Genotypic richness and dissimilarity opposingly affect ecosystem functioning

Contrasting range changes and drivers of four forest foundation species under future climate change in China

Forest foundation species, vital for shaping community structure and dynamics through non-trophic level interactions, are key to forest succession and sustainability. Despite their ecological importance, the habitat ranges of these species in China and their responses to future climate change remain unclear. Our study employed the optimal MaxEnt model to assess the range shifts and their essential drivers of four typical forest foundation species from three climatic zones in China under climate scenarios, including Acer tegmentosum, Acer pseudo-sieboldianum (temperate zone), Quercus glandulifera (subtropical zone), and Ficus hispida (tropical zone). The optimal MaxEnt model exhibited high evaluation indices (AUC values > 0.90) for the four foundation species, indicating excellent predictive performance. Currently, we observed that A. tegmentosum and A. pseudo-sieboldianum are predominantly inhabited temperate forest areas in northeastern China, Q. glandulifera is primarily concentrated in subtropical forests in southeastern China, and F. hispida is mainly distributed across the tropical forests in southern China. Climate factors, particularly temperature, emerged as the primary environmental factors influencing the potential range of forest foundation species. Moreover, precipitation strongly influenced the potential range of A. tegmentosum and A. pseudo-sieboldianum, while elevation exhibited a greater impact on the range of Q. glandulifera and F. hispida. Under future climate scenarios, suitable areas for A. tegmentosum and A. pseudo-sieboldianum tend to expand southward, F. hispida tends to expand northward, while Q. glandulifera exhibited a tendency to contract towards the center. This study advances our understanding of the spatial and temporal dynamics of forest foundation species in China under climate change, providing critical insights for conservation efforts and sustainable forest management practices.

Mild to moderate drought stress reinforces the role of functional microbiome in promoting growth of a dominant forage species (Neopallasia pectinata) in desert steppe

Background

Desert steppe ecosystems are prone to drought stress, which influences the ecological balance and sustainable development of grasslands. In addition to directly restrict plant growth, drought stress indirectly impacts plant fitness by altering the diversity and function of root-associated microbiomes. This begs the question of whether the functional microbiome of forage plants, represented by synthetic microbial communities (SynComs), can be leveraged to mitigate drought stress in desert steppes and promote the ecological restoration of these fragile ecosystems.

Methods

A pot experiment was conducted to evaluate the role of SynComs in improving the plant growth and drought stress resistance of Neopallasia pectinata (Pall.) Poljak in desert steppe in Inner Mongolia, China. Six SynComs were derived from the rhizosphere and root endosphere of 12 dominant forage species in the desert steppe. Each SynCom comprised two to three bacterial genera (Bacillus, Protomicromonospora, and Streptomyces). We examined the capacities of different SynComs for nutrient solubilization, phytohormone secretion, and enzymatic activity.

Results

Under no water stress (75% soil water holding capacity, WHC), single strains performed better than SynComs in promoting plant growth in terms of stem diameter, root length, and plant dry weight, with the greatest effects observed for Streptomyces coeruleorubidus ATCC 13740 (p < 0.05). However, under mild to moderate drought stress (55% and 35% WHC), SynComs outperformed single strains in enhancing plant biomass accumulation and inducing the production of resistance-related substances (p < 0.05). No significant effect of single strains and SynComs emerged under extreme drought stress (20% WHC).

Conclusion

This study underscores the potential of SynComs in facilitating forage plants to combat drought stress in desert steppe. Mild to moderate drought stress stimulates SynComs to benefit the growth of N. pectinata plants, despite a soil moisture threshold (21% WHC) exists for the microbial effect. The use of SynComs provides a promising strategy for the ecological restoration and sustainable utilization of desert steppes by manipulating the functional microbiome of forage plants.

Trophic interactions in microbiomes influence plant host population size and ecosystem function

Plant microbiomes that comprise diverse microorganisms, including prokaryotes, eukaryotes and viruses, are the key determinants of plant population dynamics and ecosystem function. Despite their importance, little is known about how species interactions (especially trophic interactions) between microbes from different domains modify the importance of microbiomes for plant hosts and ecosystems. Using the common duckweed Lemna minor, we experimentally examined the effects of predation (by bacterivorous protists) and parasitism (by bacteriophages) within microbiomes on plant population size and ecosystem phosphorus removal. Our results revealed that the addition of predators increased plant population size and phosphorus removal, whereas the addition of parasites showed the opposite pattern. The structural equation modelling further pointed out that predation and parasitism affected plant population size and ecosystem function via distinct mechanisms that were both mediated by microbiomes. Our results highlight the importance of understanding microbial trophic interactions for predicting the outcomes and ecosystem impacts of plant-microbiome symbiosis.

Spatial patterns and drivers of ecosystem multifunctionality in China: Arid vs. humid regions

Ecosystem multifunctionality (EMF) refers to an ecosystem's capacity to simultaneously uphold multiple ecological functions or services. In terrestrial ecosystems, the potential patterns and processes of EMF remain largely unexplored, limiting our comprehension of how ecosystems react to various driving factors. We collected environmental, soil and plant nutrient data, investigate the spatial distribution characteristics of EMF in China's terrestrial ecosystems, differentiating between arid and humid regions and examining the underlying drivers. Our findings reveal substantial spatial heterogeneity in the distribution of EMF across China's terrestrial ecosystems, with pronounced variations between arid and humid regions. In arid regions, the EMF index predominantly falls within the range of -1 to 1, including approximately 66.8 % of the total area, while in humid regions, the EMF index primarily falls within the range of 0 to 2, covering around 55.2 % of the total area. Climate, soil, and vegetation factors account for 61.4 % and 51.9 % of the total EMF variation in arid and humid regions, respectively. Notably, climate emerges as the dominant factor governing EMF variation in arid regions, whereas soil physicochemical properties take precedence in humid regions. Specifically, mean annual temperature (MAT) emerges as the primary factor influencing EMF variation in arid regions, while the normalized difference vegetation index (NDVI) and soil biodiversity index (SBI) play pivotal roles in regulating EMF variation in humid regions. Indeed, climate can exert both direct and indirect influences on EMF. In summary, our study not only compared the disparities in the spatial distribution of EMF in arid and humid regions but also unveiled the distinct controlling factors that govern EMF changes in these different regions. Our research has contributed novel insights for evaluating the drivers responsible for mediating EMF in diverse ecosystems, shedding light on the adaptability and response mechanisms of ecosystems under varying environmental conditions.

The heterogeneity-diversity-system performance nexus

Ever-growing human population and nutritional demands, supply chain disruptions, and advancing climate change have led to the realization that changes in diversity and system performance are intimately linked. Moreover, diversity and system performance depend on heterogeneity. Mitigating changes in system performance and promoting sustainable living conditions requires transformative decisions. Here, we introduce the heterogeneity-diversity-system performance (HDP) nexus as the conceptual basis upon which to formulate transformative decisions. We suggest that managing the heterogeneity of systems will best allow diversity to provide multiple benefits to people. Based on ecological theory, we pose that the HDP nexus is broadly applicable across systems, disciplines, and sectors, and should thus be considered in future decision making as a way to have a more sustainable global future.

Single-gene resolution of diversity-driven overyielding in plant genotype mixtures

In plant communities, diversity often increases productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute positive diversity effects to complementary niches occupied by different species or genotypes. However, the specific nature of niche complementarity often remains unclear, including how it is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to study positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we find that between-plant allelic differences at the AtSUC8 locus are strongly associated with mixture overyielding. AtSUC8 encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affects the biochemical activities of protein variants and natural variation at this locus is associated with different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying genes important for ecosystem functioning may ultimately allow linking ecological processes to evolutionary drivers, help identify traits underlying positive diversity effects, and facilitate the development of high-performance crop variety mixtures.

Metabolic cooperation between conspecific genotypic groups contributes to bacterial fitness

Microbial interactions are important for the survival of species and the stability of the microbial ecosystem. Although bacteria have diverse conspecific genotypes in the natural microbial ecosystem, little is known about whether wild-type strains within species would interact with each other and how the intraspecific interaction influences the growth of the species. In this work, using Lactobacillus acetotolerans, a dominant species with diverse conspecific genotypes in natural food fermentation ecosystems as a case, we studied the interactions between different genotypic groups of this species. In interspecific and intraspecific pairwise cocultures, the growth of L. acetotolerans decreased, but the increase of the phylogenetic similarity would reduce this negative effect, indicating a potential intraspecific interaction of this species. Meanwhile, the strain classification method affected the analysis of intraspecific interactions, which can be efficiently demonstrated using 99.5% average nucleotide identity (ANI) as the strain-level classification method. Using this ANI classification method, we revealed the population fitness significantly increased in cocultures of different genotypic groups. Facilitation involving 11 amino acids was identified between different ANI genotypic groups, which was beneficial for increasing population fitness. This work revealed that wild-type conspecific strains could interact with each other via cooperative metabolic changes and benefit each other to increase fitness. It shed new light on the survival and stability of species in natural microbial ecosystems.

Bacillus VOCs in the Context of Biological Control

A contemporary agricultural production system relying on heavy usage of agrochemicals represents a questionable outlook for sustainable food supply in the future. The visible negative environmental impacts and unforeseen consequences to human and animal health have been requiring a shift towards the novel eco-friendly alternatives for chemical pesticides for a while now. Microbial-based biocontrol agents have shown a promising potential for plant disease management. The bacteria of the genus Bacillus have been among the most exploited microbial active components due to several highly efficient mechanisms of action against plant pathogens, as well as a palette of additional plant-beneficial mechanisms, together with their suitable properties for microbial biopesticide formulations. Among other bioactive metabolites, volatile organic compounds (VOCs) have been investigated for their biocontrol applications, exhibiting the main advantage of long-distance effect without the necessity for direct contact with plants or pathogens. The aim of this study is to give an overview of the state-of-the-art in the field of Bacillus-based VOCs, especially in terms of their antibacterial, antifungal, and nematicidal action as the main segments determining their potential for biocontrol applications in sustainable agriculture.

High carbon resource diversity enhances the certainty of successful plant pathogen and disease control

The host-associated microbiome highly determines plant health. Available organic resources, such as food for microbes, are important in shaping microbial community structure and multifunctionality. However, how using organic resources precisely manipulates the soil microbiome and makes it supportive of plant health remains unclear. Here, we experimentally tested the influence of carbon resource diversity on the microbial trophic network and pathogen invasion success in a microcosm study. We further explored how resource diversity affects microbial evenness, community functions, and plant disease outcomes in systems involving tomato plants and the in vivo soil microbiome. Increasing available resource diversity altered trophic network architecture, increased microbial evenness, and thus increased the certainty of successful pathogen control. By contrast, the invasion resistance effects of low resource diversity were less effective and highly varied. Accordingly, increases in the evenness and connection of dominant species induced by high resource diversity significantly contributed to plant disease suppression. Furthermore, high carbohydrate diversity upregulated plant immune system regulation-related microbial functions. Our results deepen the biodiversity-invasion resistance theory and provide practical guidance for the control of plant pathogens and diseases by using organic resource-mediated approaches, such as crop rotation, intercropping, and organic amendments.

Effects of vegetation shift from needleleaf to broadleaf species on forest soil CO2 emission

Forest soil harbors diverse microbial communities with decisive roles in ecosystem processes. Vegetation shift from needleleaf to broadleaf species is occurring across the globe due to climate change and anthropogenic activities, potentially change forest soil microbial communities and C cycle. However, our knowledge on the impact of such vegetation shift on soil microbial community and activities, and its consequences on forest soil C dynamics are still not well established. Here, we examined the seasonal variation of soil CO₂ emission, soil extracellular enzyme activities (EEAs), and soil bacterial, fungal communities in subtropical forest from broadleaf, needleleaf, and mixed stands. In addition, soil CO₂ emission and soil EEAs were measured in temperate forest during the growing season. Soil organic matter (SOM) content significantly differs between broadleaf and needleleaf forests and primarily distinguish various soil chemical and microbial characteristics. Significantly higher EEAs and soil CO₂ emission in broadleaf forest compared to needleleaf forest were observed both in subtropical and temperate forests. The relative abundance of Basidiomycota positively correlated with SOM and EEAs and indirectly increase soil CO₂ emission whereas the relative abundance of Ascomycota exhibits opposite trend, suggesting that soil fungal communities play a key role in determining the different microbial activities between broadleaf and needleleaf stands. The temperature sensitivity of soil CO₂ emission was significantly higher in broadleaf forest compared to needleleaf forest, further suggesting that the soil organic carbon in broadleaf forests is more vulnerable to warming.

Insights into microbial interactive mechanism regulating dissimilatory nitrate reduction processes in riparian freshwater aquaculture sediments

Aquaculture can substantially alter the accumulation and cycling of nutrients in sediments. However, the microbial mechanisms mediating sediment dissimilatory nitrate (NO₃^-) reduction in freshwater aquaculture ponds are still unclear, which rule the removal and retention of N element. In the present study, three microbial NO₃^- reduction processes in riparian aquaculture pond sediments (i.e., crab, shrimp and fish ponds) and natural freshwater sediments (i.e., lakes and rivers) were investigated via isotopic tracing and molecular analyses. The potential rates of denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) significantly increased in the aquaculture ponds compared with the natural freshwaters. Denitrification contributed 90.40-94.22% to the total NO₃^- reduction (product as N₂), followed by 2.49-5.82% of anammox (product as N₂) and 2.09-5.18% of DRNA (product as NH₄⁺). The availability of C and N substrates, rather than functional gene abundance, regulated the activities of NO₃^- reductions and microbiome composition. Microbial mechanism based on network analysis indicated that heterotrophic denitrifiers and DNRA bacteria (e.g., Bacillus, Micromonospora, Mycobacterium and Brachybacterium) determined the community structure and function for N conversions in aquaculture ponds, whereas the such microbial network in natural freshwater sediments was manipulated by autotrophic denitrifiers (e.g., Desulfuromonas, Polaromonas, Solitalea). Collectively, this study provides an in-depth exploration of microbial nitrogen removal in freshwater aquaculture areas and supports management strategies for N pollution caused by reclamation for aquaculture in riparian zones.

Global patterns and abiotic drivers of ecosystem multifunctionality in dominant natural ecosystems

The potential patterns and processes of ecosystem multifunctionality (EMF) across global ecosystems are largely unknown, which limits our understanding of how ecosystems respond to drivers. Here we compile a global dataset that consists of 973 unique sites across the forest, grassland, and shrub ecosystems. We identify a critical global pattern of hump-shaped EMF relationship with mean annual precipitation at a threshold of ∼671 mm, where low and high precipitation patterns are discriminated. We find that climatic and soil factors jointly drive the EMF in low precipitation areas, and climatic factors dominate the EMF in high precipitation regions. However, when comparing across the three dominant ecosystems and precipitation regions, the key driver in EMF differs substantially. Specifically, climatic and soil factors dominate the EMF of low and high precipitation regions across forest ecosystems, respectively. Climatic drivers dominate the EMF under different precipitation conditions across grassland and shrub ecosystems. Overall, our findings highlight the importance of climatic and soil drivers on EMF, which should be considered in ecosystem stability models in response to global climate and land-use change scenarios.

Biotic Interactions as Mediators of Context-Dependent Biodiversity-Ecosystem Functioning Relationships

Biodiversity drives the maintenance and stability of ecosystem functioning as well as many of nature’s benefits to people, yet people cause substantial biodiversity change. Despite broad consensus about a positive relationship between biodiversity and ecosystem functioning (BEF), the underlying mechanisms and their context-dependencies are not well understood. This proposal, submitted to the European Research Council (ERC), aims at filling this knowledge gap by providing a novel conceptual framework for integrating biotic interactions across guilds of organisms, i.e. plants and mycorrhizal fungi, to explain the ecosystem consequences of biodiversity change. The overarching hypothesis is that EF increases when more tree species associate with functionally dissimilar mycorrhizal fungi. Taking a whole-ecosystem perspective, we propose to explore the role of tree-mycorrhiza interactions in driving BEF across environmental contexts and how this relates to nutrient dynamics. Given the significant role that mycorrhizae play in soil nutrient and water uptake, BEF relationships will be investigated under normal and drought conditions. Resulting ecosystem consequences will be explored by studying main energy channels and ecosystem multifunctionality using food web energy fluxes and by assessing carbon storage. Synthesising drivers of biotic interactions will allow us to understand context-dependent BEF relationships. This interdisciplinary and integrative project spans the whole gradient from local-scale process assessments to global relationships by building on unique experimental infrastructures like the MyDiv Experiment, iDiv Ecotron and the global network TreeDivNet, to link ecological mechanisms to reforestation initiatives. This innovative combination of basic scientific research with real-world interventions links trait-based community ecology, global change research and ecosystem ecology, pioneering a new generation of BEF research and represents a significant step towards implementing BEF theory for human needs.

Phylotype diversity within soil fungal functional groups drives ecosystem stability

Soil fungi are fundamental to plant productivity, yet their influence on the temporal stability of global terrestrial ecosystems, and their capacity to buffer plant productivity against extreme drought events, remain uncertain. Here we combined three independent global field surveys of soil fungi with a satellite-derived temporal assessment of plant productivity, and report that phylotype richness within particular fungal functional groups drives the stability of terrestrial ecosystems. The richness of fungal decomposers was consistently and positively associated with ecosystem stability worldwide, while the opposite pattern was found for the richness of fungal plant pathogens, particularly in grasslands. We further demonstrated that the richness of soil decomposers was consistently positively linked with higher resistance of plant productivity in response to extreme drought events, while that of fungal plant pathogens showed a general negative relationship with plant productivity resilience/resistance patterns. Together, our work provides evidence supporting the critical role of soil fungal diversity to secure stable plant production over time in global ecosystems, and to buffer against extreme climate events.

Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China

Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO₃^-, NH₄⁺, DOC/NO₃^-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.

Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant-associated microbiomes to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimized and how their effects are mediated. Here, we sought to enhance tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.

Aridity-driven shift in biodiversity-soil multifunctionality relationships

Relationships between biodiversity and multiple ecosystem functions (that is, ecosystem multifunctionality) are context-dependent. Both plant and soil microbial diversity have been reported to regulate ecosystem multifunctionality, but how their relative importance varies along environmental gradients remains poorly understood. Here, we relate plant and microbial diversity to soil multifunctionality across 130 dryland sites along a 4,000 km aridity gradient in northern China. Our results show a strong positive association between plant species richness and soil multifunctionality in less arid regions, whereas microbial diversity, in particular of fungi, is positively associated with multifunctionality in more arid regions. This shift in the relationships between plant or microbial diversity and soil multifunctionality occur at an aridity level of ∼0.8, the boundary between semiarid and arid climates, which is predicted to advance geographically ∼28% by the end of the current century. Our study highlights that biodiversity loss of plants and soil microorganisms may have especially strong consequences under low and high aridity conditions, respectively, which calls for climate-specific biodiversity conservation strategies to mitigate the effects of aridification.

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

Competitive and facilitative interactions influence bacterial community composition, diversity and functioning. However, the role of genetic diversity for determining interactions between coexisting strains of the same, or closely related, species remains poorly understood. Here, we investigated the type (facilitative/inhibitory) and potential underlying mechanisms of pairwise interactions between 24 genetically diverse bacterial strains belonging to three genospecies (gsA,C,E) of the Rhizobium leguminosarum species complex. Interactions were determined indirectly, based on secreted compounds in cell-free supernatants, and directly, as growth inhibition in cocultures. We found supernatants mediated both facilitative and inhibitory interactions that varied greatly between strains and genospecies. Overall, gsE strains indirectly suppressed growth of gsA strains, while their own growth was facilitated by other genospecies' supernatants. Similar genospecies-level patterns were observed in direct competition, where gsA showed the highest susceptibility and gsE the highest inhibition capacity. At the genetic level, increased gsA susceptibility was associated with a non-random distribution of quorum sensing and secondary metabolite genes across genospecies. Together, our results suggest that genetic variation is associated with facilitative and competitive interactions, which could be important ecological mechanisms explaining R. leguminosarum diversity.

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes

Plant pathogenic bacteria cause high crop and economic losses to human societies1-3. Infections by such pathogens are challenging to control as they often arise through complex interactions between plants, pathogens and the plant microbiome4,5. Experimental studies of this natural ecosystem at the microbiome-wide scale are rare, and consequently we have a poor understanding of how the taxonomic and functional microbiome composition and the resulting ecological interactions affect pathogen growth and disease outbreak. Here, we combine DNA-based soil microbiome analysis with in vitro and in planta bioassays to show that competition for iron via secreted siderophore molecules is a good predictor of microbe-pathogen interactions and plant protection. We examined the ability of 2,150 individual bacterial members of 80 rhizosphere microbiomes, covering all major phylogenetic lineages, to suppress the bacterium Ralstonia solanacearum, a global phytopathogen capable of infecting various crops6,7. We found that secreted siderophores altered microbiome-pathogen interactions from complete pathogen suppression to strong facilitation. Rhizosphere microbiome members with growth-inhibitory siderophores could often suppress the pathogen in vitro as well as in natural and greenhouse soils, and protect tomato plants from infection. Conversely, rhizosphere microbiome members with growth-promotive siderophores were often inferior in competition and facilitated plant infection by the pathogen. Because siderophores are a chemically diverse group of molecules, with each siderophore type relying on a compatible receptor for iron uptake8-12, our results suggest that pathogen-suppressive microbiome members produce siderophores that the pathogen cannot use. Our study establishes a causal mechanistic link between microbiome-level competition for iron and plant protection and opens promising avenues to use siderophore-mediated interactions as a tool for microbiome engineering and pathogen control.

Diversity Manipulation of Psychrophilic Bacterial Consortia for Improved Biological Treatment of Medium-Strength Wastewater at Low Temperature

Psychrophilic bacteria are valuable biocatalysts to develop robust bioaugmentation formulations for enhanced wastewater treatment at low temperatures or fluctuating temperature conditions. Here, using different biodiversity indices [based on species richness (SR), phylogenetic diversity (PD) and functional diversity (FD)], we studied the effects of microbial diversity of artificial bacterial consortia on the biomass gross yields (measured through OD₆₀₀) and removal efficiency of soluble chemical oxygen demand (mg sCOD removed/mg sCOD introduced) in synthetic, medium-strength wastewater. We built artificial consortia out of one to six bacterial strains isolated at 4°C through combinatorial biodiversity experiments. Increasing species richness resulted in improved sCOD removal efficiency (i.e., 0.266 ± 0.146, 0.542 ± 0.155, 0.742 ± 0.136, 0.822 ± 0.019 for mono-, tri-, penta-and hexacultures, respectively) and higher biomass gross yields (i.e., 0.065 ± 0.052, 0.132 ± 0.046, 0.173 ± 0.049, 0.216 ± 0.019 for mono-, tri-, penta,- and hexacultures, respectively). This positive relationship between biodiversity, sCOD removal and biomass gross yield was also observed when considering metabolic profiling (functional diversity) or evolutionary relationships (phylogenetic diversity). The positive effect of biodiversity on sCOD removal efficiency could be attributed to the selection of a particular, best-performing species (i.e., Pedobacter sp.) as well as complementary use of carbon resources among consortia members (i.e., complementarity effects). Among the biodiversity indices, PD diversity metrics explained higher variation in sCOD removal than SR and FD diversity metrics. For a more effective bioaugmentation, our results stress the importance of using phylogenetically diverse consortia, with an increased degradation ability, instead of single pure cultures. Moreover, PD could be used as an assembly rule to guide the composition of mixed cultures for wastewater bioaugmentation under psychrophilic conditions.

Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development

The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the development of microbial life history and community-level species interaction patterns that emerge during plant development. We use microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance. We show that the rhizosphere microbiome assembles from pioneer assemblages of species with random resource overlap into high-density, functionally complementary climax communities at later stages. During plant growth, fast-growing species were further replaced by antagonistic and stress-tolerant ones. Using synthetic consortia isolated from different plant growth stages, we demonstrate that the high functional diversity of 'climax' microbiomes leads to a better resistance to bacterial pathogen invasion. By demonstrating that different life-history strategies prevail at different plant growth stages and that community-level processes may supersede the importance of single species, we provide a new toolbox to understand microbiome assembly and steer its functionality at a community level.

Bacterial community richness shifts the balance between volatile organic compound-mediated microbe-pathogen and microbe-plant interactions

Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant-bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to 12 strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe-pathogen and microbe-plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems.

Microbial diversity-ecosystem function relationships across environmental gradients

In light of increasing anthropogenic pressures on ecosystems around the globe, the question how biodiversity change of organisms in the critical zone between Earth’s canopies and bedrock relates to ecosystem functions is an urgent issue, as human life relies on these functions. Particularly, soils play vital roles in nutrient cycling, promotion of plant growth, water purification, litter decomposition, and carbon storage, thereby securing food and water resources and stabilizing the climate. Soil functions are carried to a large part by complex communities of microorganisms, such as bacteria, archaea, fungi and protists. The assessment of microbial diversity and the microbiome's functional potential continues to pose significant challenges. Next generation sequencing offers some of the most promising tools to help shedding light on microbial diversity-function relationships. Studies relating microbial diversity and ecosystem functions are rare, particularly those on how this relationship is influenced by environmental gradients. The proposed project focuses on decomposition as one of the most important microbial soil ecosystem functions. The researchers from the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig combine an unparalleled range of expertise from next generation sequencing- based analysis of microbial communities (“meta-omics”) to soil ecology and biodiversity-ecosystem function research. This consortium will make use of soil samples from large international networks to assess microbial diversity both at the taxonomic and functional level and across the domains of life. By linking microbial diversity to functional measurements of decomposition and environmental gradients, the proposed project aims to achieve a comprehensive scale-independent understanding of environmental drivers and anthropogenic effects on the structural and functional diversity of microbial communities and subsequent consequences for ecosystem functioning.

More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

Biotic factors drive distinct DNRA potential rates and contributions in typical Chinese shallow lake sediments

Dissimilatory nitrate reduction to ammonia (DNRA) is an important nitrate reduction pathway in lake sediments; however, little is known about the biotic factors driving the DNRA potential rates and contributions to the fate of nitrate. This study reports the first investigation of DNRA potential rates and contributions in lake sediments linked to DNRA community structures. The results of ¹⁵N isotope-tracing incubation experiments showed that 12 lakes had distinct DNRA potentials, which could be clustered into 2 groups, one with higher DNRA potentials (rates varied from 2.7 to 5.0 nmol N g^-1 h^-1 and contributions varied from 27.5% to 35.4%) and another with lower potentials (rates varied from 0.6 to 2.3 nmol N g^-1 h^-1 and contributions varied from 8.1% to 22.8%). Sediment C/N and the abundance of the nrfA gene were the key abiotic and biotic factors accounting for the distinct DNRA potential rates, respectively. A high-throughput sequencing analysis of the nrfA gene revealed that the sediment C/N could also affect the DNRA potential rates by altering the ecological patterns of the DNRA community composition. In addition, the interactions between the DNRA community and the denitrifying community were found to be obviously different in the two groups. In the higher DNRA potential group, the DNRA community mainly interacted with heterotrophic denitrifiers, while in the lower DNRA potential group, both heterotrophic and sulfur-driven autotrophic denitrifiers might cooperate with the DNRA community. The present study highlighted the role of the sulfur-driven nitrate reduction pathway in C-limited sediments, which has always been overlooked in freshwater environments, and gave new insights into the molecular mechanism influencing the fate of nitrate.

Sediment pH, not the bacterial diversity, determines Escherichia coli O157:H7 survival in estuarine sediments

Shiga toxin-producing Escherichia coli (E. coli) O157:H7 is recognized as a hazardous microorganism in the environment. Its longer survival might contribute to higher contamination risk. In this study, E. coli O157:H7 survival in estuarine sediments collected from south Hangzhou Bay was investigated. The survival time of E. coli O157:H7 in estuarine sediments increased with the distance to the water-land junction. Sediment pH was the most important factor in regulating E. coli O157:H7 survival in estuarine sediments. In addition, sediment nutrients and texture also played significant roles in the survival of E. coli O157:H7 in the sediments. On the other hand, bacterial diversity as determined by the alpha-diversity index had no significant effect on E. coli O157:H7 survival. However, specific families of bacteria were closely associated with E. coli O157:H7 survival in the sediments. Remarkably, some potential bacterial groups, e.g., the Desulfobacteraceae, Desulfobulbaceae and Desulfarculaceae families, which are mainly involved in the sulfur cycle, showed significant negative correlation with the E. coli O157:H7 survival in the sediments. On the whole, abiotic factors showed greater effects on E. coli O157:H7 survival in the test sediments than the bacterial community. Our findings provide a comprehensive understanding of E. coli O157:H7 survival and regulatory factors in estuarine sediments, establishing foundation for the prevention of pathogen contamination.

The Dynamic of a River Model Bacterial Community in Two Different Media Reveals a Divergent Succession and an Enhanced Growth of Most Strains Compared to Monocultures

The dynamic of a community of 20 bacterial strains isolated from river water was followed in R2 broth and in autoclaved river water medium for 27 days in batch experiments. At an early stage of incubation, a fast-growing specialist strain, Acinetobater sp., dominated the community in both media. Later on, the community composition in both media diverged but was highly reproducible across replicates. In R2, several strains previously reported to degrade multiple simple carbon sources prevailed. In autoclaved river water, the community was more even and became dominated by several strains growing faster or exclusively in that medium. Those strains have been reported in the literature to degrade complex compounds. Their growth rate in the community was 1.5- to 7-fold greater than that observed in monoculture. Furthermore, those strains developed simultaneously in the community. Together, our results suggest the existence of cooperative interactions within the community incubated in autoclaved river water.

Colour polymorphism influences species' range and extinction risk

Polymorphisms in a population are expected to increase the growth rate and the stability of the population, leading to the expansion of geographical distribution and mitigation of extinction risk of a species. However, the generality of such ecological consequences of colour polymorphism remains uncertain. Here, via a comparative approach, we assessed whether colour polymorphisms influence climatic niche breadth and extinction risk in some groups of damselflies, butterflies and vertebrates. The climatic niche breadth was greater, and extinction risk was lower in polymorphic species than in monomorphic species in all taxa analysed. The results suggest that colour polymorphism facilitates range expansion and species persistence.

A multitrophic perspective on biodiversity-ecosystem functioning research

Concern about the functional consequences of unprecedented loss in biodiversity has prompted biodiversity-ecosystem functioning (BEF) research to become one of the most active fields of ecological research in the past 25 years. Hundreds of experiments have manipulated biodiversity as an independent variable and found compelling support that the functioning of ecosystems increases with the diversity of their ecological communities. This research has also identified some of the mechanisms underlying BEF relationships, some context-dependencies of the strength of relationships, as well as implications for various ecosystem services that mankind depends upon. In this paper, we argue that a multitrophic perspective of biotic interactions in random and non-random biodiversity change scenarios is key to advance future BEF research and to address some of its most important remaining challenges. We discuss that the study and the quantification of multitrophic interactions in space and time facilitates scaling up from small-scale biodiversity manipulations and ecosystem function assessments to management-relevant spatial scales across ecosystem boundaries. We specifically consider multitrophic conceptual frameworks to understand and predict the context-dependency of BEF relationships. Moreover, we highlight the importance of the eco-evolutionary underpinnings of multitrophic BEF relationships. We outline that FAIR data (meeting the standards of findability, accessibility, interoperability, and reusability) and reproducible processing will be key to advance this field of research by making it more integrative. Finally, we show how these BEF insights may be implemented for ecosystem management, society, and policy. Given that human well-being critically depends on the multiple services provided by diverse, multitrophic communities, integrating the approaches of evolutionary ecology, community ecology, and ecosystem ecology in future BEF research will be key to refine conservation targets and develop sustainable management strategies.

Ecosystem responses to exotic earthworm invasion in northern North American forests

Earth is experiencing a substantial loss of biodiversity at the global scale, while both species gains and losses are occurring at local and regional scales. The influence of these nonrandom changes in species distributions could profoundly affect the functioning of ecosystems and the essential services that they provide. However, few experimental tests have been conducted examining the influence of species invasions on ecosystem functioning. Even fewer have been conducted using invasive ecosystem engineers, which can have disproportionately strong influence on native ecosystems relative to their own biomass. The invasion of exotic earthworms is a prime example of an ecosystem engineer that is influencing many ecosystems around the world. In particular, European earthworm invasions of northern North American forests cause simultaneous species gains and losses with significant consequences for essential ecosystem processes like nutrient cycling and crucial services to humanity like soil erosion control and carbon sequestration. Exotic earthworms are expected to select for specific traits in communities of soil microorganisms (fast-growing bacteria species), soil fauna (promoting the bacterial energy channel), and plants (graminoids) through direct and indirect effects. This will accelerate some ecosystem processes and decelerate others, fundamentally altering how invaded forests function. This project aims to investigate ecosystem responses of northern North American forests to earthworm invasion. Using a novel, synthetic combination of field observations, field experiments, lab experiments, and meta-analyses, the proposed work will be the first systematic examination of earthworm effects on (1) plant communities and (2) soil food webs and processes. Further, (3) effects of a changing climate (warming and reduced summer precipitation) on earthworm performance will be investigated in a unique field experiment designed to predict the future spread and consequences of earthworm invasion in North America. By assessing the soil chemical and physical properties as well as the taxonomic (e.g., by the latest next-generation sequencing techniques) and functional composition of plant, soil microbial and animal communities and the processes they drive in four forests, work packages I-III take complementary approaches to derive a comprehensive and generalizable picture of how ecosystems change in response to earthworm invasion. Finally, in work package IV meta-analyses will be used to integrate the information from work packages I-III and existing literature to investigate if earthworms cause invasion waves, invasion meltdowns, habitat homogenization, and ecosystem state shifts. Global data will be synthesized to test if the relative magnitude of effects differs from place to place depending on the functional dissimilarity between native soil fauna and exotic earthworms. Moving from local to global scale, the present proposal examines the influence of earthworm invasions on biodiversity-ecosystem functioning relationships from an aboveground-belowground perspective in natural settings. This approach is highly innovative as it utilizes the invasion by exotic earthworms as an exciting model system that links invasion biology with trait-based community ecology, global change research, and ecosystem ecology, pioneering a new generation of biodiversity-ecosystem functioning research.

Interactions in self-assembled microbial communities saturate with diversity

How the diversity of organisms competing for or sharing resources influences community function is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we defined relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), positive and negative effects of interactions were both weak, while at moderate richness (12–26 taxa), community resource uptake increased but the carbon use efficiency decreased. Finally, beyond 26 taxa, the effect of interactions on community function saturated and further diversity increases did not affect community function. Although more diverse communities had overall greater access to resources, on average individual taxa within these communities had lower resource availability and reduced carbon use efficiency. Our results thus suggest competition and complementation simultaneously increase with diversity but both saturate at a threshold.

Balanced genetic diversity improves population fitness

Although genetic diversity within a population is suggested to improve population-level fitness and productivity, the existence of these effects is controversial because empirical evidence for an ecological effect of genetic diversity and the underlying mechanisms is scarce and incomplete. Here, we show that the natural single-gene behavioural polymorphism (Rover and sitter) in Drosophila melanogaster has a positive effect on population fitness. Our simple numerical model predicted that the fitness of a polymorphic population would be higher than that expected with two monomorphic populations, but only under balancing selection. Moreover, this positive diversity effect of genetic polymorphism was attributable to a complementarity effect, rather than to a selection effect. Our empirical tests using the behavioural polymorphism in D. melanogaster clearly supported the model predictions. These results provide direct evidence for an ecological effect of genetic diversity on population fitness and its condition dependence.

Biodiversity-ecosystem function relationships on bodies and in buildings

Biodiversity underpins the function of ecosystems. Here we discuss how biodiversity–ecosystem function theory could apply to our bodies and buildings, outline practical applications and call for further research.

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured "master" traits (like body size) might provide good predictions of overall trait differentiation.

Elevated tropospheric CO2 and O3 concentrations impair organic pollutant removal from grassland soil

The concentrations of tropospheric CO₂ and O₃ have been rising due to human activities. These rising concentrations may have strong impacts on soil functions as changes in plant physiology may lead to altered plant-soil interactions. Here, the effects of eCO₂ and eO₃ on the removal of polycyclic aromatic hydrocarbon (PAH) pollutants in grassland soil were studied. Both elevated CO₂ and O₃ concentrations decreased PAH removal with lowest removal rates at elevated CO₂ and elevated O₃ concentrations. This effect was linked to a shift in soil microbial community structure by structural equation modeling. Elevated CO₂ and O₃ concentrations reduced the abundance of gram-positive bacteria, which were tightly linked to soil enzyme production and PAH degradation. Although plant diversity did not buffer CO₂ and O₃ effects, certain soil microbial communities and functions were affected by plant communities, indicating the potential for longer-term phytoremediation approaches. Results of this study show that elevated CO₂ and O₃ concentrations may compromise the ability of soils to degrade organic pollutants. On the other hand, the present study also indicates that the targeted assembly of plant communities may be a promising tool to shape soil microbial communities for the degradation of organic pollutants in a changing world.

Community structure of rare methanogenic archaea: insight from a single functional group

The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups.

Positive diversity-functioning relationships in model communities of methanotrophic bacteria

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH₄ at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH₄ consumption and community size were positively correlated. The temporal CH₄ consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.

Effect of Simulated Climate Warming on the Ectomycorrhizal Fungal Community of Boreal and Temperate Host Species Growing Near Their Shared Ecotonal Range Limits

Ectomycorrhizal (ECM) fungi can influence the establishment and performance of host species by increasing nutrient and water absorption. Therefore, understanding the response of ECM fungi to expected changes in the global climate is crucial for predicting potential changes in the composition and productivity of forests. While anthropogenic activity has, and will continue to, cause global temperature increases, few studies have investigated how increases in temperature will affect the community composition of ectomycorrhizal fungi. The effects of global warming are expected to be particularly strong at biome boundaries and in the northern latitudes. In the present study, we analyzed the effects of experimental manipulations of temperature and canopy structure (open vs. closed) on ectomycorrhizal fungi identified from roots of host seedlings through 454 pyrosequencing. The ecotonal boundary site selected for the study was between the southern boreal and temperate forests in northern Minnesota, USA, which is the southern limit range for Picea glauca and Betula papyrifera and the northern one for Pinus strobus and Quercus rubra. Manipulations that increased air and soil temperature by 1.7 and 3.4 °C above ambient temperatures, respectively, did not change ECM richness but did alter the composition of the ECM community in a manner dependent on host and canopy structure. The prediction that colonization of boreal tree species with ECM symbionts characteristic of temperate species would occur was not substantiated. Overall, only a small proportion of the ECM community appears to be strongly sensitive to warming.

Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates

Symbiotic bacterial communities can protect their hosts from infection by pathogens. Treatment of wild individuals with protective bacteria (probiotics) isolated from hosts can combat the spread of emerging infectious diseases. However, it is unclear whether candidate probiotic bacteria can offer consistent protection across multiple isolates of globally distributed pathogens. Here, we use the lethal amphibian fungal pathogen Batrachochytrium dendrobatidis to investigate whether probiotic richness (number of bacteria) or genetic distance among consortia members influences broad-scale in vitro inhibitory capabilities of probiotics across multiple isolates of the pathogen. We show that inhibition of multiple pathogen isolates by individual bacteria is rare, with no systematic pattern among bacterial genera in ability to inhibit multiple B. dendrobatidis isolates. Bacterial consortia can offer stronger protection against B. dendrobatidis compared to single strains, and this tended to be more pronounced for consortia containing multiple genera compared with those consisting of bacteria from a single genus (i.e., with lower genetic distance), but critically, this effect was not uniform across all B. dendrobatidis isolates. These novel insights have important implications for the effective design of bacterial probiotics to mitigate emerging infectious diseases.

Fungal community structure of fallen pine and oak wood at different stages of decomposition in the Qinling Mountains, China

Historically, intense forest hazards have resulted in an increase in the quantity of fallen wood in the Qinling Mountains. Fallen wood has a decisive influence on the nutrient cycling, carbon budget and ecosystem biodiversity of forests, and fungi are essential for the decomposition of fallen wood. Moreover, decaying dead wood alters fungal communities. The development of high-throughput sequencing methods has facilitated the ongoing investigation of relevant molecular forest ecosystems with a focus on fungal communities. In this study, fallen wood and its associated fungal communities were compared at different stages of decomposition to evaluate relative species abundance and species diversity. The physical and chemical factors that alter fungal communities were also compared by performing correspondence analysis according to host tree species across all stages of decomposition. Tree species were the major source of differences in fungal community diversity at all decomposition stages, and fungal communities achieved the highest levels of diversity at the intermediate and late decomposition stages. Interactions between various physical and chemical factors and fungal communities shared the same regulatory mechanisms, and there was no tree species-specific influence. Improving our knowledge of wood-inhabiting fungal communities is crucial for forest ecosystem conservation.

The microbial community in decaying fallen logs varies with critical period in an alpine forest

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor.