FEMS Microbiology Ecology

Bacterial interactions-whether positive or negative - are crucial for the functioning of microbial communities. Though bacterial interactions are mainly expected to be negative, the sign and strength of interactions are predicted to be context dependent, with interactions typically being more positive in more stressful and nutrient-poor conditions. However, systematic studies investigating how the environment affects interactions between multiple taxa are lacking. Here, we determine if interactions between a panel of natural soil isolates change in response to the environment in which they are grown, with two different artificial media used (one simple and one complex) and a more ecologically relevant soil wash. To maximise natural variation in interactions, we collected multiple isolates from multiple sites: co-occurring (sympatric) isolates were predicted to show more negative interactions than allopatric isolates because of greater overlap in resource use. Pairwise interactions were in general negative, but more negative when grown in a complex lab-derived medium (Tryptic Soy Broth). Mutually beneficial interactions were most common in a simple resource medium (M9 minimal media) and exploitative interactions were most frequent in a soil broth. These patterns were independent of whether species originated from the same or a different site. The study supports the prediction that nutrient rich environments promote more negative interactions, and that measuring interactions of soil isolates in standard lab media is likely to misrepresent interactions occurring in natural environments.

Soil history has been shown to condition future plant-soil microbial communities up to a year after being established. However, previous experiments have also illustrated that mature, adult plants can "re-write", or mask, different soil histories through host plant-soil microbial community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Therefore, in this experiment we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere and roots of B. napus at different growth stages-- the initial seeding conditions, seedling, rosette, bolting, and flower-- from all three soil history plots. We compared the taxonomic composition and diversity of bacterial communities, as estimated using 16S rRNA metabarcoding, to identify any changes associated with soil history and growth stages on the different B. napus soil bacterial communities. We found that soil history remained significant across each growth stage in structuring the bulk soil and rhizosphere communities, but not the roots. This suggests that the host plants capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil historys identity remain present and continue to impact bacterial communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.

Hospital effluent comprises feces of many individuals, including patients undergoing antibiotic treatment. Although, hospital effluent is an important source for contamination of the environment with antibiotic resistance genes (ARGs) and pathogens, how hospital effluent in a low resistance setting contributes to antimicrobial resistance (AMR) in the environment is largely understudied. The aim of our study was to understand the microbiota and resistome of hospital effluent, and its role in the spread of AMR in the marine environment in Norway. We further aimed at describing/characterizing novel resistance factors from hospital effluent and the receiving sewage treatment plant (STP). 24-hour composite samples of the hospital effluent and the influent and effluent of the receiving STP were collected at two sampling time-points (February and April 2023) in Bergen city, Norway. Isolation of Escherichia coli and Klebsiella spp. was performed, using ECC and SCAI plates with cefotaxime, tigecycline or meropenem, followed by antibiotic susceptibility testing, using EUVSEC3 plates. Whole-genome sequencing of selected strains (n=36) and shotgun metagenomics of sewage samples (n=6) were performed, using Illumina NovaSeq. ARGs were identified with USEARCH, and known and novel ARGs were assembled with fARGene. All E. coli strains (n=66) were multidrug-resistant (MDR), while 92.3% of the Klebsiella spp. strains (n=55) showed MDR phenotype. The sequenced strains carried multiple clinically important ARGs, including carbapenemases such as NDM-5 (n=3) and KPC-3 (n=3). We obtained 238 Gigabases of sequence data from which we identified 676 unique ARGs with >200 ARGs shared across samples. We assembled 1,205 ARGs using fARGene, 365 gene sequences represented novel ARGs (< 90% amino acid (aa) identity). Both known and novel ARGs (n=54) were shared between the hospital effluent and the treated effluent of the receiving STP. We show that hospital effluent in Norway has a high diversity of both known and novel ARGs. Our study demonstrates that hospital effluent is a source of clinically relevant pathogens, as well as known and novel ARGs, reaching the marine environment in Norway through treated sewage.

Nitrogen fixation is carried out inside nodules of legumes by symbiotic rhizobia. Rhizobia dominate the nodule microbiome, however other non-rhizobial bacteria also colonise root nodules. It is not clear whether these less abundant nodule colonisers impact nodule function. In order to investigate the relationship between the nodule microbiome and nodule function as influenced by the soil microbiome, we used a metabarcoding approach to characterise the communities inside Lotus burttii, Lotus japonicus and Lotus corniculatus nodules from plants that were either starved or healthy resulting from inoculations with different soil suspensions in a closed pot experiment. We found that the nodule microbiome of all tested Lotus species differed according to inoculum, but only that of L. burttii varied with plant health. Using a machine learning algorithm, we also found that among the many non-rhizobial bacteria inside the nodule, amplicon sequence variants that were related to Pseudomonas were the most indicative signatures of a healthy plant nodule microbiome. These results support the hypothesis that legume nodule endophytes may play a role in the overall success of root-nodule symbiosis, albeit in a plant host specific manner.

1) This work explored the role of natural transformation - a mechanism by which bacteria uptake and express extracellular genes - in driving antibiotic resistance propagation in the human gut microbiome. The model extracellular antibiotic resistance gene (eARG) - a plasmid containing a kanamycin resistance (kanR) gene and a green fluorescence protein (GFP) gene - was dosed into pooled and homogenized human stool and incubated anaerobically. Cellular uptake of the eARG was assessed via droplet digital PCR, the expression of newly acquired genes was assessed by culturing on selective media and fluorescent microscopy, newly resistant isolates were identified by long-read Nanopore sequencing and the impacts on the taxonomy of the gut microbiome was assessed using shotgun Illumina sequencing. Significant gene uptake of both kanR and GFP was quantified in gut microbes, and extent of gene accumulation correlated with background kanamycin levels. Gut microbes dosed with background kanamycin expressed kanamycin resistance acquired by the eARG (as quantified by CFU on kanamycin-containing media). Newly resistant isolates, identified as Enterococcus faecium by long-read sequencing, also expressed green fluorescence acquired from the eARG. Though compositional changes of the kanamycin-resistant subpopulation were observed in the gut microbiome in response to eARG and antibiotic exposure, these changes were not reproducible among replicates and trends in taxonomy due to transformation could not be identified. This comprehensive analysis therefore establishes the significant propagation of antibiotic resistance within the human gut microbiome due to eARG exposure, while evaluating the utility of various measurements in characterizing transformation in a complex microbial community. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/625464v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1d9dfc0org.highwire.dtl.DTLVardef@f0df34org.highwire.dtl.DTLVardef@1ce04bforg.highwire.dtl.DTLVardef@99a6e2_HPS_FORMAT_FIGEXP M_FIG C_FIG 2) ImportanceInfections from antibiotic resistant bacteria in the human gut microbiome are a growing public health concern. Antibiotic resistance may develop in gut microbiota from exposure to environmentally prevalent extracellular antibiotic resistance genes (eARGs). This work explores the impact of eARG exposure on a complex human gut microbial community. It quantifies significant accumulation and expression of eARG-borne genes by endogenous gut microorganisms, thereby demonstrating that natural transformation may play a role in resistance propagation in the human gut. It also demonstrates the highly variable changes in gut taxonomy in response to eARG exposure, implying that eARGs may impact gut composition and therefore downstream human health effects. These data may be useful in characterizing and mitigating resistance propagation in the human gut, and in general, the suite of genotypic and phenotypic measurements used constitute a quantitative framework to characterize the effects of perturbations on complex microbiomes.

Most multicellular organisms harbor microbial colonizers that provide various benefits to their hosts. Although these microbial communities may be host species- or even genotype-specific, the associated bacterial communities can respond plastically to environmental changes. In this study, we estimated the relative contribution of environment and host genotype to bacterial community composition in Nematostella vectensis, an estuarine cnidarian. We isolated N. vectensis polyps from five different populations along a north-south gradient on the Atlantic coast of the United States and Canada at three different times of the year. While half of the polyps were immediately analyzed for their bacterial composition by 16S rRNA gene sequencing, the remaining polyps were cultured under laboratory conditions for one month. Bacterial community comparison analyses revealed that laboratory maintenance reduced bacterial diversity by fourfold, but maintained a population-specific bacterial colonization. Interestingly, the differences between bacterial communities correlated strongly with seasonal variations, especially with ambient water temperature. To decipher the contribution of both ambient temperature and host genotype to bacterial colonization, we generated 12 clonal lines from six different populations in order to maintain each genotype at three different temperatures for three months. The bacterial community composition of the same N. vectensis clone differed greatly between the three different temperatures, highlighting the contribution of ambient temperature to bacterial community composition. To a lesser extent, bacterial community composition varied between different genotypes under identical conditions, indicating the influence of host genotype. In addition, we identified a significant genotype x environment interaction determining microbiota plasticity in N. vectensis. From our results we can conclude that N. vectensis-associated bacterial communities respond plastically to changes in ambient temperature, with the association of different bacterial taxa depending in part on the host genotype. Future research will reveal how this genotype-specific microbiota plasticity affects the ability to cope with changing environmental conditions.

Background and aimsSoil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the plant rhizosphere remains limited. MethodsBy leveraging a natural experiment in urban farming with fields of different ages and multiple plant genotypes, we tracked the relative abundance, richness, and microbial networks of plant pathogens, mycorrhizal fungi, and saprotrophic fungi across fields over two years. ResultsWe observed an increase in the relative abundance of plant pathogens in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. Unlike plant pathogens and mycorrhizal fungi, the relative abundance of saprotrophic fungi remained similar among fields. While the richness of plant pathogens and saprotrophic fungi were similar across fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogens remained similar across fields. ConclusionOur study reveals contrasting dynamics of essential soil fungal functional groups in the plant rhizosphere, and provides a predictive insight into the potential shifts in soil function and their impact on plant productivity.

The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of symbiosis and these conditions has not been widely demonstrated. We test for these associations using Dictyostelium discoideum social amoebae and their bacterial symbionts. D. discoideum are host to endosymbiotic bacteria from three taxa: Paraburkholderia, Amoebophilus and Chlamydiae. Three species of facultative Paraburkholderia symbionts are the best studied and give hosts the ability to carry food bacteria through the dispersal stage to new environments. Amoebophilus and Chlamydiae are obligate endosymbionts with no measurable impact on host fitness. We test whether the frequency of both single infections and coinfections of these symbionts are associated with the unpredictability of their soil environments by using symbiont presence-absence data from soil isolates from 21 locations across the eastern United States. We find that that Amoebophilus and Chlamydiae obligate endosymbionts and coinfections are not associated with any of our mean measures, but that unpredictable precipitation can promote or hinder symbiosis depending on the species of Paraburkholderia symbiont.

Associations between hosts and their microbial symbionts are considered mutualistic when both partners benefit. While the advantages received by eukaryotic hosts from association with bacterial symbionts are frequently examined, benefits to the bacteria are rarely experimentally tested. Here, we consider whether the bug-Caballeronia symbiosis is truly mutualistic by measuring the effect of a leaffooted bug (Leptoglossus phyllopus) on the abundance of its horizontally acquired symbiont, Caballeronia grimmiae. We predicted that the free-living Caballeronia population would increase over time in the presence of its insect partner. We quantified Caballeronia titer in soil microcosms (i) in the presence and absence of L. phyllopus over time, and (ii) at different bug densities. Insect presence resulted in higher soil Caballeronia titer over time. As bug density increased, the soil Caballeronia population also increased. Additionally, soil moisture affected Caballeronia abundance, with moister soil supporting a larger population. These results demonstrate that the relationship between Caballeronia and L. phyllopus is truly mutualistic and add to a small but growing body of literature that has quantified the effects of eukaryotic hosts on their bacterial partners.

Many studies indicate that increases in resource variability promote plant invasion. However, it remains unknown to what extent these effects might indirectly be mediated by other organisms. To test this, we grew eight alien species in pot-mesocosms with five different native communities under eight combinations of two nutrient-availability, two nutrient-fluctuation and two soil-microbe treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of alien plants under low nutrient availability, whereas its effect was minimal under high nutrient availability. However, the opposite pattern was found when plants grew in living soil. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the soil fungal pathogen diversity under high nutrient availability, but slightly decreased it under low nutrient availability. Our findings indicate that besides its direct influence, environmental variability could also indirectly affect plant invasion via changes in soil-microbial communities.

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individual plants are colonised by different communities of soil bacteria and it is difficult to estimate if the absence of a given species was a) because it was not present in the soil to colonise a given plant or b) it went locally extinct from competition, predation or similar. To minimise this uncertainty, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, with leaf communities more susceptible to contamination. For root communities the strongest driver of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall, the results reveal that root, but not leaf communities are amenable to transplant reflecting their differing ecological drivers. This work provides the basis to develop a plant microbiome transplant system.

Since modern wheat varieties are grown with chemical inputs, we ignore if changes observed in rhizosphere microorganisms between ancient and modern varieties are due to i) breeding-induced changes in plant genotype, ii) modifications of the environment via synthetic chemical inputs, or (iii) phenotypic plasticity, defined as the interaction between the genotype and the environment. In the field, we evaluated the effects of various wheat varieties (modern and ancient) grown with or without chemical inputs (N-fertilizer, fungicide and herbicide together) in a crossed factorial design. We analysed rhizosphere bacteria and fungi by amplicons sequencing and mycorrhizal association by microscopic observations. When considered independently of plant genotype, chemical inputs were responsible for an increase in dominance for bacteria and decrease in evenness for bacteria and fungi. Independently of inputs, modern varieties had richer and more even bacterial communities compared to ancient varieties. Phenotypic plasticity had a significant effect: bacterial and fungal diversity decreased when inputs were applied in ancient varieties but not in modern ones. Mycorrhiza were more abundant in modern than ancient varieties, and less abundant when using chemical inputs. Although neglected, phenotypic plasticity is important to understand the evolution of plant-microbiota associations and a relevant target in breeding programs.

AbstractBouteloua curtipendula (sideoats grama) is a valuable prairie grass for livestock forage, supporting food webs of herbivorous insects, reducing soil erosion, and limiting weed infiltration in urban grasslands. Efficient establishment of B. curtipendula in prairie restorations and urban plantings could drastically improve long-term functionality of the space. Soil microbial communities have been linked to plant germination, growth, and drought tolerance in many plant species, however little is known about the factors contributing to B. curtipendula germination and early growth. In this study, we used sterilized soil to examine the impact of soil microbes on B. curtipendula growth under greenhouse conditions. We found Bouteloua curtipendula emergence and growth to be impaired in sterilized soil compared to non-sterilized soil. Using high throughput sequencing of the soil, we found that B. curtipendula grown in sterilized soil induced a greater proportion of plant pathogens and fewer nitrifying bacteria when grown in non- sterilized soil. For example, there was a significantly higher proportion of Acidovorax, Cellvibrio, and Xanthomonas which are known to contain plant pathogens, while plant- growth promoting bacteria, like Rhodopseudomonas, were significantly higher in the non-sterile conditions. We found that soil sterilization and growth of B. curtipendula changed the relative abundance of metabolic subsystem genes in the soil, however, by seven weeks after seeding, B. curtipendula transformed the bacterial community of sterile soil such that it was indiscernible from non-sterile soil. In contrast, fungal communities in sterilized soil were still different from non-sterilized soil seven weeks post-seeding. It appears that the bacteria are involved in the initial establishment of beneficial conditions that set the stage for a robust fungal and plant seedling development.

BackgroundPlant can evolve with a core root microbiome that maintains essential functions for host performance. However, the relative importance of plant traits and soil factors on the structure, assembly, co-occurrence networks of the core root microbiomes and their relevance for plant characteristics remain elusive. Here, we investigated how plant species identity and soil environment affect the core bacterial communities in the bulk soil, rhizosphere and root endosphere of four plants with a gradient of Cd/Zn accumulation capacity under controlled and field environments. We further tested on the role of the core bacterial isolates in plant growth and accumulation of metal and nutrients. ResultsWe identified root compartment and plant species rather than environmental parameters as the primary driver of Cd-accumulator root microbiome. Stochastic processes were more important for the assembly of endosphere generalists (58.5%) than rhizosphere counterparts (45.2%), indicating that generalists were more robust to environmental changes. Increasing host selection from epiphytes to endophytes resulted in the existence of the endosphere and rhizosphere generalist core microbiota common to different plants under varying growth environments, highlighting that shared environmental and physiological features of host plants are decisive for core microbiome establishment. Further, endophytic core microbiota conferred greater biotic connectivity within networks and was more important predictors of plant metal accumulation, whereas the rhizosphere cores were more closely linked to plant biomass and nutrient status. The divergent functions of rhizosphere and endosphere core microbes on plant characteristics were also validated by inoculating the synthetic communities comprising bacterial isolates belonging to the core microbiota. ConclusionThis study indicated the pivotal role of plant trait in the assembly of conserved and functionally important core microbiome common to different Cd-accumulators, which brings us closer to manipulating the persistent root microbial associations to accelerate the rejuvenation of metal-disturbed soils through host genetics.

BackgroundPlant-microbe interactions in two root compartments - the rhizosphere and endosphere - play vital roles in maintaining plant health and ecosystem dynamics. The microbial communities in these niches are shaped in complex ways by factors including the plants developmental stage and cultivar, and the compartment where the interactions occur. Different plant cultivars provide distinct nutritional and ecological niches and may selectively enrich specific microbial populations through the secretion of root exudates. This gives rise to complex and dynamic plant-microbe interactions; some cultivars promote the recruitment of beneficial symbionts while others may deter pathogens. To clarify these processes, this work investigated the structure of the endosphere and rhizosphere microbial communities of wild type finger millet and five domesticated cultivars across two plant developmental stages. ResultsOur results showed that the plant developmental stage, compartment, and cultivar have varying degrees of impact on root-associated microbiomes. The dominant bacterial phyla in all samples were Proteobacteria, Actinobacteria, and Bacteroidetes, while the dominant fungal phyla were Ascomycota and Basidiomycota. All of these phyla exhibited pronounced variations in abundance. In general, an increased abundance of Actinobacteria in the endosphere was accompanied by a reduced abundance of Proteobacteria. The most pronounced changes in microbial community structure were observed in the rhizosphere during the flowering stage. Changes in the microbiome patterns of the rhizosphere were driven predominantly by the genus Pseudomonas. Moreover, the host plants developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia. ConclusionsOur results show that both host developmental stage and domestication strongly affect the assembly and structure of the plant microbiome. Moreover, plant root compartments can selectively recruit specific taxa from associated core microbial communities to fulfill their needs in a manner that depends on both the plants developmental stage and the specific root compartment that is involved. These findings show that deterministic selection pressures exerted by plants during their growth and development can significantly affect their microbial communities and have important implications for efforts to create tools for manipulating the microbiome to sustainably improve primary productivity.

The phyllosphere - the aerial parts of plants - forms a vast microbial habitat that harbors diverse bacterial communities playing key roles in ecosystem function. The foliar surface is thus a promising study system to investigate biodiversity-ecosystem function relationships. Researchers have found a positive correlation between leaf bacterial diversity and ecosystem productivity, but the causality of this relationship has yet to be demonstrated. To understand how the diversity and composition of phyllosphere bacterial communities could cause variation in the growth of their host plants, we assembled synthetic communities composed of different diversity and compositions of Methylobacterium strains - a plant growth-promoting bacterial genus ubiquitous in the phyllosphere - that we inoculated on Arabidopsis thaliana grown in gnotobiotic conditions. We hypothesized that (1) increasing Methylobacterium diversity should cause an increase in host growth; (2) strains should differ in their impact on host growth; and (3) the relationship between bacterial diversity and plant productivity should be strain-dependent. Our results supported our three hypotheses but revealed unpredicted patterns in how A. thaliana leaf biomass varied according to inoculated Methylobacterium strain richness and identity. Increasing bacterial richness induced a higher host leaf biomass, but only after an initial reduction in biomass, suggesting competition alleviation by multispecies interactions. Two Methylobacterium strains showed beneficial effects on A. thaliana growth, and one strain was detrimental for the plant. Community composition shaped the relationship between diversity and productivity, highlighting the importance of community mutualistic and antagonistic interactions. Furthermore, niche complementarity was likely the main ecological mechanism driving the diversity-productivity relationship in our study system. By demonstrating the causal effects of Methylobacterium community diversity and composition on host plant growth, our experiment shed light on the importance of phyllosphere bacteria in terrestrial ecosystem functioning.

Understanding how microbes disperse in ecosystems is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about the vectors that may contribute to their migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal among French sourdoughs and flours used to make bread. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analyzed whether flour is a carrier of sourdough yeast and bacteria and studied whether microbial migration occurs between sourdoughs. The microbial community of a collection of 46 sourdough samples, as well as that of the flour from which each was made, was studied by 16S rDNA and ITS1 metabarcoding. No sourdough yeast species were detected in the flours. Sourdough lactic acid bacteria (LAB) were found in only five flour samples, and they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. The species shared between the sourdough and flour samples are commonly found on plants and are not known to be alive in sourdough. Thus, the flour microorganisms did not appear to grow in the sourdough microbial community. Dispersal between sourdoughs was also studied. Sourdoughs shared no yeast ASV, except in few cases where groups of three to five bakers shared some. These results suggest that there is little migration between sourdoughs, except in a few situations where bakers may exchange sourdough or be vectors of yeast dispersal themselves.

BackgroundRecent evidence suggests that soil microbial communities can regulate plant community dynamics. In addition, the drought tolerance of plants can be enhanced by soil microbes. So far, few studies have assessed the variation in the microbiome of specific plant species along environmental gradients. Yet understanding these dynamics is essential to improve predictions of plant-soil feedbacks and the consequences of ongoing climate changes. Here we characterized the soil microbiome of two co-occurring Mediterranean oaks along a precipitation gradient, using amplicon sequencing of phylogenetic marker genes for prokaryotes and fungi. Additionally, we identified tree-specific and locally-specific microbes potentially responsible for tree community dynamics. ResultsWe show that two co-occurring, evergreen Mediterranean oak species harbor distinct microbiomes along a precipitation gradient. The soil microbial diversity increased along the precipitation gradient, for prokaryotic and {beta} diversity and for fungal {beta} diversity. Quercus ilex harbored richer fungal communities than Quercus suber, and host-specific taxa more often belonged to fungi than to prokaryotes. Notably, the microbial communities at the dry end of the precipitation gradient harbored more locally-specific prokaryotic and fungal taxa than the microbial communities with a higher diversity, at the wet end of the gradient, suggesting higher specialization in drier areas. ConclusionsEven congeneric tree species, belonging to the same functional group, can harbor distinct and specific soil microbiomes. These microbiomes become more similar and consist of more specialized taxa under drier compared with wetter conditions. With this, our study offers a step towards a better understanding of the context-dependency of plant-soil feedbacks by going beyond and {beta} diversities and focusing on specialized taxa potentially driving community changes along environmental gradients. We hope that our study will stimulate future research assessing the importance of context-dependency of interactions between plants and soil communities in a changing world.

Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, the trends of co-occurrence networks across similar gradients remain elusive. Here, we constructed co-occurrence networks for fungal community along a 2300 m elevation gradient on Mt Norikura, Japan, hypothesizing a progressive decline in network connectivity with elevation due to reduced niche differentiation caused by declining temperature and ecosystem productivity. Results agreed broadly with predictions, with an overall decline in network connectivity with elevation for all fungi and the high abundance phyla. However, trends were not uniform with elevation, most decline in connectivity occurred between 700 m and 1500 m elevation, remaining relatively stable above this. Temperature and precipitation dominated variation in network properties, with lower mean annual temperature (MAT) and higher mean annual precipitation (MAP) at higher elevations giving less network connectivity, largely through indirect effects on soil properties. Among keystone taxa that played crucial roles in network structure, the variation in abundance along the elevation gradient was also controlled by climate and also pH. Our findings point to a major role of climate gradients in mid-latitude mountain areas in controlling network connectivity. Given the importance of the orographic precipitation effect, microbial community trends seen along elevation gradients might not be mirrored by those seen along latitudinal temperature gradients. ImportanceAlthough many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts across environmental gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation, and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Assemblages of keystone taxa playing crucial roles in network structure varied along the elevation gradient and were also largely controlled by climate. Our results provide insight into the shift of soil fungal community co-occurrence structure along elevational gradients, and possible driving mechanisms behind this. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/428196v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@12e555aorg.highwire.dtl.DTLVardef@e5c4d7org.highwire.dtl.DTLVardef@de00bdorg.highwire.dtl.DTLVardef@102967c_HPS_FORMAT_FIGEXP M_FIG C_FIG

Plasmids play a crucial role in the spread of antimicrobial resistance genes (ARGs) across One Health due to their ability to transfer a wide range of ARGs within and across bacterial species and biomes. We sequenced 173 circularised plasmids transferred from wastewater treatment plant (WWTP) effluent into Escherichia coli and subsequently characterised their genetic content. Multiple multidrug resistant plasmids were identified with a significant number of mega plasmids (>100Kb). Plasmids existing in isolation were rare and almost all existed with other plasmids. Our results suggest that positive epistasis promotes plasmid persistence in WWTP populations in a similar manner to that identified in vitro via infectious transmission, varying properties against plasmid community backgrounds, interactions with a range of other plasmids, source-sink spill-over transmission within the plasmid community rather than the host bacteria and compensatory mutations. We have demonstrated that the plasmid paradox solutions apply to plasmid communities in addition to plasmid host interactions. Our study identified that rather than existing as lone entities plasmids co-exist in small packs, the protection is afforded to the pack not by all members but by one or two and many plasmids coast within this pack as they contain no obvious advantage to the host. Our findings show that we need to enter a new paradigm and study plasmids in packs rather than as single entities in order to understand their transmission across One Health.