased plant biomass and NH4 (+) availability. This study provided novel insights into how eCO2 shapes soil fungal communities in grassland ecosystems.

Fungal Community Responses to Past and Future Atmospheric CO2 Differ by Soil Type

Soils sequester and release substantial atmospheric carbon, but the contribution of fungal communities to soil carbon balance under rising CO2 is not well understood. Soil properties likely mediate these fungal responses but are rarely explored in CO2 experiments. We studied soil fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2 gradient (250 to 500 ppm) in a black clay soil and a sandy loam soil. Sanger sequencing and pyrosequencing of the rRNA gene cluster revealed that fungal community composition and its response to CO2 differed significantly between soils. Fungal species richness and relative abundance of Chytridiomycota (chytrids) increased linearly with CO2 in the black clay (P < 0.04, R(2) > 0.7), whereas the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) increased linearly with elevated CO2 in the sandy loam (P = 0.02, R(2) = 0.63). Across both soils, decomposition rate was positively correlated with chytrid relative abundance (r = 0.57) and, in the black clay soil, fungal species richness. Decomposition rate was more strongly correlated with microbial biomass (r = 0.88) than with fungal variables. Increased labile carbon availability with elevated CO2 may explain the greater fungal species richness and Chytridiomycota abundance in the black clay soil, whereas increased phosphorus limitation may explain the increase in Glomeromycota at elevated CO2 in the sandy loam. Our results demonstrate that soil type plays a key role in soil fungal responses to rising atmospheric CO2.

Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach

BACKGROUND

Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach.

METHODOLOGY/PRINCIPAL FINDINGS

Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H(Shannon)) and richness (S(Chao1)) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time.

CONCLUSIONS

Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment.

Seasonal dynamics of fungal communities in a temperate oak forest soil

Fungi are the agents primarily responsible for the transformation of plant-derived carbon in terrestrial ecosystems. However, little is known of their responses to the seasonal changes in resource availability in deciduous forests, including photosynthate allocation below ground and seasonal inputs of fresh litter. Vertical stratification of and seasonal changes in fungal abundance, activity and community composition were investigated in the litter, organic and upper mineral soils of a temperate Quercus petraea forest using ergosterol and extracellular enzyme assays and amplicon 454-pyrosequencing of the rDNA-ITS region. Fungal activity, biomass and diversity decreased substantially with soil depth. The highest enzyme activities were detected in winter, especially in litter, where these activities were followed by a peak in fungal biomass during spring. The litter community exhibited more profound seasonal changes than did the community in the deeper horizons. In the litter, saprotrophic genera reached their seasonal maxima in autumn, but summer typically saw the highest abundance of ectomycorrhizal taxa. Although the composition of the litter community changes over the course of the year, the mineral soil shows changes in biomass. The fungal community is affected by season. Litter decomposition and phytosynthate allocation represent important factors contributing to the observed variations.

Microbial diversity in the era of omic technologies

Human life and activity depends on microorganisms, as they are responsible for providing basic elements of life. Although microbes have such a key role in sustaining basic functions for all living organisms, very little is known about their biology since only a small fraction (average 1%) can be cultured under laboratory conditions. This is even more evident when considering that >88% of all bacterial isolates belong to four bacterial phyla, the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Advanced technologies, developed in the last years, promise to revolutionise the way that we characterize, identify, and study microbial communities. In this review, we present the most advanced tools that microbial ecologists can use for the study of microbial communities. Innovative microbial ecological DNA microarrays such as PhyloChip and GeoChip that have been developed for investigating the composition and function of microbial communities are presented, along with an overview of the next generation sequencing technologies. Finally, the Single Cell Genomics approach, which can be used for obtaining genomes from uncultured phyla, is outlined. This tool enables the amplification and sequencing of DNA from single cells obtained directly from environmental samples and is promising to revolutionise microbiology.

Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important implications for both managed and natural grassland ecosystems.