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Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10−2-1.5 × 10−1 copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas.

Abstract Introduction Protists are unicellular eukaryotes including important predators, parasites and phototrophs, and play pivotal roles in organic matter decomposition, biogeochemical nutrient cycling and various ecosystem functions. Unravelling the impact of climate warming on soil protists is paramount in predicting how these microorganisms will continue to provide essential ecosystem services in the face of changing climatic conditions. Materials and Methods We examined the effects of 5‐year simulated climate warming scenario, with temperatures increased by 4°C above ambient levels, on the diversity and community composition of soil protists, as well as their interactions with other microorganisms in both natural and plantation forest ecosystems during three seasons: summer, autumn and winter. Results We found a season‐dependent response of protists to climate warming, with a significant decrease in protist diversity during winter in natural forests. Furthermore, we identified significant alterations in the community compositions of protists during summer in both natural and plantation forests, as well as during winter in both forest types, under warming. Our analysis pinpointed specific functional protist taxa, such as consumers, parasites and phototrophs, which exhibited significant shifts in their relative abundances under warming. Additionally, we found that warming facilitated trophic interactions between protists and bacteria, while also strengthening interactions between bacterial and fungal communities. Warming could induce direct modifications in protist community compositions or indirectly affect them by modifying bacterial and fungal communities, as revealed by structural equation modelling. Conclusion These findings demonstrate the substantial impact of warming on the taxonomic and functional compositions of protists in forest ecosystems, with the magnitude of these effects varying across seasons. Our study implicates that ongoing climate warming could have significant consequences for the profiles of soil protists, as well as their trophic interactions with bacteria and fungi, highlighting the importance of considering these effects for the sustainable provision of ecosystem functions.

ABSTRACTPlant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil–plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Abstract Introduction Fungal communities are key players in the soil biogeochemical processes of forest ecosystems. Although it has been illustrated that soil fungi are susceptible to environmental changes, little is known about the interactive effects of nitrogen (N) and phosphorus (P) enrichment on the soil fungal functional guild. Materials and Methods Here, a 5‐year N and P addition manipulation experiment was conducted in two growing stages (i.e., tree ages 80 years) of a subtropical forest, in which soil fungal diversity and functional guilds were investigated using a multiple‐time sampling strategy. Results Fungal species richness and Shannon indices were significantly different across sampling times. Fungal community composition was significantly affected by both N and P addition but not by forest age. Old forest had a higher fungal network complexity than young forest, and fertilisation decreased soil fungal network complexity and generated looser and more random networks in comparison with the control. The community composition of symbiotrophic and saprotrophic fungi was significantly impacted by N and P addition and correlated with soil available P and total P contents and soil C:P and N:P. Conclusions Our findings highlight that soil P availability has a strong effect on soil fungal communities and their functional guild composition in the subtropical forest.

Abstract Predatory protists are widely recognized as critical biotic forces driving soil microbial communities, but their top‐down controls on ammonia‐oxidizing microorganisms (AOMs), the major players in nitrification, are largely unresolved. Here, we investigated the communities of predatory protists and their associations with AOMs using high‐throughput sequencing and network analysis in soil aggregates following various long‐term organic substitutions. We found that organic substitutions increased while soil aggregation decreased the alpha diversity of predatory protists. Predatory protistan communities were significantly associated with AOMs. Variosea, an important group of Amoebozoa, were the keystone predatory protists associated with the AOMs. Collectively, our findings highlight the importance of predatory protists, especially Variosea, in regulating the communities of AOMs in an acidic Ultsisol, with implications for managing nitrification by predatory protists in agricultural soils.

Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.

Widespread forest fires pose significant challenges to the diverse communities of soil-dwelling organisms and the multiple ecosystem functions they support. However, whether the biodiversity and interactions of various taxonomic groups respond to fire consistently in terms of direction and extent, and their relative role in regulating post-fire soil functioning, remains largely unexplored. In this study, we investigated whether the diversity and co-occurrence networks of soil organisms across various trophic levels (including bacteria, fungi, protists, and invertebrates) in subtropical forests exhibit consistent responses to fire. Furthermore, we investigated their contribution to regulating soil multifunctionality, which is measured by a range of soil extracellular enzyme activities, available nutrients and reduced potential fungal plant pathogens. Our findings revealed that fire led to a decline in the richness of fungi, protists, and invertebrates, without significantly impacting bacterial richness. Fire also simplified the microbial co-occurrence networks while complexifying the invertebrate networks. Interestingly, soil multifunctionality tended to decrease with the richness of lower-trophic communities (i.e., bacteria), whereas it increased with that of high-trophic communities (i.e., protists and invertebrates). Moreover, fire indirectly influenced soil multifunctionality by altering biodiversity and network complexity, particularly pronounced in high-trophic communities. Overall, our results underscored the divergent vulnerability of biodiversity and networks to fires across taxa groups, highlighting the crucial role of biodiversity and interactions of higher trophic taxa groups in shaping the recovery and functionality of fire-affected soils.

This study investigated the abundance of comammox bacteria and canonical ammonia-oxidizing bacteria (AOB) and archaea (AOA), and their relative contribution to nitrification along a chronosequence of deglaciated forelands. The results showed that nitrification related gene abundance tended to increase with glacier retreat, with comammox bacteria and AOA appearing to be the most critical drivers for soil nitrification rates. These findings provide new evidence for the presence of comammox bacteria in glacier forelands and enhance our understanding of the niche differentiation of canonical nitrifier and comammox bacteria.

Abstract Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.

Abstract Background Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. Results We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. Conclusions Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract

Abstract Introduction Nitrification inhibitors and straw incorporation are used to reduce microbial mediated nitrogen (N) losses, thereby increasing N use efficiency (NUE) in cropland soil, but their effects on nitrous oxide (N2O) emission across different soil types and the underlying molecular mechanisms remain less understood. Materials and Methods In this study, we investigated how nitrification inhibitor nitrapyrin and straw incorporation affected soil N balance, N2O emission, nitrifiers and denitrifiers in three cropland soils (black, fluvo‐aquic and red soils). Results Compared with fertilization‐only treatment (N), nitrapyrin addition increased ammonium, while it decreased nitrate concentration in all soils; however, the performance of straw incorporation was less significant. Nitrapyrin decreased N2O emission only in the fluvo‐aquic soil, while straw incorporation strongly increased N2O emission in the red soil. Terminal restriction fragment length polymorphism analysis revealed that the denitrifier community was distinct across the three soils, but not strongly structured by nitrapyrin or straw incorporation. Compared with the N treatment, straw incorporation and nitrapyrin increased nosZ gene abundance only in the black soil. Structural equational modelling further confirmed that, after accounting for different soil properties, straw incorporation significantly increased N2O emission from black and red soils, and a decrease in nosZ gene abundance was the main biological factor for increased N2O emission in red soil. Conclusion Taken together, our work provides new knowledge that the performance of nitrification inhibitor and straw incorporation on N2O emission is soil type‐dependent, and management practices should be used as per soil type to balance NUE and N2O emission.

Screening high-tolerant microorganisms to cadmium (Cd) and revealing their bio-obstruction mechanism could be significant for Cd regulation from farmland to the food chain. We examined the tolerance and bio-removal efficiency of Cd ions of two bacterial strains, Pseudomonas putida 23483 and Bacillus sp. GY16, and measured the accumulation of Cd ions in rice tissues and its different chemical forms in soil. The results showed that the two strains had high tolerance to Cd, but the removal efficiency was decreased successively with increasing Cd concentrations (0.05 to 5 mg kg−1). Cell-sorption accounted for the major proportion of Cd removal compared with excreta binding in both strains, which was conformed to the pseudo-second-order kinetics. At the subcellular level, Cd was mostly taken up by the cell mantle and cell wall, and only a small amount entered into the cytomembrane and cytoplasmic with time progressed (0 to 24 h) in each concentration. The cell mantle and cell wall sorption decreased with increasing Cd concentration, especially in the cytomembrane and cytoplasmic. The scanning electron microscope (SEM) and energy dispersive X-ray (EDS) analysis verified that Cd ions were attached to the cell surface, and the functional groups of C-H, C-N, C=O, N-H, and O-H in the cell surface may participate in cell-sorption process tested by the FTIR analysis. Furthermore, inoculation of the two strains significantly decreased Cd accumulation in rice straw and grain but increased in the root, increased Cd enrichment ratio in root from soil, decreased Cd translocation ratio from root to straw and grain, and increased the Cd concentrations of Fe–Mn binding form and residual form in rhizosphere soil. This study highlights that the two strains mainly removed Cd ions in solution through biosorption and passivated soil Cd as Fe–Mn combined form ascribe to its characteristics of manganese-oxidizing, eventually achieving bio-obstruction of Cd from soil to rice grain.

Abstract Background Metal(loid)s can promote the spread and enrichment of antibiotic resistance genes (ARGs) in the environment through a co-selection effect. However, it remains unclear whether exposure of microorganisms to varying concentrations of selenium (Se), an essential but potentially deleterious metal(loid) to living organisms, can influence the migration and distribution of ARGs in forest soils. Results Precisely 235 ARGs conferring resistance to seven classes of antibiotics were detected along a Se gradient (0.06–20.65 mg kg−1) across 24 forest soils. (flor)/(chlor)/(am)phenicol resistance genes were the most abundant in all samples. The total abundance of ARGs first increased and then decreased with an elevated available Se content threshold of 0.034 mg kg−1 (P = 2E−05). A structural equation model revealed that the dominant mechanism through which Se indirectly influences the vertical migration of ARGs is by regulating the abundance of the bacterial community. In addition, the methylation of Se (mediated by tehB) and the repairing of DNA damages (mediated by ruvB and recG) were the dominant mechanisms involved in Se resistance in the forest soils. The co-occurrence network analysis revealed a significant correlated cluster between Se-resistance genes, MGEs and ARGs, suggesting the co-transfer potential. Lelliottia amnigena YTB01 isolated from the soil was able to tolerate 50 μg mL−1 ampicillin and 1000 mg kg−1 sodium selenite, and harbored both Se resistant genes and ARGs in the genome. Conclusions Our study demonstrated that the spread and enrichment of ARGs are enhanced under moderate Se pressure but inhibited under severe Se pressure in the forest soil (threshold at 0.034 mg kg−1 available Se content). The data generated in this pilot study points to the potential health risk associated with Se contamination and its associated influence on ARGs distribution in soil.

Summary It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant‐associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome‐based innovations to promote plant productivity and contribute to the end of hunger.

Abstract Introduction Fungal plant pathogens are an emerging threat to economically important crop production worldwide and a significant risk to global food security. However, we have limited knowledge of how agricultural management practices drive the emergence and spread of pathogens within crop microbiomes and the underlying ecological mechanisms. Materials and Methods We characterized the profiles of potential fungal plant pathogens, as well as bacterial and protistan communities, in sorghum phyllosphere, root endosphere, and rhizosphere and bulk soils collected from a long‐term experiment with multiple inorganic and organic fertilization regimes. Results We found contrasting patterns of fungal plant pathogens across the four sorghum–soil compartments and that organic fertilization regime significantly reduced the diversity and proportions of fungal plant pathogens in rhizosphere and bulk soils. We further found that the changes in fungal plant pathogens were driven more by resident bacterial and protistan communities than by soil physicochemical parameters. There was a significantly negative relationship between the diversity of fungal plant pathogens in the rhizosphere and bulk soils with sorghum yield and protein contents. Structural equation modeling revealed that long‐term organic fertilization regimes contributed to the suppression of fungal plant pathogens mainly through modulating the resident bacterial and protistan communities. Conclusion These findings advance our understanding of the responses of fungal plant pathogens in crop microbiomes to fertilization regimes, with implications for more targeted strategies to manage the impacts of fungal pathogens on plant health and economic losses.

Abstract Introduction Phyllosphere microbiome is intrinsically linked to plant performance and ecosystem functioning. However, our knowledge about the role of ecological processes in shaping the biogeography of different phyllosphere microbial communities is scarce. Materials and Methods Here, we compared the biogeographic patterns of bacterial and fungal communities in phyllosphere samples of plants belonging to the genus of Eucalyptus of the Myrtaceae family collected from an over 4000 km transect. We investigated the relative importance of two major ecosystem processes (stochastic vs. deterministic) in shaping phyllosphere microbial community assemblies. Results Our results demonstrated that the neutral community model, which can quantify the degree of a community assembly determined by stochastic processes, explained 64.2% of the variations in bacterial community assembly, which had a normalized stochasticity ratio of 71.8%. These results suggest that the dominant role of stochastic processes in shaping bacterial community assembly. In contrast, phyllosphere fungal community assembly was mainly shaped by deterministic processes as revealed by a relatively small explanation rate of the neutral community model (48.7%) and a normalized stochasticity ratio of 25.1%. Variation partitioning analysis and random forest modelling results indicated that climatic factors, particularly mean annual precipitation and aridity index, were important in driving both bacterial and fungal biogeographic patterns in the phyllosphere. Edaphic factors, such as soil organic and mineral nitrogen content, were more closely related to fungal community assembly than to bacterial community assembly. The differential responses of bacterial and fungal communities to environmental factors could be attributed to the different traits of bacteria and fungi, that is, the higher potential dispersal rate and wider habitat niche of bacteria than fungi. Conclusion Our findings demonstrated that phyllosphere bacterial and fungal communities followed distinct community assembly processes, which is supported by the ‘size plasticity’ hypothesis that smaller organisms (bacteria) are less influenced by environmental conditions and are more homogeneous across space than larger organisms (fungi). These findings provide new insights into the microbial ecology of plant phyllosphere microbiomes.

Abstract Background Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. Results Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. Conclusions The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.

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

The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha−1) application, rather than medium-rate (18 Mg ha−1) and high-rate (27 Mg ha−1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.

ABSTRACT Deciphering the relationships between microbes and their host plants is critical for a better understanding of microbial diversity maintenance and community stability. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a subtropical common-garden experiment. The results showed that fungal community structures significantly differed across compartments (leaf, root, and soil) and different tree species. Higher α-diversity was observed in the phyllosphere than in the roots and rhizospheric soil. Fungal community composition (β-diversity) was significantly affected by both compartment and species identity. The fungal community compositions were significantly correlated with soil pH in the roots and the soils as well as with soil nitrate and leaf total phosphorus in the leaves. We found that fungal community assemblies were mainly driven by deterministic processes, regardless of compartments. Moreover, host preference analyses indicated that stronger plant/fungus preferences occurred in leaves than in roots and soils. Our results highlight the differences in tree mycobiome between aboveground and belowground compartments and have important implications for the promotion of biodiversity conservation and management sustainability for the subtropical forest. IMPORTANCE Subtropical mountain forests are widely distributed in Southern China and are characterized by high biodiversity. The interactions between plants and fungi play pivotal roles in biodiversity maintenance and community stability. Nevertheless, knowledge of fungal diversity and of the community assembly patterns of woody plants is scarce. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a common-garden experiment. We found that both compartment and plant identity influenced fungal diversity, community, and guild compositions, while deterministic processes mainly governed the fungal community assembly, especially in the rhizospheric fungal communities. Our results demonstrate that tree leaves represent stronger host/fungi preferences than do roots and soils. Together, our findings enhance the understanding of the roles of compartment and plant identity in structuring fungal communities as well as promote fungal diversity maintenance in subtropical mountain forest ecosystems.

ABSTRACT Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.

Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling.

Soil age is thought to be an important driver of ecosystem development. Here, the authors perform a global survey of soil chronosequences and meta-analysis to show that, contrary to expectations, soil age is a relatively minor ecosystem driver at the biome scale once other drivers such as parent material, climate, and vegetation type are accounted for.

Globally, tomato is the second most cultivated vegetable crop next to potato, preferentially grown in temperate climates. Processing tomatoes are generally produced in field conditions, in which soilborne pathogens have serious impacts on tomato yield and quality by causing diseases of the tomato root system. Major processing tomato-producing countries have documented soilborne diseases caused by a variety of pathogens including bacteria, fungi, nematodes, and oomycetes, which are of economic importance and may threaten food security. Recent field surveys in the Australian processing tomato industry showed that plant growth and yield were significantly affected by soilborne pathogens, especially Fusarium oxysporum and Pythium species. Globally, different management methods have been used to control diseases such as the use of resistant tomato cultivars, the application of fungicides, and biological control. Among these methods, biocontrol has received increasing attention due to its high efficiency, target-specificity, sustainability and public acceptance. The application of biocontrol is a mix of different strategies, such as applying antagonistic microorganisms to the field, and using the beneficial metabolites synthesized by these microorganisms. This review provides a broad review of the major soilborne fungal/oomycete pathogens of the field processing tomato industry affecting major global producers, the traditional and biological management practices for the control of the pathogens, and the various strategies of the biological control for tomato soilborne diseases. The advantages and disadvantages of the management strategies are discussed, and highlighted is the importance of biological control in managing the diseases in field processing tomatoes under the pressure of global climate change.

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

Honeybees provide crucial pollination services and valuable apiarian products. The symbiotic intestinal communities facilitate honeybee health and fitness by promoting nutrient assimilation, detoxifying toxins, and resisting pathogens.

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.

Abstract Nitrogen (N) fertilization has boosted grain production during the past century, while excess N fertilization with declining N use efficiency (NUE) has led to severe pollution in many regions. To achieve the goal of sustainable food production, Technologies and Management Practices (TMPs, e.g., optimum N application rate and methods, N‐transformation inhibitors) have been developed to improve crop yield and NUE and to reduce N losses. However, it remains unclear how N fate has been changed by environmental factors and TMPs. Here, we compiled a dataset of 366 field 15N tracer observations from 74 publications worldwide and conducted a meta‐analysis to examine how environmental conditions and management practices influence the fertilizer‐N fate one growing season after the fertilization of maize. We show that the proportion of 15N taken up by aboveground biomass (NUE15N), was significantly lower in China (33%) than that in North America (42%) and the European Union (54%). Soil organic carbon was the most critical environmental factor positively correlated with NUE15N. Among the nine selected categories of TMPs, deep placement of fertilizer and split application increased the grain yield and decreased the fertilizer‐N loss consistently among studies. Reducing the fertilizer‐N rate could increase the NUE15N but presents risks of yield reduction in some regions. This study demonstrates the importance of SOC and varying impacts of TMPs on the efficiency of fertilizer use in cropping systems globally and provides critical information for farmers and policymakers to improve N management for higher productivity and less pollution.

Soil microbial communities play a central role in driving multiple ecosystem functions and ecological processes that are key to maintaining the plant productivity. However, we lack sound evidence for the linkage between soil microbial diversity and plant productivity, which hinders our ability to predict the consequences of microbial diversity loss for food security under the context of global environmental change. Here, we used the dilution-to-extinction approach to test the consequences of soil microbial diversity loss for the aboveground plant biomass in a glasshouse experiment. Compared with original soils, the bacterial alpha-diversity (Observed operational taxonomic units and Shannon index) significantly decreased in treatments with serially diluted inoculum. Principal coordinates analysis showed that the overall bacterial community compositions (beta-diversity) in original soils were clearly separated from the treatments with serially diluted inoculum. The aboveground biomass of lettuce harvested from the original soils was significantly higher than that from the sterilized soils regardless of the inoculation. The ordinary least squares regression model showed a significant linear relationship between the plant biomass and bacterial alpha-diversity, indicating that reduction in soil microbial diversity could result in a significant decline in the biomass of lettuce. No significant correlation was observed between plant biomass and soil processes including soil basal respiration and denitrification rates. Structural equation models suggested that the effects of soil microbial diversity on the plant biomass were maintained even when simultaneously accounting for other drivers (soil properties and biological processes). Our study provides experimental evidence that soil microbial diversity is important to the maintenance of the plant productivity and suggests that the functional redundancy in soil microbial communities may be overestimated especially in the agroecological system.

Abstract Background The ecological consequences of mercury (Hg) pollution—one of the major pollutants worldwide—on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites. Results We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction). Conclusions Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.

Urban green spaces are closely related to the activities and health of urban residents. Turf grass and soil are two major interfaces between the environmental and human microbiome, which represent potential pathways for the spread of antibiotic resistance genes (ARGs) from environmental to human microbiome through skin-surface contact. However, the information regarding the prevalence of ARGs in urban green spaces and drivers in shaping their distribution patterns remain unclear. Here, we profiled a wide spectrum of ARGs in grass phyllosphere and soils from 40 urban parks across Greater Melbourne, Australia, using high throughput quantitative PCR. A total of 217 and 218 unique ARGs and MGEs were detected in grass phyllosphere and soils, respectively, conferring resistance to almost all major classes of antibiotics commonly used in human and animals. The plant microbiome contained a core resistome, which occupied >84% of the total abundance of ARGs. In contrast, no core resistome was identified in the soil microbiome. The difference between plant and soil resistome composition was attributed to the difference in bacterial community structure and intensity of environmental and anthropogenic influence. Most importantly, the abundance of ARGs in urban green spaces was significantly positively related to industrial factors including total number of business, number of manufacturing, and number of electricity, gas, water and waste services in the region. Structural equation models further revealed that industrial distribution was a major factor shaping the ARG profiles in urban green spaces after accounting for multiple drivers. These findings have important implications for mitigation of the potential risks posed by ARGs to urban residents. Keywords: Resistome, Urban green spaces, Phyllosphere, Anthropogenic activities, Public health

The increasing antimicrobial resistance in manure-amended soil can potentially enter food chain, representing an important vehicle for antibiotic resistance genes (ARGs) transmission into human microbiome. However, the pathways for transmission of ARGs from soil to plant remain unclear. Here, we explored the impacts of poultry and cattle manure application on the patterns of resistome in soil and lettuce microbiome including rhizosphere, root endosphere, leaf endosphere and phyllosphere, to identify the potential transmission routes of ARGs in the soil-plant system. After 90 days of cultivation, a total of 144 ARGs were detected in all samples using high-throughput quantitative PCR. Rhizosphere soil samples harbored the most diverse ARGs compared with other components of lettuce. Cattle manure application increased the abundance of ARGs in root endophyte, while poultry manure application increased ARGs in rhizosphere, root endophyte and phyllosphere, suggesting that poultry manure may have a stronger impact on lettuce resistomes. The ARG profiles were significantly correlated with the bacterial community, and the enrichment of soil and plant resistomes was strongly affected by the bacterial taxa including Solibacteres, Chloroflexi, Acidobacteria, Gemm-1 and Gemmatimonadetes, as revealed by the network analyses. Moreover, the overlaps of ARGs between lettuce tissues and soil were identified, which indicated that plant and environmental resistomes are interconnected. Our findings provide insights into the transmission routes of ARGs from manured soil to vegetables, and highlight the potential risks of plant resistome migration to the human food chain. Keywords: Antibiotic resistance genes, Manure-amended soil, Plant resistome, Endophyte, Phyllosphere

Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The oprJ and mexF genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mexF gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence.

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH4 and N2O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH4 and N2O emissions. However, little is known about their interactive effect on CH4 and N2O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH4 and N2O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH4 emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH4 emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N2O emissions at low input rate (S1) but significantly increased N2O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N2O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH4 and N2O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Knowledge about the biogeography of organisms has long been a focus in ecological research, including the mechanisms that generate and maintain diversity. In this study, we targeted a microbial group relatively underrepresented in the microbial biogeographic literature, the soil Archaea. We surveyed the archaeal abundance and community composition using real-time quantitative PCR and T-RFLP approaches for 105 soil samples from 2 habitat types to identify the archaeal distribution patterns and factors driving these patterns. Results showed that the soil archaeal community was affected by spatial and environmental variables, and 79% and 51% of the community variation was explained in the non-flooded soil (NS) and flooded soil (FS) habitat, respectively, showing its possible biogeographic distribution. The diversity patterns of soil Archaea across the landscape were influenced by a combination of stochastic and deterministic processes. The contribution from neutral processes was higher than that from deterministic processes associated with environmental variables. The variables pH, sample depth and longitude played key roles in determining the archaeal distribution in the NS habitat, while sampling depth, longitude and NH4 (+)-N were most important in the FS habitat. Overall, there might be similar ecological drivers in the soil archaeal community as in macroorganism communities.

During the past decades, extensive nitrogen fertilization and acid deposition have greatly contributed to soil acidification in agroecosystems. Liming, the addition of calcium- and magnesium-rich material to soil, is an effective management strategy used to improve fertility and productivity of agricultural soils degraded by acidification. Nitrification plays a central role in nitrogen (N) availability in agroecosystems and contributes to soil acidification. However, little is known regarding the effects of liming on this process and microbial populations that drive it. Here, we investigated population dynamics and activity of ammonia oxidizers in response to a 2-year liming field trial in acidic soils received long-term fertilization with chemical N fertilizers and short-term lime amendment in microcosm incubations. Our results showed that activity, abundance and population structure of both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were sensitive to liming in fertilized acidic soils. AOB abundance and potential nitrification rates increased in field plots subjected to liming, whereas the opposite was observed for AOA. In microcosm incubations, AOA abundance increased progressively over 60 days, namely under low CaO levels, whereas AOB abundance was greatly stimulated only during the first week under high CaO levels. 13CO2-SIP-DNA experiments further supported that AOA were the most active ammonia oxidizers in fertilized field soils. However, in N-fertilized soils freshly amended with CaO, only autotrophic growth of AOB was observed after seven days, but not after 30 days when growth of AOA was observed. Taken together, our results indicated that both AOA and AOB play a role in nitrification following liming in fertilized acidic soils, likely through selection of better adapted clades of organisms. Although AOA were likely the main drivers of nitrification in these soils in the long-term, liming stimulated AOB activity in the short-term.