Grazing intensity alters network complexity and predator-prey relationships in the soil microbiome.

Grasslands are recognized as important reservoirs of soil biodiversity. Livestock grazing is implemented as a grassland management strategy to improve soil quality and enhance plant diversity. Soil microbial communities play a pivotal role in grassland ecosystems, so it is important to examine whether grazing practices affect the soil microbiome. Previous studies on grazing have primarily focused on bacteria and fungi, overlooking an important group-protists. Protists are vital in soil microbiomes as they drive nutrient availability and trophic interactions. Determining the impact of grazing on protists and their relationships with bacterial and fungal communities is important for understanding soil microbiome dynamics in grazed ecosystems. In this study, we investigated soil bacterial, fungal, and protist communities under four grazing levels: no grazing, moderate-use grazing, full-use grazing, and heavy-use grazing. Our results showed that heavy grazing led to a greater diversity of protists with specific groups, such as Discoba and Conosa, increasing in abundance. We also found strong associations between protist and bacterial/fungal members, indicating their intricate relationships within the soil microbiome. For example, the abundance of predatory protists increased under grazing while arbuscular mycorrhizal fungi decreased. Notably, arbuscular mycorrhizae were negatively associated with predatory groups. Furthermore, we observed that microbial network complexity increased with grazing intensity, with fungal members playing an important role in the network. Overall, our study reports the impact of temporal grazing intensity on soil microbial dynamics and highlights the importance of considering protist ecology when evaluating the effects of grazing on belowground communities in grassland ecosystems. IMPORTANCE: The significance of this study lies in its exploration of the effects of temporal grazing intensity on the dynamics of the soil microbiome, specifically focusing on the often-neglected role of protists. Our findings provide insights into the complex relationships between protists, bacteria, and fungi, emphasizing their impact on trophic interactions in the soil. Gaining a better understanding of these dynamics is essential for developing effective strategies for grassland management and conservation, underscoring the importance of incorporating protist ecology into microbiome studies in grasslands.

The role of halophyte-induced saline fertile islands in soil microbial biogeochemical cycling across arid ecosystems.

Halophyte shrubs, prevalent in arid regions globally, create saline fertile islands under their canopy. This study investigates the soil microbial communities and their energy utilization strategies associated with tamarisk shrubs in arid ecosystems. Shotgun sequencing revealed that high salinity in tamarisk islands reduces functional gene alpha-diversity and relative abundance compared to bare soils. However, organic matter accumulation within islands fosters key halophilic archaea taxa such as Halalkalicoccus, Halogeometricum, and Natronorubrum, linked to processes like organic carbon oxidation, nitrous oxide reduction, and sulfur oxidation, potentially strengthening the coupling of nutrient cycles. In contrast, bare soils harbor salt-tolerant microbes with genes for autotrophic energy acquisition, including carbon fixation, H2 or CH4 consumption, and anammox. Additionally, isotope analysis shows higher microbial carbon use efficiency, N mineralization, and denitrification activity in tamarisk islands. Our findings demonstrate that halophyte shrubs serve as hotspots for halophilic microbes, enhancing microbial nutrient transformation in saline soils.

The impact of fungi on soil protist communities in European cereal croplands.

Protists, a crucial part of the soil food web, are increasingly acknowledged as significant influencers of nutrient cycling and plant performance in farmlands. While topographical and climatic factors are often considered to drive microbial communities on a continental scale, higher trophic levels like heterotrophic protists also rely on their food sources. In this context, bacterivores have received more attention than fungivores. Our study explored the connection between the community composition of protists (specifically Rhizaria and Cercozoa) and fungi across 156 cereal fields in Europe, spanning a latitudinal gradient of 3000 km. We employed a machine-learning approach to measure the significance of fungal communities in comparison to bacterial communities, soil abiotic factors, and climate as determinants of the Cercozoa community composition. Our findings indicate that climatic variables and fungal communities are the primary drivers of cercozoan communities, accounting for 70% of their community composition. Structural equation modelling (SEM) unveiled indirect climatic effects on the cercozoan communities through a change in the composition of the fungal communities. Our data also imply that fungivory might be more prevalent among protists than generally believed. This study uncovers a hidden facet of the soil food web, suggesting that the benefits of microbial diversity could be more effectively integrated into sustainable agriculture practices.

Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling.

Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.

Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil.

Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.

Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe.

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains.

Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.

The impact of agricultural management on soil aggregation and carbon storage is regulated by climatic thresholds across a 3000 km European gradient.

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (-56%) and SOC stocks (-35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.

Soil microbiomes and one health.

The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions.

Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.

Contrasting effect of irrigation practices on the cotton rhizosphere microbiota and soil functionality in fields.

Drip irrigation under plastic film mulch is a common agricultural practice used to conserve water. However, compared to traditional flood irrigation with film mulch, this practice limit cotton root development from early flowering stage and may cause premature senescence in cotton. Changes of root will consequently shape the composition and activity of rhizosphere microbial communities, however, the effect of this farming practice on cotton rhizosphere microbiota remains poorly understood. This study investigated rhizosphere bacteria and soil functionality in response to different irrigation practices -including how changes in rhizosphere bacterial diversity alter soil nutrient cycling. Drip irrigation under plastic film mulch was shown to enhance bacterial diversity by lowering the salinity and increasing the soil moisture. However, the reduced root biomass and soluble sugar content of roots decreased potential copiotrophic taxa, such as Bacteroidetes, Firmicutes, and Gamma-proteobacteria, and increased potential oligotrophic taxa, such as Actinobacteria, Acidobacteria, and Armatimonadetes. A core network module was strongly correlated with the functional potential of soil. This module not only contained most of the keystone taxa but also comprised taxa belonging to Planctomycetaceae, Gemmatimonadaceae, Nitrosomonadaceae, and Rhodospirillaceae that were positively associated with functional genes involved in nutrient cycling. Drip irrigation significantly decreased the richness of the core module and reduced the functional potential of soil in the rhizosphere. Overall, this study provides evidence that drip irrigation under plastic film mulch alters the core bacterial network module and suppresses soil nutrient cycling.

Concerted Evaluation of Pesticides in Soils of Extensive Grassland Sites and Organic and Conventional Vegetable Fields Facilitates the Identification of Major Input Processes.

The intensive use of pesticides and their subsequent distribution to the environment and non-target organisms is of increasing concern. So far, little is known about the occurrence of pesticides in soils of untreated areas─such as ecological refuges─as well as the processes contributing to this unwanted pesticide contamination. In this study, we analyzed the presence and abundance of 46 different pesticides in soils from extensively managed grassland sites, as well as organically and conventionally managed vegetable fields (60 fields in total). Pesticides were found in all soils, including the extensive grassland sites, demonstrating a widespread background contamination of soils with pesticides. The results suggest that after conversion from conventional to organic farming, the organic fields reach pesticide levels as low as those of grassland sites not until 20 years later. Furthermore, the different pesticide composition patterns in grassland sites and organically managed fields facilitated differentiation between long-term persistence of residues and diffuse contamination processes, that is, short-scale redistribution (spray drift) and long-scale dispersion (atmospheric deposition), to offsite contamination.

Core Microbiota in the Rhizosphere of Heavy Metal Accumulators and Its Contribution to Plant Performance.

Persistent microbial symbioses can confer greater fitness to their host under unfavorable conditions, but manipulating such beneficial interactions necessitates a mechanistic understanding of the consistently important microbiomes for the plant. Here, we examined the phylogenetic profiles and plant-beneficial traits of the core microbiota that consistently inhabits the rhizosphere of four divergent Cd hyperaccumulators and an accumulator. We evidenced the existence of a conserved core rhizosphere microbiota in each plant distinct from that in the non-hyperaccumulating plant. Members of Burkholderiaceae and Sphingomonas were the shared cores across hyperaccumulators and accumulators. Several keystone taxa in the rhizosphere networks were part of the core microbiota, the abundance of which was an important predictor of plant Cd accumulation. Furthermore, an inoculation experiment with synthetic communities comprising isolates belonging to the shared cores indicated that core microorganisms could facilitate plant growth and metal tolerance. Using RNA-based stable isotope probing, we discovered that abundant core taxa overlapped with active rhizobacteria utilizing root exudates, implying that the core rhizosphere microbiota assimilating plant-derived carbon may provide benefits to plant growth and host phenotype such as Cd accumulation. Our study suggests common principles underpinning hyperaccumulator-microbiome interactions, where plants consistently interact with a core set of microbes contributing to host fitness and plant performance. These findings lay the foundation for harnessing the persistent root microbiomes to accelerate the restoration of metal-disturbed soils.

Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts.

Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope 33P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring 33P and transferred 64% more 33P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal 33P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced 33P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.

Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations.

Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. As the rhizosphere microbiome is a major determinant of plant health, we postulated that such a binary outcome may result from an early divergence in the rhizosphere microbiome assembly that may further cascade into varying disease suppression abilities. We tested this hypothesis by setting up a longitudinal study of tomato plants growing in a natural but homogenized soil infested with the soilborne bacterial pathogen Ralstonia solanacearum. Starting from an originally identical species pool, individual rhizosphere microbiome compositions rapidly diverged into multiple configurations during the plant vegetative growth. This variation in community composition was strongly associated with later disease development during the later fruiting state. Most interestingly, these patterns also significantly predicted disease outcomes 2 weeks before any difference in pathogen density became apparent between the healthy and diseased groups. In this system, a total of 135 bacterial OTUs were associated with persistent healthy plants. Five of these enriched OTUs (Lysinibacillus, Pseudarthrobacter, Bordetella, Bacillus, and Chryseobacterium) were isolated and shown to reduce disease severity by 30.4-100% when co-introduced with the pathogen. Overall, our results demonstrated that an initially homogenized soil can rapidly diverge into rhizosphere microbiomes varying in their ability to promote plant protection. This suggests that early life interventions may have significant effects on later microbiome states, and highlights an exciting opportunity for microbiome diagnostics and plant disease prevention.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield.

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of 15N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the ß-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and ß-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Halophytes increase rhizosphere microbial diversity, network complexity and function in inland saline ecosystem.

Salinization is an important global environmental problem influencing sustainable development of terrestrial ecosystems. Salt-tolerant halophytes are often used as a promising approach to remedy the saline soils. Yet, how rhizosphere microbes' association and functions vary with halophytes in saline ecosystems remains unclear, restricting our ability to assess the role of halophytes in remedying saline ecosystems. Herein, we examined bacterial and fungal diversities, compositions, and co-occurrence networks in the rhizospheres of six halophytes and bulk soils in a semiarid inland saline ecosystem, and related these parameters to microbial functions. The microbiomes were more diverse and complex and microbial activity and residues were higher in rhizospheres than bulk soils. The connections of taxa in the rhizosphere microbial communities increased with fungi-fungi and bacteria-fungi connections and fungal diversity. The proportion of the fungi-related central connections were larger in rhizospheres (13-73%) than bulk soils (3%). Moreover, microbial activity and residues were significantly correlated with microbial composition and co-occurrence network complexity. These results indicated that enhanced association between fungi and bacteria increased microbial co-occurring network complexity in halophytes rhizosphere, which contributed to the higher microbial functions (microbial activities and residue) in this inland saline ecosystem.

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.

BACKGROUND: Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. RESULTS: We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. CONCLUSIONS: Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.

Compositional and functional succession of bacterial and fungal communities is associated with changes in abiotic properties during pig manure composting.

While both bacteria and fungi are important for the degradation and humification of organic matter during composting, it is unclear to what extent their roles are associated with abiotic compost properties. This study evaluated changes in abiotic compost properties and the succession of bacterial and fungal communities during pig manure composting for 90 days. The compost rapidly reached thermophilic phase (>58 ℃), which lasted for 15 days. Both bacterial and fungal community compositions changed drastically during composting and while bacterial diversity increased, the fungal diversity decreased during the thermophilic phase of composting. Two taxa dominated both bacterial (Bacillales and Clostridiales) and fungal (Eurotiales and Glomerellales) communities and these showed alternating abundance fluctuations following different phases of composting. The abundance fluctuations of most dominant bacterial and fungal taxa could be further associated with decreases in the concentrations of fulvic acid, cellulose, hemicellulose and overall biodegradation potential in the compost. Moreover, bacterial predicted metabolic gene abundances dominated the first three phases of composting, while predicted fungal saprotrophic functional genes increased consistently, reaching highest abundances towards the end of composting. Finally, redundancy analysis (RDA) showed that changes in abiotic compost properties correlated with the bacterial community diversity and carbohydrate metabolism and fungal wood saprotrophic function. Together these results suggests that bacterial and fungal community succession was associated with temporal changes in abiotic compost properties, potentially explaining alternating taxa abundance patterns during pig manure composting.

Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage.

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.