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Soil microorganisms are known to significantly contribute to climate change through soil carbon (C) cycle feedbacks. However, it is challenging to incorporate these feedbacks into predictions of future patterns of terrestrial C cycling, largely because of the vast diversity of soil microorganisms and their responses to environmental conditions. Here, we show that the composition of the bacterial community can provide information about the microbial community-level thermal response (MCTR), which drives ecosystem-scale soil C-climate feedbacks. The dominant taxa from 169 sites representing a gradient from tropical to boreal forest mainly belonged to the phyla Actinobacteria and Acidobacteria. Moreover, we show that the MCTR in warm biomes and acidic soils was linked primarily to bacteria, whereas the MCTR in cold biomes and alkaline soils was primarily associated with fungi. Our results provide strong empirical evidence of linkages between microbial composition and the MCTR across a wide range of forests, and suggest the importance of specific microorganisms in regulating soil C-climate feedbacks.

The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach is also applied to eukaryotic marker genes to characterize the diversity and distribution of soil eukaryotes. However, understanding the properties and limitations of eukaryotic marker sequences is essential for correctly analysing, interpreting, and synthesizing the resulting data. Here, we illustrate several biases from sequencing data that affect measurements of biodiversity that arise from variation in morphology, taxonomy and phylogeny between organisms, as well as from sampling designs. We recommend analytical approaches to overcome these limitations, and outline how the benchmarking and standardization of sequencing protocols may improve the comparability of the data.

Despite knowledge of the interaction between climate change factors significant uncertainty exists concerning the individual and interactive effects of elevated carbon dioxide (eCO2) and elevated temperature (eT) on the soil microbiome and function. Here we examine the individual and interactive effects of eCO2 and eT on tree growth, soil respiration (Rsoil), biomass, structural and functional composition of microbial community, nitrogen (N) mineralisation and N availability in a whole tree chamber experiment. Eucalyptus globulus plants were grown from seedling to ca. 10 m tall for 15 months in a nutrient-poor sandy soil under ambient and elevated (+ 240 ppm) atmospheric CO2 concentrations combined with ambient or elevated temperatures (+ 3 °C) in a full factorial design. Plant growth was strongly stimulated under eCO2, but eT had little impact on any measured plant property. In contrast, Rsoil was not consistently affected by eCO2 or eT, but correlated strongly with root and leaf biomass. The response of N-mineralisation and nutrient availability to eCO2 and eT varied across time, and available N correlated strongly with plant height. Further, the C:N ratio of the microbial biomass and leaves were both higher under eCeT treatment. However, these functional measures were not significantly linked to either structural or functional diversity of the soil microbiome. Taken together, these results suggest that in this low-nutrient soil, belowground processes are principally driven by aboveground productivity. Our work provides novel insight into mechanisms underlying above- and belowground response to climate change, and the potential to sequester C in a low-nutrient status soil under future climatic conditions may be limited .

The phyllosphere harbors diverse microbial communities that influence ecosystem functioning. Emerging evidence suggests that plants impaired in genetic networks harbor an altered microbiome and develop dysbiosis in the phyllosphere, which pinpoints plant genetics as a key driver of the phyllosphere microbiome assembly and links the phyllosphere microbiome to plant health.

Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions. In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.

Plants are subjected to diverse biotic and abiotic stresses in life. These can induce changes in transcriptomics and metabolomics, resulting in changes to root and leaf exudates and, in turn, altering the plant-associated microbial community. Emerging evidence demonstrates that changes, especially the increased abundance of commensal microbes following stresses, can be beneficial for plant survival and act as a legacy, enhancing offspring fitness. However, outstanding questions remain regarding the microbial role in plant defense, many of which may now be answered utilizing a novel synthetic community approach. In this article, building on our current understanding on stress-induced changes in plant microbiomes, we propose a 'DefenseBiome' concept that informs the design and construction of beneficial microbial synthetic communities for improving fundamental understanding of plant-microbial interactions and the development of plant probiotics.

Malaria infection induces complex and diverse immune responses. To elucidate the mechanisms underlying host–parasite interaction, we performed a genetic screen during early (24 h) Plasmodium yoelii infection in mice and identified a large number of interacting host and parasite genes/loci after transspecies expression quantitative trait locus (Ts-eQTL) analysis. We next investigated a host E3 ubiquitin ligase gene (March1) that was clustered with interferon (IFN)-stimulated genes (ISGs) based on the similarity of the genome-wide pattern of logarithm of the odds (LOD) scores (GPLS). March1 inhibits MAVS/STING/TRIF-induced type I IFN (IFN-I) signaling in vitro and in vivo. However, in malaria-infected hosts, deficiency of March1 reduces IFN-I production by activating inhibitors such as SOCS1, USP18, and TRIM24 and by altering immune cell populations. March1 deficiency increases CD86(+)DC (dendritic cell) populations and levels of IFN-γ and interleukin 10 (IL-10) at day 4 post infection, leading to improved host survival. T cell depletion reduces IFN-γ level and reverse the protective effects of March1 deficiency, which can also be achieved by antibody neutralization of IFN-γ. This study reveals functions of MARCH1 (membrane-associated ring-CH–type finger 1) in innate immune responses and provides potential avenues for activating antimalaria immunity and enhancing vaccine efficacy.

Our knowledge of host-associated microorganisms and their role in host functions is rapidly evolving. Stress-affected plants assemble beneficial microbes in their rhizosphere to maximize survival and growth. Similarly, insects have gut microbiomes that extend their functional repertoire in fighting stress. A strong microbial linkage between soil, plants, and pollinators is emerging and this can influence pollination services and overall ecosystem health. Yet, the nature of microbial interactions between different ecosystem components remains poorly understood. Here we highlight the acquisition pathways of beneficial microbes and their functions in protecting hosts against stress. By adopting a new 'eco-holobiont' approach, which explicitly incorporates biotic feedbacks, we can significantly expand our ecological understanding and better develop sustainable environmental management.

Cystic fibrosis is an autosomal-recessive disease that is caused by a mutant CFTR (cystic fibrosis transmembrane conductance regulator) gene and is characterized by chronic bacterial lung infections and inflammation. Complementation with functional CFTR normalizes anion transport across the airway surface. Adeno-associated virus (AAV) is a useful vector for gene therapy because of its low immunogenicity and ability to persist for months to years. However, because its episomal expression may decrease after cell division, readministration of the AAV vector may be required. To overcome this, we designed an integrating AAV-based CFTR-expressing vector, termed piggyBac (PB)/AAV, carrying CFTR flanked by the terminal repeats of the piggyBac transposon. With codelivery of the piggyBac transposase, PB/AAV can integrate into the host genome. Because of the packaging constraints of AAV, careful consideration was required to ensure that the vector would package and express its CFTR cDNA cargo. In this short-term study, PB/AAV-CFTR was aerosolized to the airways of CF pigs in the absence of the transposase. Two weeks later, transepithelial Cl(−) current was restored in freshly excised tracheal and bronchial tissue. Additionally, we observed an increase in tracheal airway surface liquid pH and bacterial killing in comparison with untreated CF pigs. Airway surface liquid from primary airway cells cultured from treated CF pigs exhibited increased pH correlating with decreased viscosity. Together, these results show that complementing CFTR in CF pigs with PB/AAV rescues the anion transport defect in a large-animal CF model. Delivery of this integrating viral vector system to airway progenitor cells could lead to persistent, life-long expression in vivo.

Measles virus (MeV) is the most contagious human virus. Unlike most respiratory viruses, MeV does not directly infect epithelial cells upon entry in a new host. MeV traverses the epithelium within immune cells that carry it to lymphatic organs where amplification occurs. Infected immune cells then synchronously deliver large amounts of virus to the airways. However, our understanding of MeV replication in airway epithelia is limited. To model it, we use well-differentiated primary cultures of human airway epithelial cells (HAE) from lung donors. In HAE, MeV spreads directly cell-to-cell forming infectious centers that grow for ~3–5 days, are stable for a few days, and then disappear. Transepithelial electrical resistance remains intact during the entire course of HAE infection, thus we hypothesized that MeV infectious centers may dislodge while epithelial function is preserved. After documenting by confocal microscopy that infectious centers progressively detach from HAE, we recovered apical washes and separated cell-associated from cell-free virus by centrifugation. Virus titers were about 10 times higher in the cell-associated fraction than in the supernatant. In dislodged infectious centers, ciliary beating persisted, and apoptotic markers were not readily detected, suggesting that they retain functional metabolism. Cell-associated MeV infected primary human monocyte-derived macrophages, which models the first stage of infection in a new host. Single-cell RNA sequencing identified wound healing, cell growth, and cell differentiation as biological processes relevant for infectious center dislodging. 5-ethynyl-2’-deoxyuridine (EdU) staining located proliferating cells underneath infectious centers. Thus, cells located below infectious centers divide and differentiate to repair the dislodged infected epithelial patch. As an extension of these studies, we postulate that expulsion of infectious centers through coughing and sneezing could contribute to MeV’s strikingly high reproductive number by allowing the virus to survive longer in the environment and by delivering a high infectious dose to the next host., Author summary Measles virus (MeV) is a respiratory pathogen that infects millions worldwide each year. Although sometimes mischaracterized as an innocuous childhood disease, measles remains a leading cause of death for children under five. MeV is the most contagious human virus and requires vaccination rates above 90% to maintain herd immunity. Global decreases in vaccination rates over the past ten years contributed to recent, widespread MeV outbreaks. We uncover here a novel mechanism by which MeV exits the human airways that may explain why it is much more contagious than other viruses. We document that infected cells containing cell-associated virus detach en masse from the airway epithelial sheet. These dislodged infectious centers are metabolically active and can transmit infection to primary human monocyte-derived macrophages via cell-cell contact as efficiently as cell-free virus particles. Thus, cell-associated MeV could spread host-to-host and is a potentially vital strategy for efficient respiratory virus transmission.

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.

Grazing is a major driver of the composition of microbial communities, which play important roles in soil functioning. Mechanisms whereby grazing might regulate the spatial heterogeneity of microbial communities within ecological networks remain largely untested. We used network analysis to identify the impacts of increasing grazing intensity by livestock (cattle, sheep, goats), and native (kangaroos) and wild (rabbits) animals, on the spatial heterogeneity of the relative abundance of eight ecological clusters of co-occurring soil microbial taxa: four from Grasslands and four from Forests. Grazing effects on microbial spatial heterogeneity were strongly nuanced and depended on (1) plant community type, (2) herbivore type and (3) microbial identity. Microbial within-site spatial heterogeneity was greater in Grasslands than in Forests, and most effects of grazing on microbial spatial heterogeneity were in Forests, effecting three of the four Forest clusters, but only one Grassland cluster. The associations between grazing intensity and microbial heterogeneity were driven indirectly by changes in the spatial heterogeneity of litter cover and soil pH. For Grasslands, we also detected a direct effect of grazing intensity on the heterogeneity of particular microbial groups. Our results indicate that increased grazing intensity will advantage some microbial clusters but disadvantage others. Together, our study provides evidence that grazing intensity regulates the abundance and spatial heterogeneity of microbial communities within ecological networks. Knowing the potential effects of herbivores on different microbial clusters can help us predict the likely effects of grazing on soil function. This has important implications for future sustainable management and conservation policies.

The consequences of microbial functional diversity loss on key ecosystem processes remain debatable due to lack of firm evidence from observational or manipulative experiments for a link between microbial functional diversity and specialized ecosystem functions. Here, we conducted a microcosm experiment to test for a link between multiple microbial functional diversity (nitrifiers, methanotrophs and denitrifiers) and corresponding specialized soil functions (nitrate availability, methane, and nitrous oxide flux) using the dilution-to-extinction approach. We found that reductions in functional microbial diversity led to declines in the rates of specialized soil processes. Additionally, partial correlations provided statistical evidence that the correlations between microbial functional diversity and specialized functions were maintained after accounting for functional gene abundance (qPCR data) and substrate availability. Our analyses further suggested little redundancy in the relationship between microbial functional diversity and specialized ecosystem functions. Our work provides experimental evidence that microbial functional diversity is critical and directly linked to maintaining the rates of specialized soil processes in terrestrial ecosystems.

Rising global air temperature and atmospheric CO2 are expected to have considerable effects on soil nutrient cycling and plant productivity. Soil nitrification controlled by ammonia-oxidizing bacteria and archaea (AOB and AOA) communities plays a key role in contributing to plant nitrogen (N) availability; however, response of soil nitrification and functional microbial communities to climate change and subsequent consequences for crop yields remain largely unknown. Cotton productivity is a function of temperature and N availability under well-watered conditions. In general, cotton growth responds positively to elevated CO2, but simultaneous warming may offset benefits of rising CO2. In this study, cotton was used as a model system to elucidate the short-term response of soil nitrification and ammonia-oxidizing communities to elevated temperature and elevated CO2 using field-based environmentally-controlled chambers. Elevated temperature (ambient + 1.1 °C) altered the AOA community, while elevated temperature and elevated CO2 (ambient + 132 ppm) significantly increased soil nitrification rate and shifted AOB and AOA communities, but these effects depended on cotton developmental stages. Ammonia-oxidizing community abundance and structure were statistically correlated with nitrifying activity. Our findings suggest that climate change will positively affect soil nitrifying communities, leading to an increase in process rates and subsequent N availability, which is directly linked to crop productivity.

The signs of climate change are undeniable, and the inevitable impact for Earth and all its inhabitants is a serious concern. Ice is melting, sea levels are rising, biodiversity is declining, precipitation has increased, atmospheric levels of carbon dioxide and greenhouse gases are alarmingly high, and extreme weather conditions are becoming increasingly common. But what role do microorganisms have in this global challenge? In this Viewpoint article, several experts in the field discuss the microbial contributions to climate change and consider the effects of global warming, extreme weather, flooding and other consequences of climate change on microbial communities in the ocean and soil, on host-microbiota interactions and on the global burden of infectious diseases and ecosystem processes, and they explore open questions and research needs.

Mixed plantations of Eucalyptus and N2-fixing trees are ecologically beneficial because they stimulate organic matter cycling and increase carbon (C) and nitrogen (N) pools in the soil. However, the microbial mechanisms that contribute to the improvement of C and N dynamics remain poorly understood in managed forest ecosystems. Here, we evaluated interactions between the bacterial community and biological functions involved in C and N cycles in the soil and litter layers resulting from pure or mixed Eucalyptus grandis and Acacia mangium plantations. We hypothesized that the mixed plantations induce changes in the bacterial community that would drive increases in C and N pools in soil and litter layers. We established a field experiment with treatments including pure E. grandis without (E) and with nitrogen fertilization (E + N), pure A. mangium (A), and mixed E. grandis and A. mangium (E + A). Soil and litter from all treatments were sampled 27 and 39 months after planting. We evaluated the soil and litter bacterial community and biological functions involved in C and N cycles (i.e., microbial and enzyme activities, functional gene abundance, and soil-litter nutrient cycling). The treatments A and E + A showed an increase in C and N contents in the organic soil fractions. We found higher bacterial diversity and OTU richness in soil and litter, and higher nifH gene abundance in the soil under A and E + A, when compared to pure E. grandis (especially E + N) plantation. Our data suggest that the total N content influences the bacterial community structure of the litter, which undergoes alterations according to the treatment and forest age. Equally, Rhizobium, Bradyrhizobium and Sphingomonas showed a positive correlation with nifH and soil N. Our study provided evidence that changes in the microbial community in mixed A. mangium and E. grandis plantations is correlated with increased C and N cycling. These findings have implications for increased productivity and environmental sustainability, besides allowing for the optimization of mineral fertilization in forest plantations.

Little is known about the role of ant colonies in regulating the distribution and diversity of soil microbial communities across large spatial scales. Here, we conducted a survey across >1000 km in eastern Australia and found that, compared with surrounding bare soils, ant colonies promoted the richness (number of phylotypes) and relative abundance of rare taxa of fungi and bacteria. Ant nests were also an important reservoir for plant pathogens. Our study also provides a portfolio of microbial phylotypes only found in ant nests, and which are associated with high nutrient availability. Together, our work highlights the fact that ant nests are an important refugia for microbial diversity.

Measles virus (MeV) is the most contagious human virus, but we do not fully understand why. Unlike most respiratory viruses, MeV does not infect the airway epithelium immediately. MeV traverses the epithelium within immune cells that carry it to lymphatic organs where amplification occurs. Infected immune cells then synchronously deliver large amounts of virus to the airways. However, our understanding of MeV replication in airway epithelia is limited. To model it, we use well-differentiated primary cultures of human airway epithelial cells (HAE) from lung donors. In HAE, MeV spreads directly cell-to-cell forming infectious centers that grow for ∼3-5 days, are stable for a few days, and then disappear. Transepithelial electrical resistance remains intact during the entire course of HAE infection, thus we hypothesized that MeV infectious centers may slough off while preserving epithelial function. After documenting by confocal microscopy that infectious centers progressively detach from HAE, we recovered apical washes and separated cell-associated from cell-free virus by centrifugation. Virus titers were about 10 times higher in the cell-associated fraction than in the supernatant. In sloughed infectious centers, ciliary beating persisted and apoptotic markers were not readily detected, suggesting that they retain functional metabolism. Cell-associated MeV infected primary human monocyte-derived macrophages, modeling the first stage of infection in a new host. Single-cell RNA sequencing identified wound healing, cell growth, and cell differentiation as biological processes relevant for infectious center sloughing. 5-ethynyl-2’-deoxyuridine (EdU) staining located proliferating cells underneath infectious centers. Thus, cells located below infectious centers divide and differentiate to repair the extruded infected epithelial patch. As an extension of these studies, we postulate that expulsion of infectious centers through coughing and sneezing could contribute to MeV’s strikingly high reproductive number by allowing the virus to survive longer in the environment and by delivering a high infectious dose to the next host.AUTHOR SUMMARYMeasles virus (MeV) is a respiratory pathogen that infects millions worldwide each year. Although sometimes mischaracterized as an innocuous childhood disease, measles remains a leading cause of death for children under five. MeV is the most contagious human virus and requires vaccination rates above 90% to maintain herd immunity. Global decreases in vaccination rates over the past ten years contributed to recent, widespread MeV outbreaks. We uncover here a novel mechanism by which MeV exits the human airways that may explain why it is much more contagious than other viruses. We document that infected cells containing cell-associated virus sloughen massefrom the airway epithelial sheet. These expelled infectious centers are metabolically active and can transmit infection to primary human monocyte-derived macrophages more efficiently than cell-free virus particles. Thus, cell-associated MeV can transmit host-to-host, a new paradigm for efficient respiratory virus transmission.

BackgroundPlants live with diverse microbial communities which profoundly affect multiple facets of host performance such as nutrition acquisition, disease suppression and productivity, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils (rhizosphere and bulk soil), plant epiphytic and endophytic niches (phylloplane, rhizoplane, leaf and root endosphere), and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.ResultsOur results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartment niches than in soils, with the strongest effect in the phylloplane. Air (represented by fake plants) was an important source of phylloplane microbiomes which were co-shaped by both plant development and seasonal environmental factors. Further, we demonstrated that bacterial and fungal communities in plant compartment niches exhibited contrasting response to host developmental stages, with higher alpha diversity and stronger deterministic assembly within bacterial microbiomes at the early stage but a similar pattern within mycobiomes at the late stage. Moreover, we found that bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity and functional genes involved in nutrient provision and disease resistance at the early stage than the late stage. Conclusions Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different plant development stages. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection to meet the physiological requirement of plant developmental stages. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity.

Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. Results Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. Conclusions Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity.

The functional traits of organisms within multispecies assemblages regulate biodiversity effects on ecosystem functioning. Yet how traits should assemble to boost multiple ecosystem functions simultaneously (multifunctionality) remains poorly explored. In a multibiome litter experiment covering most of the global variation in leaf trait spectra, we showed that three dimensions of functional diversity (dispersion, rarity, and evenness) explained up to 66% of variations in multifunctionality, although the dominant species and their traits remained an important predictor. While high dispersion impeded multifunctionality, increasing the evenness among functionally dissimilar species was a key dimension to promote higher multifunctionality and to reduce the abundance of plant pathogens. Because too-dissimilar species could have negative effects on ecosystems, our results highlight the need for not only diverse but also functionally even assemblages to promote multifunctionality. The effect of functionally rare species strongly shifted from positive to negative depending on their trait differences with the dominant species. Simultaneously managing the dispersion, evenness, and rarity in multispecies assemblages could be used to design assemblages aimed at maximizing multifunctionality independently of the biome, the identity of dominant species, or the range of trait values considered. Functional evenness and rarity offer promise to improve the management of terrestrial ecosystems and to limit plant disease risks., This work was funded by the British Ecological Society (SR17\1297 grant, PI: P.G.-P.) and by the European Research Council (ERC Grant Agreement #647038, BIODESERT, PI: F.T.M.). Y.L.B.-P. was supported by a Marie Sklodowska-Curie Actions Individual Fellowship within the European Program Horizon 2020 (DRYFUN Project #656035). H.S. was supported by a Juan de la Cierva-Formación grant from the Span ish Ministry of Economy and Competitiveness (FJCI-2015-26782). F.T.M. and S.A. were supported from the Generalitat Valenciana (CIDEGENT/ 2018/041). M.D. was supported by a Formación del Profesorado Universi tario (FPU) fellowship from the Spanish Ministry of Education, Culture and Sports (FPU-15/00392). S.A. was supported by the Spanish MINECO for financial support via the DIGGING_DEEPER project through the 2015 to 2016 BiodivERsA3/FACCE‐JPI joint call for research proposals. B.K.S. re search on biodiversity-ecosystem functions was supported by the Austra lian Research Council (DP170104634 and DP190103714). P.G.-P. was supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-024766-I). R.M. was supported by MINECO (Grants CGL2014-56567-R and CGL2017-83855-R)

Ensuring food security in an environmentally sustainable way is a global challenge. To achieve this agriculture productivity requires increasing by 70 % under increasingly harsh climatic conditions without further damaging the environmental quality (e.g. reduced use of agrochemicals). Most governmental and inter-governmental agencies have highlighted the need for alternative approaches that harness natural resource to address this. Use of beneficial phytomicrobiome, (i.e. microbes intimately associated with plant tissues) is considered as one of the viable solutions to meet the twin challenges of food security and environmental sustainability. A diverse number of important microbes are found in various parts of the plant, i.e. root, shoot, leaf, seed, and flower, which play significant roles in plant health, development and productivity, and could contribute directly to improving the quality and quantity of food production. The phytomicrobiome can also increase productivity via increased resource use efficiency and resilience to biotic and abiotic stresses. In this article, we explore the role of phytomicrobiome in plant health and how functional properties of microbiome can be harnessed to increase agricultural productivity in environmental-friendly approaches. However, significant technical and translation challenges remain such as inconsistency in efficacy of microbial products in field conditions and a lack of tools to manipulate microbiome in situ. We propose pathways that require a system-based approach to realize the potential to phytomicrobiome in contributing towards food security. We suggest if these technical and translation constraints could be systematically addressed, phytomicrobiome can significantly contribute towards the sustainable increase in agriculture productivity and food security.

In recent decades, endophytes have attracted significant attention for their beneficial role in plant health and fitness and have been proposed as effective alternatives to synthetic fertilizers and pesticides. As such, knowledge on nature and mechanisms underpinning plant-endophyte interactions represents an important advancement to enhance our understanding of how plants can benefit from their microbial partners. In this chapter, we review the role of the rhizosphere microbiome in the recruitment of this major subgroup of plant-associated microbes and other factors in the rhizosphere (root exudates, soil properties, and plant genotype) that, together with a range of gene expression and epigenetic mechanisms, directly regulate endophytic colonization. We conclude by highlighting emerging strategies to manipulate these associations to benefit plant health and productivity. The information and facts gathered from current plant microbiome research will greatly improve our ability to harness rhizosphere/endophytic microbiome for viable strategies to improve agricultural production.

Huanglongbing (HLB), a deadly citrus disease which has significantly downsized the entire industry worldwide. The intractable and incurable disease has brought the citriculture an enormous loss of productivity. With no resistant varieties available, failure of chemical treatments despite repeated applications, and hazardous consequences to environmental health, have led to large-scale research to find a sustainable cure. Inside plants, the key determinants of health and safety, live the endophytic microbes. Endophytes possess unrivaled plant benefiting properties. The progression of HLB is known to cause disturbance in endophytic bacterial communities. Given the importance of the plant endophytic microbiome in disease progression, the notion of engineering microbiomes through indigenous endophytes is attracting scientific attention which is considered revolutionary as it precludes the incompatibility concerns associated with the use of alien (microbes from other plant species) endophytes. In this review, we briefly discuss the transformation of the plant-pathogen-environment to the plant-pathogen-microbial system in a disease triangle. We also argue the employment of indigenous endophytes isolated from a healthy state to engineer the diseased citrus endophytic microbiomes that can provide sustainable solution for vascular pathogens. We evaluated the plethora of microbiomes responses to the re-introduction of endophytes which leads to disease resistance in the citrus host. The idea is not merely confined to citrus-HLB, but it is globally applicable for tailoring a customized cure for general plant-pathogen systems particularly for the diseases caused by the vascular system-restricted pathogens.

The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential., This paper is an output from the EU project MicrobiomeSupport, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 818116., info:eu-repo/semantics/publishedVersion

The fungal community plays an important role in forest ecosystems via the provision of resources to plant nutrition and productivity. However, the ecology of the fungal network and its relationship with phosphorus (P) dynamics remain poorly understood in mixed forest plantations. Here, we analyzed the fungal community using the amplicon sequencing in plantations of pure Eucalyptus grandis, with (E + N) and without N fertilization (E), besides pure Acacia mangium (A), and in a consortium of E. grandis and A. mangium (E + A), at 27 and 39 months after planting. We analyzed chemical, physical and biochemical soil and litter attributes related to P cycling, and the fungal community structure to find out if mixed plantations can increase fungal connections and to identify their role in the P dynamics in the soil-litter system. Soil organic fraction (OF), phosphorus in OF, total-P and acid phosphatase activity were significantly higher in E + A and A treatments regardless of the sampling period. Total N and P, richness, and Shannon diversity of the fungi in the litter was significantly higher in the treatments E + A and A. The fungal community structure in litter differed between treatments and sampling periods, and E + A showed an intermediate structure between the two pure treatments (E) and (A). E + A correlated highly with P dynamics when evaluated by both Pearson and redundancy analyses, particularly in the litter layer. Co-occurrence networks of fungal taxa became simpler in pure E. grandis plantations, whereas mixed system (E + A) showed a more connected and complex network. Our findings provide novel evidence that mixed forest plantations promote positive responses in the fungal community connections, which are closely related to P availability in the system, prominently in the litter layer. This indicates that the litter layer represents a specific niche to improve nutrient cycling by fungi in mixed forest ecosystems.

SummaryEmerging experimental framework suggests that plants under biotic stress may actively seek help from soil microbes, but empirical evidence underlying such a ‘cry for help’ strategy is limited.We used integrated microbial community profiling, pathogen and plant transcriptive gene quantification and culture-based methods to systematically investigate a three-way interaction between the wheat plant, wheat-associated microbiomes and Fusarium pseudograminearum (Fp).A clear enrichment of a dominant bacterium, Stenotrophomonas rhizophila (SR80), was observed in both the rhizosphere and root endosphere of Fp-infected wheat. SR80 reached 3.7×107 cells g-1 in the rhizosphere and accounted for up to 11.4% of the microbes in the root endosphere. Its abundance had a positive linear correlation with the pathogen load at base stems and expression of multiple defense genes in top leaves. Upon re-introduction in soils, SR80 enhanced plant growth, both the below- and above-ground, and induced strong disease resistance by priming plant defense in the aboveground plant parts, but only when the pathogen was presentTogether, the bacterium SR80 seems to have acted as an early warning system for plant defense. This work provides novel evidence for the potential protection of plants against pathogens by an enriched beneficial microbe via modulation of the plant immune system.

Infection by malaria parasites triggers dynamic immune responses leading to diverse symptoms and pathologies; however, the molecular mechanisms responsible for these reactions are largely unknown. We performed Trans-species Expression Quantitative Trait Locus analysis to identify a large number of host genes that respond to malaria parasite infections. Here we functionally characterize one of the host genes called receptor transporter protein 4 (RTP4) in responses to malaria parasite and virus infections. RTP4 is induced by type I IFN (IFN-I) and binds to the TANK-binding kinase (TBK1) complex where it negatively regulates TBK1 signaling by interfering with expression and phosphorylation of both TBK1 and IFN regulatory factor 3. Rtp4(−/−) mice were generated and infected with malaria parasite Plasmodiun berghei ANKA. Significantly higher levels of IFN-I response in microglia, lower parasitemia, fewer neurologic symptoms, and better survival rates were observed in Rtp4(−/−) than in wild-type mice. Similarly, RTP4 deficiency significantly reduced West Nile virus titers in the brain, but not in the heart and the spleen, of infected mice, suggesting a specific role for RTP4 in brain infection and pathology. This study reveals functions of RTP4 in IFN-I response and a potential target for therapy in diseases with neuropathology.

An emerging experimental framework suggests that plants under biotic stress may actively seek help from soil microbes, but empirical evidence underlying such a 'cry for help' strategy is limited. We used integrated microbial community profiling, pathogen and plant transcriptive gene quantification and culture-based methods to systematically investigate a three-way interaction between the wheat plant, wheat-associated microbiomes and Fusarium pseudograminearum (Fp). A clear enrichment of a dominant bacterium, Stenotrophomonas rhizophila (SR80), was observed in both the rhizosphere and root endosphere of Fp-infected wheat. SR80 reached 3.7 × 107 cells g-1 in the rhizosphere and accounted for up to 11.4% of the microbes in the root endosphere. Its abundance had a positive linear correlation with the pathogen load at base stems and expression of multiple defence genes in top leaves. Upon re-introduction in soils, SR80 enhanced plant growth, both the below-ground and above-ground, and induced strong disease resistance by boosting plant defence in the above-ground plant parts, but only when the pathogen was present. Together, the bacterium SR80 seems to have acted as an early warning system for plant defence. This work provides novel evidence for the potential protection of plants against pathogens by an enriched beneficial microbe via modulation of the plant immune system.

The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes.

Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant-mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil-plant continuums (rhizosphere, phyllosphere and endosphere) in the maize-wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.

1. The importance of soil phosphorus (P) is likely to increase in coming decades due to the growing atmospheric nitrogen (N) deposition originated by industrial and agricultural activities. We currently lack a proper understanding of the main drivers of soil P pools in coastal dunes, which rank among the most valued priority conservation areas worldwide. 2. Here, we evaluated the joint effects of biotic (i.e. microbial abundance and richness, vegetation and cryptogams cover) and abiotic (i.e. pH and aridity) factors on labile, medium‐lability and recalcitrant soil P pools across a wide aridity gradient in the Atlantic coast of the Iberian Peninsula. 3. Climate determined the availability of medium‐lability, recalcitrant and total P, but had a minor net effect on labile P, which was positively and significantly related to the presence of plants, mosses and lichens. Medium‐lability P was significantly influenced by soil bacterial richness and abundance (positively and negatively, respectively). 4. Our results suggest that micro‐organisms transfer P from medium‐lability pool to more labile one. At the same time, increases in bacterial richness associated to biofilms might be involved in the thickening of the medium‐lability P pool in our climosequence. 5. These bacterial‐mediated transfers would confer resistance to the labile P pool under future climate change and uncover an important role of soil micro‐organisms as modulators of the geochemical P cycle. This project was financed by FEDER/Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación/Proyect (CGL2017-88124-R), European Research Council (ERC Grant Agreement 647038 [BIODESERT]) and the Fundaçã o para Ciência e Tecnologia (IF/00950/2014) and the FEDER, within the PT2020 Partnership Agreement and COMPETE 2020 (UID/BIA/04004/2013). F.T.M. acknowledges support from Generalitat Valenciana (CIDEGENT/2018/041). B.K.S. acknowledge research support on microbes and ecosystem functions from the Australian Research Council (DP170104634) and Research Award from the Humboldt Foundation.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term ``microbiome.'' Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role., The study was funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 818116 (Project MicrobiomeSupport)., info:eu-repo/semantics/publishedVersion

The Australian sugarcane industry is facing a new threat of the currently undiagnosed Yellow Canopy Syndrome (YCS). Here, we investigated if YCS is linked to detrimental shifts in soil microbial function and/or altered physico-chemical soil properties. We examined changes in rhizosphere soil microbial assemblages, functional gene profiles and microbial activity associated with YCS development. Shifts in soil bacterial and fungal community assemblages with YCS appeared variety-specific with limited consistent trends emerging. However, significant, consistent shifts in the rhizosphere soil metagenome with YCS were found, suggesting that YCS incidence might be linked to changes in specific soil microbial functions. Functional gene categories involved in prokaryotic immune response and in metabolism of compounds present in root exudates were consistently detected in higher abundance in the rhizosphere of YCS-affected plants, while gene categories involved in DNA, RNA and protein processing were consistently less abundant. Soil nutrient status (C, N), extracellular enzyme activity and substrate-induced respiration either did not significantly differ between affected and healthy fields of three sugarcane varieties, or showed inconsistent trends with variety. Altogether, our results did not show a direct link between soil microbial richness, overall soil microbial activity, soil nutrient status and YCS incidence. However, rhizosphere microbial communities responded consistently to YCS incidence by enrichment of genes encoding functions involved in defence against pathogens and root exudate metabolism which may have potential implications for the future development of diagnostic tools and an effective management practice to minimise impact of YCS on farm productivity. Refereed/Peer-reviewed

The ability of viral particles to directly spread cell to cell within the airways without particle release is considered to be highly advantageous to many respiratory viruses. Our previous studies in well-differentiated, primary human airway epithelial cells suggest that measles virus (MeV) spreads cell to cell by eliciting the formation of intercellular membrane pores. Based on a newly generated ribonucleoprotein complex (RNP) “tracker” virus, we document by live-cell microscopy that MeV RNPs move along F-actin rings before entering a new cell. Thus, rather than diffusing through the cytoplasm of a newly infected columnar cell, RNPs take advantage of the cytoskeletal infrastructure to rapidly spread laterally across the human airway epithelium. This results in rapid horizontal spread through the epithelium that does not require particle release., Measles virus (MeV) is a highly contagious human pathogen that continues to be a worldwide health burden. One of the challenges for the study of MeV spread is the identification of model systems that accurately reflect how MeV behaves in humans. For our studies, we use unpassaged, well-differentiated primary cultures of airway epithelial cells from human donor lungs to examine MeV infection and spread. Here, we show that the main components of the MeV ribonucleoprotein complex (RNP), the nucleocapsid and phosphoprotein, colocalize with the apical and circumapical F-actin networks. To better understand how MeV infections spread across the airway epithelium, we generated a recombinant virus incorporating chimeric fluorescent proteins in its RNP complex. By live cell imaging, we observed rapid movement of RNPs along the circumapical F-actin rings of newly infected cells. This strikingly rapid mechanism of horizontal trafficking across epithelia is consistent with the opening of pores between columnar cells by the viral membrane fusion apparatus. Our work provides mechanistic insights into how MeV rapidly spreads through airway epithelial cells, contributing to its extremely contagious nature.

Cystic fibrosis (CF) is a common genetic disease caused by mutations in the gene coding for cystic fibrosis transmembrane conductance regulator (CFTR). Although CF affects multiple organ systems, chronic bacterial infections and inflammation in the lung are the leading causes of morbidity and mortality in people with CF. Complementation with a functional CFTR gene repairs this defect, regardless of the disease-causing mutation. In this study, we used a gene delivery system termed piggyBac/adenovirus (Ad), which combines the delivery efficiency of an adenoviral-based vector with the persistent expression of a DNA transposon-based vector. We aerosolized piggyBac/Ad to the airways of pigs and observed widespread pulmonary distribution of vector. We quantified the regional distribution in the airways and observed transduction of large and small airway epithelial cells of non-CF pigs, with ∼30–50% of surface epithelial cells positive for GFP. We transduced multiple cell types including ciliated, non-ciliated, basal, and submucosal gland cells. In addition, we phenotypically corrected CF pigs following delivery of piggyBac/Ad expressing CFTR as measured by anion channel activity, airway surface liquid pH, and bacterial killing ability. Combining an integrating DNA transposon with adenoviral vector delivery is an efficient method for achieving functional CFTR correction from a single vector administration.

Background The Leishmania spp. protozoa are introduced into humans through a sand fly blood meal, depositing the infectious metacyclic promastigote form of the parasite into human skin. Parasites enter a variety of host cells, although a majority are found in macrophages where they replicate intracellularly during chronic leishmaniasis. Symptomatic leishmaniasis causes considerable human morbidity in endemic regions. The Leishmania spp. evade host microbicidal mechanisms partially through virulence-associated proteins such as the major surface protease (MSP or GP63), to inactivate immune factors in the host environment. MSP is a metalloprotease encoded by a tandem array of genes belonging to three msp gene classes, whose mRNAs are differentially expressed in different life stages of the parasite. Like other cells, Leishmania spp. release small membrane-bound vesicles called exosomes into their environment. The purpose of this study was to detect MSP proteins in exosomal vesicles of Leishmania spp. protozoa. Methods Using mass spectrometry data we determined the profile of MSP class proteins released in L. infantum exosomes derived from promastigotes in their avirulent procyclic (logarithmic) stage and virulent stationary and metacyclic stages. MSP protein isoforms belonging to each of the three msp gene classes could be identified by unique peptides. Results Metacyclic promastigote exosomes contained the highest, and logarithmic exosomes had the lowest abundance of total MSP. Among the MSP classes, MSPC class had the greatest variety of isoforms, but was least abundant in all exosomes. Nonetheless, all MSP classes were present at higher levels in exosomes released from stationary or metacyclic promastigotes than logarithmic promastigotes. Conclusions The data suggest the efficiency of exosome release may be more important than the identity of MSP isoform in determining the MSP content of Leishmania spp. exosomes. Electronic supplementary material The online version of this article (10.1186/s13071-018-2937-y) contains supplementary material, which is available to authorized users.

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.

Waterlogging may affect soil nitrification rates, resulting in changes in plant-available nitrogen (N), and hence potentially influencing crop productivity. Because nitrification is a microbially-driven process and ammonia-oxidizing communities regulate soil nitrification rates, the aim of this study was to investigate the mechanistic response of ammonia-oxidizing communities and nitrification rates to waterlogging. A field study was conducted by experimentally imposing two short-term waterlogging events when cotton plants were at the early- and late-flowering stages. Soil physicochemical properties, nitrification rates, and ammonia-oxidizing community abundance and structure in response to waterlogging were examined. Soil nitrate (NO3−) content, potential nitrification rates (PNR) and the abundance of ammonia-oxidizing communities significantly decreased upon waterlogging. Shifts in ammonia-oxidizing community structure were also observed. Both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) responded to waterlogging. PNR was significantly correlated with the abundance and structure of both AOB and AOA. Waterlogging had strong negative effects on soil nitrification rates by altering the ammonia-oxidizing community abundance and structure, resulting in reduced soil N availability. Decreased plant-available N is likely to negatively affect primary productivity.

Archaeal community has important contributors to nutrient cycling in the forest ecosystems. However, how soil-litter attributes shift their community structure remains poorly understood. To date, the structure of the archaeal community has never been reported either in pure or in mixed eucalypt and acacia plantations, especially in tropical soils. Here, we analyzed the archaeal community and performed correlations with C, N and P attributes in soil-litter layers of pure Eucalyptus grandis without (E) and with N fertilization (E + N), a mixed system of E. grandis and Acacia mangium (E + A), and a pure A. mangium (A) plantation. We extracted DNA from soil (0–20 cm) and litter samples at 27 and 39 months after planting and sequenced the archaeal 16S rRNA gene. We also analyzed the abundance of 16S rRNA and amoA genes by quantitative PCR and assessed the correlations between molecular data with soil-litter attributes (i.e., microbial and enzyme activities, and C, N and P contents). The high-throughput sequencing of the archaeal 16S rRNA gene revealed that the treatments influenced the archaeal community structure. However, the litter layer showed more significant modifications, since archaeal richness, diversity, and the relative abundance of Thaumarchaeota increased in the litter of pure acacia and mixed treatments at both, 27 and 39 months after planting. There was no clear pattern regarding the abundance of functional genes in the soil, but archaeal structure responded to treatments in the litter layer, in which NH4+, total-N and the C/N ratio were the most important attributes for community group differentiation. Our study provides novel insights into the structure and function of archaea in pure and mixed forest systems, but highlights that young mixed plantations exert a low effect on soil community structure. Archaeal community may have an important role in nutrient cycling in the litter interface, especially related to the N cycle in the initial stages of tree development.

Summary Plant‐associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real‐world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant–microbe interactions to breed ‘microbe‐optimized plants’. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security.

The legacy impacts of past climates on the current distribution of soil microbial communities are largely unknown. Here, we use data from more than 1,000 sites from five separate global and regional datasets to identify the importance of palaeoclimatic conditions (Last Glacial Maximum and mid-Holocene) in shaping the current structure of soil bacterial communities in natural and agricultural soils. We show that palaeoclimate explains more of the variation in the richness and composition of bacterial communities than current climate. Moreover, palaeoclimate accounts for a unique fraction of this variation that cannot be predicted from geographical location, current climate, soil properties or plant diversity. Climatic legacies (temperature and precipitation anomalies from the present to ~20 kyr ago) probably shape soil bacterial communities both directly and indirectly through shifts in soil properties and plant communities. The ability to predict the distribution of soil bacteria from either palaeoclimate or current climate declines greatly in agricultural soils, highlighting the fact that anthropogenic activities have a strong influence on soil bacterial diversity. We illustrate how climatic legacies can help to explain the current distribution of soil bacteria in natural ecosystems and advocate that climatic legacies should be considered when predicting microbial responses to climate change. Analysing data from more than 1,000 sites globally, the authors show that palaeoclimatic legacies explain a greater amount of variation in bacterial community richness and composition than current climate.

Summary Global change models indicate that rainfall patterns are likely to shift towards more extreme events concurrent with increasing atmospheric carbon dioxide concentration ([CO2]). Both changes in [CO2] and rainfall regime are known to impact above- and belowground communities, but the interactive effects of these global change drivers have not been well explored, particularly belowground. In this experimental study, we examined the effects of elevated [CO2] (ambient + 240 ppm; [eCO2]) and changes in rainfall patterns (seasonal drought) on soil microbial communities associated with forest ecosystems. Our results show that bacterial and archaeal communities are highly resistant to seasonal drought under ambient [CO2]. However, substantial taxa specific responses to seasonal drought were observed at [eCO2], suggesting that [eCO2] compromise the resistance of microbial communities to extreme events. Within the microbial community we were able to identify three types of taxa specific responses to drought: tolerance, resilience and sensitivity that contributed to this pattern. All taxa were tolerant to seasonal drought at [aCO2], whereas resilience and sensitivity to seasonal drought were much greater in [eCO2]. These results provide strong evidence that [eCO2] moderates soil microbial community responses to drought in forests, with potential implications for their long-term persistence and ecosystem functioning. This article is protected by copyright. All rights reserved.

Uncovering potential soil drivers of soils pathogen suppression represent an essential step in order to develop alternative and sustainable management strategies for disease control and increased soil health. In this study, we tested the potential role of keystone microbial taxa and chemical/physical properties in the suppression (referred to as soil suppressiveness) of the soil-borne model pathogen Fusarium oxysporum using soil samples from various crop producing agro-ecosystems in Australia. Using random forest, we identified bacteria belonging to the phyla Actinobacteria , Firmicutes and Acidobacteria as the major microbial predictors for soil suppressiveness at a continental scale. Structural equation modeling approach revealed strong relationship between the relative abundance of phylum Actinobacteria and soil functions carried out by soil microbial communities (soil functioning) with pathogen inhibition. Overall our study provided a mechanistic framework showing how microbial communities, soil functionality, and abiotic properties being antagonistic to soil pathogens are linked and interactively shape the suppressive potential of soils at continental scale. This information, upon further validation can be incorporated in risk management tools for developing novel concepts such as “ Know before you Sow ” leading to increased farm productivity and profitability.

Atmospheric concentrations of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) are predicted to increase as a consequence of fossil fuel emissions and the impact on biosphere–atmosphere interactions. Forest ecosystems in general, and forest soils in particular, can be sinks or sources for CO2, CH4, and N2O. Environmental studies traditionally target soil temperature and moisture as the main predictors of soil greenhouse gas (GHG) flux from different ecosystems; however, these emissions are primarily biologically driven. Thus, little is known about the degree of regulation by soil biotic vs. abiotic factors on GHG emissions, particularly under predicted increase in global temperatures, and changes in intensity and frequency of precipitation events. Here we measured net CO2, CH4 and N2O fluxes after 5 years of experimental warming (+3.4°C), and 2 years of ≈45% summer rainfall reduction, in two forest sites in a boreal–temperate ecotone under different habitat conditions (closed or open canopy) in Minnesota, USA. We evaluated the importance of microbial gene abundance and climo-edaphic factors (soil texture, canopy, seasonality, climate, and soil physicochemical properties) driving GHG emissions. We found that changes in CO2 fluxes were predominantly determined abiotically by temperature and moisture, after accounting for bacterial abundance. Methane fluxes on the other hand, were determined both abiotically, by gas diffusivity (via soil texture) and microbially, by methanotroph pmoA gene abundance, whereas, N2O emissions showed only a strong biotic regulation via ammonia-oxidizing bacteria amoA gene abundance. Warming did not significantly alter CO2 and CH4 fluxes after 5 years of manipulation, while N2O emissions were greater with warming under open canopy. Our findings provide evidence that soil GHG emissions result from multiple direct and indirect interactions of microbial and abiotic drivers. Overall, this study highlights the need to include both microbial and climo-edaphic properties in predictive models in order to provide improved mechanistic understanding for the development of future mitigation strategies. A lay summary is available for this article.

Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend. We used two independent approaches (i.e. experimental and observational), and applied statistical modeling to identify the role and relative importance of bacterial richness and composition in driving multifunctionality (here defined as seven measures of respiration and enzyme activities). In the observational study we measured soil microbial communities and functions in both tree- and bare soil-dominated microsites at 22 locations across a 1200 km transect in southeastern Australia. In the experimental study we used soils from two of those locations and developed gradients of bacterial diversity and composition through inoculation of sterilized soils. Microbial richness and the relative abundance of γ-Proteobacteria, Actinobacteria and Bacteroidetes were positively related to multifunctionality in both the observational and experimental approaches; however, only Bacteroidetes was consistently selected as a key predictor of multifunctionality across all experimental approaches and statistical models used here. Moreover, our results, from two different approaches, provide evidence that microbial richness and composition are both important, yet independent, drivers of multiple ecosystem functions. Overall, our findings advance our understanding of the mechanisms underpinning relationships between microbial diversity and ecosystem functionality in terrestrial ecosystems, and further suggest that information on microbial richness and composition needs to be considered when formulating sustainable management and conservation policies, and when predicting the effects of global change on ecosystem functions. This article is protected by copyright. All rights reserved.

Globally, drylands represent the largest terrestrial biome and are projected to expand by 23% by the end of this century. Drylands are characterized by extremely low levels of water and nutrients and exhibit highly heterogeneous distribution in plants and biocrusts which make microbial processes shaping the dryland functioning rather unique compared with other terrestrial ecosystems. Nitrous oxide (N2 O) is a powerful greenhouse gas with ozone depletion potential. Despite of the pivotal influences of microbial communities on the production and consumption of N2 O, we have limited knowledge of the biological pathways and mechanisms underpinning N2 O emissions from drylands, which are estimated to account for 30% of total gaseous nitrogen emissions on Earth. In this article, we describe the key microbial players and biological pathways regulating dryland N2 O emissions, and discuss how these processes will respond to emerging global changes such as climate warming, extreme weather events and nitrogen deposition. We also provide a conceptual framework to precisely manipulate the dryland microbiome to mitigate N2 O emissions in situ using emerging technologies with great specificity and efficacy. These cross-disciplinary efforts will enable the development of novel and environmental-friendly microbiome-based solutions to future mitigation strategies of climate change.

It is well established that resource quantity and elemental stoichiometry play major roles in shaping below and aboveground plant biodiversity, but their importance for shaping microbial diversity in soil remains unclear. Here, we used statistical modeling on a regional database covering 179 locations and six ecosystem types across Scotland to evaluate the roles of total carbon (C), nitrogen (N) and phosphorus (P) availabilities and ratios, together with land use, climate and biotic and abiotic factors, in determining regional scale patterns of soil bacterial diversity. We found that bacterial diversity and composition were primarily driven by variation in soil resource stoichiometry (total C:N:P ratios), itself linked to different land uses, and secondarily driven by other important biodiversity drivers such as climate, soil spatial heterogeneity, soil pH, root influence (plant-soil microbe interactions) and microbial biomass (soil microbe-microbe interactions). In aggregate, these findings provide evidence that nutrient stoichiometry is a strong predictor of bacterial diversity and composition at a regional scale.

Acid sulfate soil (ASS) is sensitive to redox fluctuations induced by climate change and human activities. Oxidation of sulfur and sulfide in ASS leads to the release of acid and consequently metals, posing severe hazards to coastal environment, while microbial contribution and response to oxidation is poorly understood. Here we used metagenomic sequencing to delineate the shift in microbial community structures and functional genes in ASS upon exposure to aerobic conditions. Aerobic incubation resulted in significant shifts in microbial communities in both topsoil and parent material. Archaea decreased significantly in the parent material after aerobic incubation. The relative abundance of sulfur cycling genes in the parent material layer was significantly higher than those in the topsoil, and multiple sulfide oxidation genes increased after aerobic oxidation. Metagenomic assembly enabled construction of eight key draft genomes from ASS. Three of them (GS3, GS6 and GT3) are novel strains of Thermoplasmatales, Acidothermales (Acidothermus) and Acidimicrobiales, respectively. Functional gene annotation of these population genomes revealed a dominance of sulfur cycling genes and acid tolerant genes. These findings highlight the microbial response to environmental change and identify the ecological adaptation and survival strategies of microbial communities in acid sulfate soils.