Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda

Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.

Changes and driving factors of microbial community composition and functional groups during the decomposition of Pinus massoniana deadwood

Clarifying changes in the microbial community in deadwood at different stages of decomposition is crucial for comprehending the role of deadwood in the biogeochemical processes and the sustainability of forest development. However, there have been no reports on the dynamics of microbial community during the decomposition of Pinus massoniana. We used the "space-for-time" substitution to analyze the characteristics of microbial community changes and the key influencing factors in the P. massoniana deadwood during different decomposition stages by 16S and ITS rRNA gene sequencing. The results suggest that the microbial community structure of the early decomposition (decay class I) was significantly different from the other decay classes, while the diversity and richness of the microbial community were the highest in the late decomposition (decay class V). The Linear Discriminant Analysis Effect Size analysis revealed that most bacterial and fungal taxa were significantly enriched in decay classes I and V deadwood. During the initial stages of decomposition, the relative abundance of the bacterial functional group responsible for carbohydrate metabolism was greater than the later stages. As decomposition progressed, the relative abundance of saprophytic fungi gradually decreased, and there was a shift in the comparative abundance of mixed saprophytic-symbiotic fungi from low to high before eventually decreasing. Total organic carbon, total nitrogen, carbon-to-nitrogen ratio, total potassium, total phenol, condensed tannin, lignin, and cellulose were significantly correlated with microbial community structure, with the carbon-to-nitrogen ratio having the greatest effect. Our results indicate that the physicochemical properties of deadwood, microbial community structural composition and functional group changes were related to the decay class, among which the carbon-to-nitrogen ratio may be an important factor affecting the composition and diversity of microbial communities.

Structural and functional microbial diversity in deadwood respond to decomposition dynamics

We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.

Bacterial, but not fungal, communities show spatial heterogeneity in European beech (Fagus sylvatica L.) deadwood

Deadwood decomposition and other environmental processes mediated by microbial communities are generally studied with composite sampling strategies, where deadwood is collected from multiple locations in a large volume, that produce an average microbial community. In this study, we used amplicon sequencing to compare fungal and bacterial communities sampled with either traditional, composite samples, or small, 1 cm3 cylinders from a discrete location within decomposing European beech (Fagus sylvatica L.) tree trunks. We found that bacterial richness and evenness is lower in small samples when compared to composite samples. There was no significant difference in fungal alpha diversity between different sampling scales, suggesting that visually defined fungal domains are not restricted to a single species. Additionally, we found that composite sampling may obscure variation in community composition and this affects the understanding of microbial associations that are detected. For future experiments in environmental microbiology, we recommend that scale is explicitly considered as a factor and properly selected to correspond with the questions asked. Studies of microbial functions or associations may require samples to be collected at a finer scale than is currently practised.

Characteristics and Traceability Analysis of Microbial Assemblage in Fine Particulate Matter from a Pig House

Fine particulate matter (PM2.5) can carry numerous substances and penetrate deep into the respiratory tract due to its small particle size; associated harmful microorganisms are suspected to increase health risks for humans and animals. To find out the microbial compositions of PM2.5 in piggeries, their interaction and traceability, we collected PM2.5 samples from a piggery while continuously monitoring the environmental indicators. We also identified pathogenic bacteria and allergens in the samples using high-throughput sequencing technology. We analyzed the microbial differences of PM2.5 samples at different heights and during different times of day and investigated the microbial dynamics among the PM2.5 samples. To better understand the interaction between microorganisms and environmental factors among different microbial communities, we applied the network analysis method to identify the correlation among various variables. Finally, SourceTracker, a commonly used microbial traceability tool, was used to predict the source of airborne microorganisms in the pig house. We identified 14 potential pathogenic bacteria and 5 allergens from PM2.5 in the pig houses, of which Acinetobacter was the dominant bacterium in all samples (relative abundance > 1%), which warrants attention. We found that bacteria and fungi directly affected the the microbial community. The bacterial community mainly played a positive role in the microbial community. Environmental variables mainly indirectly and positively affected microbial abundance. In the SourceTracker analysis using fecal matter and feed as sources and PM2.5 sample as sink, we found that fecal matter made the greatest contribution to both bacterial and fungal components of PM2.5. Our findings provide important insights into the potential risks of pathogens in PM2.5 to human and animal health and their main sources.

The Necrobiome of Deadwood: The Life after Death

In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and habitats for a wide variety of saprotrophic and heterotrophic organisms and significantly contributes to soil formation and carbon storage. Deadwood is inhabited by a plethora of organisms from various kingdoms that have evolved the ability to utilize decaying organic matter. This community, consisting of both eukaryotic and prokaryotic species, can be defined as “necrobiome”. Through the interactions between its various members, the necrobiome influences the decay rates of deadwood and plays a crucial role in the balance between organic matter decomposition, carbon sequestration, and gas exchanges (e.g., CO2) with the atmosphere. The present work aims to provide an overview of the biodiversity and role of the microbial communities that inhabit deadwood and their possible involvement in greenhouse gas (CO2, N2O, and CH4) emissions.

Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing

Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.

Which Is the Best Substrate to Regenerate? A Comparative Pot Experiment for Tree Seedling Growth on Decayed Wood and in Soil

Dead wood is an important microsite for seedling regeneration in forest ecosystems. Although recent studies have found important associations between fungal wood decay type (white rot and brown rot) and both density and species composition of regenerating seedlings, its abiotic and biotic mechanisms are unknown. In the present study, pot experiments were conducted with the seedlings of two ectomycorrhizal tree species (Abies veitchii and Betula ermanii) and two arbuscular mycorrhizal tree species (Chamaecyparis obtusa and Cryptomeria japonica) to evaluate their growth using three substrates: brown rot wood, white rot wood, and soil. Results showed that the shoot growth of B. ermanii grown in white rot wood was greater than in other substrates, but this effect disappeared in sterilized substrates, suggesting some biotic positive effects occur in white rot wood. The seedling weights of Cr. japonica and Ch. obtusa were found to be greater in soil than in wood, and this may be partly attributable to the high mycorrhizal rate of their roots in soil. Colonization of arbuscular and ectomycorrhizal fungi was restricted to the seedlings in unsterilized soil. These results demonstrate the importance of the biological mechanisms affecting seedlings’ preferences for a variety of regeneration microsites and illustrate the need for future experiments to include larger sets of seedling species.

Habitat Significantly Affect CWD Decomposition but No Home-Field Advantage of the Decomposition Found in a Subtropical Forest, China

The home-field advantage (HFA) effect has been reported to occur in coarse woody debris (CWD) and litter. It is thought that the HFA effect may be due to the specialization of decomposers in their original habitats. However, the relative contribution of microorganisms, particularly fungi and bacteria, to deadwood decomposition is unclear because of differences in their functional at-tributes and carbon requirements, and the microorganisms that drive the HFA effect of deadwood are also unclear. Here, we analysed a dataset of microbial PLFA and substrate properties collected from the soil and CWD of two subtropical trees, Cryptomeria japonica and Platycarya strobilacea, from forests dominated by one or the other of the two species, with both species present in the forests. Our results showed that habitat and tree types all significantly affected CWD respiration rates, the CWD respiration rates were significantly higher in the deciduous broadleaf forests (DBF) than in the coniferous forest (CF) regardless of tree types, but no a large HFA of CWD decomposition found (HFA index was 4.75). Most biomarkers indicated bacteria and fungi were more abundant in the DBF than in the CF, and the concentration of microbial PLFAs was higher in Platycarya strobilacea than in Cryptomeria japonica. In addition, the relative abundance of fungi and soil B/F were remarkably positively correlated with CWD respiration, indicating that fungi may be the primary decomposers of CWD. In conclusion, our work highlights the importance of interactions between the three primary drivers (environment, substrate quality and microbes) on CWD decomposition.

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and ¹⁵N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N₂ fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and ¹⁵N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

Biofertilizers can enhance nitrogen use efficiency of sugarcane

Fertilizers are costly inputs into crop systems. To compensate for inefficiencies and losses from soil, farmers apply on average double the amount of nitrogen (N) fertilizer acquired by crops. We explored if N efficiency improves with biofertilizers formulated with organic waste, mineral N or plant growth-promoting rhizobacteria (PGPR). We compared treatments receiving mineral N fertilizer or biofertilizers at industry-recommended (100%) or lower (60%) N rates at two commercial sugarcane farms. Biofertilizer at the 60% N-rate generated promising results at one farm with significantly higher biomass and sugar yield than the no-N control, which matched the 100% mineral N treatment. This yield difference was accompanied by a shift in microbial diversity and composition. Correlation analysis confirmed that shifts in microbial communities were strongly linked to soil mineral N levels, as well as crop productivity and yield. Microbial co-occurrence networks further revealed that biofertilizer, including treatments with an added PGPR, can enhance bacterial associations, especially in the context of complex fungal networks. Collectively, the results confirm that biofertilizers have quantifiable effects on soil microbial communities in a crop system setting, which underscores the opportunities for biofertilizers to promote N use efficiency and the circular N economy.

Nitrogen fixing bacteria facilitate microbial biodegradation of a bio-based and biodegradable plastic in soils under ambient and future climatic conditions

We discovered a biological mechanism supporting microbial degradation of bio-based poly(butylene succinate-co-adipate) (PBSA) plastic in soils under ambient and future climates. Here, we show that nitrogen-fixing bacteria facilitate the microbial degradation of PBSA by enhancing fungal abundance, accelerating plastic-degrading enzyme activities, and shaping/interacting with plastic-degrading fungal communities.

Back to the Future: Decomposability of a Biobased and Biodegradable Plastic in Field Soil Environments and Its Microbiome under Ambient and Future Climates

Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28-33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.

A Seed Mucilage-Degrading Fungus From the Rhizosphere Strengthens the Plant-Soil-Microbe Continuum and Potentially Regulates Root Nutrients of a Cold Desert Shrub

Seed mucilage plays important roles in the adaptation of desert plants to the stressful environment. Artemisia sphaerocephala is an important pioneer plant in the Central Asian cold desert, and it produces a large quantity of seed mucilage. Seed mucilage of A. sphaerocephala can be degraded by soil microbes, but it is unknown which microorganisms can degrade mucilage or how the mucilage-degrading microorganisms affect rhizosphere microbial communities or root nutrients. Here, mucilage-degrading microorganisms were isolated from the rhizosphere of A. sphaerocephala, were screened by incubation with mucilage stained with Congo red, and were identified by sequencing and phylogenetic analyses. Fungal-bacterial networks based on high-throughput sequencing of rhizosphere microbes were constructed to explore the seasonal dynamic of interactions between a mucilage-degrading microorganism and its closely related microorganisms. The structural equation model was used to analyze effects of the mucilage-degrading microorganism, rhizosphere fungal-bacterial communities, and soil physicochemical properties on root C and N. The fungus Phanerochaete chrysosporium was identified as a mucilage-degrading microorganism. Relative abundance of the mucilage-degrading fungus (MDF) was highest in May. Subnetworks showed that the abundance of fungi and bacteria closely related to the MDF also were highest in May. Interactions between the MDF and related fungi and bacteria were positive, which might enhance mucilage degradation. In addition, the MDF might regulate root C and N by affecting rhizosphere microbial community structure. Our results suggest that MDF from the rhizosphere strengthens the plant-soil-microbe continuum, thereby potentially regulating microbial interactions and root nutrients of A. sphaerocephala.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Facilitation in the soil microbiome does not necessarily lead to niche expansion

BACKGROUND

The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown.

RESULTS

Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent.

CONCLUSIONS

Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.

Amplicon Sequencing-Based Bipartite Network Analysis Confirms a High Degree of Specialization and Modularity for Fungi and Prokaryotes in Deadwood

Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling.

Fungi and prokaryotes are dominant colonizers of wood and mediate its decomposition. Much progress has been achieved to unravel these communities and link them to specific wood properties. However, comparative studies considering both groups of organisms and assessing their relationships to wood resources are largely missing. Bipartite interaction networks provide an opportunity to investigate this colonizer-resource relationship more in detail and aim to directly compare results between different biotic groups. The main questions were as follows. Are network structures reflecting the trophic relationship between fungal and prokaryotic colonizers and their resources? If so, do they reflect the critical role of these groups, especially that of fungi, during decomposition? We used amplicon sequencing data to analyze fungal and prokaryotic interaction networks from deadwood of 13 temperate tree species at an early to middle stage of decomposition. Several diversity- and specialization-related indices were determined and the observed network structures were related to intrinsic wood traits. We hypothesized nonrandom bipartite networks for both groups and a higher degree of specialization for fungi, as they are the key players in wood decomposition. The results reveal highly modular and specialized interaction networks for both groups of organisms, demonstrating that many fungi and prokaryotes are resource-specific colonizers. However, as the level of specialization of fungi significantly surpassed that of prokaryotes, our findings reflect the strong association between fungi and their host. Our novel approach shows that the application of bipartite interaction networks is a useful tool to explore, quantify, and compare the deadwood-colonizers relationship based on sequencing data.

IMPORTANCE Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling. The aim of this study was to explore and quantify the relationship between these two main wood-inhabiting organism groups and their corresponding host trees. Two independent DNA-based amplicon sequencing data sets (fungi and prokaryotes) were analyzed via bipartite interaction networks. The links in the networks represent the interactions between the deadwood colonizers and their deadwood hosts. The networks allowed us to analyze whether many colonizing species interact mostly with a restricted number of deadwood tree species, so-called specialization. Our results demonstrate that many prokaryotes and fungi are resource-specific colonizers. The direct comparison between both groups revealed significantly higher specialization values for fungi, emphasizing their strong association to respective host trees, which reflects their dominant role in exploiting this resource.

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition

Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers.

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.

IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.

Fungal and Bacterial Diversity Patterns of Two Diversity Levels Retrieved From a Late Decaying Fagus sylvatica Under Two Temperature Regimes

Environmental fluctuations are a common occurrence in an ecosystem, which have an impact on organismic diversity and associated ecosystem services. The aim of this study was to investigate how a natural and a species richness-reduced wood decaying community diversity were capable of decomposing Fagus sylvatica dead wood under a constant and a fluctuating temperature regime. Therefore, microcosms with both diversity levels (natural and species richness-reduced) were prepared and incubated for 8 weeks under both temperature regimes. Relative wood mass loss, wood pH, carbon dioxide, and methane emissions, as well as fungal and bacterial community compositions in terms of Simpson‘s diversity, richness and evenness were investigated. Community interaction patterns and co-occurrence networks were calculated. Community composition was affected by temperature regime and natural diversity caused significantly higher mass loss than richness-reduced diversity. In contrast, richness-reduced diversity increased wood pH. The bacterial community composition was less affected by richness reduction and temperature regimes than the fungal community composition. Microbial interaction patterns showed more mutual exclusions in richness-reduced compared to natural diversity as the reduction mainly reduced abundant fungal species and disintegrated previous interaction patterns. Microbial communities reassembled in richness-reduced diversity with a focus on nitrate reducing and dinitrogen-fixing bacteria as connectors in the network, indicating their high relevance to reestablish ecosystem functions. Therefore, a stochastic richness reduction was followed by functional trait based reassembly to recover previous ecosystem productivity.

Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood

Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions.

Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood’s properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood.

IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups

Eukaryote-associated microbiomes vary across host taxa and environments but the key factors underlying their diversity and structure in fungi are still poorly understood. Here we determined the structure of bacterial communities in fungal fruitbodies in relation to the main chemical characteristics in ectomycorrhizal (EcM) and saprotrophic (SAP) mushrooms as well as in the surrounding soil. Our analyses revealed significant differences in the structure of endofungal bacterial communities across fungal phylogenetic groups and to a lesser extent across fungal guilds. These variations could be partly ascribed to differences in fruitbody chemistry, particularly the carbon-to-nitrogen ratio and pH. Fungal fruitbodies appear to represent nutrient-rich islands that derive their microbiome largely from the underlying continuous soil environment, with a larger overlap of operational taxonomic units observed between SAP fruitbodies and the surrounding soil, compared with EcM fungi. In addition, bacterial taxa involved in the decomposition of organic material were relatively more abundant in SAP fruitbodies, whereas those involved in release of minerals were relatively more enriched in EcM fruitbodies. Such contrasts in patterns and underlying processes of the microbiome structure between SAP and EcM fungi provide further evidence that bacteria can support the functional roles of these fungi in terrestrial ecosystems.

Future Climate Significantly Alters Fungal Plant Pathogen Dynamics during the Early Phase of Wheat Litter Decomposition

Returning wheat residues to the soil is a common practice in modern agricultural systems and is considered to be a sustainable practice. However, the negative contribution of these residues in the form of “residue-borne pathogens” is recognized. Here, we aimed to investigate the structure and ecological functions of fungal communities colonizing wheat residues during the early phase of decomposition in a conventional farming system. The experiment was conducted under both ambient conditions and a future climate scenario expected in 50–70 years from now. Using MiSeq Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2), we found that plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome. Destructive wheat fungal pathogens such as Fusarium graminearum, Fusarium tricinctum, and Zymoseptoria tritci were detected under ambient and future climates. Moreover, future climate enhanced the appearance of new plant pathogenic fungi in the plant residues. Our results based on the bromodeoxyuridine (BrdU) immunocapture technique demonstrated that almost all detected pathogens are active at the early stage of decomposition under both climate scenarios. In addition, future climate significantly changed both the richness patterns and the community dynamics of the total, plant pathogenic and saprotrophic fungi in wheat residues as compared with the current ambient climate. We conclude that the return of wheat residues can increase the pathogen load, and therefore have negative consequences for wheat production in the future.

Successional Variation in the Soil Microbial Community in Odaesan National Park, Korea

Succession is defined as variation in ecological communities caused by environmental changes. Environmental succession can be caused by rapid environmental changes, but in many cases, it is slowly caused by climate change or constant low-intensity disturbances. Odaesan National Park is a well-preserved forest located in the Taebaek mountain range in South Korea. The forest in this national park is progressing from a mixed-wood forest to a broad-leaved forest. In this study, microbial community composition was investigated using 454 sequencing of soil samples collected from 13 different locations in Odaesan National Park. We assessed whether microbial communities are affected by changes in environmental factors such as water content (WC), nutrient availability (total carbon (TC) and total nitrogen (TN)) and pH caused by forest succession. WC, TC, TN and pH significantly differed between the successional stages of the forest. The WC, TC and TN of the forest soils tended to increase as succession progressed, while pH tended to decrease. In both successional stages, the bacterial genus Pseudolabrys was the most abundant, followed by Afipia and Bradyrhizobium. In addition, the fungal genus Saitozyma showed the highest abundance in the forest soils. Microbial community composition changed according to forest successional stage and soil properties (WC, TC, TN, and pH). Furthermore, network analysis of both bacterial and fungal taxa revealed strong relationships of the microbial community depending on the soil properties affected by forest succession.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood

Deadwood decomposition is relevant in nature and wood inhabiting fungi (WIF) are its main decomposers. However, climate influence on WIF community and their interactions with bacteria are poorly understood. Therefore, we set up an in-field mesocosm experiment in the Italian Alps and monitored the effect of slope exposure (north- vs. south-facing slope) on the decomposition of Picea abies wood blocks and their microbiome over two years. Unlike fungal richness and diversity, we observed compositional and functional differences in the WIF communities as a function of exposure. Wood-degrading operational taxonomic units (OTUs) such as Mycena, and mycorrhizal and endophytic OTUs were characteristic of the south-facing slope. On the north-facing one, Mucoromycota, primarily Mucor, were abundant and mixotrophic basidiomycetes with limited lignin-degrading capacities had a higher prevalence compared to the southern slope. The colder, more humid conditions and prolonged snow-coverage at north exposure likely influenced the development of the wood-degrading microbial communities. Networks between WIF and N2-fixing bacteria were composed of higher numbers of interacting microbial units and showed denser connections at the south-facing slope. The association of WIF to N2-fixing Burkholderiales and Rhizobiales could have provided additional competitive advantages, especially for early wood colonization.

Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil

P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.

This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens. Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.

IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.

Nitrogen-obtaining and -conserving strategies in xylotrophic basidiomycetes

Nitrogen in sufficient quantities is strictly necessary for all living organisms. In this study, the ability of some xylotrophic basidiomycetes to grow extremely long on a solid growth medium full of carbon nutrition but lacking a nitrogen source in its composition was discovered. The nitrogen oligotrophy of wood-decaying fungi is associated with their adaptation to live in a wood substrate, which is also deficient in nitrogen content. This nitrogen-depleted cultural growth is called "pseudo-foraging" and can be used as a simplified model of wood-decaying growth. Four main nitrogen-obtaining and -conserving strategies (nitrogen concentration, using alternative sources of nitrogen, economy of growth, and nutritional recycling), which are attributed to wood-colonizing xylotrophs in the literature, were revised studying the pseudo-foraging model. Based on the results, some aspects of the behavior of xylotrophs deep in undecomposed wood were predicted. For example, one of the results is that for pseudo-foraging xylotrophs, the main way to obtain nitrogen is its concentration in their mycelium from the nutrient medium in which nitrogen is contained in the impurities of the components of the medium. The result suggests that in bulk solid wood, the nitrogen concentration strategy also dominates the strategy of using diazotrophic and other alternative nitrogen. In addition, three individual unprecedented mechanisms, which supposedly help the xylotrophic fungi to colonize wood in nature (generation of fine mycelium, macrovesicular endocytosis, formation and conversion of super-elongated mitochondria), were investigated in the laboratory.

Microbial metaproteome data from decayed beech dead wood

Wood-decomposition in terrestrial ecosystems is a very important process with huge ecologic consequences. This decomposition process is a combination of biological respiration, leaching and fragmentation, mainly triggered by organismic activities. In order to gain a deeper insight into these microbial communities and their role in deadwood decay, we used metaproteomics. Metaproteomics is an important tool and offers the ability to characterize the protein complement of environmental microbiota at a given point in time. In this dataset, we provide data of an exemplary beech wood log and applied different extraction methods to provide the proteome profile of beech dead wood and their corresponding fungal-bacterial community.

Highly competitive fungi manipulate bacterial communities in decomposing beech wood (Fagus sylvatica)

The bacterial communities in decomposing wood are receiving increased attention, but their interactions with wood-decay fungi are poorly understood. This is the first field study to test the hypothesis that fungi are responsible for driving bacterial communities in beech wood (Fagus sylvatica). A meta-genetic approach was used to characterise bacterial and fungal communities in wood that had been laboratory-colonised with known wood-decay fungi, and left for a year at six woodland sites. Alpha-, Beta- and Gammaproteobacteria and Acidobacteria were the proportionally dominant bacterial taxa, as in previous studies. Pre-colonising wood with decay fungi had a clear effect on the bacterial community, apparently via direct fungal influence; the bacterial and fungal communities present at the time of collection explained nearly 60% of their mutual covariance. Site was less important than fungal influence in determining bacterial communities, but the effects of pre-colonisation were more pronounced at some sites than at others. Wood pH was also a strong bacterial predictor, but was itself under considerable fungal influence. Burkholderiaceae and Acidobacteriaceae showed directional responses against the trend of the bacterial community as a whole.

The Effect of Size of Black Cherry Stumps on the Composition of Fungal Communities Colonising Stumps

We investigated fungal communities colonising black cherry stumps. We tested the hypothesis that black cherry stumps of greater diameter should be characterised by more diverse fungal communities than stumps of smaller diameter. The material for analyses came from Podanin Forest District. DNA was extracted using a Plant Genomic DNA purification kit. The results were subjected to bioinformatic analysis and statistical analysis. The OTU sequences were compared using the BLAST algorithm with reference sequences from the UNITE database. In total, 8192 raw sequences were obtained from samples of black cherry stumps applying the Illumina sequencing technique. The results of the statistical analysis indicate a trend towards increased diversity in bigger black cherry stumps. The dominant share of fungi associated with wood decomposition indicates the progressing process of decomposition in stumps. Identification of the role and functions of the individual components of fungal communities colonising stumps may provide insight into the overall ecology of these organisms and provide a basis for improved plant protection, with a view to limiting the occurrence of black cherries in the future in undesirable locations outside their natural range.

First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

Mangrove forest trees play important ecological functions at the interface between terrestrial and marine ecosystems. However, despite playing crucial roles in plant health and productivity, there is little information on microbiomes of the tree species in mangrove ecosystems. Thus, in this study we aimed to characterize the microbiome in soil (rhizosphere) and plant (root, stem, and leaf endosphere) compartments of the widely distributed mangrove tree Rhizophora stylosa. Surprisingly, bacterial operational taxonomic units (OTUs) were only confidently detected in rhizosphere soil, while fungal OTUs were detected in all soil and plant compartments. The major detected bacterial phyla were affiliated to Proteobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Several nitrogen-fixing bacterial OTUs were detected, and the presence of nitrogen-fixing bacteria was confirmed by nifH gene based-PCR in all rhizosphere soil samples, indicating their involvement in N acquisition in the focal mangrove ecosystem. We detected taxonomically (54 families, 83 genera) and functionally diverse fungi in the R. stylosa mycobiome. Ascomycota (mainly Dothideomycetes, Eurotiomycetes, Sordariomycetes) were most diverse in the mycobiome, accounting for 86% of total detected fungal OTUs. We found significant differences in fungal taxonomic and functional community composition among the soil and plant compartments. We also detected significant differences in fungal OTU richness (p < 0.002) and community composition (p < 0.001) among plant compartments. The results provide the first information on the microbiome of rhizosphere soil to leaf compartments of mangrove trees and associated indications of ecological functions in mangrove ecosystems.

Home-Field Advantage in Wood Decomposition Is Mainly Mediated by Fungal Community Shifts at "Home" Versus "Away"

The home-field advantage (HFA) hypothesis has been used intensively to study leaf litter decomposition in various ecosystems. However, the HFA in woody substrates is still unexplored. Here, we reanalyzed and integrated existing datasets on various groups of microorganisms collected from natural deadwood of two temperate trees, Fagus sylvatica and Picea abies, from forests in which one or other of these species dominates but where both are present. Our aims were (i) to test the HFA hypothesis on wood decomposition rates of these two temperate tree species, and (ii) to investigate if HFA hypothesis can be explained by diversity and community composition of bacteria and in detail N-fixing bacteria (as determined by molecular 16S rRNA and nifH gene amplification) and fungi (as determined by molecular ITS rRNA amplification and sporocarp surveys). Our results showed that wood decomposition rates were accelerated at "home" versus "away" by 38.19% ± 20.04% (mean ± SE). We detected strong changes in fungal richness (increase 36-50%) and community composition (R_ANOSIM = 0.52-0.60, P < 0.05) according to HFA hypothesis. The changes of fungi were much stronger than for total bacteria and nitrogen fixing for both at richness and community composition levels. In conclusion, our results support the HFA hypothesis in deadwood: decomposition rate is accelerated at home due to specialization of fungal communities produced by the plant community above them. Furthermore, the higher richness of fungal sporocarps and nitrogen-fixing bacteria (nifH) may stimulate or at least stabilize wood decomposition rates at "home" versus "away."

More obvious air pollution impacts on variations in bacteria than fungi and their co-occurrences with ammonia-oxidizing microorganisms in PM2.5

Based on long-term systematic sampling, information is currently limited regarding the impacts of different air pollution levels on variations of bacteria, fungi and ammonia-oxidizing microorganisms (AOMs) in fine particulate matter (PM_2.5), especially their interactions. Here, PM_2.5 samples were weekly collected at different air pollution levels in Beijing, China during one-year period. Microbial composition was profiled using Illumina sequencing, and their interactions were further investigated to reveal the hub genera with network analysis. Diversity of bacteria and fungi showed obvious seasonal variations, and the heavy- or severe-pollution levels mainly affected the diversity and composition of bacteria, but not fungi. While, the community structure of both bacteria and fungi was influenced by the combination of air pollution levels and seasons. The most abundant bacterial genera and some genera with highest abundance in heavy- or severe-pollution days were the hub bacteria in PM_2.5. Whereas, only the dominant fungi in light-pollution days in winter were the hub fungi in PM_2.5. The complex positive correlations of bacterial or fungal pathogens would aggravate the air pollution effects on human health, despite of their low relative abundances. Moreover, the strong co-occurrence and co-exclusion patterns of bacteria and fungi in PM_2.5 were identified. Furthermore, the hub environmental factors (e.g., relative humidity and atmospheric pressure) may play central roles in the distributions of bacteria and fungi, including pathogens. Importantly, AOMs showed significant co-occurrence patterns with the main bacterial and fungal genera and potential pathogens, providing possible microbiological evidences for controlling ammonia emissions to effectively reduce PM_2.5 pollution. These results highlighted the more obvious air pollution impacts on bacteria than fungi, and the complex bacterial-fungal interactions, as well as the important roles of AOMs in airborne microbial interactions webs, improving our understanding of bioaerosols in PM_2.5.

Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen)

Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions - we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.

Carbon flux from decomposing wood and its dependency on temperature, wood N2 fixation rate, moisture and fungal composition in a Norway spruce forest

Globally 40-70 Pg of carbon (C) are stored in coarse woody debris on the forest floor. Climate change may reduce the function of this stock as a C sink in the future due to increasing temperature. However, current knowledge on the drivers of wood decomposition is inadequate for detailed predictions. To define the factors that control wood respiration rate of Norway spruce and to produce a model that adequately describes the decomposition process of this species as a function of time, we used an unprecedentedly diverse analytical approach, which included measurements of respiration, fungal community sequencing, N₂ fixation rate, nifH copy number, ¹⁴ C-dating as well as N%, δ¹³ C and C% values of wood. Our results suggest that climate change will accelerate C flux from deadwood in boreal conditions, due to the observed strong temperature dependency of deadwood respiration. At the research site, the annual C flux from deadwood would increase by 27% from the current 117 g C/kg wood with the projected climate warming (RCP4.5). The second most important control on respiration rate was the stage of wood decomposition; at early stages of decomposition low nitrogen content and low wood moisture limited fungal activity while reduced wood resource quality decreased the respiration rate at the final stages of decomposition. Wood decomposition process was best described by a Sigmoidal model, where after 116 years of wood decomposition mass loss of 95% was reached. Our results on deadwood decomposition are important for C budget calculations in ecosystem and climate change models. We observed for the first time that the temperature dependency of N₂ fixation, which has a major role at providing N for wood-inhabiting fungi, was not constant but varied between wood density classes due to source supply and wood quality. This has significant consequences on projecting N₂ fixation rates for deadwood in changing climate.

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype

Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting plant health and disease. The plant microbiome is shaped by plant species, plant genotype, soil and environmental conditions, but the contributions of these variables are hard to disentangle from each other in natural systems. We used bioassay common garden experiments to decouple plant genotype and soil property impacts on fungal and bacterial community structure in the Populus rhizobiome. High throughput amplification and sequencing of 16S, ITS, 28S and 18S rDNA was accomplished through 454 pyrosequencing. Co-association patterns of fungal and bacterial taxa were assessed with 16S and ITS datasets. Community bipartite fungal-bacterial networks and PERMANOVA results attribute significant difference in fungal or bacterial communities to soil origin, soil chemical properties and plant genotype. Indicator species analysis identified a common set of root bacteria as well as endophytic and ectomycorrhizal fungi associated with Populus in different soils. However, no single taxon, or consortium of microbes, was indicative of a particular Populus genotype. Fungal-bacterial networks were over-represented in arbuscular mycorrhizal, endophytic, and ectomycorrhizal fungi, as well as bacteria belonging to the orders Rhizobiales, Chitinophagales, Cytophagales, and Burkholderiales. These results demonstrate the importance of soil and plant genotype on fungal-bacterial networks in the belowground plant microbiome.

Copper in Wood Preservatives Delayed Wood Decomposition and Shifted Soil Fungal but Not Bacterial Community Composition

Copper-based fungicides are routinely used for wood and plant protection, which can lead to an enrichment of copper-tolerant microbial communities in soil. To investigate the effect of such wood preservatives on the soil fungal and bacterial community compositions, five different vineyard and fruit-growing soil environments were evaluated using incubation studies over time. Pine sapwood specimens were impregnated with either water or different biocide treatment solutions containing a mixture of copper, triazoles, and quaternary ammonium compounds (CuTriQAC), a mixture of triazoles and quaternary ammonium compounds (TriQAC), or copper alone (Cu). Specimens were incubated in soil from each sample site for 8, 16, 24, and 32 weeks. The effects of preservative treatment on the modulus of elasticity (MOE) of the wood specimens and on the soil fungal as well as bacterial community composition at the soil-wood interface were assessed by quantitative PCR and amplicon sequencing of the fungal internal transcribed spacer (ITS) region and bacterial 16S rRNA gene. Specimens impregnated with CuTriQAC and Cu showed decreased MOE and reduced fungal and bacterial copy numbers over time compared to those impregnated with water and TriQAC. Fungal but not bacterial community composition was significantly affected by wood preservative treatment. The relative abundance of members of the family Trichocomaceae compared to other genera increased in the presence of the Cu and CuTriQAC treatments at three sites, suggesting these to be Cu-tolerant fungi. In conclusion, the copper-containing treatments resulted in marginally increased MOE, lowered microbial gene copy numbers compared to those in the TriQAC and water treatments, and thus enhanced wood protection against soil microbial wood degradation.IMPORTANCE Copper-containing rather than TRIQAC formulations are efficient wood preservatives irrespective of the origin and composition of the soil microbial communities. However, some fungi appear to be naturally insensitive to copper and should be the focus of future wood preservative formulations to facilitate the life span of wooden construction in contact with soil while also minimizing the overall environmental impact.

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype

Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting plant health and disease. The plant microbiome is shaped by plant species, plant genotype, soil and environmental conditions, but the contributions of these variables are hard to disentangle from each other in natural systems. We used bioassay common garden experiments to decouple plant genotype and soil property impacts on fungal and bacterial community structure in the Populus rhizobiome. High throughput amplification and sequencing of 16S, ITS, 28S and 18S rDNA was accomplished through 454 pyrosequencing. Co-association patterns of fungal and bacterial taxa were assessed with 16S and ITS datasets. Community bipartite fungal-bacterial networks and PERMANOVA results attribute significant difference in fungal or bacterial communities to soil origin, soil chemical properties and plant genotype. Indicator species analysis identified a common set of root bacteria as well as endophytic and ectomycorrhizal fungi associated with Populus in different soils. However, no single taxon, or consortium of microbes, was indicative of a particular Populus genotype. Fungal-bacterial networks were over-represented in arbuscular mycorrhizal, endophytic, and ectomycorrhizal fungi, as well as bacteria belonging to the orders Rhizobiales, Chitinophagales, Cytophagales, and Burkholderiales. These results demonstrate the importance of soil and plant genotype on fungal-bacterial networks in the belowground plant microbiome.

Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment

Despite the important role of wood-inhabiting fungi (WIF) in deadwood decomposition, our knowledge of the factors shaping the dynamics of their species richness and community composition is scarce. This is due to limitations regarding the resolution of classical methods used for characterizing WIF communities and to a lack of well-replicated long-term experiments with sufficient numbers of tree species. Here, we used a large scale experiment with logs of 11 tree species at an early stage of decomposition, distributed across three regions of Germany, to identify the factors shaping WIF community composition and Operational Taxonomic Unit (OTU) richness using next generation sequencing. We found that tree species identity was the most significant factor, corresponding to (P < 0.001) and explaining 10% (representing 48% of the explainable variance) of the overall WIF community composition. The next important group of variables were wood-physicochemical properties, of which wood pH was the only factor that consistently corresponded to WIF community composition. For overall WIF richness patterns, we found that approximately 20% of the total variance was explained by wood N content, location, tree species identity and wood density. It is noteworthy that the importance of determinants of WIF community composition and richness appeared to depend greatly on tree species group (broadleaved vs. coniferous) and it differed between the fungal phyla Ascomycota and Basidiomycota.

Bacteria associated with decomposing dead wood in a natural temperate forest

Dead wood represents an important pool of organic matter in forests and is one of the sources of soil formation. It has been shown to harbour diverse communities of bacteria, but their roles in this habitat are still poorly understood. Here, we describe the bacterial communities in the dead wood of Abies alba, Picea abies and Fagus sylvatica in a temperate natural forest in Central Europe. An analysis of environmental factors showed that decomposing time along with pH and water content was the strongest drivers of community composition. Bacterial biomass positively correlated with N content and increased with decomposition along with the concurrent decrease in the fungal/bacterial biomass ratio. Rhizobiales and Acidobacteriales were abundant bacterial orders throughout the whole decay process, but many bacterial taxa were specific either for young (<15 years) or old dead wood. During early decomposition, bacterial genera able to fix N2 and to use simple C1 compounds (e.g. Yersinia and Methylomonas) were frequent, while wood in advanced decay was rich in taxa typical of forest soils (e.g. Bradyrhizobium and Rhodoplanes). Although the bacterial contribution to dead wood turnover remains unclear, the community composition appears to reflect the changing conditions of the substrate and suggests broad metabolic capacities of its members.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of the N2 -fixing community depending on depth and agricultural use of soil

In this survey, a total of 80 787 reads and 28 171 unique NifH protein sequences were retrieved from soil RNA. This dataset extends our knowledge about the structure and diversity of the functional diazotrophic communities in agricultural soils from Argentinean Pampas. Operational taxonomic unit (OTU)‐based analyses showed that nifH phylotypes related to Geobacter and Anaeromyxobacter (44.8%), Rhizobiales (29%), Cyanobacteria (16.7%), and Verrucomicrobiales (8%) are key microbial components of N₂ fixation in soils associated with no‐till management and soil depth. In addition, quantification of nifH gene copies related to Geobacter and Cyanobacteria revealed that these groups are abundant in soils under maize–soybean rotation and soybean monoculture, respectively. The correlation of physicochemical soil parameters with the diazotrophic diversity and composition showed that soil stability and organic carbon might contribute to the functional signatures of particular nifH phylotypes in fields under no‐till management. Because crop production relies on soil‐borne microorganism's activities, such as free N₂ fixation, the information provided by our study on the diazotrophic population dynamics, associated with the edaphic properties and land‐use practices, represents a major contribution to gain insight into soil biology, in which functionally active components are identified.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales-the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique

The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics (Schima superba and Pinus massoniana) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima. The two deadwood species differed significantly in WIF OTU richness (Pinus > Schima) and community composition (P < 0.001). Variations in WIF community composition of both tree species were significantly explained by wood pH and ecological factors (biotic: deadwood species, basal area and abiotic: soil pH), but the WIF communities derived from each tree species correlated differently with abiotic factors. Interestingly, we found that deadwood decomposition rate significantly correlated with WIF communities and negatively correlated with WIF OTU richness. We conclude that the pattern of WIF OTU richness and community composition are controlled by multiple interacting biotic and abiotic factors. Overall, our study provides an in-depth picture of the deadwood mycobiome in this subtropical forest. Furthermore, by comparing our results to results from temperate and boreal forests we contribute to a better understanding of patterns of WIF communities across different biomes and geographic locations.