RESUMEN
Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.
Asunto(s)
Biología Computacional , Cartilla de ADN , Eucariontes , ARN Ribosómico 18S , Microbiología del Suelo , ARN Ribosómico 18S/genética , Biología Computacional/métodos , Eucariontes/genética , Eucariontes/clasificación , Cartilla de ADN/genética , Biodiversidad , Temperatura , Suelo/parasitología , Suelo/química , Reacción en Cadena de la PolimerasaRESUMEN
Highly diverse and abundant organisms coexist in soils. However, the contribution of biotic interactions between soil organisms to microbial community assembly remains to be explored. Here, we assess the extent to which soil fauna can shape microbial community assembly using an exclusion experiment in a grassland field to sort soil biota based on body size. After 1 year, the exclusion of larger fauna favoured phagotrophic protists, with increases up to 32% in their proportion compared to the no-mesh treatment. In contrast, members of the bacterial community and to a lesser extent of the fungal community were negatively impacted. Shifts in bacterial but not in fungal communities were best explained by the response of the protistan community to exclusion. Our findings provide empirical evidence of top-down control on the soil microbial communities and underline the importance of integrating higher trophic levels for a better understanding of the soil microbiome assembly.
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Bacterias , Hongos , Pradera , Microbiota , Microbiología del Suelo , Hongos/fisiología , Animales , Eucariontes/fisiología , Suelo/química , Tamaño CorporalRESUMEN
Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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Eucariontes , Eucariontes/genética , ARN Ribosómico 18S/genética , Bases de Datos Genéticas , Bases de Datos de Ácidos Nucleicos , Animales , Genes de ARNr/genética , FilogeniaRESUMEN
Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.
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Embryophyta , Microbiota , Microbiología del Suelo , Biodiversidad , Suelo/químicaRESUMEN
Predatory protists play a central role in nutrient cycling and are involved in other ecosystem functions by predating the microbiome. While most soil predatory protist species arguably are bacterivorous, some protist species can prey on eukaryotes. However, studies about soil protist feeding mainly focused on bacteria as prey and rarely tested both bacteria and eukaryotes as potential prey. In this study, we aimed to decipher soil predator-prey interactions of three amoebozoan and three heterolobosean soil protists and potential bacterial (Escherichia coli; 0.5-1.5 µm), fungal (Saccharomyces cerevisiae; 5-7 µm) and protist (Plasmodiophora brassicae; 3-5 µm) prey, either as individual prey or in all their combinations. We related protist performance (relative abundance) and prey consumption (qPCR) to the protist phylogenetic group and volume. We showed that for the six soil protist predators, the most suitable prey was E. coli, but some species also grew on P. brassicae or S. cerevisiae. While protist relative abundances and growth rates depended on prey type in a protist species-specific manner, phylogenetic groups and volume affected prey consumption. Yet we conclude that protist feeding patterns are mainly species-specific and that some known bacterivores might be more generalist than expected, even preying on eukaryotic plant pathogens such as P. brassicae.
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Suelo , Especificidad de la Especie , Suelo/parasitología , Suelo/química , Escherichia coli/fisiología , Conducta Predatoria/fisiología , Cadena Alimentaria , Microbiología del Suelo , Saccharomyces cerevisiae/fisiología , Eucariontes/fisiología , Eucariontes/clasificación , FilogeniaRESUMEN
Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2â¯mm; small macroaggregates, 0.25-2â¯mm; and microaggregates, < 0.25â¯mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower ß-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.
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Nematodos , Suelo , Animales , Suelo/química , Microbiología del Suelo , Hongos , Tamaño Corporal , Carbono , Nitrógeno , Fósforo , AzufreRESUMEN
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.
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Biodiversidad , Ecosistema , Biomasa , Agricultura , SueloRESUMEN
Trait-based approaches are being increasingly adopted to understand species' ecological strategies and how organisms influence ecosystem function. Trait-based research on soil organisms, however, remains poorly developed compared with that for plants. The abundant and diverse soil nematodes are prime candidates to advance trait-based approaches belowground, but a unified trait framework to describe nematode ecological strategies and assess their linkages with ecosystem function is lacking. We categorized nematode traits as morphological, physiological, life history, and community clusters, and proposed the nematode economics spectrum (NES) to better understand nematode ecological strategies and their association with ecosystem function. We argue that bridging the NES and the plant economics spectrum will facilitate a more holistic understanding of ecosystem carbon and nutrient cycling under global change.
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Ecosistema , Nematodos , Animales , Nematodos/fisiología , Suelo/parasitología , Suelo/química , Rasgos de la Historia de Vida , Plantas/parasitologíaRESUMEN
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.
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Solanum lycopersicum , Incidencia , Microbiología del Suelo , Eucariontes , Bacterias , SueloRESUMEN
Urbanization negatively impacts aboveground biodiversity, such as bird and insect communities. City parks can reduce these negative impacts by providing important habitat. However, it remains poorly understood how the degree of urbanization and vegetation types within city parks (e.g., lawns, woodland) impact soil biodiversity. Here we investigated the impact of the degree of urbanization (urban vs. suburban) and vegetation type (lawn, shrub-lawn, tree-lawn and tree-shrub mixtures) on soil biodiversity in parkland systems. We used eDNA metabarcoding to characterize soil biodiversity of bacteria, fungi, protists, nematodes, meso- and macrofauna across park vegetation types in urban and suburban regions in Xiamen, China. We observed a strong effect of the degree of urbanization on the richness of different soil biota groups, with higher species richness of protists and meso/macrofauna in urban compared to suburban areas, while the richness of bacteria and fungi did not differ, and the difference of nematode richness depended on vegetation type. At the functional level, increased degree of urbanization associated with greater species richness of bacterivores, plant pathogens and animal parasites. These urbanization effects were at least partly modulated by higher soil phosphorous levels in urban compared to suburban sites. Also, the vegetation type impacted soil biodiversity, particularly fungal richness, with the richness of pathogenic and saprotrophic fungi increasing from lawn to tree-shrub mixtures. Tree-shrub mixtures also had the highest connectedness between biotas and lowest variation in the soil community structure. Overall, we show that soil biodiversity is strongly linked to the degree of urbanization, with overall richness increasing with urbanization, especially in bacterivores, plant pathogens and animal parasites. Targeted management of vegetation types in urban areas should provide a useful way to help mitigate the negative effect of urbanization on soil biodiversity.
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Biodiversidad , Urbanización , Animales , Biota , China , SueloRESUMEN
Microbiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the role of microbiome predators in soil functioning? (2) How does global change affect microbiome predators and their functions? (3) How can microbiome predators be applied in agriculture? We show that there is sufficient evidence for the vital role of microbiome predators in soils and stress that global changes impact their functions, something that urgently needs to be addressed to better understand soil functioning as a whole. We are convinced that there is a potential for the application of microbiome predators in agricultural settings, as they may help to sustainably increase plant growth. Therefore, we plea for more applied research on microbiome predators.
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Microbiota , Suelo , Agricultura , Microbiología del SueloRESUMEN
Aboveground, large and higher trophic-level organisms often respond more strongly to environmental changes than small and lower trophic-level organisms. However, whether this trophic or size-dependent sensitivity also applies to the most abundant animals, microscopic soil-borne nematodes, remains largely unknown. Here, we sampled an altitudinal transect across the Tibetan Plateau and applied a community-weighted mean (CWM) approach to test how differences in climatic and edaphic properties affect nematode CWM biomass at the level of community, trophic group and taxon mean biomass within trophic groups. We found that climatic and edaphic properties, particularly soil water-related properties, positively affected nematode CWM biomass, with no overall impact of altitude on nematode CWM biomass. Higher trophic-level omnivorous and predatory nematodes responded more strongly to climatic and edaphic properties, particularly to temperature, soil pH, and soil water content than lower trophic-level bacterivorous and fungivorous nematodes. However, these differences were likely not (only) driven by size, as we did not observe significant interactions between climatic and edaphic properties and mean biomasses within trophic groups. Together, our research implies a stronger, size-independent trophic sensitivity of higher trophic-level nematodes compared with lower trophic-level ones. Therefore, our findings provide new insights into the mechanisms underlying nematode body size structure in alpine grasslands and highlight that traits independent of size need to be found to explain increased sensitivity of higher trophic-level nematodes to climatic and edaphic properties, which might affect soil functioning.
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Nematodos , Animales , Biomasa , Suelo , Tamaño Corporal , Agua , EcosistemaRESUMEN
Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.
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Ecosistema , Suelo , Eucariontes/genética , Ecología , Biodiversidad , BacteriasRESUMEN
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.
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Biodiversidad , Ecosistema , Biomasa , Suelo/química , Estado NutricionalRESUMEN
Plant-nematode interactions are mainly considered from the negative aspect with a focus on plant-parasitic nematodes (PPNs), which is justified considering the agronomic losses caused by PPNs. Despite the fact that PPNs are outnumbered by nonparasitic free-living nematodes (FLNs), the functional importance of FLNs, especially with regard to plant performance, remains largely unknown. Here, we provide a comprehensive overview and most recent insights into soil nematodes by showing direct and indirect links of both PPNs and FLNs with plant performance. We especially emphasize the knowledge gaps and potential of FLNs as important indirect players in driving plant performance such as stimulating the resistance to pests via improving the disease suppressive activity of the rhizobiome. Together, we present a holistic view of soil nematodes as positive and negative contributors to plant performance, accentuating the positive but underexplored role of FLNs.
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Nematodos , Enfermedades de las Plantas , Animales , Enfermedades de las Plantas/parasitología , Plantas/parasitología , Agricultura/métodos , SueloRESUMEN
Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging-if not impossible-without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, archaea, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet is severely understudied. In this perspective, we (i) synthesize existing knowledge about virus-microbe-temperature interactions and (ii) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands-globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs.
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Virosis , Virus , Humanos , Ecosistema , Calentamiento Global , Cambio Climático , CarbonoRESUMEN
The physiological performance of organisms depends on their environmental context, resulting in performance-response curves along environmental gradients. Parasite performance-response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we (1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and (2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesize knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host-parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance-response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions.
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Interacciones Huésped-Parásitos , Parásitos , Animales , Interacciones Huésped-Parásitos/fisiología , Temperatura , Aclimatación , Adaptación Fisiológica , Cambio ClimáticoRESUMEN
Host-associated fungi can help protect plants from pathogens, and empirical evidence suggests that such microorganisms can be manipulated by introducing probiotic to increase disease suppression. However, we still generally lack the mechanistic knowledge of what determines the success of probiotic application, hampering the development of reliable disease suppression strategies. We conducted a three-season consecutive microcosm experiment in which we amended banana Fusarium wilt disease-conducive soil with Trichoderma-amended biofertilizer or lacking this inoculum. High-throughput sequencing was complemented with cultivation-based methods to follow changes in fungal microbiome and explore potential links with plant health. Trichoderma application increased banana biomass by decreasing disease incidence by up to 72%, and this effect was attributed to changes in fungal microbiome, including the reduction in Fusarium oxysporum density and enrichment of pathogen-suppressing fungi (Humicola). These changes were accompanied by an expansion in microbial carbon resource utilization potential, features that contribute to disease suppression. We further demonstrated the disease suppression actions of Trichoderma-Humicola consortia, and results suggest niche overlap with pathogen and induction of plant systemic resistance may be mechanisms driving the observed biocontrol effects. Together, we demonstrate that fungal inoculants can modify the composition and functioning of the resident soil fungal microbiome to suppress soilborne disease.
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Fusarium , Musa , Trichoderma , Enfermedades de las Plantas/prevención & control , Enfermedades de las Plantas/microbiología , Microbiología del Suelo , Suelo , Musa/microbiologíaRESUMEN
There have been major developments in the molecular characterization of soil protist and micrometazoan diversity, leading to a better understanding of these minute soil eukaryotes. Like in all newly developing research fields, several approaches are currently used in parallel to study these organisms. Here, we synthesize these various approaches and propose a best practice manual that should help researchers to efficiently target soil eukaryotic diversity as a whole. We cover the whole working pipeline, ranging from sampling to nucleic acids extraction to bioinformatic processing and sequence identification. Synchronous approaches to molecularly survey microbial-sized eukaryotes and other soil biodiversity groups are needed in order to provide a cumulative knowledge of soil biodiversity, as here shown for the soil eukaryome. This will be crucial in understanding the important ecosystem functions provided by soil biodiversity.
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Eucariontes , Suelo , Eucariontes/genética , Ecosistema , Biodiversidad , Código de Barras del ADN TaxonómicoRESUMEN
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.