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Effective conservation strategies are needed to prevent further loss of biodiversity. This requires a comprehensive assessment of species' presence, distribution, and population sizes. Such assessments can be extremely challenging for species-rich taxa, like fungi, which are difficult to detect and identify. In recent years, metabarcoding applied to environmental samples has proven to be a promising method for fungal detection. However, its potential against traditional fruit body surveys in monitoring threatened fungal species has rarely been tested. Here, we utilized data on deadwood-inhabiting fungi from 569 deadwood objects across five sites in Central Europe to compare the effectiveness of fruit body surveys and metabarcoding (of low and high sampling intensity) in detecting threatened species. Across objects, sites, and per object, metabarcoding was more effective in detecting threatened species than fruit body surveys, regardless of sampling intensity. Eleven percent of all threatened species across all objects and sites could be detected by both methods, 70 % exclusively by metabarcoding and 18 % exclusively by fruit body surveys. The number of species detected by both methods on the same object was <4 %. Effects of high sampling intensity metabarcoding were stronger than low sampling intensity at object level. The effectiveness of the survey method was mainly independent of deadwood object characteristics. We suggest that metabarcoding is a valuable tool for threatened fungal species monitoring and conservation status assessments. However, for a comprehensive assessment, fruit body surveys are still needed, as this method detected a unique set of species and indicates the presence of vital fungal individuals.

Effective conservation strategies are needed to prevent further loss of biodiversity. This requires a comprehensive assessment of species' presence, distribution, and population sizes. Such assessments can be extremely challenging for species-rich taxa, like fungi, which are difficult to detect and identify. In recent years, metabarcoding applied to environmental samples has proven to be a promising method for fungal detection. However, its potential against traditional fruit body surveys in monitoring threatened fungal species has rarely been tested. Here, we utilized data on deadwood-inhabiting fungi from 569 deadwood objects across five sites in Central Europe to compare the effectiveness of fruit body surveys and metabarcoding (of low and high sampling intensity) in detecting threatened species. Across objects, sites, and per object, metabarcoding was more effective in detecting threatened species than fruit body surveys, regardless of sampling intensity. Eleven percent of all threatened species across all objects and sites could be detected by both methods, 70 % exclusively by metabarcoding and 18 % exclusively by fruit body surveys. The number of species detected by both methods on the same object was <4 %. Effects of high sampling intensity metabarcoding were stronger than low sampling intensity at object level. The effectiveness of the survey method was mainly independent of deadwood object characteristics. We suggest that metabarcoding is a valuable tool for threatened fungal species monitoring and conservation status assessments. However, for a comprehensive assessment, fruit body surveys are still needed, as this method detected a unique set of species and indicates the presence of vital fungal individuals.

Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and—within fungal taxa—increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.&nbsp

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes, and viruses from metagenomes exist. However, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool accessible for non-bioinformaticians that make it easy to recover genomes of prokaryotes, eukaryotes, and viruses from metagenomes, either alone or in combination. We tested MuDoGer using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR.

Microorganisms dominate all ecosystems on Earth and play a key role in the turnover of organic matter. By producing enzymes, they degrade complex carbohydrates, facilitating the recycling of nutrients and controlling the carbon cycle. Despite their importance, our knowledge regarding microbial carbohydrate utilization has been limited to genome-sequenced taxa and thus heavily biased to specific groups and environments. Here, we used the Genomes from Earth's Microbiomes (GEM) catalog to describe the carbohydrate utilization potential in >7000 bacterial and archaeal taxa originating from a range of terrestrial, marine and host-associated habitats. We show that the production of carbohydrate-active enzymes (CAZymes) is phylogenetically conserved and varies significantly among microbial phyla. High numbers of carbohydrate-active enzymes were recorded in phyla known for their versatile use of carbohydrates, such as Firmicutes, Fibrobacterota, and Armatimonadota, but also phyla without cultured representatives whose carbohydrate utilization potential was so far unknown, such as KSB1, Hydrogenedentota, Sumerlaeota, and UBP3. Carbohydrate utilization potential reflected the specificity of various habitats: the richest complements of CAZymes were observed in MAGs of plant microbiomes, indicating the structural complexity of plant biopolymers.IMPORTANCE This study expanded our knowledge of the phylogenetic distribution of carbohydrate-active enzymes across prokaryotic tree of life, including new phyla where the carbohydrate-active enzymes composition have not been described until now and demonstrated the potential for carbohydrate utilization of numerous yet uncultured phyla. Profiles of carbohydrate-active enzymes are largely habitat-specific and reflect local carbohydrate availability by selecting taxa with appropriate complements of these enzymes. This information should aid in the prediction of functions in microbiomes of known taxonomic composition and helps to id

The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2,3,4,5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.

This paper was originally published under standard Springer Nature copyright (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license. The error has been corrected in the print, HTML and PDF versions of the article.

The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2–5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle.

The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2,3,4,5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle.

The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2–5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle.

Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.

Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.

Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil.

Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass.

Forest soils represent important terrestrial carbon (C) pools, where C is primarily fixed in plant biomass and then is incorporated in the biomass of fungi and bacteria. Although classical concepts assume that fungi are the main decomposers of the recalcitrant organic matter within plant and microbial biomass, whereas bacteria are considered to mostly utilize simpler compounds, recent studies have shown that fungi and bacteria overlap in substrate utilization. Here, we studied the microbial contribution to the recycling of dead biomass by analyzing the bacterial and fungal communities in soil microcosms supplemented with 13C-labeled biomass of plant, fungal, and bacterial origin using a combination of DNA-stable isotope probing and metagenomics. Both fungi and bacteria contributed actively to the degradation of complex components of plant and microbial biomass. Specific families of carbohydrate-active enzymes (CAZyme) were involved in the degradation of each biomass type. Moreover, the analysis of five bacterial metagenome-assembled genomes indicated the key role of some bacterial genera in the degradation of plant biomass (Cytophaga and Asticcacaulis) and microbial biomass (Herminiimonas). The enzymatic systems utilized by bacteria are highly complex and complementary but also highly diverse among taxa. The results confirm the importance of bacteria, in addition to fungi, as decomposers of complex organic matter in forest soils.

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here, we used a meta-analysis of completely annotated extant genomes of 377 taxonomically distinct fungal species to predict the total fungal microbiome functionality on Earth with accumulation curves (ACs) of all known functions from the level 3 of KEGG Orthology using both parametric and non-parametric estimates in an explorative data-mining approach. The unsaturated model extrapolating functional diversity as a function of species richness described the ACs significantly better than the saturated model that assumed a limited total number of functions, which suggested the presence of widespread and rare functions. Based on previous estimates of 3.8 million fungal species on Earth, we propagated the unsaturated model to predict a total of 42.4 ± 0.5 million KEGG level 3 functions of which only 0.06% are known today. Our approach not only highlights the presence of widespread and rare functions but points toward the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

Intermittent rivers and ephemeral streams (IRES) encompass fluvial ecosystems that eventually stop flowing and run dry at some point in space and time. During the dry phase, channels of IRES consist mainly of dry riverbeds (DRBs), prevalent yet widely unexplored ecotones between dry and wet phases that can strongly influence the biogeochemistry of fluvial networks. DRBs are often overlooked because they do not strictly belong to either domain of soil or freshwater science. Due to this dual character of DRBs, we suggest that concepts and knowledge from soil science can be used to expand the understanding of IRES biogeochemistry. Based on this idea, we propose that DRBs can be conceptually understood as early stage soils exhibiting many similarities with soils through two main forces: i) time since last sediment transport event, and ii) the development status of stabilizing structures (e.g. soil crusts and/or vascular plants). Our analysis suggests that while DRBs and soils may differ in master physical attributes (e.g. soil horizons vs fluvial sedimentary facies), they become rapidly comparable in terms of microbial communities and biogeochemical processes. We further propose that drivers of DRBs biogeochemistry are similar to those of soils and, hence, concepts and methods used in soil science are transferable to DRBs research. Finally, our paper presents future research directions to advance the knowledge of DRBs and to understand their role in the biogeochemistry of intermittent fluvial networks. © 2018 The Authors

Intermittent rivers and ephemeral streams (IRES) encompass fluvial ecosystems that eventually stop flowing and run dry at some point in space and time. During the dry phase, channels of IRES consist mainly of dry riverbeds (DRBs), prevalent yet widely unexplored ecotones between dry and wet phases that can strongly influence the biogeochemistry of fluvial networks. DRBs are often overlooked because they do not strictly belong to either domain of soil or freshwater science. Due to this dual character of DRBs, we suggest that concepts and knowledge from soil science can be used to expand the understanding of IRES biogeochemistry. Based on this idea, we propose that DRBs can be conceptually understood as early stage soils exhibiting many similarities with soils through two main forces: i) time since last sediment transport event, and ii) the development status of stabilizing structures (e.g. soil crusts and/or vascular plants). Our analysis suggests that while DRBs and soils may differ in master physical attributes (e.g. soil horizons vs fluvial sedimentary facies), they become rapidly comparable in terms of microbial communities and biogeochemical processes. We further propose that drivers of DRBs biogeochemistry are similar to those of soils and, hence, concepts and methods used in soil science are transferable to DRBs research. Finally, our paper presents future research directions to advance the knowledge of DRBs and to understand their role in the biogeochemistry of intermittent fluvial networks. © 2018 The Authors

The growth and survival of plants in semiarid Mediterranean forests can be improved through the benefits conferred by thinning, a forest management practice that removes trees and reduces the competition between the remaining ones. Here, we evaluate the impacts of induced drought (the exclusion of 25% of the natural rainfall for 5 years) and thinning, and their interaction, with the objective of determining whether the thinning of Holm oak (Quercus ilex L.) modulates the resistance of the soil microbial community to drought. Sequencing of 16S rRNA and ITS amplicons revealed that drought, thinning, and their interaction influenced the composition of the bacterial community, while the fungal community was exclusively affected by thinning. Thinning consisted of the removal of the aboveground parts of the Holm oak trees, which were thereafter left in forest stand. Thinning contributed to the C and N contents, with parallel increases in microbial biomass, particularly in summer. Drought increased the amounts of total organic C and total N, likely due to the reduced enzyme activities. Indeed, the composition of the bacterial community was modulated primarily by the indirect and long-term effects of drought - the accumulation of soil organic matter - rather than by the direct effect of the lower water content imposed by the drought treatments. Thinning under drought conditions did not increase soil organic C (SOC) content. However, the resistance of the soil microbial community to drought was fostered by thinning, particularly at the functional level, as indicated by the enzyme activities related to C, N and P cycles. These responses were associated to variations in the composition of the microbial communities in thinned, drought-exposed plots, in comparison to unthinned, drought-exposed plots. In conclusion, the interaction between forest management and drought influenced the soil microbial community of a Holm oak-dominated Mediterranean ecosystem.

Intermittent rivers and ephemeral streams (IRES) encompass fluvial ecosystems that eventually stop flowing and run dry at some point in space and time. During the dry phase, channels of IRES consist mainly of dry riverbeds (DRBs), prevalent yet widely unexplored ecotones between dry and wet phases that can strongly influence the biogeochemistry of fluvial networks. DRBs are often overlooked because they do not strictly belong to either domain of soil or freshwater science. Due to this dual character of DRBs, we suggest that concepts and knowledge from soil science can be used to expand the understanding of IRES biogeochemistry. Based on this idea, we propose that DRBs can be conceptually understood as early stage soils exhibiting many similarities with soils through two main forces: i) time since last sediment transport event, and ii) the development status of stabilizing structures (e.g. soil crusts and/or vascular plants). Our analysis suggests that while DRBs and soils may differ in master physical attributes (e.g. soil horizons vs fluvial sedimentary facies), they become rapidly comparable in terms of microbial communities and biogeochemical processes. We further propose that drivers of DRBs biogeochemistry are similar to those of soils and, hence, concepts and methods used in soil science are transferable to DRBs research. Finally, our paper presents future research directions to advance the knowledge of DRBs and to understand their role in the biogeochemistry of intermittent fluvial networks. © 2018 The Authors

Compost production is a critical component of organic waste management. One of the most important properties of compost is its ability to suppress soil-borne pathogens such as Phytophthora nicotianae in pepper plants. Both the physico-chemical and biological properties of composts can be responsible for the suppression of pathogens, although biological properties are the main driver. In this study, we analyzed composts with various levels of suppressiveness against P. nicotianae. We analyzed both physico-chemical properties like pH and electrical conductivity and biological properties like microbial activity, amplicon sequencing and metaproteomics. We believed that the link between community structures and proteins could provide deep insights into the mechanism of compost suppressiveness. Our results indicate that there are differences between suppressive and non-suppressive composts at the phylogenetic level (sequencing) and at the functional level (based on analysis of the cluster of orthologous groups, COGs). The proteins identified were assigned to the carbohydrate process, cell wall structure and inorganic ion transport and metabolism. Proteobacteria could also be new indicators of P. nicotianae suppression.

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning—that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 60 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial c

The decomposition of dead plant biomass contributes to the carbon cycle and is one of the key processes in temperate forests. While fungi in litter decomposition drive the chemical changes occurring in litter, the bacterial community appears to be important as well, especially later in the decomposition process when its abundance increases. In this paper, we describe the bacterial community composition in live Quercus petraea leaves and during the subsequent two years of litter decomposition. Members of the classes Alpha-, Beta- and Gammaproteobacteria and the phyla Actinobacteria, Bacteroidetes and Acidobacteria were dominant throughout the experiment. Bacteria present in the oak phyllosphere were rapidly replaced by other taxa after leaf senescence. There were dynamic successive changes in community composition, in which the early-stage (months 2-4), mid-stage (months 6-8) and late-stage (months 10-24) decomposer communities could be distinguished, and the diversity increased with time. Bacteria associated with dead fungal mycelium were important during initial decomposition, with sequence relative abundances of up to 40% of the total bacterial community in months 2 and 4 when the highest fungal biomass was observed. Cellulose-decomposing bacteria were less frequent, with abundance ranging from 4% to 15%. The bacterial community dynamics reflects changes in the availability of possible resources either of the plant or microbial origin.

As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum Tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal functional and phylogenetic diversity. The weight loss of both leaves and tubers in litterbags were analysed after 1, 3 and 6 months of incubation in soils and combined with measurements of fungal extracellular enzyme activities (laccases, Mn-peroxidases and cellulases) as well as molecular analyses of the fungal community (ITS regions and cellobiohydrolase I (cbhI) genes). The study revealed that initial (after one month) decomposition of both tubers and leaves of the parental isoline was significantly faster than that of the genetically modified (GM)-variety. This coincided with differences in fungal community composition. After this initial difference, no significant differences in any of the parameters measured could be detected after 3 and 6 months of decomposition illustrating the transient nature of the initial difference between the cultivars. Thus, it can be concluded that the starch modified tubers are not harmful to the fungal decomposer community and that despite initial differences in decomposition, the final decomposition rate of tissues from the GM-variety was similar to that of tissues from the parental variety. Furthermore, interesting dynamics of fungal phyla and species during decomposition were observed; the basidiomycetal yeasts and ascomycetes were primary colonizers of the potato tissue while basidiomycetes were dominant in the more decomposed and lignin-rich litter., As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum Tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal functional and phylogenetic diversity. The weight loss of both leaves and tubers in litterbags were analysed after 1, 3 and 6 months of incubation in soils and combined with measurements of fungal extracellular enzyme activities (laccases, Mn-peroxidases and cellulases) as well as molecular analyses of the fungal community (ITS regions and cellobiohydrolase I (cbhI) genes). The study revealed that initial (after one month) decomposition of both tubers and leaves of the parental isoline was significantly faster than that of the genetically modified (GM)-variety. This coincided with differences in fungal community composition. After this initial difference, no significant differences in any of the parameters measured could be detected after 3 and 6 months of decomposition illustrating the transient nature of the initial difference between the cultivars. Thus, it can be concluded that the starch modified tubers are not harmful to the fungal decomposer community and that despite initial differences in decomposition, the final decomposition rate of tissues from the GM-variety was similar to that of tissues from the parental variety. Furthermore, interesting dynamics of fungal phyla and species during decomposition were observed; the basidiomycetal yeasts and ascomycetes were primary colonizers of the potato tissue while basidiomycetes were dominant in the more decomposed and lignin-rich litter.

As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum Tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal functional and phylogenetic diversity. The weight loss of both leaves and tubers in litterbags were analysed after 1, 3 and 6 months of incubation in soils and combined with measurements of fungal extracellular enzyme activities (laccases, Mn-peroxidases and cellulases) as well as molecular analyses of the fungal community (ITS regions and cellobiohydrolase I (cbhI) genes). The study revealed that initial (after one month) decomposition of both tubers and leaves of the parental isoline was significantly faster than that of the genetically modified (GM)-variety. This coincided with differences in fungal community composition. After this initial difference, no significant differences in any of the parameters measured could be detected after 3 and 6 months of decomposition illustrating the transient nature of the initial difference between the cultivars. Thus, it can be concluded that the starch modified tubers are not harmful to the fungal decomposer community and that despite initial differences in decomposition, the final decomposition rate of tissues from the GM-variety was similar to that of tissues from the parental variety. Furthermore, interesting dynamics of fungal phyla and species during decomposition were observed; the basidiomycetal yeasts and ascomycetes were primary colonizers of the potato tissue while basidiomycetes were dominant in the more decomposed and lignin-rich litter., As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum Tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal functional and phylogenetic diversity. The weight loss of both leaves and tubers in litterbags were analysed after 1, 3 and 6 months of incubation in soils and combined with measurements of fungal extracellular enzyme activities (laccases, Mn-peroxidases and cellulases) as well as molecular analyses of the fungal community (ITS regions and cellobiohydrolase I (cbhI) genes). The study revealed that initial (after one month) decomposition of both tubers and leaves of the parental isoline was significantly faster than that of the genetically modified (GM)-variety. This coincided with differences in fungal community composition. After this initial difference, no significant differences in any of the parameters measured could be detected after 3 and 6 months of decomposition illustrating the transient nature of the initial difference between the cultivars. Thus, it can be concluded that the starch modified tubers are not harmful to the fungal decomposer community and that despite initial differences in decomposition, the final decomposition rate of tissues from the GM-variety was similar to that of tissues from the parental variety. Furthermore, interesting dynamics of fungal phyla and species during decomposition were observed; the basidiomycetal yeasts and ascomycetes were primary colonizers of the potato tissue while basidiomycetes were dominant in the more decomposed and lignin-rich litter.

Mycorrhizal fungi constitute a considerable sink for carbon in most ecosystems. This carbon is used for building extensive mycelial networks in the soil as well as for metabolic activity related to nutrient uptake. A number of methods have been developed recently to quantify production, standing biomass and turnover of extramatrical mycorrhizal mycelia (EMM) in the field. These methods include minirhizotrons, in-growth mesh bags and cores, and indirect measurements of EMM based on classification of ectomycorrhizal fungi into exploration types. Here we review the state of the art of this methodology and discuss how it can be developed and applied most effectively in the field, Furthermore, we also discuss different ways to quantify fungal biomass based on biomarkers such as chitin, ergosterol and PLFAs, as well as molecular methods, such as qPCR. The evidence thus far indicates that mycorrhizal fungi are key components of microbial biomass in many ecosystems. We highlight the need to extend the application of current methods to focus on a greater range of habitats and mycorrhizal types enabling incorporation of mycorrhizal fungal biomass and turnover into biogeochemical cycling models.

There is growing evidence of the importance of extramatrical mycelium (EMM) of mycorrhizal fungi in carbon (C) cycling in ecosystems. However, our understanding has until recently been mainly based on laboratory experiments, and knowledge of such basic parameters as variations in mycelial production, standing biomass and turnover as well as the regulatory mechanisms behind such variations in forest soils is limited. Presently, the production of EMM by ectomycorrhizal (EM) fungi has been estimated at similar to 140 different forest sites to be up to several hundreds of kg per ha per year, but the published data are biased towards Picea abies in Scandinavia. Little is known about the standing biomass and turnover of EMM in other systems, and its influence on the C stored or lost from soils. Here, focussing on ectomycorrhizas, we discuss the factors that regulate the production and turnover of EMM and its role in soil C dynamics, identifying important gaps in this knowledge. C availability seems to be the key factor determining EMM production and possibly its standing biomass in forests but direct effects of mineral nutrient availability on the EMM can be important. There is great uncertainty about the rate of turnover of EMM. There is increasing evidence that residues of EM fungi play a major role in the formation of stable N and C in SOM, which highlights the need to include mycorrhizal effects in models of global soil C stores.

White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2–8 109 colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus., White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2–8 109 colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus.

White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2–8 109 colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus., White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2–8 109 colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus.