FEMS microbiology ecology最新文献

Subsurface microbiology is at a crossroads, evolving from asking 'who's home' to seeking clarity on microbes' functionality and the key processes that constrain subsurface life. Importantly, the processes subsurface microorganisms mediate are central to societal needs to mitigate climate change and address waste storage, as proposed solutions to both involve subsurface habitats. However, subsurface sampling opportunities and funding remain limited and, in some cases, have diminished. This perspective article is aimed at scientists who have or might develop an interest in the geomicrobiology of the subsurface, for funding agencies worldwide, and for scientists and engineers engaged in the extractive and waste disposal industries. It briefly reviews subsurface science's history and current status and proposes some actions for moving forward. In particular, we see the continued need for engaging early-career microbiologists in drilling projects, increasing access through industry partnerships, microbiology-led drilling projects, and creating interdisciplinary drilling projects by including microbiologists during the drilling project planning.

The WHO has identified rising antibiotic resistance as a 'global threat,' highlighting the urgent need to understand how resistance spreads. A key concept is the minimum selective concentration (MSC)-the threshold at which resistant bacteria gain a competitive advantage. While MSC studies typically use single antibiotics under controlled conditions, real-world environments often contain fluctuating levels and mixtures of antibiotics from sources such as wastewater, complicating the dynamics of resistance spread. This study presents a mathematical model that simulates antibiotic accumulation in aquatic systems to evaluate the resulting influence on resistance selection in microbial communities. It incorporates antibiotic inputs, their photolytic and/or biotic degradation, and microbial competition. Results show that antibiotic accumulation from environmental pulses depends on parameters such as pulse frequency and half-life and may drive the selection of resistant strains. Importantly, combinations of antibiotics significantly alter bacterial competition depending on their interaction type. Synergistic combinations can potentially intensify selection for resistance even when individual antibiotic concentrations are below their respective MSCs. These findings help to understand effects of changing concentrations of multiple antibiotics and to plan mitigation strategies.

Climate warming is likely to increase the physical connectivity of ecosystems with their surroundings. For Arctic lakes, increasing meltwater and precipitation may enhance the inputs of nutrients, organic matter and microorganisms from their catchments, and the increasingly ice-free, open-water conditions of the Arctic Ocean may favor increased inputs of marine aerosols, including microbiota. This study therefore aimed to determine how changing connectivity to terrestrial and marine habitats may affect the dispersal, sorting, and establishment of bacterial communities in a coastal High Arctic lake. Three habitats in this model system were sampled for ice, water, and snow: the lake, inflowing water tracks over permafrost soils, and an adjacent ice-dammed bay connected to the Arctic Ocean. Lake water chemistry confirmed the hydrological connection between the lake and terrestrial habitats, with the lake fed by terrestrial carbon sources via snow and groundwater run-off. Sequencing of 16S rDNA and rRNA showed evidence of a small marine and terrestrial influence on the lake, but few bacterial phylotypes were common to all three connected habitats. These results imply ongoing strong environmental filtering by habitat type, despite the apparent and potentially rising connectivity, and provide an example of bacterial resilience in a region of rapid climate change.

This study addresses a significant research gap in understanding the impacts of captivity on the bacteriome and physiology of saltwater crocodiles (Crocodylus porosus). Despite their ecological and cultural significance, crocodilians are a taxon that remains underexplored in microbiome research. We investigated cloacal bacteriome samples from both wild and captive populations to identify compositional and functional differences resulting from captivity. Our findings reveal significant alterations in bacterial diversity and community structure in captive crocodiles, with notable shifts at both phylum and family levels; specifically, Bacteroidota and Fusobacteriota dominate in captivity, whereas wild crocodiles exhibit a higher prevalence of Pseudomonadota and Bacillota. The Shannon diversity index indicates a significant reduction in bacterial diversity among captive individuals, likely due to husbandry practices that foster a microbially depauperate environment. Additionally, serum metabolomics analysis shows an enrichment of alcohol sugars in captive crocodiles, alongside a decrease in pantothenic acid. While this is the first study to characterize these traits in saltwater crocodiles, further research is necessary to determine the physiological consequences of these bacterial and metabolic changes on host fitness and adaptability. Longitudinal studies are essential for understanding how bacterial communities evolve over time and in response to environmental factors, which will inform conservation strategies and improve the management of captive populations of crocodilians intended for reintroduction into the wild.

Understanding plant growth-promoting bacteria interaction is essential for developing of effective multi-strain inoculants. Here, we investigated how Azospirillum baldaniorum Sp245 and Pseudomonas fluorescens A506 interact when establishing biofilms under rhizospheric conditions and its impact on root colonization and plant growth. Mixed biofilms assembled in vitro on root exudates revealed competition between both strains, with Sp245 outcompeting A506. On lettuce roots, they formed spatially segregated biofilms according to their individual niche preferences: Sp245 exhibited dense biofilms on and along the main root, while A506 grew preferentially associated to root hairs. Both strains co-localized only in certain hotspots on the root surface and hairs bases. Yet when colonizing roots in substrate, their colonization was mutually enhanced, suggesting that cooperation prevails under these conditions. Co-inoculation of Sp245 and A506 promoted lettuce growth synergistically, increasing leaf area, fresh and dry biomass, and root dry weight. Moreover, co-inoculated plants showed enhanced survival and growth after heat stress. Our findings unveil a complex yet complementary interaction between Sp245 and A506 in the rhizosphere, where their spatial segregation does not preclude cooperation and synergistic plant-beneficial effects. Likewise, the results highlight the potential of simplified two-strain synthetic communities for enhancing crop productivity and resilience under climatic stress.

A key question in microbial ecology is how the microbiota regulates host invasion by pathogens. Several ecological theories link the diversity, abundance and assembly processes of the microbiota with its resistance to invasion, but the specific properties of microbial communities that confer protection to the host are poorly understood. We addressed this question for the oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. Using state-of-the-art microbial ecology methods, we compared microbial communities associated with asymptomatic and symptomatic leaf tissues to elucidate pathogen-microbiota interactions. Despite visible symptoms, P. viticola infection induced only subtle changes in microbial community composition. Symptomatic tissues showed enrichment in basidiomycete yeasts and Bacillus species, both known for their biocontrol activity, and exhibited a higher degree of determinism in community assembly processes. Asymptomatic tissues hosted more diverse microbiota, but lacked consistent associations with known biocontrol agents. Instead, they were often associated with other airborne grapevine pathogens. These findings suggest a novel interaction scenario: upon infection, P. viticola reshapes locally the leaf microbiota, excluding other pathogens and selecting for beneficial microbes. Although further studies are needed to uncover the underlying mechanisms, these findings underscore the relevance of targeting disease lesions in the search for protective microbial consortia.

Extreme rainfall and flooding are expected to increase in Northern subboreal habitats, altering soil hydrology and impacting greenhouse gas (GHG) fluxes by shifting redox potential and microbial communities as soils transition from aerobic to anaerobic conditions. This study examined the effects of a 2-week growing-season flash flood on bacterial, archaeal, and fungal communities and microbial processes driving CH4 and N2O fluxes in riparian alder (Alnus incana) forests. Flooding reduced soil nitrate accumulation as determined by quantitative polymerase chain reaction and promoted dinitrogen-fixing, nifH gene-carrying bacteria like Geomonas. Sequencing data showed that anaerobic bacteria (Oleiharenicola, Pelotalea) increased during the flood, while N2O emissions declined, indicating a shift towards complete denitrification to N2. However, drier patches within the flooded area emitted N2O, suggesting nitrification or incomplete denitrification. A diverse arbuscular mycorrhizal community was detected, including genera Acaulospora, Archaeospora, Claroideoglomus, Diversispora, and Paraglomus. Flooding increased the abundance of the fungal genera Naucoria, Russula, and Tomentella and the family Thelephoraceae, which symbiotically support alder trees in nitrogen uptake and carbon sequestration. Microtopographic differences of 0.3-0.7 m created spatial variability in GHG emissions during flooding, with some waterlogged areas emitting CH4, while others enhanced CH4 oxidation (determined by FAPROTAX) and promoted nitrification-driven N2O emissions in drier, elevated zones. We conclude that flash flooding during the active growing season significantly affects nitrogen-fixing and nitrifying microbes and alters symbiotic fungal community composition, creating spatial variability in GHG emissions.

Rice is a staple crop relevant to present and future human feeding. However, these agroecosystems significantly contribute to greenhouse gas methane emissions. In Uruguay, a traditional low-intensity, reduced-tillage rice system alternates annual rice crops with pastures for livestock. We hypothesize that rice crop intensification impacts aerobic methanotrophic communities associated with rice roots, which are crucial in mitigating methane emissions. The pmoA gene abundance, methane oxidation potential (MOP), and methanotrophic community composition by 16S rRNA gene Illumina MiSeq (V4 region) allowed us to determine the dynamics of these communities in bulk and rhizospheric soils from continuous rice (CR) and rice-pastures (RP) rotations throughout the crop cycle. Results showed that rice crop intensification significantly affected MOP and pmoA abundance in both compartments. The tillering stage showed the greatest pmoA abundance and MOP. Rhizospheric methanotrophic communities from the CR and RP systems at flowering differed greatly. While Methylocystis dominated rhizospheric CR soil, Methylocella predominated in those from RP rotation. Active rhizospheric methanotrophic communities at flowering detected by 13CH4 DNA-SIP were dominated by distinct Methylocystis-affiliated ASVs in both cropping systems. However, other active genera were differentially enriched in the two contrasting cropping systems. These results suggest aerobic methanotrophs could be a microbial guild sensitive to crop intensification.