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Next‐generation sequencing (NGS) has significantly increased knowledge of microbial communities and their distribution. However, it is still not common to apply NGS technology to microbial conservation. We sought to use NGS technologies to evaluate conservation strategies for wood‐inhabiting fungi. Evaluating a deadwood experiment 3 years after it was established, we specifically examined which tree species combinations promoted the highest richness of wood‐inhabiting fungi. Deadwood enrichment was an effective strategy and logs of 6 tree species, either those with the highest wood‐inhabiting fungal α and γ diversity or those with the highest β diversity, maintained >1,000 operational taxonomic units (OTUs) spread over a wide range of taxonomic groups. In comparison, a conservation strategy based only on the results of sporocarp surveys yielded 591 OTUs. This result highlights the need to use NGS approaches to inform microbial conservation strategies. We also determined that 5 tree species with the highest saproxylic beetle γ diversity simultaneously conserved wood‐inhabiting fungi. Apart from deadwood volume, we suggest data on deadwood quality and species also be included as indicators, especially for wood‐inhabiting fungal diversity, and incorporated quickly in forest assessment and monitoring systems in Central Europe. Article impact statement: Enrichment of the species diversity of deadwood is an effective strategy for wood‐inhabiting fungal conservation in temperate forests. [ABSTRACT FROM AUTHOR]

Summary: Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood‐inhabiting fungi (WIF) and their related ecological functions and processes in a highly N‐limited deadwood habitat. Based on high‐throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat. Nevertheless, we detected several switches in presence/absence (gain/loss) of wood‐inhabiting fungal OTUs due to the effect of N addition. The responses of WIF differed from previous studies carried out with fungi living in soil and leaf‐litter, which represent less N‐limited fungal habitats. Our results suggest that adaptation at different levels of organization and functional redundancy may explain this buffered response and the resistant microbial‐mediated ecosystem function and processes against N deposition in highly N‐limited habitats. [ABSTRACT FROM AUTHOR]

Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial ecosystems. Due to the permanently changing litter quality during decomposition, studies of both fungi and bacteria at a fine taxonomic resolution are required during the whole process. Here we investigated microbial community succession in decomposing leaf litter of temperate beech forest using pyrotag sequencing of the bacterial 16S and the fungal internal transcribed spacer ( ITS) rRNA genes. Our results reveal that both communities underwent rapid changes. Proteobacteria, Actinobacteria and Bacteroidetes dominated over the entire study period, but their taxonomic composition and abundances changed markedly among sampling dates. The fungal community also changed dynamically as decomposition progressed, with ascomycete fungi being increasingly replaced by basidiomycetes. We found a consistent and highly significant correlation between bacterial richness and fungal richness ( R = 0.76, P < 0.001) and community structure ( RMantel = 0.85, P < 0.001), providing evidence of coupled dynamics in the fungal and bacterial communities. A network analysis highlighted nonrandom co-occurrences among bacterial and fungal taxa as well as a shift in the cross-kingdom co-occurrence pattern of their communities from the early to the later stages of decomposition. During this process, macronutrients, micronutrients, C:N ratio and pH were significantly correlated with the fungal and bacterial communities, while bacterial richness positively correlated with three hydrolytic enzymes important for C, N and P acquisition. Overall, we provide evidence that the complex litter decay is the result of a dynamic cross-kingdom functional succession. [ABSTRACT FROM AUTHOR]

To understand the fine-scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long-term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae-Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88 706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic- (farmyard manure), mineral- and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co-occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels. [ABSTRACT FROM AUTHOR]

Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition. [ABSTRACT FROM AUTHOR]

Fungi are important members of soil microbial communities with a crucial role in biogeochemical processes. Although soil fungi are known to be highly diverse, little is known about factors influencing variations in their diversity and community structure among forests dominated by the same tree species but spread over different regions and under different managements. We analyzed the soil fungal diversity and community composition of managed and unmanaged European beech dominated forests located in three German regions, the Schwäbische Alb in Southwestern, the Hainich-Dün in Central and the Schorfheide Chorin in the Northeastern Germany, using internal transcribed spacer (ITS) rDNA pyrotag sequencing. Multiple sequence quality filtering followed by sequence data normalization revealed 1655 fungal operational taxonomic units. Further analysis based on 722 abundant fungal OTUs revealed the phylum Basidiomycota to be dominant (54%) and its community to comprise 71.4% of ectomycorrhizal taxa. Fungal community structure differed significantly (p≤0.001) among the three regions and was characterized by non-random fungal OTUs co-occurrence. Soil parameters, herbaceous understory vegetation, and litter cover affected fungal community structure. However, within each study region we found no difference in fungal community structure between management types. Our results also showed region specific significant correlation patterns between the dominant ectomycorrhizal fungal genera. This suggests that soil fungal communities are region-specific but nevertheless composed of functionally diverse and complementary taxa. [ABSTRACT FROM AUTHOR]

Abstract: The soil fungal diversity and community partitioning between the bulk soil and stone compartments was investigated using PCR based approaches targeting the barcoding internal transcribed spacer (ITS) of rDNA and the laccase encoding functional gene as genetic markers. Soil samples were collected from the B-horizon of spruce and beech forests at the Hainich Biodiversity Exploratory, central Germany. The targeted markers were amplified from the respective DNA extracts using general fungal primers and basidiomycete laccase gene specific primers, cloned and sequenced. Differences in the fungal community composition between the two forest types and the soil compartments were indicated by both markers. When the effects of ecological factors were considered, the two markers produced different patterns of results. The ITS rDNA marker revealed communities principally influenced by forest type, while those detected with the functional marker were mainly affected by soil pH. The fungal communities detected by the functional marker in particular, differed significantly between soils and stones, indicating that laccase-producing fungi are specifically adapted to degrade organic matter in soils rather than weathering of stones. The study underlines the fact that coherent and complementary results may be obtained with both genetic markers used. [Copyright &y& Elsevier]

Large-scale (temporal and/or spatial) molecular investigations of the diversity and distribution of arbuscular mycorrhizal fungi (AMF) require considerable sampling efforts and high-throughput analysis. To facilitate such efforts, we have developed a TaqMan real-time PCR assay to detect and identify AMF in environmental samples. First, we screened the diversity in clone libraries, generated by nested PCR, of the nuclear ribosomal DNA internal transcribed spacer (ITS) of AMF in environmental samples. We then generated probes and forward primers based on the detected sequences, enabling AMF sequence type-specific detection in TaqMan multiplex real-time PCR assays. In comparisons to conventional clone library screening and Sanger sequencing, the TaqMan assay approach provided similar accuracy but higher sensitivity with cost and time savings. The TaqMan assays were applied to analyze the AMF community composition within plots of a large-scale plant biodiversity manipulation experiment, the Jena Experiment, primarily designed to investigate the interactive effects of plant biodiversity on element cycling and trophic interactions. The results show that environmental variables hierarchically shape AMF communities and that the sequence type spectrum is strongly affected by previous land use and disturbance, which appears to favor disturbance-tolerant members of the genus Glomus. The AMF species richness of disturbance-associated communities can be largely explained by richness of plant species and plant functional groups, while plant productivity and soil parameters appear to have only weak effects on the AMF community. [ABSTRACT FROM AUTHOR]

A new arbuscular mycorrhizal fungal species of the genus Glomus, Glomus indicum (Glomeromycota), forming small, hyaline spores in hypogeous aggregates is described and illustrated. The spores are globose to subglobose, (17–)32(–52) µm in diameter, rarely egg-shaped, oblong to irregular, 17–38 µm × 19–43 µm. The single spore wall of G. indicum consists of two hyaline layers: a mucilaginous, short-lived, thin outer layer staining pinkish to pink in Melzer’s reagent and a laminate, smooth, permanent, thicker inner layer. Glomus indicum was found in the rhizosphere of Euphorbia heterophylla L. naturally growing in coastal sands of Alappuzha in Kerala State of South India and Lactuca sativa L. cultivated in Asmara, Eritrea, North East Africa. In single-species cultures with Plantago lanceolata L. as the host plant, G. indicum formed vesicular-arbuscular mycorrhiza. Molecular analysis of the phylogenetic position of G. indicum based on both SSU and ITS rDNA sequences showed the fungus to be a new species with its own cluster. Besides the sites where the spores were observed, sequence types belonging to the G. indicum cluster were documented from environmental samples mainly in the USA, Estonia, and Australia, suggesting the wide occurrence of the species. A key to all known species of the Glomeromycota producing hyaline to light-coloured glomoid spores is provided. [ABSTRACT FROM AUTHOR]

The molecular diversity of arbuscular mycorrhizal (AM) fungi colonizing roots of Podocarpus falcatus (Thunb.) R.Br. (Podocarpaceae) in the dry Afromontane forests of Ethiopia was investigated. The nuclear gene coding for small subunit ribosomal RNA (nucSSU rDNA) was amplified from colonized roots of P. falcatus, cloned, and sequenced using AM fungal specific primers. Phylogenetic analyses revealed that the glomeromycetous sequences from mycorrhizae of P. falcatus belong to the Glomeraceae, Diversisporaceae, and Archaeosporaceae. Overall, 16 Glomus, three Diversispora, and one Archaeospora sequence types were identified. These sequence types were distinct and only distantly related to sequences from the available defined species. The composition of the AM fungal communities differed significantly between the two study sites. Comparison of the AM fungal community composition of P. falcatus with that of previously investigated Juniperus procera Hochst. ex Endl. (Cupressaceae), the only coexisting indigenous conifer tree species in the dry Afromontane forest ecosystem, yields that the two tree species are colonized by distinct AM fungal communities. This suggests that fungal communities are host plant specific in the natural stand conditions. Therefore, in the conservation of these endangered species and restoration of the degraded ecosystem, the use of appropriate mycorrhizal fungi should be taken into account in future projects. [ABSTRACT FROM AUTHOR]

Abstract: The endangered indigenous tree species Juniperus procera, commonly known as African Pencil Cedar, is an important component of the dry Afromontane vegetation of Ethiopia and was shown to be AM in earlier studies. Here we describe the composition of AM fungi in colonized roots of J. procera from two dry Afromontane forests of Ethiopia. The nuSSU rDNA gene was amplified from colonized roots, cloned and sequenced using AM fungal specific primers that were partly developed for this study. Molecular phylogenetic analysis revealed that all the glomeralean sequences obtained belonged exclusively to the genus Glomus (Glomeraceae). Seven distinct Glomus sequence types were identified that all are new to science. The composition of the AM fungal communities between the sampled trees, and between the two study sites in general, differed significantly. Isolation and utilization of the indigenous AM fungal taxa from the respective sites might be required for successful enrichment plantation of this threatened Juniperus species. [Copyright &y& Elsevier]

Features a study that aimed to illustrate morphological characteristics of Taxus baccata mycorrhizas and to investigate the molecular diversity of arbuscular mycorrhizal fungi (AMF) species in roots of Taxus baccata growitn in southern Germany. Use of polymerase chain reaction based molecular techniques; Amplification of the internal transcribed spacer region of the DNA from AMF within the roots; Phylogenetic position of the AMF sequences obtained.

Summary: Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet the influence of tree mycorrhizal types, species identity, and diversity on tree‐tree interactions and their root‐associated fungal communities remains poorly understood.Our study addresses this gap by investigating root‐associated fungal communities of different arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species pairs (TSPs) in a subtropical tree diversity experiment, spanning monospecific, two‐species, and multi‐species mixtures, utilizing Illumina sequencing of the ITS2 region.The study reveals that tree mycorrhizal type significantly impacts the alpha diversity of root‐associated fungi in monospecific stands. Meanwhile, tree species identity's influence is modulated by overall tree diversity. Tree‐related variables and spatial distance emerged as major drivers of variations in fungal community composition. Notably, in multi‐species mixtures, compositional differences between root fungal communities of AM and EcM trees diminish, indicating a convergence of fungal communities irrespective of mycorrhizal type. Interestingly, dual mycorrhizal fungal communities were observed in these multi‐species mixtures.This research underscores the pivotal role of mycorrhizal partnerships and the interplay of biotic and abiotic factors in shaping root fungal communities, particularly in varied tree diversity settings, and its implications for effective forest management and biodiversity conservation. [ABSTRACT FROM AUTHOR]

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines. [ABSTRACT FROM AUTHOR]

Land management is known to have consequences for biodiversity; however, our synthetic understanding of its effects is limited due to highly variable results across studies, which vary in the focal taxa and spatial grain considered, as well as the response variables reported. Such synthetic knowledge is necessary for management of agroecosystems for high diversity and function.To fill this knowledge gap, we investigated the importance of scale‐dependent effects of land management (LM) (pastures vs. meadows), on plant and soil microbe diversity (fungi and bacteria) across 5 study sites in Central Germany. Analyses included diversity partitioning of species richness and related biodiversity components (i.e., density of individuals, species‐abundance distribution, and spatial aggregation) at two spatial grains (α‐ and γ‐scale, 1 m2 and 16 km2, respectively).Our results show scale‐dependent patterns in response to LM to be the norm rather than the exception and highlight the importance of measuring species richness and its underlying components at multiple spatial grains.Our outcomes provide new insight to the complexity of scale‐dependent responses within and across taxonomic groups. They suggest that, despite close associations between taxa, LM responses are not easily extrapolated across multiple spatial grains and taxa. Responses of biodiversity to LM are often driven by changes to evenness and spatial aggregation, rather than by changes in individual density. High‐site specificity of LM effects might be due to a variety of context‐specific factors, such as historic land management, identity of grazers, and grazing regime.Synthesis and applications: Our results suggest that links between taxa are not necessarily strong enough to allow for generalization of biodiversity patterns. These findings highlight the importance of considering multiple taxa and spatial grains when investigating LM responses, while promoting management practices that do the same and are tailored to local and regional conditions. [ABSTRACT FROM AUTHOR]

Forest ecosystems are critical for their carbon sequestration potential. Increasing tree diversity has been shown to enhance both forest productivity and litter decomposition. Litter diversity increases litter decomposability by increasing the diversity of substrates offered to decomposers. However, the relative importance of litter decomposability and decomposer community in mediating tree diversity effects on decomposition remains unknown. Moreover, tree diversity modulation of litterfall spatial distribution, and consequently litter decomposition, has rarely been tested. We studied tree diversity effects on leaf litter decomposition and its mediation by the amount of litterfall, litter species richness and decomposability, and soil microorganisms in a large‐scale tree diversity experiment in subtropical China. Furthermore, we examined how litter functional identity and diversity affect leaf litter decomposability. Finally, we tested how leaf functional traits, tree biomass, and forest spatial structure drive the litterfall spatial distribution. We found evidence that tree species richness increased litter decomposition by increasing litter species richness and the amount of litterfall. We showed that soil microorganisms in this subtropical forest perform 84–87% of litter decomposition. Moreover, changes in the amount of litterfall and microbial decomposition explained 19–37% of the decomposition variance. Additionally, up to 20% of the microbial decomposition variance was explained by litter decomposability, while litter decomposability itself was determined by litter functional identity, diversity, and species richness. Tree species richness increased litter species richness and the amount of litterfall (+200% from monoculture to eight‐species neighborhood). We further demonstrated that the amount of species‐specific litterfall increased with increasing tree proximity and biomass, and was modulated by leaf functional traits. These litterfall drivers increased the spatial heterogeneity of litter distribution, and thus litter decomposition. We highlighted multiple biomass‐ and diversity‐mediated effects of tree diversity on ecosystem properties driving forest nutrient cycling. We conclude that considering spatial variability in biotic properties will improve our mechanistic understanding of ecosystem functioning. [ABSTRACT FROM AUTHOR]

Carbon‐focused climate mitigation strategies are becoming increasingly important in forests. However, with ongoing biodiversity declines we require better knowledge of how much such strategies account for biodiversity. We particularly lack information across multiple trophic levels and on established forests, where the interplay between carbon stocks, stand age, and tree diversity might influence carbon–biodiversity relationships. Using a large dataset (>4600 heterotrophic species of 23 taxonomic groups) from secondary, subtropical forests, we tested how multitrophic diversity and diversity within trophic groups relate to aboveground, belowground, and total carbon stocks at different levels of tree species richness and stand age. Our study revealed that aboveground carbon, the key component of climate‐based management, was largely unrelated to multitrophic diversity. By contrast, total carbon stocks—that is, including belowground carbon—emerged as a significant predictor of multitrophic diversity. Relationships were nonlinear and strongest for lower trophic levels, but nonsignificant for higher trophic level diversity. Tree species richness and stand age moderated these relationships, suggesting long‐term regeneration of forests may be particularly effective in reconciling carbon and biodiversity targets. Our findings highlight that biodiversity benefits of climate‐oriented management need to be evaluated carefully, and only maximizing aboveground carbon may fail to account for biodiversity conservation requirements. [ABSTRACT FROM AUTHOR]

Forests are ecosystems critical to understanding the global carbon budget, due to their carbon sequestration potential in both aboveground and belowground compartments, especially in species‐rich forests. Soil carbon sequestration is strongly linked to soil microbial communities, and this link is mediated by the tree community, likely due to modifications of microenvironmental conditions (i.e., biotic conditions, soil properties, and microclimate). We studied soil carbon concentration and the soil microbial biomass of 180 local neighborhoods along a gradient of tree species richness ranging from 1 to 16 tree species per plot in a Chinese subtropical forest experiment (BEF‐China). Tree productivity and different tree functional traits were measured at the neighborhood level. We tested the effects of tree productivity, functional trait identity, and dissimilarity on soil carbon concentrations, and their mediation by the soil microbial biomass and microenvironmental conditions. Our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentrations. In addition, soil carbon concentration increased with tree productivity and tree root diameter, while it decreased with litterfall C:N content. Moreover, tree productivity and tree functional traits (e.g., fungal root association and litterfall C:N ratio) modulated microenvironmental conditions with substantial consequences for soil microbial biomass. We also showed that soil history and topography should be considered in future experiments and tree plantations, as soil carbon concentrations were higher at sites where historical (i.e., at the beginning of the experiment) carbon concentrations were high, themselves being strongly affected by the topography. Altogether, these results implied that the quantification of the different soil carbon pools is critical for understanding microbial community–soil carbon stock relationships and their dependence on tree diversity and microenvironmental conditions. [ABSTRACT FROM AUTHOR]

Summary: Plant–soil feedbacks (PSFs) underlying grassland plant richness and productivity are typically coupled with nutrient availability; however, we lack understanding of how restoration measures to increase plant diversity might affect PSFs. We examined the roles of sward disturbance, seed addition and land‐use intensity (LUI) on PSFs.We conducted a disturbance and seed addition experiment in 10 grasslands along a LUI gradient and characterized plant biomass and richness, soil microbial biomass, community composition and enzyme activities.Greater plant biomass at high LUI was related to a decrease in the fungal to bacterial ratios, indicating highly productive grasslands to be dominated by bacteria. Lower enzyme activity per microbial biomass at high plant species richness indicated a slower carbon (C) cycling. The relative abundance of fungal saprotrophs decreased, while pathogens increased with LUI and disturbance. Both fungal guilds were negatively associated with plant richness, indicating the mechanisms underlying PSFs depended on LUI.We show that LUI and disturbance affect fungal functional composition, which may feedback on plant species richness by impeding the establishment of pathogen‐sensitive species. Therefore, we highlight the need to integrate LUI including its effects on PSFs when planning for practices that aim to optimize plant diversity and productivity. [ABSTRACT FROM AUTHOR]

Opencast limestone mines or limestone quarries are considered challenging ecosystems for soil fungi as they are highly degraded land with specific conditions, including high temperature, prolonged sunlight exposure, and a lack of organic matter, moisture, and nutrients in soil. In such ecosystems, certain fungi can survive and have a crucial function in maintaining soil ecosystem functions. Unfortunately, we know very little about taxonomic diversity, potential functions, and the ecology of such fungi, especially for a limestone quarry in a tropical region. Here, we characterized and compared the living soil fungal communities in an opencast limestone mine, including mining site and its associated rehabilitation site (9 months post-rehabilitation), with the soil fungal community in a reference forest, using the amplicon sequencing of enrichment culture. Our results showed that living fungal richness in the quarry areas was significantly lower than that in the reference forest, and their community compositions were also significantly different. Living fungi in the mining sites mostly comprised of Ascomycota (Eurotiomycetes and Sordariomycetes) with strongly declined abundance or absence of Basidiomycota and Mucoromycota. After nine months of rehabilitation, certain taxa were introduced, such as Hypoxylon spp. and Phellinus noxius, though this change did not significantly differentiate fungal community composition between the mining and rehabilitation plots. The majority of fungi in these plots are classified as saprotrophs, which potentially produce all fifteen soil enzymes used as soil health indicators. Network analysis, which was analyzed to show insight into complex structures of living fungal community in the limestone quarry, showed a clear modular structure that was significantly impacted by different soil properties. Furthermore, this study suggests potential taxa that could be useful for future rehabilitation. [ABSTRACT FROM AUTHOR]

Summary: There is limited knowledge on how the association of trees with different mycorrhizal types shapes soil microbial communities in the context of changing tree diversity levels. We used arbuscular (AM) and ectomycorrhizal (EcM) tree species as con‐ and heterospecific tree species pairs (TSPs), which were established in plots of three tree diversity levels including monocultures, two‐species mixtures and multi‐tree species mixtures in a tree diversity experiment in subtropical China. We found that the tree mycorrhizal type had a significant effect on fungal but not bacterial alpha diversity. Furthermore, only EcM but not AM TSPs fungal alpha diversity increased with tree diversity, and the differences between AM and EcM TSPs disappeared in multi‐species mixtures. Tree mycorrhizal type, tree diversity and their interaction had significant effects on fungal community composition. Neither fungi nor bacteria showed any significant compositional variation in TSPs located in multi‐species mixtures. Accordingly, the most influential taxa driving the tree mycorrhizal differences at low tree diversity were not significant in multi‐tree species mixtures. Collectively, our results indicate that tree mycorrhizal type is an important factor determining the diversity and community composition of soil microbes, and higher tree diversity levels promote convergence of the soil microbial communities. Significance statement: More than 90% of terrestrial plants have symbiotic associations with mycorrhizal fungi which could influence the coexisting microbiota. Systematic understanding of the individual and interactive effects of tree mycorrhizal type and tree species diversity on the soil microbiota is crucial for the mechanistic comprehension of the role of microbes in forest soil ecological processes. Our tree species pair (TSP) concept coupled with random sampling within and across the plots, allowed us the unbiased assessment of tree mycorrhizal type and tree diversity effects on the tree‐tree interaction zone soil microbiota. Unlike in monocultures and two‐species mixtures, we identified species‐rich and converging fungal and bacterial communities in multi‐tree species mixtures. Consequently, we recommend planting species‐rich mixtures of EcM and AM trees, for afforestation and reforestation regimes. Specifically, our findings highlight the significance of tree mycorrhizal type in studying 'tree diversity – microbial diversity – ecosystem function' relationships. [ABSTRACT FROM AUTHOR]

In this study, drivers for ammonia-oxidation and the related microbial communities (ammonia-oxidizing bacteria and archaea) were investigated in grassland soils on the local as well as on the regional scale focusing on the role of land-use intensity (LUI). To this end, 150 sites from three distinct regions across Germany were selected, covering the whole range of LUI levels (from natural grasslands up to intensive managed meadows). Furthermore, the role of contrasting soil types was analyzed in one of the regions (high vs low organic matter content) for ammonia-oxidation. We revealed a significant increase in potential nitrification rates and abundance of ammonia-oxidizing microbes at two sites on the local level from extensively to intensively managed sites, which indicates that the response pattern of ammonia-oxidizing microbes in grassland soils is likely triggered to a large extent by LUI. However at a third site, where two different soil types were investigated, no correlation between LUI and potential nitrification rates was observed, and only a site-specific effect was apparent. At this site, on the one hand the specific soil type (Histosol) and the related continuous nutrient mobilization from the former peat matrix, as well as the high groundwater level, which could induce a high abundance of methane- oxidizing microbes in the top soil, may be of greater importance as a driver for potential nitrification rates and abundance of ammonia- oxidizing microbes than LUI. On the other hand, the mineral soils of this site were characterized by extreme water shortage, which may also explain the lack of potential nitrification and the abundance of ammonia-oxidizing bacteria and archaea. Thus any extrapolation of local data to regional predictions must be made with care, as factors other than LUI may be of importance if the nitrification potential of a soil is to be described. [ABSTRACT FROM AUTHOR]

Oaks ( Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags ( ESTs) have been characterized in ectomycorrhizal ( EM) symbioses., We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone ( DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum., Using the Mimicking Intelligent Read Assembly ( MIRA) and Trinity assembler, the OakContig DF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated., In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees. [ABSTRACT FROM AUTHOR]

The genomes of two novel Dehalococcoides mccartyi strains, DCMB5 and BTF08, enriched from the heavily organohalide-contaminated megasite around Bitterfeld ( Germany), were fully sequenced and annotated. Although overall similar, the genome sequences of the two strains reveal remarkable differences in their genetic content, reflecting a specific adaptation to the contaminants at the field sites from which they were enriched. The genome of strain BTF08 encodes for 20 reductive dehalogenases, and is the first example of a genome containing all three enzymes that are necessary to couple the complete reductive dechlorination of PCE to ethene to growth. The genes encoding trichloroethene and vinyl chloride reductive dehalogenases, tceA and vcrA, are located within mobile genetic elements, suggesting their recent horizontal acquisition. The genome of strain DCMB5 contains 23 reductive dehalogenase genes, including cbrA, which encodes a chlorobenzene reductive dehalogenase, and a gene cluster encoding arsenic resistance proteins, both corresponding to typical pollutants at its isolation site. [ABSTRACT FROM AUTHOR]

Benzene is a major contaminant in various environments, but the mechanisms behind its biodegradation under strictly anoxic conditions are not yet entirely clear. Here we analyzed a benzene-degrading, sulfate-reducing enrichment culture originating from a benzene-contaminated aquifer by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). The time-resolved, quantitative analysis of carbon fluxes within the community supplied with either 13C-labeled benzene or 13C-labeled carbonate yielded different functional groups of organisms, with their peptides showing specific time dependencies of 13C relative isotope abundance indicating different carbon utilization. Through a detailed analysis of the mass spectrometric (MS) data, it was possible to quantify the utilization of the initial carbon source and the metabolic intermediates. The functional groups were affiliated to Clostridiales, Deltaproteobacteria and Bacteroidetes/Chlorobi. The Clostridiales-related organisms were involved in benzene degradation, putatively by fermentation, and additionally used significant amounts of carbonate as a carbon source. The other groups of organisms were found to perform diverse functions, with Deltaproteobacteria degrading fermentation products and Bacteroidetes/Chlorobi being putative scavengers feeding on dead cells. A functional classification of identified proteins supported this allocation and gave further insights into the metabolic pathways and the interactions between the community members. This example shows how protein-SIP can be applied to obtain temporal and phylogenetic information about functional interdependencies within microbial communities. [ABSTRACT FROM AUTHOR]

Schall et al. (2020) assessed how a combination of different forest management systems in managed forest landscapes dominated by European beech may affect the biodiversity (alpha, beta and gamma) of 14 taxonomic groups. Current forest policy and nature conservation often demand for combining uneven‐aged managed and unmanaged, set‐aside for nature conservation, beech forests in order to promote biodiversity. In contrast to this, Schall et al. (2020) found even‐aged shelterwood forests, represented by different developmental phases, to support highest regional (gamma) diversity.By pointing out that unmanaged forests included in our study are not old‐growth forests, Bruun and Heilmann‐Clausen (2021) challenge our conclusion as not providing sound scientific advice to societies. It is true that the studied unmanaged forests are not representing old‐growth forests as defined in the literature. However, we demonstrate the representativeness of our unmanaged forests for current beech forest landscapes of Central Europe, where managed forests were more or less recently set‐aside in order to develop old‐growth structures. We also show that the managed and recently unmanaged forests in our study already differ distinctively in their forest structures.We use this response to stress the role of forest reserves for promoting certain species groups, and to emphasise their importance as valuable research sites today and in the future.Synthesis and applications. We see two main conclusions from our study. First, unmanaged forests still matter. We agree with Bruun and Heilmann‐Clausen (2021) on the general importance of unmanaged, old‐growth or long‐untouched forests, and we do not question the importance of set‐aside forests for biodiversity conservation. However, a complete complementarity to managed systems may only reveal after many decades of natural development. Second, safeguarding biodiversity in largely managed forest landscapes should focus on providing a landscape matrix of different developmental phases with varying environmental conditions rather than on maximising the vertical structure within stands. Such landscapes can partly compensate for structures that are still missing in vital, dense and closed forests recently set‐aside or for unsuitable phases that may occur due to a cyclic synchronisation of forest structures in unmanaged forests. [ABSTRACT FROM AUTHOR]

Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar‐associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions. [ABSTRACT FROM AUTHOR]

Leaf fungal pathogens alter their host species’ performance and, thus, changes in fungal species composition can translate into effects at the tree community scale. Conversely, the functional diversity of tree species in a host tree’s local neighbourhood can affect the host’s foliar fungal infestation. Therefore, understanding the factors that affect fungal infestations is important to advance our understanding of biodiversity-ecosystem functioning (BEF) relationships. Here we make use of the largest BEF tree experiment worldwide, the BEF-China experiment, where we selected tree host species with different neighbour species. Identifying fungal taxa by microscopy and by high-throughput DNA sequencing techniques based on the internal transcribed spacer (ITS) rDNA region, we analysed the fungal richness and infestation rates of our target trees as a function of local species richness. Based on the visual microscopic assessment, we found that a higher tree diversity reduced fungal richness and host-specific fungal infestation in the host’s local neighbourhood, while molecular fungal richness was unaffected. This diversity effect was mainly explained by the decrease in host proportion. Thus, the dilution of host species in the local neighbourhood was the primary mechanism in reducing the fungal disease severity. Overall, our study suggests that diverse forests will suffer less from foliar fungal diseases compared to those with lower diversity. View Full-Text [ABSTRACT FROM AUTHOR]

Plant diversity begets diversity at other trophic levels. While species richness is the most commonly used measure for plant diversity, the number of evolutionary lineages (i.e. phylogenetic diversity) could theoretically have a stronger influence on the community structure of co‐occurring organisms. However, this prediction has only rarely been tested in complex real‐world ecosystems.Using a comprehensive multitrophic dataset of arthropods and fungi from a species‐rich subtropical forest, we tested whether tree species richness or tree phylogenetic diversity relates to the diversity and composition of organisms.We show that tree phylogenetic diversity but not tree species richness determines arthropod and fungi community composition across trophic levels and increases the diversity of predatory arthropods but decreases herbivorous arthropod diversity. The effect of tree phylogenetic diversity was not mediated by changed abundances of associated organisms, indicating that evolutionarily more diverse plant communities increase niche opportunities (resource diversity) but not necessarily niche amplitudes (resource amount).Our findings suggest that plant evolutionary relatedness structures multitrophic communities in the studied species‐rich forests and possibly other ecosystems at large. As global change non‐randomly threatens phylogenetically distinct plant species, far‐reaching consequences on associated communities are expected. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Forest management greatly influences biodiversity across spatial scales. At the landscape scale, combining management systems that create different stand properties might promote biodiversity due to complementary species assemblages. In European beech forests, nature conservation and policy advocate a mixture of unmanaged (UNM) forests and uneven‐aged (UEA) forests managed at fine spatial grain at the expense of traditionally managed even‐aged shelterwood forests (EA). Evidence that such a landscape composition enhances forest biodiversity is still missing.We studied the biodiversity (species richness 0D, Shannon diversity 1D, Simpson diversity 2D) of 14 taxonomic groups from bacteria to vertebrates in 'virtual' beech forest landscapes composed of varying shares of EA, UEA and UNM and investigated how γ‐diversity responds to landscape composition. Groups were sampled in the largest contiguous beech forest in Germany, where EA and UEA management date back nearly two centuries, while management was abandoned 20–70 years ago (UNM). We used a novel resampling approach that created all compositional combinations of management systems.Pure EA landscapes preserved a maximum of 97.5% γ‐multidiversity (0D, 1D) across all taxa. Pure and mixed UEA/UNM landscapes reduced γ‐multidiversity by up to 12.8% (1D). This effect was consistent for forest specialists (1D: −15.3%). We found only weak complementarity among management systems.Landscape composition significantly affected γ‐diversity of 6–9 individual taxa, depending on the weighting of species frequencies with strongest responses for spiders, beetles, vascular plants and birds. Most showed maximum diversity in pure EA landscapes. Birds benefited from UNM in EA‐dominated landscapes. Deadwood fungi showed highest diversity in UNM.Synthesis and applications. Our study shows that combining fine‐grained forest management and management abandonment at the landscape scale will reduce, rather than enhance, regional forest biodiversity. We found an even‐aged shelterwood management system alone operating at intermediate spatial scales and providing stands with high environmental heterogeneity was able to support regional biodiversity. However, some taxa require certain shares of uneven‐aged and unmanaged forests, emphasizing their general importance. We encourage using the here presented resampling approach to verify our results in forest landscapes of different composition and configuration across the temperate zone. [ABSTRACT FROM AUTHOR]

Summary: Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha‐ and beta‐diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta‐diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome. [ABSTRACT FROM AUTHOR]

While the number of studies on the role of biodiversity on ecosystem functioning is steadily increasing, a key component of biogeochemical cycling in forests, dead wood decay, has been largely neglected. It remains widely unknown whether and how dead wood decay is affected by diversity loss in forests. We studied the hierarchical effects of tree species diversity on wood decay rates in a subtropical forest landscape in southeast China via its influence on fungal OTU richness and invertebrate diversity using piecewise structural equation models. The experiment was conducted in natural forest plots that span a wide gradient of tree species diversity embedded in a heterogeneous topography. To account for interactions between macro‐invertebrates and fungi, that potentially modify the influence of tree biodiversity and climate on dead wood decay, we compared a macro‐invertebrate exclusion treatment with a control treatment that allowed access to all types of decomposers. Diversity effects of trees on wood decay rates were mostly negative and mediated by the diversity of macro‐invertebrates. However, the effects of tree species diversity or fungal OTU richness and macro‐invertebrate diversity on wood decay rates were comparatively weak. Temperature affected decay rates positively and had the strongest influence in all treatments. While the exclusion of macro‐invertebrates did not lead to a reduction of wood decay rates, our results suggest that they may however have a mediating role in the process. In the presence of invertebrates the predictability of wood decay rates was higher and we observed a tendency of a stronger temperature control. Our results suggest that there is evidence for diversity effects on wood decomposition, but the temperature control is still more important. Thus, an increase in mean annual temperature will increase carbon and nutrient turnover through wood decomposition in subtropical forest irrespective of biotic composition. [ABSTRACT FROM AUTHOR]

Abstract A major gap in understanding the relationship between tree diversity and litter decomposition concerns knowledge of the saprotrophic fungal communities mediating decomposition processes. Making use of experimental tree diversity plots in subtropical China, our objective was to disentangle the effects of tree species richness on diversity, abundance, and composition of saprotrophic fungal communities in freshly fallen leaf litter. We employed a meta-genomic approach and analysed enzymatic decomposition. Our results indicate the dominance of Ascomycota, with species from this phylum colonizing leaf litter more rapidly than Basidiomycota. Furthermore, Ascomycota was the most abundant when tree richness was intermediate. Both Ascomycota and Basidiomycota differed significantly in their species composition in response to varying tree species richness. However, saprotrophic fungal species diversity did not respond to tree species richness. Instead, litter C/N ratio, litter Ca and plot altitude were the strongest determinants of fungal species diversity. Carbon-degradation enzyme activities were also significantly associated with litter C/N ratio, Ca and Fe concentration and, in addition, with tree species richness. The responses of fungal species and enzyme activity to tree species richness were uncoupled from each other, although the two variables were significantly correlated. Overall, our findings highlight a significant effect of tree species richness on litter fungal species composition, but not diversity. Our findings also provide insight into the importance of enzyme-mediated C degradation for the response to tree species richness in early-stage leaf decay in subtropical forests. Highlights • Fungal diversity in litter did not respond to the increase of tree species richness. • Tree richness affect Ascomycota composition rather than Basidiomycota fungi. • Ascomycota fungi were highest at intermediate tree species richness level. • Carbon degradation-related enzymes were significantly affected by tree richness. [ABSTRACT FROM AUTHOR]

Abstract Although fungi play important roles in biogeochemical cycling in aquatic ecosystems and have received a great deal of attention, much remains unknown about the living fractions of fungal communities in aquifers of the terrestrial subsurface in terms of diversity, community dynamics, functional roles, the impact of environmental factors and presence of fungal pathogens. Here we address this gap in knowledge by using RNA-based high throughput pair-end illumina sequencing analysis of fungal internal transcribed spacer (ITS) gene markers, to target the living fractions of groundwater fungal communities from fractured alternating carbonate-/siliciclastic-rock aquifers of the Hainich Critical Zone Exploratory. The probed levels of the hillslope multi-storey aquifer system differ primarily in their oxygen and nitrogen content due to their different connections to the surface. We discovered highly diverse living fungal communities (384 Operational Taxonomic Units, OTUs) with different taxonomic affiliations and ecological functions. The observed fungal communities primarily belonged to three phyla: Ascomycota, Basidiomycota and Chytridiomycota. Perceived dynamics in the composition of living fungal communities were significantly shaped by the concentration of ammonium in the moderately agriculturally impacted aquifer system. Apart from fungal saprotrophs, we also detected living plant and animal pathogens for the first time in this aquifer system. This work also demonstrates that the RNA-based high throughput pair-end illumina sequencing method can be used in future for water quality monitoring in terms of living fungal load and subsequent risk assessments. In general, this study contributes towards the growing knowledge of aquatic fungi in terrestrial subsurface biogeosphere. Highlights • First RNA-based study using Illumina platform studying fungi in the aquifer system. • A diverse pool of living aquatic fungal species detected in subsurface aquifers. • NH 4 + and TIC supply correlate with the living fungal community composition in the aquifers. • Saprotrophs along with animal and plant pathogens were most frequently detected living functional groups. [ABSTRACT FROM AUTHOR]

Soil and root-associated fungi are important in ecosystem functioning, and it is essential to understand driving factors of these fungi in natural ecosystems. In the present study, soil and root fungal communities in a fine-scale grassland were determined using high through-put sequencing, and our aims are to evaluate the relative importance of plant composition, soil elements and space factors on these two fungal communities. Our results showed that (1) fungal communities in soil and plant roots were distinct from each other, and OTU richness in soil was significantly higher than that in plant roots; (2) biomass of perennial rhizome grass, soil carbon content, and soil C/P ratio were key drivers for both soil and root fungal community; (3) dissimilarity of the soil fungal community significantly correlated with spatial distance, while no significant correlations were found between dissimilarity of root-associated fungal community and spatial distance. These results suggest the different spatial patterns of root and soil fungal communities which may contribute to a better understanding of the mechanisms maintaining root and soil fungal communities at small scales in this grassland ecosystem. [ABSTRACT FROM AUTHOR]

Negative relationships between species richness and elevation are common and attributed to changes in single environmental properties associated to elevation, such as temperature and habitat area. However, research has lacked taxonomic breadth and comprehensive elevation studies that consider multiple groups from different trophic levels are rare. We thus analysed 24 groups of plants, arthropods, and microorganisms grouped into six trophic guilds (predators, detritivores, herbivores, plants, bacteria and fungi) along a relatively short elevational gradient (~600 m) in a subtropical forest in south‐east China. The total species richness of all organisms was not related to elevation, nor was the richness of plants, herbivores or microorganisms. However, species richness and abundance in two major trophic guilds of arthropods changed with elevation, which was mediated by changes in elevation‐associated habitat properties. Specifically, deadwood mass increased with elevation, which increased detritivore richness indirectly via detritivore abundance, thus supporting the ‘more individuals hypothesis’. In contrast, lower predator richness at higher elevations was directly related to lower mean temperatures, which had no effect on abundance. Our study demonstrates that even along relatively short gradients, elevation can have strong direct and abundance‐mediated effects on species richness, but with effects varying from positive to negative signs depending on local resource availability and the characteristics of groups or trophic guilds. If elevation positively influences local environmental properties that benefit a given group, richness can increase towards higher elevations. Thus, the effect of global change in mountainous regions should be evaluated within the local environmental context using multi‐taxon approaches. [ABSTRACT FROM AUTHOR]

Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent coexistence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF–plant association. Our results show the woody plant–AMF networks to be highly interconnected and nested, but in antimodular and antispecialized manners. The nonrandom pattern in the woody plant–AMF network was explained by plant and AMF phylogenies, with a tendency for a stronger phylogenetic signal by plant than AMF phylogeny. This study suggests that the phylogenetic niche conservatism in woody plants and their AMF symbionts could contribute to interdependent AMF and plant community assembly in this subtropical forest ecosystem. [ABSTRACT FROM AUTHOR]

Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients. [ABSTRACT FROM AUTHOR]

Intensive land use is a major cause of biodiversity loss, but most studies comparing the response of multiple taxa rely on simple diversity measures while analyses of other community attributes are only recently gaining attention. Species-abundance distributions (SADs) are a community attribute that can be used to study changes in the overall abundance structure of species groups, and whether these changes are driven by abundant or rare species. We evaluated the effect of grassland management intensity for three land-use modes (fertilization, mowing, grazing) and their combination on species richness and SADs for three belowground (arbuscular mycorrhizal fungi, prokaryotes and insect larvae) and seven aboveground groups (vascular plants, bryophytes and lichens; arthropod herbivores; arthropod pollinators; bats and birds). Three descriptors of SADs were evaluated: general shape (abundance decay rate), proportion of rare species (rarity) and proportional abundance of the commonest species (dominance). Across groups, taxonomic richness was largely unaffected by land-use intensity and only decreased with increasing mowing intensity. Of the three SAD descriptors, abundance decay rate became steeper with increasing combined land-use intensity across groups. This reflected a decrease in rarity among plants, herbivores and vertebrates. Effects of fertilization on the three descriptors were similar to the combined land-use intensity effects. Mowing intensity only affected the SAD descriptors of insect larvae and vertebrates, while grazing intensity produced a range of effects on different descriptors in distinct groups. Overall, belowground groups had more even abundance distributions than aboveground groups. Strong differences among aboveground groups and between above- and belowground groups indicate that no single taxonomic group can serve as an indicator for effects in other groups. In the past, the use of SADs has been hampered by concerns over theoretical models underlying specific forms of SADs. Our study shows that SAD descriptors that are not connected to a particular model are suitable to assess the effect of land use on community structure. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH. [ABSTRACT FROM AUTHOR]

Environmental selection and dispersal limitation are two of the primary processes structuring biotic communities in ecosystems, but little is known about these processes in shaping soil microbial communities during secondary forest succession., We examined the communities of ectomycorrhizal ( EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing., The EM fungal community consisted of 393 operational taxonomic units ( OTUs), belonging to 21 EM fungal lineages, in which three EM fungal lineages and 11 EM fungal OTUs showed significantly biased occurrence among the young, intermediate and old forests. The EM fungal community was structured by environmental selection and dispersal limitation in old forest, but only by environmental selection in young, intermediate, and whole forests. Furthermore, the EM fungal community was affected by different factors in the different forest successional stages, and the importance of these factors in structuring EM fungal community dramatically decreased along the secondary forest succession series., This study suggests that different assembly mechanisms operate on the EM fungal community at different stages in secondary subtropical forest succession. [ABSTRACT FROM AUTHOR]

S ulfurospirillum multivorans, a free-living ε-proteobacterium, is among the best studied organisms capable of organohalide respiration. It is able to use several halogenated ethenes as terminal electron acceptor. In this report, the complete genome sequence of S . multivorans including a comparison with genome sequences of two related non-dehalogenating species, S ulfurospirillum deleyianum and S ulfurospirillum barnesii, is described. The 3.2 Mbp genome of S . multivorans revealed a ∼ 50 kbp gene region encoding proteins required for organohalide respiration and corrinoid cofactor biosynthesis. This region includes genes for components not detected before in organohalide-respiring organisms. A transcript analysis of genes coding for some of these proteins indicates the involvement of a putative quinol dehydrogenase in organohalide respiration. The presence of genes encoding a variety of oxidoreductases reflects the organism's metabolic versatility. This was confirmed by growth studies with different electron acceptors including perchlorate and several sulfur-containing compounds. A comparison with other ε-proteobacteria indicates horizontal acquisition of many genes in the S . multivorans genome, which might be the basis of the bacterium's catabolic flexibility. [ABSTRACT FROM AUTHOR]

Abstract: Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D1), Simpson's dominance (D2), Simpson's evenness (E), and Berger–Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P. lanceolata molecular and chemical diversity. Including these trait‐based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system. [ABSTRACT FROM AUTHOR]

Exploring the relationships between the biodiversity of groups of interacting organisms yields insight into ecosystem stability and function (Hooper et al. ; Wardle ). We demonstrated positive relationships between host plant richness and ectomycorrhizal ( EM) fungal diversity both in a field study in subtropical China (Gutianshan) and in a meta-analysis of temperate and tropical studies (Gao et al. ). However, based on re-evaluation of our data sets, Tedersoo et al. () argue that the observed positive correlation between EM fungal richness and EM plant richness at Gutianshan and also in our metastudies was based mainly from (i) a sampling design with inconsistent species pool and (ii) poor data compilation for the meta-analysis. Accordingly, we checked our data sets and repeated the analysis performed by Tedersoo et al. (). In contrast to Tedersoo et al. (), our re-analysis still confirms a positive effect of plant richness on EM fungal diversity in Gutianshan, temperate and tropical ecosystems, respectively. [ABSTRACT FROM AUTHOR]

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa. [ABSTRACT FROM AUTHOR]

Highlights: [•] PLFA data and enzyme activities were studied in managed grasslands at regional scale. [•] OC, pH and soil moisture impacted microbial parameters independent of study region. [•] Water stagnation modifies relations between OC and microbial biomass and activity. [•] Soil properties control soil microbiological properties more than management. [ABSTRACT FROM AUTHOR]