Biotic and abiotic factors distinctly drive contrasting biogeographic patterns between phyllosphere and soil resistomes in natural ecosystems

Exploring the dichotomy: Shotgun metagenomics reveals diversity of beneficial and pathogenic protist community in arid wetlands of northeastern South Africa

Arid regions harbor seasonal and permanent wetlands, as biodiversity hotspots crucial for ecosystem services despite harsh conditions. These wetlands, typically dependent on episodic intense rainfall, are understudied compared to their humid counterparts. While the diversity of plants and animals in these wetlands is well-known, the microbial communities remain largely unexplored. To address this knowledge gap, we employed metagenome sequencing technologies to profile protist communities, including pathogenic protozoa, and their associated functional pathways, in sediment of permanent and seasonal arid freshwater wetlands across northern South Africa. Results revealed a core community of protists dominated by phylum Apicomplexa (66.73 %), Euglenazoa (19.03 %), Bacillariophyta (5.44 %), Metamonada (4.65 %), Cryptophyta (1.90 %), and Amoebazoa (1.21 %). Seasonal wetlands showed significantly higher protist diversity compared to permanent wetlands (Shannon index, p = 0.019; Chao1, p = 0.0095). A high abundance and diversity of human and zoonotic pathogenic protists (87.67 %) was observed, with lower levels of photoautotrophs (6.69 %) and limited diversity of phagotrophs (5.64 %). Key photoautotrophs identified included diatoms (Thalassiosiraceae and Phaeodactylaceae) and cryptophytes (genus Hemiselmis and Cryptophyta), with consumers/phagotrophs exhibited a correlation with the bacterial community abundance (r2 = 0.218, p < 0.001). Pathogenic protozoans identified, include malaria-causing Plasmodium, kinetoplastids (genus Besnoita, Theilleria, Neospora, Toxoplasma, Encephalitozoon, and Babesia) and waterborne protozoans of public health importance (such as Cryptosporidium parvum and Giardia lamblia). Furthermore, the enrichment of pathogenesis-associated pathways (amino acid biosynthesis, peptidoglycan maturation, heme biosynthesis and degradation, and the Calvin-Benson-Bassham cycle), along with virulence gene families identified, highlighted these wetlands as potential reservoirs for infectious diseases. Our results unveil a baseline protist taxonomic and functional composition within arid wetlands, including beneficial and pathogenic protozoa. The close proximity of these wetlands to human activity raises concern for local and transboundary spread of these pathogens. Thus, continued monitoring is vital for disease control and preserving these unique ecosystems.

Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland

The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.

Nanoplastics promote the dissemination of antibiotic resistance genes and diversify their bacterial hosts in soil

The wide application of plastics has led to the ubiquitous presence of nanoplastics and microplastics in terrestrial environments. However, few studies have focused on the mechanism underlying the effects of plastic particles on soil microbiomes and resistomes, especially the differences between nanoplastics and microplastics. This study investigated the microbiome and resistome in soil exposed to polystyrene microplastics (mPS) or nanoplastics (nPS) through 16S rRNA and shotgun metagenomic sequencing. Distinct microbial communities were observed between mPS and nPS exposure groups, and nPS exposure significantly changed the bacterial composition even at the lowest amended rate (0.01%, w/w). The abundance of antibiotic resistance genes (ARGs) in nPS exposure (1%) was 0.26 copies per cell, significantly higher than that in control (0.21 copies per cell) and mPS exposure groups (0.21 copies per cell). It was observed that nanoplastics, bacterial community, and mobile genetic elements (MGEs) directly affected the ARG abundance in nPS exposure groups, while in mPS exposure groups, only MGEs directly induced the change of ARGs. Streptomyces was the predominant host for multidrug in the control and mPS exposure, whereas the primary host was changed to Bacillus in nPS exposure. Additionally, exposure to nPS induced several bacterial hosts to exhibit possible multi-antibiotic resistance characteristics. Our results indicated that the effects of plastic particles on the soil microbial community were size-dependent, and nano-sized plastic particles exhibited more substantial impacts. Both microplastics and nanoplastics promoted ARG transfer and diversified their bacterial hosts. These findings bear implications for the regulation of plastic waste and ARGs.

Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions

Rhizosphere microorganisms play a vital role in enhancing plant health, productivity, and the accumulation of secondary metabolites. Currently, there is a limited understanding of the ecological processes that control the assembly of community. To address the role of microbial interactions in assembly and for functioning of the rhizosphere soil microbiota, we collected rhizosphere soil samples from Anisodus tanguticus on the Tibetan Plateau spanning 1500 kilometers, and sequenced the bacteria, fungi, archaea, and protist communities. We observed a significant but weak distance-decay relationship in the microbial communities of rhizosphere soil. Our comprehensive analysis of spatial, abiotic, and biotic factors showed that trophic relationships between protists and bacteria and fungi predominantly influenced the alpha and beta diversity of bacterial, fungal, and protistan communities, while abiotic factors had a greater impact on archaeal communities, including soil pH, available phosphorus, total phosphorus and mean annual temperature. Importantly, microbial interactions had a more significant influence on Anisodus tanguticus physiological and ecological functions compared to individual microorganisms. Network analyses revealed that bacteria occupy a central position of the co-occurrence network and play a crucial role of connector within this community. The addition of protists increased the stability of bacterial, fungal, and archaeal networks. Overall, our findings indicate that trophic relationships play an important role in assembly and for functioning of the rhizosphere soil microbiota. Bacterial communities serve as a crucial link between different kingdoms of microorganisms in the rhizosphere community. These findings help us to fully harness the beneficial functions of rhizosphere microorganisms for plants and achieve sustainable use of biological resources.

Pathogenic Bacteria Are the Primary Determinants Shaping PM2.5-Borne Resistomes in the Municipal Food Waste Treatment System

Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs) have received little attention. Herein, 48 metagenomic data were applied to study the prevalence of PM2.5-borne ARGs in and around full-scale food waste treatment plants (FWTPs). Overall, FWTP PM2.5 (2.82 ± 1.47 copies/16S rRNA gene) harbored comparable total abundance of ARGs to that of municipal wastewater treatment plant PM2.5 (WWTP), but was significantly enriched with the multidrug type (e.g., AdeC/I/J; p < 0.05), especially the abundant multidrug ARGs could serve as effective indicators to define resistome profiles of FWTPs (Random Forest accuracy >92%). FWTP PM2.5 exhibited a decreasing enrichment of total ARGs along the FWTP-downwind-boundary gradient, eventually reaching levels comparable to urban PM2.5 (1.46 ± 0.21 copies/16S rRNA gene, N = 12). The combined analysis of source-tracking, metagenome-assembled genomes (MAGs), and culture-based testing provides strong evidence that Acinetobacter johnsonii-dominated pathogens contributed significantly to shaping and disseminating multidrug ARGs, while abiotic factors (i.e., SO42-) indirectly participated in these processes, which deserves more attention in developing strategies to mitigate airborne ARGs. In addition, the exposure level of FWTP PM2.5-borne resistant pathogens was about 5-11 times higher than those in urban PM2.5, and could be more severe than hospital PM2.5 in certain scenarios (<41.53%). This work highlights the importance of FWTP in disseminating airborne multidrug ARGs and the need for re-evaluating the air pollution induced by municipal FWTP in public health terms.

Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than hydrochar in an agricultural soil

Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.

pH drives the spatial variation of antibiotic resistance gene profiles in riparian soils at a watershed scale

Owing to convenient water access, riparian areas are often sites for intensive livestock breeding industries and agriculture, which can increase the spread of antibiotic resistance genes (ARGs). However, studies on ARG profiles in riparian soils are limited and there is little information regarding the factors influencing ARGs at a watershed scale. Here, we analyzed ARG profiles, bacterial communities, and soil properties in riparian soils under different land-use types. A total of 124 ARGs and 25 mobile genetic elements (MGEs) were detected in the riparian soils, which covered almost all major classes of antibiotics. Non-metric multidimensional scaling analysis showed that both the distance to the water reservoir and land-use types played important roles in shaping ARG profiles in riparian soils at a watershed scale. Downstream soils harbored three times the abundance of ARGs compared with upstream and midstream soils. Distance-decay analysis indicated that the similarity of ARG profiles and bacterial community composition decreased significantly with the increase of geographical distance (p < 0.001). When taking the land-use type into consideration, the relative abundance and diversity of ARGs and MGEs in orchard and farmland soils were significantly higher than those in wasteland soils. This indicated that anthropogenic activities can also affect ARG patterns in riparian soils. MGE abundance was identified as major driving factors of ARG profiles. In addition, among all the examined soil properties, soil pH was found to be more important than nutrients and organic carbon in shaping ARG profiles. Our findings provide valuable data on ARG distribution in riparian soils in a reservoir catchment and highlight downstream soils is crucial for ensuring water source security.

Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere

The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.

Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat

The spread of antibiotic-resistance genes (ARGs) has posed a significant threat to human health over the past decades. Despite the fact that the phyllosphere represents a crucial pool of microorganisms, little is known about the profile and drivers of ARGs in less human interference natural habitats. In order to minimize the influence of environmental factors, here we collected leaf samples from the early-, middle- and late-successional stages across a primary vegetation successional sequence within 2 km, to investigate how the phyllosphere ARGs develop in natural habitats. Phyllosphere ARGs were determined using high-throughput quantitative PCR. Bacterial community and leaf nutrient content were also measured to assess their contribution to the phyllosphere ARGs. A total of 151 unique ARGs were identified, covering almost all recognized major antibiotic classes. We further found that there was some stochastic and a core set of the phyllosphere ARGs during the plant community succession process, due to the fluctuant phyllosphere habitat and specific selection effect of plant individuals. The ARG abundance significantly decreased due to the reduction of the phyllosphere bacterial diversity, community complexity, and leaf nutrient content during the plant community succession process. While the closer links between soil and fallen leaf resulted in a higher ARG abundance in leaf litter than in fresh leaf. In summary, our study reveals that the phyllosphere harbors a broad spectrum of ARGs in the natural environment. These phyllosphere ARGs are driven by various environmental factors, including the plant community composition, host leaf properties, and the phyllosphere microbiome.

Plant identity shapes phyllosphere microbiome structure and abundance of genes involved in nutrient cycling

The phyllosphere is a fluctuant micro-environment habitat that harbors diverse microbial communities that have the potential to influence plant growth through their effect on host fitness. However, we know little about the driving factors of phyllosphere microbial functional traits, e.g., genes related to nutrient cycling and microbial community structure under anthropic disturbance. Here, we characterized phyllosphere microbial communities and the abundance of genes related to nutrient cycling from diverse plant species between urban and natural habitats. We measured leaf functional traits to investigate the potential drivers of the phyllosphere microbial profile. Results indicated that phyllosphere microbial communities differed significantly between urban and natural habitats, and that this variation was dependent upon plant species. Host plant species had a greater influence on the abundance of genes involved in nutrient cycling in the phyllosphere than habitat. In addition, phyllosphere microbial diversity and functional gene abundance were significantly correlated. Furthermore, host leaf functional traits (e.g., specific leaf area and nutrient content) were potential driving factors of both phyllosphere microbial community structure and the abundance of genes involved in nutrient cycling. These findings contribute to a better understanding of the phyllosphere microbiome and its biotic and abiotic controlling factors, which improves our understanding of plant-microbe interactions and their ecosystem functions under anthropic disturbance.

Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus

Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.

Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil

Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (Cu^R) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the Cu^R bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.

Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland

The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.

Host species and microplastics differentiate the crop root endophytic antibiotic resistome

The increasing One-Health concept calls for a more in-depth understanding of the dissemination of antibiotic resistance in plant microbiomes. While there is considerable published evidence that microplastics can promote the spread of antibiotic resistance genes (ARGs) in the environment, whether and how microplastics impact the plant endophytic resistome are largely unknown. Here we examined the ARGs along the soil-root continuum of maize and wheat under the pressure of microplastics. Amendment with heavy metals was also included as they can apply the selective pressure for ARG spread as well. The crop species and genotypes had significant effects on the root endophytic ARG abundance and diversity. The greatest ARG abundance was observed in the maize ZD958 endophytes (0.215 copies per 16S rRNA gene), followed by the maize XY335 (0.092 copies per 16S rRNA gene). For each crop genotype, amendment with microplastics and heavy metals significantly increased the ARG abundances and changed their profiles in root endophytes. The endophytic ARG variances were closely associated with the endophytic microbiome, the rhizosphere bacterial communities and resistome. Additionally, the level of endophytic ARGs was positively relevant to the abundance of mobile genetic elements (MGEs). These findings suggested that the root endophytic resistome was primarily affected by the crop species, and microplastics might show enhancement effects on the endophytic resistome via changing the root-associated microbiome and facilitating the MGE mediation. Overall, this study, for the first time, highlights the root endophytic ARG emergence and dissemination induced by microplastics.

Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment

Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.

Supercarriers of antibiotic resistome in a world's large river

BACKGROUND

Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large rivers that are regarded as "terrestrial gut."

RESULTS

By creating the integral pattern for ARGs and antibiotic-resistant microbes in water and sediment along a 4300-km continuum of the Yangtze River, we found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively. Moreover, the planktonic HPB harbored 79 ARG combinations that are dominated by "natural" supercarriers (e.g., Rheinheimera texasensis and Noviherbaspirillum sp. Root189) in river basins.

CONCLUSIONS

We confirmed that terrestrial HPB are the major ARG hosts in the river, rather than conventional supercarriers (e.g., Enterococcus spp. and other fecal indicator bacteria) that prevail in the human gut. The discovery of HPB as natural supercarriers in a world's large river not only interprets the inconsistency between the spatial dissimilarities in ARGs and their hosts, but also highlights the top priority of controlling terrestrial HPB in the future ARG-related risk management of riverine ecosystems globally. Video Abstract.

Climate warming increases the proportions of specific antibiotic resistance genes in natural soil ecosystems

Understanding the future distribution of antibiotic resistance in natural soil ecosystems is important to forecast their impacts on ecosystem and human health under projected climate change scenarios. Therefore, it is critical and timely to decipher the links between climate warming and antibiotic resistance, two of Earth's most imminent problems. Here, we explored the role of five-year simulated climate warming (+ 4 °C) on the diversity and proportions of soil antibiotic resistance genes (ARGs) across three seasons in both plantation and natural forest ecosystems. We found that the positive effects of warming on the number and proportions of ARGs were dependent on the sampling seasons (summer, autumn and winter), and seasonality was a key factor driving the patterns of ARG compositions in forest soils. Fifteen ARGs, conferring resistance to common antibiotics including aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin B, multidrug, sulfonamide, and tetracycline, were significantly enriched in the warming treatment. We showed that changes in soil properties and community compositions of bacteria, fungi and protists can explain the changes in soil ARGs under climate warming. Taken together, these findings advance our understanding of environmental ARGs under the context of future climate change and suggest that elevated temperature may promote the abundance of specific soil ARGs, with important implications for ecosystem and human health.

Salicylic Acid-Mediated Disturbance Increases Bacterial Diversity in the Phyllosphere but Is Overcome by a Dominant Core Community

Plant microbiomes and immune responses have coevolved through history, and this applies just as much to the phyllosphere microbiome and defense phytohormone signaling. When in homeostasis, the phyllosphere microbiome confers benefits to its host. However, the phyllosphere is also dynamic and subject to stochastic events that can modulate community assembly. Investigations into the impact of defense phytohormone signaling on the microbiome have so far been limited to culture-dependent studies; or focused on the rhizosphere. In this study, the impact of the foliar phytohormone salicylic acid (SA) on the structure and composition of the phyllosphere microbiome was investigated. 16S rRNA amplicons were sequenced from aerial tissues of two Arabidopsis mutants that exhibit elevated SA signaling through different mechanisms. SA signaling was shown to increase community diversity and to result in the colonization of rare, satellite taxa in the phyllosphere. However, a stable core community remained in high abundance. Therefore, we propose that SA signaling acts as a source of intermediate disturbance in the phyllosphere. Predictive metagenomics revealed that the SA-mediated microbiome was enriched for antibiotic biosynthesis and the degradation of a diverse range of xenobiotics. Core taxa were predicted to be more motile, biofilm-forming and were enriched for traits associated with microbe-microbe communication; offering potential mechanistic explanation of their success despite SA-mediated phyllospheric disturbance.