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.

Propionic acid (HPr) accumulation is a major indicator of anaerobic digestion (AD) dysfunction, yet the relative contributions of acidity, undissociated HPr, and propionate ions (Pr-) to process inhibition remain poorly understood. We investigated these effects in mesophilic batch AD microcosms fed with municipal sewage sludge, using a comparative design involving HPr, sodium propionate (NaPr), NaCl, and HCl treatments across two series of experiments. While 20 mM HPr caused a 22% reduction in the maximal methane production rate, 81 mM HPr led to complete inhibition, with the initial pH dropping to 5.1. By contrast, 81 mM NaPr reduced methane production rate by only 40%, and 81 mM NaCl caused no inhibition, demonstrating that acidity is the dominant inhibitory factor, with Pr- exerting a secondary concentration-dependent effect. 16S rRNA gene amplicon sequencing revealed strong, compound-specific shifts in microbial community composition, affecting key functional groups including syntrophs and methanogenic archaea. The proportion of methanogens dropped from 2-3% in control reactors to less than 0.2% under 81 mM HPr, consistent with the observed methane production inhibition. Under HPr81, over 100 ASVs were differentially abundant compared to controls, a pattern largely shared with HCl-treated reactors, further confirming the predominant role of acidity. The number of differentially abundant ASVs was negatively correlated with methane production rates (R{superscript 2} = 0.97), underscoring the link between community reshaping and process impairment. These results provide a unifying framework for propionate inhibition in AD and suggest that microbial community profiling could serve as an early warning tool for process imbalance detection.

O_LIPhyllosphere microbiomes are subject to microbial import from various sources and undergo substantial changes during phenological changes of plants. However, these processes are still poorly understood for forest canopies. We propose that phenology-driven changes in host properties, and rainwater-mediated, within-canopy transport shape the phyllosphere microbiome in temperate forests. Leaves and throughfall samples were collected from oak, ash and linden trees at top, mid, and bottom canopy positions at the Leipzig canopy crane facility (Germany) at time points representing early, mid and late phenological stages. Bacterial community composition was assessed by 16S rRNA gene amplicon sequencing. C_LIO_LIPhenological stages explained 19% of phyllosphere bacterial community variation, followed by tree species identity (12%) and canopy position (2%). Later phenological stages exhibited more homogeneous and functionally redundant phyllosphere communities along with a strong decline of plant pathogens and increasing potential for microbially mediated biocontrol mechanisms. Throughfall transported up to 1011 bacterial cells per litre with maximum bacterial fluxes at the canopy top. C_LIO_LIOur findings demonstrate that in temperate forests, phenology-driven effects on the phyllosphere microbiome are far more important than tree species specific effects. Extent and selectivity of throughfall-mediated mobilization may play a crucial role for the spatial heterogeneity of microbial communities in tree crowns. C_LI

Emergence of multi-drug resistant (MDR) pathogens is facilitated by the mobilization of resistance genes from bacteria in animal and environmental habitats, a process often mediated by plasmids. While fertilization of agricultural soils with manure is hypothesized to serve as a pathway for transferring antimicrobial resistance plasmids to soil and crop bacteria, evidence is limited. In this study, we aimed to determine whether MDR-plasmids from manure transfer in soil, leading to the formation of long-term agricultural resistance reservoirs. To this end, we introduced a known MDR plasmid to agricultural soil where barley was subsequently grown and monitored spread of the plasmid over the course of a growing season (up to 190 days). Our experimental design mimicked conventional agricultural practices at a microcosm scale. A digital droplet PCR approach indicated plasmid transfer in the rhizosphere, which was confirmed by a targeted Hi-C method (termed Hi-C+). This demonstrated transfer of the plasmid to soil bacteria 10 days after barley planting but was not observed afterwards. The new plasmid hosts could not be identified, as plasmid-associated host Hi-C reads were absent from existing databases. This implies these hosts were rare and likely unculturable members of the soil microbiome. Our findings demonstrate that plasmid transfer from manure to soil can occur under conditions reflecting those found in agricultural settings. Furthermore, rare and uncharacterized members of the soil microbiomes may participate in acquiring MDR plasmids from manure bacteria, raising important questions about their role in spreading resistance plasmids.

O_LIThe causal factors shaping plant-associated microbiota are incompletely known. Elevated concentrations of the micronutrients zinc (Zn), manganese (Mn) and copper (Cu), and exposure to non-essential trace elements including cadmium (Cd) and arsenic (As), can be toxic. Here we explored whether differences in metal(loid) sensitivity between plants and bacteria influence phyllosphere bacterial community composition. C_LIO_LI224 representative Arabidopsis thaliana phyllosphere bacterial strains were screened on metal(loid) concentration series in synthetic media. We obtained leaf apoplastic fluid ionomes for comparisons with bacteriotoxicity profiles, and tested for relationships between strain-wise metal(loid) tolerances, phylogeny and gene content. C_LIO_LILeaf apoplastic Zn2+ and Cd2+ concentrations were the most likely to arrest growth of metal-sensitive bacteria in planta. Soil bacterial strains were several-fold more sensitive to both these metals than leaf strains, consistent with selection for increased bacterial Zn and Cd tolerance in the phyllosphere. Strains known to govern bacterial community structure were metal-sensitive, with only minor influences of between-metal and between-strain interactions. Bacterial genus explained considerable proportions of the variances in metal(loid)-related gene content and tolerance phenotypes. Bacterial Cd tolerance correlated with the presence and copy number of known Cd-related genes. C_LIO_LIOur results suggest that plant metal homeostasis contributes to structuring bacterial communities in the leaf endosphere. C_LI

Aridification and climate stress threaten global plant productivity, but the survival strategies of desert plants remain only partly understood. In this study, we examined how the microbiome of Citrullus colocynthis, a hardy desert cucurbit valued for its ecological and medicinal benefits, may influence the plants ability to withstand harsh conditions. Using 16S rRNA amplicon sequencing, shotgun metagenomics, and culture-based methods, we analyzed microbiome changes across two regions of the UAE during the rainy and dry seasons. Leaf and root bacterial communities showed clear seasonal shifts, with greater richness in winter and higher evenness in summer, while soil microbiomes remained stable. Dominant bacterial groups, Actinomycetota and Pseudomonadota, varied seasonally, indicating trade-offs between stress tolerance and metabolic flexibility. Fungal communities (mainly Ascomycota and Basidiomycota) were stable at the phylum level but reorganized by order between seasons; archaeal populations showed little change. Among 24 cultured bacterial isolates, including three potential new species, we identified multiple stress tolerance and plant growth-promoting traits. Genomic data revealed biosynthetic clusters for antimicrobial and stress-protective functions, as well as adaptation genes in Pseudomonas orientalis. These results demonstrate that the dynamic, functionally diverse microbiome of C. colocynthis enhances its resilience to desert stress, offering potential for arid-land agriculture.

Characterizing the household bacterial microbiome allows for a stronger understanding of the various microbes that a person is exposed to everyday in their home. Exploring household microbiomes in different countries around the world increases - our understanding of the impact cultural differences might have on niche microbial communities in the house. The goal of this study was to use shotgun metagenomics to characterize the microbiome for ten locations around the home in ten different houses from three different countries (Mysuru, India; Dubai, United Arab Emirates (UAE); and Tucson, United States of America (USA)). There was a significant difference in alpha diversity between the three countries (ANOVA, p<0.05) with homes in Mysuru, India showing significantly higher bacterial diversity compared to Dubai, UAE and Tucson, AZ, USA. Beta diversity analysis of the homes found that bacterial communities significantly differed between cities (PERMANOVA, p<0.01) and within cities by household locations (PERMANOVA, p<0.001). Locations such as underneath the toilet rim, bathroom and kitchen sinks had the highest levels of bacterial diversity across the three cities compared to other sampling areas. A core microbiome of Actinomycetes and Gammaproteobacteria was found in all homes in all three cities. Within each city, a core microbiome was identified at the species level within specific household locations in each city. Over 90% of bacterial taxa found in the homes were a part of the human-associated phyla Actinomycetes (eg. genera Brevibacterium, Corynebacterium, and Microbacterium), Pseudomonadota (eg. genera Acinetobacter, Moraxella, Pantoea, Paracoccus, and Psuedomonas), and Bacillota (genus Streptococcus), which was comparable to previous studies. The household microbiome is variable in different locations in the house and on a global scale. Factors such as human activity, cultural practices, climate, and surface type and use may drive this diversity. Characterizing the household microbiome on a global scale allows for a better understanding of what drives microbial diversity, increasing our understanding of how microbial communities are shaped by the environment and how humans influence their dynamics, as well as any risks to human health that the built microbiome may potentially pose. Impact StatementThis research contributes to the understanding of the built microbiome, specifically how it varies within the house, within cities, and across the globe. This can aid in our understanding of microbial dynamics in environments with heavy human influence and help develop and improve hygiene habits and products which are mindful of the existing microbiome. Data SummaryDNA sequence data from this research is publicly available on the NCBIs Sequence Read Archive under BioProject PRJNA1416920. Data was analyzed using python and R code. Analysis protocols and information on software versions, packages, and more can be found within the text and in the following github repository: https://github.com/carolinescranton01/Global_Household_Microbiome. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

Bacterial communities and the bacteriophages infecting them are the basis of every ecosystem, including holobionts. The various ways in which these microorganisms interact with each other in complex communities over the life of the host affects the holobiont fitness. Despite being ubiquitous and environmentally relevant, plant-associated microbial communities remain understudied, especially in the phyllosphere, mainly because of the low abundance of microbes and the complexity of the system. In this work we followed bacteria and phage community dynamics in the phyllosphere over a growing cycle of Arabidopsis thaliana, to understand the ecology and relevance of bacteriophages in complex bacterial communities. We focused on Pseudomonas, a common plant pathogen and commensal, and the phages infecting them, in three setups of increasing complexity: in vitro, controlled experiments in planta and in wild populations of A. thaliana. We found that bacterial communities are resilient to phage infection, and more dynamic than the phages infecting them over the growing season, suggesting that although ubiquitous and abundant, bacteriophages exert selective pressures on leaf bacterial communities only intermittently.

Microbial communities can shift under drought in ways that enhance plant performance during drought ("microbe-mediated acclimation"). However, it is also possible for microbial communities to shift in ways that worsen the effects of drought ("mal-acclimation"). It is unclear how and where microbe-mediated acclimation vs. mal-acclimation occurs, or if there are types of soils or microbial communities that are more likely to harbor microbes that enhance plant acclimation and limit mal-acclimation. We tested for microbe-mediated plant acclimation/mal-acclimation to drought in soils from 21 maize farms in the midwestern United States, spanning a range of climate, soil types, and management practices. We first conditioned soil microbial communities to drought vs. well-watered conditions in a greenhouse and then tested for microbe-mediated acclimation by growing maize in soils inoculated with the conditioned microbial communities under drought and well-watered conditions. Drought-conditioned soils did not enhance plant performance under drought. In fact, one third of the farms exhibited mal-acclimation, especially under well-watered conditions where wet-conditioned soils reduced plant performance in well-watered contemporary conditions. Farm management practices, climate, soil texture, and microbial diversity generally did not predict when this microbe-mediated mal-acclimation occurred. Overall, these results suggest that in agricultural soils, microbes may frequently impede-rather than facilitate-plant acclimation to soil moisture levels. Open research statementThe plant and soil data used in this study are available via the Environmental Data Initiative repository at https://doi.org/10.6073/pasta/f4a0db3a076cf6d8cef908947f82736e. The bacterial and fungal amplicon sequence data are available via the European Nucleotide Archive under accessions PRJEB110071 and PRJEB109827, respectively.

There is disagreement on whether secondary endosymbionts are found in the major cereal pest aphid, Rhopalosiphum padi. Some papers report a diversity of secondary bacterial endosymbionts while others have failed to find evidence of these bacteria in this species. Here we revisit this issue by summarizing the relevant literature and through additional sampling of the species in Australia, China and Denmark using a combination of molecular approaches. We find a general absence of secondary endosymbionts beyond the obligate endosymbiont Hamiltonella defensa in R. padi. While the inconsistency in survey results may reflect rapid changes in endosymbiont turnover in populations and/or the impact of ecological factors such as host plant type on endosymbiont diversity, we are concerned that technical issues may be at least partly responsible for inconsistencies in the literature. This leads us to emphasize the importance of multiple sources of evidence required to establish and characterize endosymbiont infections, including PCR and qPCR assays, DNA Sanger sequencing and 16SrRNA gene metabarcoding. We note that several major aphid pests show a low incidence of secondary endosymbionts which raises issues about the importance of these endosymbionts in aphids that constitute pests, even though endosymbionts can in some cases increase host fitness and therefore pest impact.

Spartina alterniflora, the dominant plant species in salt marshes along the Atlantic and Gulf of Mexico coastlines of the Americas, is affected by disease and sudden vegetation dieback. Despite the foundational role of S. alterniflora in low-elevation salt marshes, the response of the native leaf-associated microbiome (i.e., phyllosphere microbiome) to leaf damage resulting from disease and environmental stress has not been explored. We hypothesized that healthy and damaged plants would show differentiation in their phyllosphere microbiomes following primary infection or exposure to environmental stressors. Here, we analyzed changes in prokaryotic and fungal relative abundance, diversity, and community composition in the S. alterniflora phyllosphere microbiome. We compared natural marsh and greenhouse plants in Georgia and South Carolina, USA, and collected leaves from healthy and damaged natural plants across two contrasting Spartina phenotypes that differ in their exposure to environmental stress. Our results show that plant origin (i.e., greenhouse vs. natural marsh), plant health status (i.e., healthy vs. damaged), and plant phenotype (i.e., short vs. tall Spartina) affect microbial relative abundance, alpha diversity, and community composition in the S. alterniflora phyllosphere. Damaged leaves presented higher microbial abundance and alpha diversity than healthy leaves, suggesting microbial proliferation following leaf damage. Plants raised from seeds in the greenhouse presented the lowest microbial abundance and Shannon diversity for both prokaryotic and fungal communities, indicating that in natural ecosystems the phyllosphere microbiota is acquired predominantly through horizontal transmission from the environment. Overall, this study provides novel insights into the assembly of the S. alterniflora phyllosphere microbiome. ImportanceSalt marshes are tidally influenced coastal wetlands that provide a range of ecosystem services to global and local communities, including protection from storm surge, water purification, and carbon sequestration. Spartina alterniflora is the dominant plant species in Atlantic and Gulf of Mexico marshes within the Americas. Fungal disease and exposure to environmental stressors have previously been described in marsh ecosystems and linked to extensive and sudden vegetation dieback in the southeastern U.S. In this study, we show that microbial proliferation follows plant damage caused by either fungal disease or environmental stress, leading to a profound change in native leaf-associated microbiota abundance, diversity, and composition (i.e., leaf microbiome dysbiosis). Using greenhouse plants as a control, we also demonstrate that microbes colonizing marsh leaves are acquired predominantly from the environment. Overall, this study advances our understanding of the leaf-associated microbiome of S. alterniflora, with implications for ecosystem management and restoration practices.

Sourdough starters contain simple microbial communities typically consisting of a few bacterial species and one or two yeast species. The yeast Maudiozyma humilis and the lactic acid bacterium Fructilactobacillus sanfranciscensis often co-occur in sourdough starters, and have been presumed to exist in a trophic relationship supported by glucose cross-feeding. However, previous research has highlighted a lack of evidence showing that yeast strains consume the glucose that F. sanfranciscensis produces. We have investigated the interaction between sourdough isolates of M. humilis and F. sanfranciscensis in a synthetic wheat sourdough medium, allowing us to control substrate composition and use flow cytometry to enumerate living and dead cells. M. humilis fitness was found to be lower in co-culture with F. sanfranciscensis than when grown alone. Analysis of spent medium composition highlighted the reliance of M. humilis on glucose rather than maltose for growth. Comparisons of predicted and measured co-culture metabolite content also revealed that F. sanfranciscensis consumed less maltose in co-culture than when grown alone. For the first time, we examined potential amino acid cross-feeding between M. humilis and F. sanfranciscensis, and found that within the pairing, F. sanfranciscensis was the main producer of amino acids. Our findings suggest that the M. humilis-F. sanfranciscensis interaction is likely to be neutral, or even competitive, with the strain identity of F. sanfranciscensis playing a defining role in the observed dominance of the bacteria and spent medium metabolite composition. ImportanceThe association of the yeast Maudiozyma humilis and the bacterium Fructilactobacillus sanfranciscensis in sourdough starters is well-documented, and together this pairing makes key functional and organoleptic contributions to the final bread product. Their relationship has historically been thought to be stabilised by cross-feeding of glucose to M. humilis. However, this theory has been drawn into question by recent research which found no evidence that M. humilis consumes the glucose produced by F. sanfranciscensis. Our understanding of cooperation, coexistence, and competition in microbial consortia affects approaches to ecosystem management in a broad variety of applied fields. The significance of our research is in demonstrating that this pairing does not interact mutualistically within a specified setting, providing support for neutral or competitive interactions as drivers of ecological stability. Research areas:

BackgroundPelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This algaes microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment. ResultsHere, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after a period of recovery post-induction. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to a relative loss of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization. ConclusionDue to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that significantly contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.

Ectomycorrhizal (EcM) fungi are well-recognized symbionts impacting tree health and ecosystem functioning globally, yet understanding of their timing of proliferation in soils across seasons and years remains limited. We analyzed monthly patterns of EcM fungal abundance and community structure over two years in five temperate monodominant forest plots via quantitative PCR and Illumina sequencing. We found that the phenological dynamics of EcM fungi differed significantly by host tree leaf habit, fungal exploration type, fungal genus, and soil moisture. Overall, total EcM fungal abundances based on qPCR consistently peaked in autumn, and were more dynamic in evergreen than deciduous plots, supporting ideas of surplus carbon and asymmetric above-belowground dynamics. Longer-distance exploration types peaked earlier and were more stable than shorter-distance types, suggesting an independent and supportive role in releasing spring nutrients. About half of 20 focal taxa consistently peaked in either autumn, summer, or spring, while others were either host- and/or year-dependent. Our findings highlight that phenology is a key EcM fungal trait best explained by both host and fungal contributions, and future studies across biomes should consider seasonal shifts and sampling to elucidate phenological traits. Summary- The timing of belowground production and seasonal community dynamics remain poorly understood for ectomycorrhizal (EcM) fungi. - We collected soils monthly for two years from five temperate monodominant forest plots. - Fungal production peaked in autumn, shorter-distance and evergreen-associated spanned wider ranges, and half of focal fungal genera showed seasonal preference, emphasizing autumn surplus carbon and spring nutrients from long-distance types. - Future studies should consider seasonal shifts when sampling EcM fungal communities, and forest carbon models should include asymmetric above-belowground phenology. Translated Summary (Spanish)- La fenologia de la produccion y composicion de comunidades de hongos ectomicorrizicos (EcM) es poco estudiada. - Recolectamos suelos mensualmente por dos anos de cinco parcelas mono-dominantes templados. - Produccion maxima de hongos ocurrio en otono, hongos asociados con arboles siempreverdes y de exploracion de corta-distancia observaron rangos mas amplios, y la mitad de generos de hongos focales observaron preferencia estacional, enfatizando extra carbono en otono y nutrientes en primavera de tipos larga-distancia. - Estudios deben considerar cambios estacionales para el muestreo de hongos EcM, y modelos de carbono deben incluir fenologia asimetrica entre hojas y hongos. Plain language summaryEctomycorrhizal fungi are critical for the global carbon cycle, but their seasonal and inter-annual growth patterns remain unclear. We sample soil DNA monthly over two years across five different monodominant temperate forest stands. We find an overall belowground peak in autumn, with significantly later growth under wetter conditions, more dynamism with evergreen trees, and distinct spring growth by longer-distance fungi.

The study of microbial volatile organic compounds (mVOCs) is a growing area of research, with applications ranging from agriculture to human health. The majority of the mVOC data are from in vitro liquid cultures, while few analyses of bacterial and fungal volatilomes on solid media cultures exist. Studies comparing liquid versus solid cultures of bacteria and fungi show significant changes to the soluble metabolites that are produced, suggesting that large differences would be observed for mVOCs based on the culture conditions. To test this idea, we characterized the volatilomes of Chromobacterium violaceum (strain ATCC(R) 12472) and C. vaccinii (strain MWU328), and those of their isogenic cviR- quorum sensing mutants cultured on solid versus liquid Kings Medium B media. VOCs were sampled using thin-film solid-phase microextraction (TF-SPME) and analyzed by two-dimensional gas chromatography-time-of-flight mass spectrometry (GCxGC-TOFMS). Of the three variables examined - Chromobacterium species, media type, and quorum sensing ability - growth on liquid versus solid media caused the most significant differences in the volatilomes. Bacterial species and quorum sensing ability were also influential, but to a lesser degree. Our findings indicate the importance of growth conditions in microbial volatilomics, and therefore, more consideration should be given to how microorganisms are cultured for volatilome analyses. ImportanceThe purpose of this work is to elucidate the differences in the volatile metabolic profiles of Chromobacterium spp. by exploring them through the lens of three variables: growth conditions, species, and the ability to quorum sense. Work on organismal metabolic differences stemming from factors such as liquid versus solid media types remains broadly overlooked. Understanding these effects will allow future researchers to design more robust experiments that better translate to native microbial ecosystems such as rhizosphere and phyllosphere, where volatile compounds may influence plant-pathogen or plant-saprobe interactions.

Seed microbiota play a crucial role in plant health and development, yet remain understudied compared to other plant-associated microbial communities. This study aimed to characterize seed microbiota diversity across four major crops (common bean, rapeseed, tomato, and wheat) and establish a comprehensive strain collection of seed-borne microorganisms (bacteria and fungi). We employed a combination of culture-dependent and culture-independent approaches to analyze 68 seed samples representing diverse genotypes and production modes. Our results revealed highly variable seed microbiota, with bacterial colonization ranging from 10 to 100 million bacterial CFUs per gram of seeds, and microbial richness varying from 4 to 351 bacterial and 16 to 138 fungal amplicon sequence variants (ASVs) per sample. Both plant genotype and production mode significantly influenced microbiota composition, with each seed sample produced harboring a distinct microbial assemblage. Interestingly, seeds produced in confined environments exhibited lower bacterial colonization but higher microbial richness compared to field-produced seeds. We observed divergent ecological drivers shaping bacterial and fungal communities. Bacterial assemblages were more host-specific and variable, while fungal communities showed greater stability and a substantial core microbiome shared across plant species. Our culturomics approach yielded a collection of 2,510 bacterial and 837 fungal isolates, representing 10-21% of the seed microbiota diversity detected by metabarcoding and the majority of the prevalent and abundant taxa. Notably, 44-60% of cultured bacterial isolates were not detected by metabarcoding, highlighting the complementary nature of these approaches to detect rare or under amplified taxa in PCR. This study provides insights into the complexity and variability of seed microbiota across different crops and production conditions. Our findings emphasize the importance of combining culturomics and sequencing methods for comprehensive characterization of seed microbiota to uncover the potential of seed-borne microorganisms as bioinoculants for sustainable agriculture.

Near-shore coral reefs in southern Guam (Mariana Islands) experience severe sedimentation, in particular during the wet season when rainfall and erosion are high. We sampled fragments of the reef-forming coral Porites lobata from opposite ends of a sedimentation gradient in Fouha Bay, southern Guam, during dry and wet seasons. Using DNA metabarcoding, we characterized the diversity and composition of P. lobata-associated Symbiodiniaceae and bacterial microbiome communities. As in many species of Porites, Symbiodiniaceae communities of P. lobata were dominated by variants of Cladocopium C15 with sites showing differences in Symbiodiniaceae communities attributable to variation in these Cladocopium C15 variants. Bacterial microbiomes of P. lobata were dominated by Endozoicomonadaceae, a family of putative coral bacterial endosymbionts involved in nutrient cycling. Site and seasonal differences in bacterial diversity and community composition were apparent. In close proximity to the mouth of the river draining into Fouha Bay, bacterial diversity was highest during the wet season when sedimentation is generally severe. Microbiome reorganization in response to sedimentation may explain this result, but we also found overrepresentation of bacteria associated with terrestrial origin close to the river mouth and/or during the wet season. Together these patterns highlight that coral Symbiodiniaceae and bacterial communities are both spatially and temporally structured in this disturbed system. IMPORTANCEThis study provides a time series dataset of coral-associated microorganisms, including dinoflagellate algae and bacteria, from a tropical bay impacted by sedimentation that results from upstream erosion of disturbed soils. Characterizing temporal patterns of coral-associated microbes provides insights into the dynamic nature of these communities. While microbiome variability across sites and seasons may be a result of acclimatization to different environmental conditions, we identified bacterial groups of putative terrestrial origin in sampled coral microbiomes that may have been exported from eroded soils to the near-shore reef. Considering that disturbed soils act as hotspots for the proliferation of potentially harmful substances, such as antimicrobial resistance genes, understanding microbial community connections at the marine-freshwater-terrestrial interface is an important step toward evaluating environmental impacts across connected ecosystems from ridge to reef.

BackgroundGlobally, seagrass ecosystems are threatened by anthropogenic activities that are leading to increased levels of eutrophication, coastal pollution and thermal conditions. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. ResultsOur cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, which reflected 18% of the total microbial diversity of the starting inoculum. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51%), dissimilatory nitrate reduction to ammonia (71%), and C-N bond cleavage (83%). Six of the isolates, which represent new lineages of Agarivorans, coded for the nitrogenase gene cassette. Additionally, 52% of the genomes had genes for sulfur and/or thiosulfate oxidation, 88.5% for phosphorus solubilization, and 60.5% for IAA production. Genomic analysis also revealed that some pathways, including denitrification and dissimilatory nitrite to ammonia DNRA, required cross-species cooperation as no one taxa contained all the genes needed to complete these metabolic pathways. Based on draft genome models and results from phenotypic assays, isolates Streptomyces sp. (Iso23 and Iso384), Mesobacillus sp (Iso127), Roseibuim sp. (Iso195), Peribacillus sp. (Iso49), and Agarivorans sp. (Iso311) represent a minimal microbial community that is likely to promote seagrass growth and enhance restoration efforts. ConclusionOur work provides a detailed genomic and phenotypic analysis of bacteria isolated from Z. marina and identifies a minimal microbial community with complementary PGP traits. Isolating, identifying and characterizing bacteria that promote seagrass growth is critical towards enhancing restoration efforts of seagrass meadows.

Climate change is reshaping soil microbial communities, yet the impact of warming in bacterial-fungal interactions (BFIs) remains underexplored. We investigated whether heatwave temperature influence BFIs and the mechanism supporting the interaction. Using co-culture experiments with two bacterial and two fungal strains isolated from heathland soil, we compared mono- and co-cultures final abundances under ambient (18{degrees}C) and heatwave (25{degrees}C) soil temperatures. Our results revealed strongly asymmetric interactions, where fungi benefited by around 5% from bacterial presence, while bacterial abundance was inhibited by around 68%, regardless of temperature. Analyses of pH confirmed that acidification by fungi was probably the main cause of this inhibition. Moreover, warming did not affect the strength or direction of these interactions, though it slightly increased fungal abundance. These findings provide direct experimental evidence that fungi can impact bacteria via acidification, and that the interaction is unaffected by temperature. Understanding these mechanisms is crucial for improving predictions of microbial community dynamics and ecosystem functioning in warming environments.

ObjectivesBiofilms are the dominant mode of bacterial life. The gut microbiota itself has characteristics of a biofilm that grows on the intestinal mucosa. C. difficile and VRE are commonly co-isolated from patients but biofilm formation has not been studied in a multi-species context. Here we study the interactions between C. difficile and VRE in surface adherent community. ResultsWe found that VRE inhibits C. difficile biofilm formation in dual-species culture in the presence of excess glucose. Robust dual-species biofilms were produced when the carbon source was changed to a non-fermentable sugar such as fucose and xylose. We observed a high level of vancomycin tolerance in C. difficile biofilms that was not affected by the presence of VRE. Finally we also found that a nutrient step-change is sufficient to induce dispersion of single and dual-species biofilms. ConclusionsVRE can inhibit the development of C. difficile biofilms in the presence of a fermentable carbon source. VRE does not appear to affect vancomycin tolerance or nutrient-induced dispersion of C. difficile biofilms. Highlights- VRE inhibits C. difficile biofilm formation in the presence of fermentable glucose. - Stable VRE - C. difficile biofilms are formed by managing the available carbon source. - VRE does not affect C. difficile vancomycin tolerance in this model. - A 10-fold increase in available nutrients is sufficient to induce biofilm dispersion in C. difficile and VRE.