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Abstract Background Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown. Results Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum. Conclusions Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. Video Abstract

Abstract Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a ‘slow-fast’ axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that ‘slow’ and ‘fast’ strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.

Abstract Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.

Abstract The clubroot pathogen Plasmodiophora brassicae is a major and growing problem for the cultivation of Brassica crops. As conventional control disease management methods are ineffective or prohibited due to their ecological impact, and crop resistance is frequently broken, biological control of the pathogen has become a key focus for the development of sustainable agricultural systems. Here we provide a perspective review on the unexplored impact of soil microbiome predators, and their potential use as biocontrol agents, using clubroot disease as an example. We highlight several pathways by which microbiome predators can reduce clubroot in soils, including directly through predation and indirectly by inducing a clubroot‐suppressive microbiome. We further discuss how some microbiome predators might, in contrast, benefit clubroot disease spread through mechanisms such as phoresy toward hosts. We highlight that gaps in knowledge need to be filled that hinder wider application of microbiome predators against P. brassicae alone, and in combination with known biocontrol agents.

Abstract Background For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. Results We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass. Conclusions Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract

Introduction: The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to retain microbiome functioning under drought. Objectives: This work aims to reveal if fertilization with organic fertilizer, can enhance resistance and resilience of bacterial communities and their function in extreme drought and subsequent rewetting compared with conventional fertilizers. Methods: In soil mesocosms, we induced a long-term drought for 80 days with subsequent rewetting for 170 days to follow bacterial community dynamics in organic (NOF) and chemical (NCF) fertilization regimes. Results: Our results showed that bacterial diversity was higher with NOF than with NCF during drought. In particular, the ecological resilience and recovery of bacterial communities under NOF were higher than in NCF. We found these bacterial community features to enhance pathogen-inhibiting functions in NOF compared to NCF during late recovery. The other soil ecology functional analyses revealed that bacterial biomass recovered in the early stage after rewetting, while soil respiration increased continuously following prolonged time after rewetting. Conclusion: Together, our study indicates that organic fertilization can enhance the stability of the soil microbiome and ensures that specific bacterial-driven ecosystem functions recover after rewetting. This may provide the basis for more sustainable agricultural practices to counterbalance negative climate change-induced effects on soil functioning.

The soil microbiome is dynamically structured at the local soil aggregate level by a combination of bottom-up and top-down processes. The soil microbiome is structured at the local soil aggregate scale by a dynamic interplay of bottom-up and top-down processes, yet less attention has been given to the latter (e.g., predation). We aimed to identify distinct groups of predators (protists and nematodes) and prey (bacteria) to determine the effect of predation on microbial gene abundances associated with carbon and nitrogen metabolisms. We partitioned soil aggregate size at three distinct levels to distinguish potential differences in predator–prey microbe interactions that take place at the soil micro-structure level. Our results revealed that the bacterial diversity and the abundance of protists were significantly higher in microaggregates than in macroaggregates. Correlation analysis, structural equation modeling, and co-occurrence networks suggested that predation by protists and nematodes impacted the diversity (Shannon index) and stability (average variation degree) of soil bacterial community, with a more pronounced effect on the bacterial community in soil macroaggregates than in smaller microaggregates. Compared to microaggregates, the higher frequency of predation within macroaggregates was found to promote faster microbiome turnover with direct implications for the abundance of genes involved in carbon and nitrogen metabolisms. Lastly, we also studied the importance of predation as a mechanism promoting bacterial diversity using field and microcosm studies, with a specific focus on the dominant bacterivorous nematode Protorhabditis. We addressed the influence of top-down processes on soil microbiome diversity and modulation of the genetic potential of genes involved in carbon and nitrogen metabolisms. Our study provides evidence for the importance of predation impacting the diversity and stability of soil bacterial communities. In addition, it shows that predation alters the abundance of microbial genes associated with carbon and nitrogen metabolisms at the soil aggregate level.

Abstract Biodiversity is widely linked to human health, however, connections between human health and soil biodiversity in urban environments remain poorly understood. Here, we stress that reductions in urban soil biodiversity elevate risks to human health, but soil biodiversity can improve human health through pathways including suppressing pathogens, remediating soil, shaping a beneficial human microbiome and promoting immune fitness. We argue that targeted enhancement of urban soil biodiversity could support human health, in both outdoor and indoor settings. The potential of enhanced urban soil biodiversity to benefit human health reflects an important yet understudied field of fundamental and applied research.

Abstract Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect and interactive effects of global change drivers on soil communities and ecosystems across environmental contexts, not only today but also in the near future. This is particularly relevant for international efforts to tackle climate change like the Paris Agreement, and considering the failure to achieve the 2020 biodiversity targets, especially the target of halting soil degradation. Here, we outline the main frontiers related to soil ecology that were presented and discussed at the thematic sessions of the World Biodiversity Forum 2022 in Davos, Switzerland. We highlight multiple frontiers of knowledge associated with data integration, causal inference, soil biodiversity and function scenarios, critical soil biodiversity facets, underrepresented drivers, global collaboration, knowledge application and transdisciplinarity, as well as policy and public communication. These identified research priorities are not only of immediate interest to the scientific community but may also be considered in research priority programmes and calls for funding.

Traditional rice production is often reliant on the unsustainable practice of utilizing intensive inputs in monoculture cropping systems. Alternatives fallow cover cropping and rice–fish coculture (RFC) offer promising solutions. However, the potential of fallow cover cropping in RFC remains underexplored, and its impact on soil microbes is poorly understood. In this study, assessments of soil–plant–microbe interactions were conducted across three cover cropping systems: Chinese milk vetch (Astragalus sinicus L.) single cropping (CM), Rapeseed (Brassica napus L.) single cropping (RP), and a combination of Chinese milk vetch and rapeseed intercropping (CM_RP). These systems were evaluated with and without nitrogen (N) addition, encompassing both the RFC and rice monoculture (RMC) systems. The findings indicate a notable increase in soil microbial biomass nitrogen (MBN) with CM. Soil microbial biomass carbon (MBC), influenced more by N-fertilizer than crop species, decreased with N addition. In the RFC system, the soil bacterial co-occurrence network exhibited more connections, yet negative links increased. CM_RP displayed similarities to CM without N but shifted closer to RP with N addition. N addition in intercropping significantly increased the root–shoot ratio (R/S) of A. sinicus, associated with decreased aboveground biomass and total root length. Compared to RMC, RFC with N addition reduced the relative abundance of Anaerolineaceae in CM while increasing Bacillus and Pontibacter across cover cropping systems. Overall, with N addition, both RFC and RMC showed decreased soil bacterial diversity indices. Changes in soil bacterial diversity correlated significantly with soil MBC, MBN, and plant R/S. Continuous fallow cover cropping altered soil microbial biomass and affected cover crop biomass distribution, impacting bacterial composition in paddy soil. These results shed light on how bacterial communities respond to N addition and fallow cover cropping in RFC and RMC systems, offering insights for sustainable nutrient management in paddy systems.

ABSTRACT As important ecosystem engineers in soils, earthworms strongly influence carbon cycling through their burrowing and feeding activities. Earthworms do not perform these roles in isolation, because their intestines create a special habitat favorable for complex bacterial communities. However, how the ecological functioning of these earthworm-microbe interactions regulates carbon cycling remains largely unknown. To fill this knowledge gap, we investigated the bacterial community structure and carbon metabolic activities in the intestinal contents of earthworms and compared them to those of the adjacent soils in a long-term fertilization experiment. We discovered that earthworms harbored distinct bacterial communities compared to the surrounding soil under different fertilization conditions. The bacterial diversity was significantly larger in the adjacent soils than that in the earthworm gut. Three statistically identified keystone taxa in the bacterial networks, namely, Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans, were shared across the earthworm gut and adjacent soil. Environmental factors (pH and organic matter) and keystone taxa were important determinants of the bacterial community composition in the earthworm gut. Both PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) and FAPROTAX (Functional Annotation of Prokaryotic Taxa) predicted that carbon metabolism was significantly higher in adjacent soil than in the earthworm gut, which was consistent with the average well color development obtained by the Biolog assay. Structural equation modeling combined with correlation analysis suggested that pH, organic matter, and potential keystone taxa exhibited significant relationships with carbon metabolism. This study deepens our understanding of the mechanisms underlying keystone taxa regulating carbon cycling in the earthworm gut. IMPORTANCE The intestinal microbiome of earthworms is a crucial component of the soil microbial community and nutrient cycling processes. If we could elucidate the role of this microbiome in regulating soil carbon metabolism, we would make a crucial contribution to understanding the ecological role of these gut bacterial taxa and to promoting sustainable agricultural development. However, the ecological functioning of these earthworm-microbe interactions in regulating carbon cycling has so far not been fully investigated. In this study, we revealed, first, that the bacterial groups of Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans were core keystone taxa across the earthworm gut and adjacent soil and, second, that the environmental factors (pH and organic carbon) and keystone taxa strongly affected the bacterial community composition and exhibited close correlations with microbial carbon metabolism. Our results provide new insights into the community assembly of the earthworm gut microbiome and the ecological importance of potential keystone taxa in regulating carbon cycling dynamics.

Abstract We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth's systems with eukaryotes in freshwater sediments being among the least known. In this study, we used high‐throughput sequencing of the 18S rRNA gene to investigate the entire diversity of benthic eukaryotes in three distinct habitats (littoral sediment and hard substrate, profundal sediment) of Lake Ohrid, the oldest European lake. Eukaryotic sequences were dominated by annelid and arthropod animals (54% of all eukaryotic reads) and protists (Ochrophyta and Ciliophora; together 40% of all reads). Eukaryotic diversity was 15% higher in the deep profundal than on either near‐surface hard substrates or littoral sediments. The three habitats differed in their taxonomic and functional community composition. Specifically, heterotrophic organisms accounted for 92% of the reads in the profundal, whereas phototrophs accounted for 43% on the littoral hard substrate. The profundal community was the most homogeneous, and its network was the most complex, suggesting its highest stability among the sampled habitats.

Beyond interacting with neighboring plants, crop performance is affected by the microbiome that includes pathogens and mutualists. While the importance of plant–plant interactions in explaining overyielding in intercropping is well known, the role of the microbiome, in particular how the presence of microbes from heterospecific crop species inhibit pathogens of the focal plants in affecting yield remains hardly explored. Here we performed both field samplings and pot experiments to investigate the microbial interactions in the maize/faba bean intercropping system, with the focus on the inhibition of Fusarium oxysporum in faba bean plants. Long-term field measurements show that maize/faba bean intercropping increased crop yield, reduced the gene copies of F. oxysporum by 30–84% and increased bacterial richness and Shannon index compared to monocropping. Bacterial networks in intercropping were more stable with more hub nodes than the respective monocultures. Furthermore, the observed changes of whole microbial communities were aligned with differences in the number of siderophore-producing rhizobacteria in maize and pathogen abundances in faba bean. Maize possessed 71% more siderophore-producing rhizobacteria and 33% more synthetases genes abundance of nonribosomal peptides, especially pyochelin, relative to faba bean. This was further evidenced by the increased numbers of siderophore-producing bacteria and decreased gene copies of F. oxysporum in the rhizosphere of intercropped faba bean. Four bacteria (Pseudomonas spp. B004 and B021, Bacillus spp. B005 and B208) from 95 isolates antagonized F. oxysporum f. sp. fabae. In particular, B005, which represented a hub node in the networks, showed particularly high siderophore-producing capabilities. Intercropping increased overall bacterial diversity and network complexity and the abundance of siderophore-producing bacteria, leading to facilitated pathogen suppression and increased resistance of faba bean to F. oxysporum. This study has great agronomic implications as microorganisms might be specifically targeted to optimize intercropping practices in the future.

Abstract Background Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes. Results Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer. Conclusions We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers. Video abstract

ABSTRACT Nematode predation plays an essential role in determining changes in the rhizosphere microbiome. These changes affect the local nutrient balance and cycling of essential nutrients by selectively structuring interactions across functional taxa in the system. Currently, it is largely unknown to what extent nematode predation induces shifts in the microbiome associated with different rates of soil phosphorous (P) mineralization. Here, we performed an 7-year field experiment to investigate the importance of nematode predation influencing P availability and cycling. These were tracked via the changes in the alkaline phosphomonoesterase (ALP)-producing bacterial community and ALP activity in the rhizosphere of rapeseed. Here, we found that the nematode addition led to high predation pressure and thereby caused shifts in the abundance and composition of the ALP-producing bacterial community. Further analyses based on cooccurrence networks and metabolomics consistently showed that nematode addition induced competitive interactions between potentially keystone ALP-producing bacteria and other members within the community. Structural equation modeling revealed that the outcome of this competition induced by stronger predation pressure of nematodes was significantly associated with higher diversity of ALP-producing bacteria, thereby enhancing ALP activity and P availability. Taken together, our results provide evidence for the importance of predator-prey and competitive interactions in soil biology and their direct influences on nutrient cycling dynamics. IMPORTANCE Nematode predation plays an essential role in determining the rhizosphere microbiome. In doing so, predation dynamically affects the soil nutrient cycling, for instance, by shifting the availability of phosphorus (P) for plant uptake. However, the role of nematode predation inducing selective changes in the microbiome and affecting rates of P mineralization remains still largely unknown. Here, we used a field site treated with different fertilizers to investigate the importance of nematode predation influencing P availability and plant productivity, via changes in bacterial taxa producing alkaline phosphomonoesterases (ALP) and ALP activity in the rhizosphere of rapeseed. We integrated field and laboratory experiments to show that nematode predation induces bacterial keystone taxa to compete with the connected members and results in the modulation of ALP-producing bacterial populations and ALP activity in the rhizosphere. Taken together, our study provides novel insights into microbially mediated mechanisms of competitive interaction induced by nematode predation in enhancing P availability in the plant rhizosphere.

Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, consumption of dead organic matter, and interactions with microbial and plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, microbial communities, and vegetation, limits our understanding of biological interactions in soil systems and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities, (2) to describe key environmental drivers of soil animal communities and food webs, (3) to assess the efficiency of conservation approaches for the protection of soil animal communities, (4) to describe soil food webs and their association with soil functioning globally, (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics, (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs at sites associated with the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, climate, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems.

It is unclear whether body size affects community assembly mechanisms of soil biota. Here, the authors analyse soil microbial and nematode communities sampled along a 4000-km transect in China and global soil microbiome data to show that bacterial assembly is governed by high dispersal, whereas larger taxa are more influenced by deterministic processes.

Abstract Background The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fungi (AMF) that provide phosphorous (P) to plants. While plant hosts and abiotic parameters are known to structure AMF communities, it remains largely unknown how higher trophic level organisms, including protists and nematodes, affect AMF abundance and community composition. Results Here, we explored the connections between AMF, fungivorous protists and nematodes that could partly reflect trophic interactions, and linked those to rhizosphere P dynamics and plant performance in a long-term manure application setting. Our results revealed that manure addition increased AMF biomass and the density of fungivorous nematodes, and tailored the community structures of AMF, fungivorous protists, and nematodes. We detected a higher abundance of AMF digested by the dominant fungivorous nematodes Aphelenchoides and Aphelenchus in high manure treatments compared to no manure and low manure treatments. Structural equation modeling combined with network analysis suggested that predation by fungivorous protists and nematodes stimulated AMF biomass and modified the AMF community composition. The mycorrhizal-fungivore interactions catalyzed AMF colonization and expression levels of the P transporter gene ZMPht1;6 in maize roots, which resulted in enhanced plant productivity. Conclusions Our study highlights the importance of predation as a key element in shaping the composition and enhancing the biomass of AMF, leading to increased plant performance. As such, we clarify novel biological mechanism of the complex interactions between AMF, fungivorous protists, and nematodes in driving P absorption and plant performance. Video Abstract

Abstract Background Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. Results To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. Conclusion Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function. Video Abstract

Abstract Background Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators—protists—are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. Results We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. Conclusions We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. Video Abstract

Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.

ABSTRACT Microbes dominate the planet’s biodiversity in terms of species number and by driving essential Earth system functions such as the carbon cycle. Soils contain most of this microbial biodiversity. Only recently, we have started to better understand the diversity of bacteria and fungi at the global scale. Here, I list my views on some shortcomings of contemporary soil microbiome studies and potential solutions to overcome them. In particular, I highlight that (soil) microbiome studies should become more holistic in terms of (i) taxa and resolution targeted, (ii) by adding functional to taxonomic information, and (iii) by integrating temporal analysis into spatial analyses. Considering those elements with the methodology that is now available will advance our understanding on (soil) microbiomes to reliably address major ecological hypotheses and to advance insights into the importance for life on Earth.

Microscopic organisms are the dominant and most diverse organisms on Earth. Nematodes, as part of this microscopic diversity, are by far the most abundant animals and their diversity is equally high. Molecular metabarcoding is often applied to study the diversity of microorganisms, but has yet to become the standard to determine nematode communities. As such, the information metabarcoding provides, such as in terms of species coverage, taxonomic resolution and especially if sequence reads can be linked to the abundance or biomass of nematodes in a sample, has yet to be determined. Here, we applied metabarcoding using three primer sets located within ribosomal rRNA gene regions to target assembled mock-communities consisting of 18 different nematode species that we established in 9 different compositions. We determined abundances and biomass of all species added to examine if relative sequence abundance or biomass can be linked to relative sequence reads. We found that nematode communities are not equally represented by the three different primer sets and we found that relative read abundances almost perfectly correlated positively with relative species biomass for two of the primer sets. This strong biomass-read number correlation suggests that metabarcoding reads can reveal biomass information even amongst more complex nematode communities as present in the environment and possibly can be transferred to better study other groups of organisms. This biomass-read link is of particular importance for more reliably assessing nutrient flow through food-webs, as well as adjusting biogeochemical models through user-friendly and easily obtainable metabarcoding data.

Most studies of plant–soil feedbacks and associated traits look at remotely-related species. Here the authors look at congeners, and show that nematode-driven plant–soil feedbacks depend on root chemical and morphological traits, independent of phylogenetic distance.

Abstract Background Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. Results We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Conclusions Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth’s habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.

Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.

Soils host most biodiversity on Earth, with a major fraction of its taxonomic diversity still to be uncovered and most of its functional knowledge to be determined. Much focus has been - and still is - on bacteria, fungi and animals. Clearly, without any of those components, soils would not function as they do. However, the group that constitutes the bulk of eukaryotic diversity and plays a central role for soil functioning is missing: protists. As the main consumers of the microbiome, protists shape its composition and functioning. Other less known functions performed by protists may be equally important. Protists also include primary producers, decomposers, animal parasites and plant pathogens. We briefly review the many functions protists perform in soils and argue that soil biodiversity studies that ignore protists miss some potential mechanistic insight into the drivers of observed patterns. We highlight that the immense functional repertoire of protist affects virtually every soil process, from carbon cycling to primary production, including crop production. Therefore, we call for truly integrated biodiversity assessments including protists, without which the soil food-web and processes cannot reliably be understood: protists matter!

ABSTRACT We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications. IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Effects of habitat restoration on belowground organisms and ecosystem processes are poorly understood. Morriën and colleagues show that changes in the composition and network interactions of soil biota lead to improved carbon uptake efficiency when formerly cultivated land is restored.

Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria. Keywords: Antibiotic resistance genes, Antibiotic residue, Hyperthermophilic composting, Horizontal gene transfer, Plasmids

Soil-borne diseases, especially those caused by fungal pathogens, lead to profound annual yield losses. One key example for such a disease is Fusarium wilt disease in banana. In some soils, plants do not show disease symptoms, even if the disease-causing pathogens are present. However, the underlying agents that make soils suppressive against Fusarium wilt remain elusive. In this study, we aimed to determine the underlying microbial agents governing soil disease-suppressiveness. We traced the shift of microbiomes during the invasion of disease-causing Fusarium oxysporum f. sp. cubense in disease-suppressive and disease-conducive soils. We found distinct microbiome structures in the suppressive and conducive soils after pathogen invasion. The alpha diversity indices increased (or did not significantly change) and decreased, respectively, in the suppressive and conducive soils, indicating that the shift pattern of the microbiome with pathogen invasion was notably different between the suppressive and conductive soils. Microbiome networks were more complex with higher numbers of links and revealed more negative links, especially between bacterial taxa and the disease-causing Fusarium, in suppressive soils than in conducive soils. We identified the bacterial genera Chryseolinea, Terrimonas, and Ohtaekwangia as key groups that likely confer suppressiveness against disease-causing Fusarium. Overall, our study provides the first insights into agents potentially underlying the disease suppressiveness of soils against Fusarium wilt pathogen invasion. The results of this study may help to guide efforts for targeted cultivation and application of these potential biocontrol agents, which might lead to the development of effective biocontrol agents against Fusarium wilt disease.

The use of antibiotics in humans and animals results in a release of excess antibiotic residues into the environment through wastewaters and insufficient removal in wastewater treatment plants (WWTP), leading to increasing numbers of bacteria enriched in antibiotic resistance genes (ARG). However, the potential transfer of ARG and their host bacteria between different environments remains largely unexplored. Since many factors need to be fulfilled for a transfer between different environments, we hypothesized that antibiotic resistance (ABR) is less frequently transferred between environments in the same geographical region but rather develops and clusters in each distinct environment, leading to characteristic metagenome patterns in samples of different environments. We sampled agricultural soils, a WWTP and private households and performed metagenomic analyses to evaluate differences and potential overlaps in bacterial communities and resistomes of different environments. Wastewater revealed significantly higher richness of ARG (n = 40) and mobile genetic elements (n = 52) than soil and household samples. Bacterial communities differed between the environments and antibiotic resistance factors clustered distinctly. Overall, only few overlaps of ARG between the environments were observed, leading to the conclusion that ABR predominantly develops in individual environments as caused by environmental filtering for ARG, while a transfer between different environments is less likely.

Climate change is accelerating the spread of plants and their associated species to new ranges. The differences in range shift capacity of the various types of species may disrupt long-term co-evolved relationships especially those belowground, however, this may be less so for seed-borne endophytic microbes. We collected seeds and soil of the range-expanding Centaurea stoebe and the congeneric Centaurea jacea from three populations growing in Slovenia (native range of both Centaurea species) and the Netherlands (expanded range of C. stoebe, native range of C. jacea). We isolated and identified endophytic fungi directly from seeds, as well as from roots of the plants grown in Slovenian, Dutch or sterilized soil to compare fungal endophyte composition. Furthermore, we investigated whether C. stoebe hosts a reduced community composition of endophytes in the expanded range due to release from plant-species specific fungi while endophyte communities in C. jacea in both ranges are similar. We cultivated 46 unique and phylogenetically diverse endophytes. A majority of the seed endophytes resembled potential pathogens, while most root endophytes were not likely to be pathogenic. Only one endophyte was found in both roots and seeds, but was isolated from different plant species. Unexpectedly, seed endophyte diversity of southern C. stoebe populations was lower than of populations from the north, while the seed endophyte community composition of northern C. stoebe populations was significantly different southern C. stoebe as well as northern and southern C. jacea populations. Root endophyte diversity was considerably lower in C. stoebe than in C. jacea independent of plant and soil origin, but this difference disappeared when plants were grown in sterile soils. We conclude that the community composition of fungal endophytes not only differs between related plant species but also between populations of plants that expand their range compared to their native habitat. Our results suggest that fungal endophytes of two Centaurea species are not able to systemically infect plants. We highlight that endophytes remain poorly studied and further work should investigate the functional importance of endophytes.