Natural Microbiome Research Articles

Microbiome transfer from native to invasive species may increase invasion risk.

In a fast-changing world, understanding how organisms adapt to their environment is a pressing necessity. Research has focused on genetic adaptation, while our understanding of non-genetic modes is still in its infancy. The host-associated microbiome can be considered a non-genetic mode of adaptation, which can strongly influence an organism's ability to cope with its environment. However, the role of the microbiome in host ecological dynamics is largely unexplored, particularly in animal communities. Here, we discuss the following hypothesis: invasive species may rapidly adapt to local conditions by adopting beneficial microbes from similar co-occurring native species. This occurs when the invader's fitness is influenced by adaptation to local conditions that is facilitated by microbes acquired from native microbiomes. We present a minimal mathematical model to explore this hypothesis and show that a delayed acquisition of native microbes may explain the occurrence of an invasion lag. Overall, our results contribute to broadening the conceptualization of rapid adaptation via microbiome transfer and offer insights towards designing early intervention strategies for invasive species management.

Native woody species depend on the soil microbiome to establish on burned soils, while non‐native do not

Abstract Wildfires are important natural disturbances with profound ecological impacts. However, our understanding of how to restore plant–soil microbiome interactions following wildfires remains limited, revealing a key knowledge gap in post‐wildfire ecosystem restoration. To assess the restoration of plant‐microbiome interactions in fire‐affected ecosystems, we conducted greenhouse experiments simulating wildfire effects on soil collected from Maulino Coastal Forest of central Chile, a biodiversity hotspot. We measured the plant height and photosynthesis over 90 days, and two‐year survival probability, of three common native (Aristotelia chilensis, Nothofagus glauca and N. alessandrii) and three non‐native species (Eucalyptus globulus, Pinus radiata and Genista monspessulana) planted in three soils (unburned, burned and burned soil inoculated with the native microbiome). Available nutrient concentrations (N, P and K) and activities of microbial enzymes (dehydrogenase, β‐glucosidase and urease) were also measured over 360 days. Available nutrient concentrations were consistently higher in burned and burned‐inoculated soils than in unburned soils. Enzyme activities in unburned and burned‐inoculated soils remained higher than in burned soil, indicating that the native microbiome restored microbial enzyme activities. The increase in height over 90 days was lower in burned soils compared with unburned soils for native species. However, inoculation with the native microbiome mitigated this negative effect, resulting in height increases similar to those in unburned soils. For non‐native species, burning and inoculation had negligible effects on the height increases. Similar patterns were observed for the increase in photosynthetic rate, with native species showing a reduced rate in burned soils, which was offset by microbiome inoculation, while non‐native species were unaffected by both treatments. Survival probability of native species declined in burned soil, but was the same in burned‐inoculated soil as in unburned soil. That of non‐native species was unaffected by burning or by inoculation with the native microbiome. Synthesis and applications. Native microbiomes are evidently promising tools to safeguard ecosystem functionality and mitigate species extinction risks arising from climate change and human‐induced wildfires. We advocate integrating microbiomes into future active restoration strategies for fire‐affected ecosystems.

Microbiome Geographic Population Structure (mGPS) Detects Fine-Scale Geography.

Over the past decade, sequencing data generated by large microbiome projects showed that taxa exhibit patchy geographical distribution, raising questions about the geospatial dynamics that shape natural microbiomes and the spread of antimicrobial resistance (AMR) genes. Answering these questions requires distinguishing between local and non-local microorganisms and identifying the source sites for the latter. Predicting the source sites and migration routes of microbiota has been envisioned for decades but was hampered by the lack of data, tools, and understanding of the processes governing biodiversity. State-of-the-art biogeographical tools suffer from low resolution and cannot predict biogeographical patterns at a scale relevant to ecological, medical, or epidemiological applications. Analyzing urban, soil, and marine microorganisms, we found that some taxa exhibit regional-specific composition and abundance, suggesting they can be used as biogeographical biomarkers. We developed the Microbiome Geographic Population Structure (mGPS), a machine-learning-based tool that utilizes microbial relative sequence abundances to yield a fine-scale source site for microorganisms. mGPS predicted the source city for 92% of the samples and the within-city source for 82% of the samples, though they were often only a few hundred meters apart. mGPS also predicted soil and marine sampling sites for 86% and 74% of the samples, respectively. We demonstrated that mGPS differentiated local from non-local microorganisms and used it to trace the global spread of AMR genes. mGPS's ability to localize samples to their waterbody, country, city, and transit stations opens new possibilities in tracing microbiomes and has applications in forensics, medicine, and epidemiology.

Native intra-articular knee microbiome is a matter of facts: a systematic review of clinical evidence.

Growing interest surrounds the role of human gut microbiome in the development of degenerative pathologies such as osteoarthritis (OA), but microbes have recently been detected also in other sites previously considered to be sterile. Evidence emerged suggesting that even native and osteoarthritic knee joints may host several microbial species possibly involved in the osteoarthritic degeneration. This is the first systematic review critically collecting all the available evidence on the existence and composition of knee intra-articular microbiome. A systematic research on the PubMed, Cochrane and Google Scholar databases was performed. Human clinical studies investigating the presence of intra-articular microbiome in native osteoarthritic knee joints with next-generation sequencing techniques were collected. A total of eight studies were included reporting data on 255 knees. All the included studies reported evidence supporting the existence of an intra-articular microbiome in native knee joints, with detection rates varying from 5.8% to 100%. Bacteria from the Proteobacteria phylum were found to be among the most identified followed by the Actinobacteria, Firmicutes, Fusobacteria, and Bacteroideta phyla. Proteobacteria phylum were also found to be more common in osteoarthritic knees when compared to healthy joints. Furthermore, several pathways correlating those microbes to knee OA progression have been suggested and summarized in this review. Evidence collected in this systematic review suggests that the native knee joint, previously presumed to be a sterile environment, hosts a peculiar intra-articular microbiome with a unique composition. Furthermore, its alteration may have a link with the progression of knee osteoarthritis.

Glucosinolate structural diversity shapes recruitment of a metabolic network of leaf-associated bacteria

Host defenses can have broader ecological roles, but how they shape natural microbiome recruitment is poorly understood. Aliphatic glucosinolates (GLSs) are secondary defense metabolites in Brassicaceae plant leaves. Their genetically defined structure shapes interactions with pests in Arabidopsis thaliana leaves, and here we find that it also shapes bacterial recruitment. In model genotype Col-0, GLSs (mostly 4-methylsulfinylbutyl-GLS) have no clear effect on natural leaf bacterial recruitment. In a genotype from a wild population, however, GLSs (mostly allyl-GLS) enrich specific taxa, mostly Comamonadaceae and Oxalobacteraceae. Consistently, Comamonadaceae are also enriched in wild A. thaliana, and Oxalobacteraceae are enriched from wild plants on allyl-GLS as carbon source, but not on 4-methylsulfinylbutyl-GLS. Recruitment differences between GLS structures most likely arise from bacterial myrosinase specificity. Community recruitment is then defined by metabolic cross-feeding among bacteria. The link of genetically defined metabolites to recruitment could lead to new strategies to shape plant microbiome balance.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (~1:100), but a much larger ratio of phage genomes to bacterial genomes (~4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage, phage-plasmids, etc.). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occurs at a low average rate (~0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone, while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

Evaluating the coral microbiome during cryopreservation

Coral reefs are threatened by various local and global stressors, including elevated ocean temperatures due to anthropogenic climate change. Coral cryopreservation could help secure the diversity of threatened corals. Recently, isochoric vitrification was used to demonstrate that coral fragments lived to 24 hr post-thaw; however, in this study, they were stressed post-thaw. The microbial portion of the coral holobiont has been shown to affect host fitness and the impact of cryopreservation treatment on coral microbiomes is unknown. Therefore, we examined the coral-associated bacterial communities pre- and post-cryopreservation treatments, with a view towards informing potential future stress reduction strategies. We characterized the microbiome of the Hawaiian finger coral, Porites compressa in the wild and at seven steps during the isochoric vitrification process. We observed significant changes in microbiome composition, including: 1) the natural wild microbiomes of P. compressa were dominated by Endozoicomonadaceae (76.5 % relative abundance) and consistent between samples, independent of collection location across Kāneʻohe Bay; 2) Endozoicomonadaceae were reduced to <6.9 % in captivity, and further reduced to <0.5 % relative abundance after isochoric vitrification; and 3) Vibrionaceae dominated communities post-thaw (58.5–74.7 % abundance). Thus, the capture and cryopreservation processes, are implicated as possible causal agents of dysbiosis characterized by the loss of putatively beneficial symbionts (Endozoicomonadaceae) and overgrowth of potential pathogens (Vibrionaceae). Offsetting these changes with probiotic restoration treatments may alleviate cryopreservation stress and improve post-thaw husbandry.

Organic fungicides and diphenylamine shift microbiomes of ‘Fuji’ apples during storage

The native microbiome plays an important role in biocontrol efficacy, but less is known about how the microbiome responds to conventional and organic natural product fungicides. This study investigated the effects of the conventional fungicide fludioxonil and the organic fungicide natamycin, with and without the superficial scald inhibitor diphenylamine (DPA) on the microbiomes of ‘Fuji’ apples from 1 to 28 d of storage at 0.5 °C plus 7 d at 20 °C. We hypothesized that fungicide applications would shift the microbiome, with a more pronounced effect from natamycin due to the target specificity of fludioxonil. We also predicted that the antioxidant properties of DPA would shift both bacterial and fungal microbiomes. We found that natamycin resulted in modest fungal shifts and fludioxonil resulted in no observed shifts, while DPA strongly affected the fungal microbiome over time. Chemical treatment was not a predictor of bacterial microbiome variation, but bacterial communities shifted throughout storage. However, many of the trends that occurred during storage were reversed during the 7-d shelf life period at 20 °C after storage. Time in cold storage decreased the relative abundance of Pseudomonas, while DPA application reduced the relative abundance of Aureobasidium, both notable biocontrol genera. These results highlight how chemical applications such as DPA may have unintended effects on beneficial microbes that protect fruit from pathogen infection.

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome

Managed colonies of the European honey bee, Apis mellifera, have faced considerable losses in recent years. A widespread contributing factor is a microsporidian pathogen, Nosema ceranae, which occurs worldwide, is increasingly resistant to antibiotic treatment, and can alter the host’s immune response and nutritional uptake. These obligate gut pathogens share their environment with a natural honey bee microbiome whose composition can affect pathogen resistance. We tested the effect of N. ceranae infection on this microbiome by feeding 5 day-old adult bees that had natural, fully developed microbiomes with live N. ceranae spores (40,000 per bee) or a sham inoculation, sterile 2.0 M sucrose solution. We caged and reared these bees in a controlled lab environment and tracked their mortality over 12 d, after which we dissected them, measured their infection levels (gut spore counts), and analyzed their microbiomes. Bees fed live spores had two-fold higher mortality by 12 d and 36.5-fold more spores per bee than controls. There were also strong colony effects on infection levels, and 9% of spore-inoculated bees had no spore counts at all (defined as fed-spores-but-not-infected). Nosema ceranae infection had significant but subtle effects on the gut microbiomes of experimentally infected bees, bees with different infection levels, and fed-spores-but-not-infected vs. bees with gut spores. Specific bacteria, including Gilliamella ASVs, were positively associated with infection, indicating that multiple strains of core gut microbes either facilitate or resist N. ceranae infection. Future studies on the interactions between bacterial, pathogen, and host genotypes would be illuminating.

Overcoming toxicity: why boom-and-bust cycles are good for non-antagonistic microbes.

Antagonistic interactions are critical determinants of microbial community stability and composition, offering host benefits such as pathogen protection and providing avenues for antimicrobial control. While the ability to eliminate competitors confers an advantage to antagonistic microbes, it often incurs a fitness cost. Consequently, many microbes only produce toxins or engage in antagonistic behavior in response to specific cues like population density or environmental stress. In laboratory settings, antagonistic microbes typically dominate over sensitive ones, raising the question of why both antagonistic and non-antagonistic microbes are found in natural environments and host microbiomes. Here, using both theoretical models and experiments with killer strains of Saccharomyces cerevisiae , we show that boom-and-bust dynamics caused by temporal environmental fluctuations can favor non-antagonistic microbes that do not incur the growth rate cost of toxin production. Additionally, using control theory, we derive bounds on the competitive performance and identify optimal regulatory toxin-production strategies in various boom-and-bust environments where population dilutions occur either deterministically or stochastically over time. Our findings offer a new perspective on how both antagonistic and non-antagonistic microbes can thrive under varying environmental conditions.

Persistence and Microbiome Modification in Rhizoctonia solani-Inoculated Rhizosphere Following Amendment with a Bacillus Biocontrol Agent

Bacterial biocontrol agents that antagonize soilborne pathogens are increasingly considered alternatives to chemical pesticides, but their in vivo efficacy is often inconsistent, restricting commercial use. The efficacy of a biocontrol agent can depend on rhizosphere competence and its interaction with native microbiomes, which can affect ecosystem functioning. This study investigated the capacity of a Bacillus cereus sensu lato biocontrol strain (S-25) to persist on roots and in the rhizosphere of cucumber and evaluated its impact on bacterial and fungal community composition in the rhizosphere in the absence and presence of Rhizoctonia solani, the causative agent of damping-off disease in young seedlings. Following amendment, S-25 abundance in the cucumber rhizosphere decreased by two orders of magnitude but remained relatively high for the duration of the experiment, in contrast to the root surface, where it was not detected. Amendment with S-25 significantly reduced the incidence of disease caused by R. solani without reducing the relative abundance of the fungal pathogen. Interestingly, R. solani did not substantially alter the rhizosphere microbial community, whereas S-25 reduced bacterial diversity and facilitated a shift in community composition, with increased relative abundance of Acidobacteriota and Actinomycetota, and reduced abundance of Pseudomonadota, Bacteroidota, and Verrucomicrobiota. Collectively, this study provides important insights into the mode of persistence of biocontrol agents and their effect on native microbiomes in the rhizosphere of pathogen-inoculated plants. It demonstrates that amendment can significantly alter local microbiomes and suggests that optimizing amendment regimes or selecting strains with higher rhizosphere competence can enhance future biocontrol agents.

Superiority of native soil core microbiomes in supporting plant growth

Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.

Repercussions of Prolonged Pesticide Use on Natural Soil Microbiome Dynamics Using Metagenomics Approach.

The residual pesticides in soil can affect the natural microbiome composition and genetic profile that drive nutrient cycling and soil fertility. In the present study, metagenomic approach was leveraged to determine modulations in nutrient cycling and microbial composition along with connected nexus of pesticide, antibiotic, and heavy metal resistance in selected crop and fallow soils having history of consistent pesticide applications. GC-MS analysis estimated residuals of chlorpyrifos, hexachlorbenzene, and dieldrin showing persistent nature of pesticides that pose selective pressure for microbial adaptation. Taxonomic profiling showed increased abundance of pesticide degrading Streptomyces, Xanthomonas, Cupriavidus, and Pseudomonas across the selected soils. Genes encoding for pesticide degrading cytochrome p450, organophosphorus hydrolase, aldehyde dehydrogenase, and oxidase were predominant and positively correlated with Bacillus, Sphingobium, and Burkholderia. Nitrogen-fixing genes (nifH, narB, and nir) were relatively less abundant in crop soils, correlating to the decrease in nitrogen-fixing bacteria (Anabaena, Pantoea, and Azotobacter). Microbial enzymes involved in carbon (pfkA, gap, pgi, and tpiA) and phosphorus cycle (gmbh and phnJ) were significantly higher in crop soils indicating extensive utilization of pesticide residuals as a nutrient source by the indigenous soil microbiota. Additionally, presence of antibiotic and heavy metal resistance genes suggested potential cross-resistance under pressure from pesticide residues. The results implied selective increase in pesticide degrading microbes with decrease in beneficial bacteria that resulted in reduced soil health and fertility. The assessment of agricultural soil microbial profile will provide a framework to develop sustainable agriculture practices to conserve soil health and fertility.

The design and development of EcoBiomes: Multi-species synthetic microbial consortia inspired by natural desert microbiome to enhance the resilience of climate-sensitive ecosystems

Synthetic microbial communities, which simplify the complexity of natural ecosystems while retaining their key features, are gaining momentum in engineering and biotechnology applications. One potential application is the development of bioinoculants, offering an eco-friendly, sustainable solution to promote plant growth and increase resilience to abiotic stresses amidst climate change. A potential source for stress-tolerant microbes is those associated with desert plants, evolved and shaped by selective pressures to promote host health under harsh environmental conditions. In our research, we aim to design and develop synthetic microbial consortia inspired by the natural microbiota of four desert plants native to the Arabian Peninsula, inferred from our previous work identifying the structure and predicting the function of these microbial communities using high throughput eDNA barcoding. To obtain culturable microbes that are manageable and traceable yet still representative of natural microbial communities, we combined multiple experimental protocols coupled with compatibility and synergy assessments, along with in planta testing. We isolated a total of 75 bacteria and conducted detailed biological evaluations, revealing that an overwhelming majority (84 %) of all isolates produced indole acetic acid (IAA), with 73 % capable of solubilizing phosphate, 60 % producing siderophores, 47 % forming biofilms, and 35 % producing ACC deaminase, all contributing to plant growth and stress tolerance. We constructed four synthetic microbial consortia, named EcoBiomes, consisting of synergistic combinations of multiple species that can co-exist without significant antagonism. Our preliminary data indicate that EcoBiomes enhance the resilience of heterologous host plants under simulated environmental stresses, including drought, heat, and salinity. EcoBiomes offer a unique, sustainable, and eco-friendly solution to mitigate the impact of climate change on sensitive ecosystems, ultimately affecting global food security.

Compost-diatomite-based phytostabilization course under extreme environmental conditions in terms of high pollutant contents and low temperatures

The effects of changes in environmental temperatures on the immobilization or removal of cationic potentially toxic elements (PTE) in heavily polluted soils are often poorly understood, although both are widely studied in the context of phytostabilization. To address this issue, a novel compost-diatomite hybrid (CDH) amendment was developed and applied for assisted phytostabilization at two external temperature regimes. (Cd/Ni/Cu/Zn)-extremely polluted soils (unenriched and CDH-enriched) were cultivated with perennial ryegrass and native soil microbiome under greenhouse conditions and then transferred to freeze-thaw conditions (FTC). The decrease in metal potential toxicity in soils subjected to phytostabilization following both temperature treatments was characterized by a combination of sequential extraction and atomic absorption measurements. The soil microbiome was characterized by high-throughput sequencing. In a relative comparison, the greatest decrease in the content of all PTEs in CDH-enriched soil (compared to unenriched soil) appeared in FTC. Furthermore, under the influence of FTC, in the relative comparison between two CDH-enriched soils (exposed-, and not-exposed- to FTC) and two unenriched soils (exposed-, and not-exposed- to FTC), the content of all PTEs decreased more sharply in the CDH-enriched series than in the unenriched series. The largest redistribution into four sequentially extracted fractions in CDH-enriched soil was found for Zn. Based on the distribution pattern, Zn immobilization was greater in CDH-enriched soil in FTC. CDH increased species richness in the soil, while FTC stimulated the growth of Bacteroidia, Alphaproteobacteria, Theromomicrobia, and Gammaproteobacteria. The analysis of the functionalities of the microbiome indicated enhanced metal transportation and defense systems in samples exposed to FTC. The current research is crucial for understanding how extreme environmental conditions in both cases high pollutant levels and low temperatures affect the movement and transformation of PTEs in polluted soils during phytostabilization.

Drought stress homogenizes maize growth responses to diverse natural soil microbiomes

Drought stress homogenizes maize growth responses to diverse natural soil microbiomes

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.

Methylation patterns in bacteria can be used to study Restriction-Modification (RM) or other defense systems with novel properties. While m4C and m6A methylation is well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on viral DNA and compared to host DNA, strengthening evidence for virus-host interaction. Applied to three different microbiomes, the method unveils over 1900 motifs that were deposited in REBASE. The motifs include a novel 8-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights to bacterial biology and biotechnological applications.

Environmentally dependent interactions shape patterns in gene content across natural microbiomes.

Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.

An inclusive study to elucidation the heavy metals-derived ecological risk nexus with antibiotic resistome functional shape of niche microbial community and their carbon substrate utilization ability in serpentine soil

Heavy metals (HMs) contained terrestrial ecosystems are often significantly display the antibiotic resistome in the pristine area due to increasing pressure from anthropogenic activity, is complex and emerging research interest. This study investigated that impact of chromium (Cr), nickel (Ni), cobalt (Co) concentrations in serpentine soil on the induction of antibiotic resistance genes and antimicrobial resistance within the native bacterial community as well as demonstrated their metabolic fingerprint. The full-length 16S-rRNA amplicon sequencing observed an increased abundance of Firmicutes, Actinobacteriota, and Acidobacteriota in serpentine soil. The microbial community in serpentine soil displayed varying preferences for different carbon sources, with some, such as carbohydrates and carboxylic acids, being consistently favored. Notably, 27 potential antibiotic resistance opportunistic bacterial genera have been identified in different serpentine soils. Among these, Lapillicoccus, Rubrobacter, Lacibacter, Chloroplast, Nitrospira, Rokubacteriales, Acinetobacter, Pseudomonas were significantly enriched in high and medium HMs concentrated serpentine soil samples. Functional profiling results illustrated that vancomycin resistance pathways were prevalent across all groups. Additionally, beta-lactamase, aminoglycoside, tetracycline, and vancomycin resistance involving specific bio-maker genes (ampC, penP, OXA, aacA, strB, hyg, aph, tet(A/B), otr(C), tet(M/O/Q), van(A/B/D), and vanJ) were the most abundant and enriched in the HMs-contaminated serpentine soil. Overall, this study highlighted that heavy-metal enriched serpentine soil is potential to support the proliferation of bacterial antibiotic resistance in native microbiome, and might able to spread antibiotic resistance to surrounding environment.

Genetic architecture of heritable leaf microbes.

Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown yet fundamental to the community assembly of host-associated microbiomes, with implications for the eco-evolutionary dynamics of microbes and hosts. Using Ipomoea hederacea, ivyleaf morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect Mendelian locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.IMPORTANCEWe investigated how host genetic variation affects the assembly of Ipomoea hederacea's natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance and community composition.