FEMS microbiology ecology最新文献

Soil microbial communities play a pivotal role in salt marsh ecosystem functioning, driving processes such as organic matter decomposition and greenhouse gas cycling. Despite their importance, it remains unclear how climate warming will affect the diversity and activity of salt marsh soil microbial communities, limiting our ability to predict the fate of the vast stores of soil organic carbon in these so-called blue carbon ecosystems. Here, we leveraged the Marsh Ecosystem Response to Increased Temperature (MERIT) experiment to investigate the effects of sustained warming on the structure and function of the putatively active microbial community, as assessed by rRNA transcripts, alongside measurements of exo-enzymatic activities involved in carbon and nitrogen acquisition. Our results reveal that, after 5 years of experimental warming by +1.5°C and +3.0°C, the overall structure of the active microbial community remains remarkably stable, suggesting a high degree of resilience to elevated temperatures in this dynamic environment. However, warming selectively promoted drought-tolerant phyla, particularly Actinobacteriota and Firmicutes, which are known for their ability to degrade complex organic compounds and withstand desiccation. These findings suggest that while the active microbial community is broadly resistant to warming, subtle compositional shifts may enhance decomposition of recalcitrant soil carbon.

Marine surface waters contain complex mixtures of chemicals that can adversely affect microzooplankton. There is a lack of toxicity data for this organism group, and we used two different methodologies to fill this gap. We tested the toxicity of three chemical mixtures of polar organic chemicals extracted from marine surface water, using a component-based and a whole-mixture approach. The component-based approach estimates cumulative toxic units for each mixture based on concentrations of individual compounds. The observed hazard data for zooplankton was supplemented with ECOSAR-generated QSAR daphnid LC50s when observed data was missing. ECOSAR performance was evaluated for zooplankton, where 65% of the observed hazard data for zooplankton was predicted within a factor of 10. This approach suggested that none of the mixtures should be toxic to zooplankton at their respective measured environmental concentrations. We found contrasting results using the whole-mixture approach with a reduction in ciliates and dinoflagellates, and change in microzooplankton diversity, at the measured environmental concentrations. We suggest an assessment factor of at least 1000 when using additive toxic units in a component-based risk assessment approach to cover for the extrapolation from acute to chronic toxicity data and for the range of sensitivities among microzooplankton species.

The significant advancements in understanding the roles of anaerobic fungi (AF) within microbial ecology have opened numerous avenues for biotechnological exploitation, particularly in enhancing the productivity of livestock. The efficient, unique, and complex enzyme systems of AF play a determining role in the metabolic conversion of lignocellulosic plant matter into animal products, such as milk and meat by mammalian herbivores. Mitigation of methane emissions through microbial or dietary strategies in ruminants is a major environmental climate change issue. In turn, controlled management of the interkingdom syntrophic interactions among the eukaryotic AF, prokaryotic bacteria, and archaea can lead to the production of valuable biofuels, (biomethane, biohydrogen, and bioethanol), and organic acids. These products can also serve as building blocks in numerous processes to generate high value chemicals in circular bioeconomy.

The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in aboveground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.

Zygnematophycean "glacier algae" form extensive blooms on ablating glacier surfaces despite the ultra-oligotrophic conditions apparent. Previous work has postulated that this oligotrophic bloom paradox is due to (i) lower nutrient requirements of glacier algae, (ii) efficient uptake and storage of the nutrients available, and/or (iii) ineffective characterisation of the actual nutrient environment that glacier algae experience. We investigate the latter here by directly sampling the thin (∼2 mm) melt water film in which glacier algal cells reside across three glaciers in Svalbard during the 2023 melt season, comparing to outcomes from more typical bulk ice sampling techniques. Micromelt samples generally contained increased concentrations of ammonium (NH4+), nitrate (NO3-), nitrite (NO2-), and phosphate (PO43-), though trends were not uniform, and concentrations remained well within oligotrophic levels. Several major ion species were significantly increased in micromelt fractions as compared to bulk samples, indicating aeolian deposition and marine aerosol influences on the glacier algal environment. In turn, enhanced micromelt dissolved organic carbon concentrations (DOC) indicated likely DOC delivery by glacier algae to the microbial food web from the onset of bloom formation. Taken together, datasets reveal new fine-scale heterogeneity in the glacier algal meltwater environment.

Interactions among plants and belowground microbes form complex networks that underpin ecosystem functions, yet the specific roles of prokaryotes and fungi and their links to plant diversity and productivity remain unclear. In a North American grassland, we examined biomass, diversity, and community composition across four communities-plants, root fungi, soil fungi, and soil prokaryotes-along a water-driven edaphic gradient. Drier habitats had lower plant biomass but higher diversity and more complex belowground networks. All communities, except soil fungi, varied significantly across habitats, producing distinct network structures. Bacterial biomass was more strongly correlated with plant biomass than fungal biomass, and bacterial families had greater predictive power for plant productivity. However, many keystone taxa with high network degrees and betweenness were fungi, and the proportion of fungal network hubs increased in wetter habitats. Core fungal families such as Glomeraceae and Herpotrichiellaceae consistently showed high richness and degree across habitats, while core prokaryotic families differed between wet and dry sites, suggesting more localized roles. These findings enhance our understanding of the relationships between the biomass and diversity of plants and belowground microbial communities, highlighting the importance of distinguishing microbial functional roles to better understand belowground ecological processes.

Pseudomonas aeruginosa is a model organism for studying social behaviors in bacteria, such as the exploitation of exoprotease by social cheaters. The current paradigm holds that continuous culture of exoprotease-producing individuals with protein as the sole carbon source selects for exoprotease non-producers mutants with an impaired quorum-sensing regulator, LasR, which controls exoprotease expression. However, recent studies reveal that some isolates lacking functional LasR still produce exoproteases under the control of another regulator, RhlR. Here, we extended this study to two clinical strains, AUS 411 and AUS 531, isolated from cystic fibrosis patients and harboring functional LasR. Surprisingly, in AUS 411, exoprotease-non-producers appeared from the first growth passage, but most cells lost exoprotease production only transiently, with stable non-producers isolated only in late passages. In contrast, AUS 531 slowly selected stable non-producers with limited cheating ability, which neither accumulated to high proportions nor caused population collapses. Contrary to the paradigm, these non-producers had no inactivating mutations in lasR yet were more fit than laboratory-derived lasR deletion mutants in both casein and casamino acid media. Our findings demonstrate that social behavior can differ significantly from that in reference strains, suggesting that some P. aeruginosa strains evolve quorum-sensing networks with robust resistance to exploitation.

Leaf litter decomposition is a vital ecosystem process in which macroinvertebrate-shredders produce substantial amounts of fine particulate organic matter (FPOM) via sloppy feeding and defecation, creating a substratum and substrate for microbial assemblages. However, microbial communities colonizing the shredder-produced FPOM are understudied compared to those in streams and on original leaves. Here, we investigated the bacterial community composition on shredder-produced FPOM in a laboratory experiment. We fed alder, beech, and maple leaves conditioned under oxic or anoxic conditions to Sericostoma (Insecta: Trichoptera) larvae. We collected shredded leaf particles and faecal pellets as shredder-produced FPOM at different times and examined their microbial communities using 16S rRNA amplicon sequencing. We hypothesized that shredder-produced FPOM types harbor diverse, distinct, and specialized microbial taxa in response to leaf species and conditioning. We found significantly higher alpha diversity on shredded leaves compared to faecal pellets. Microbial communities on faecal pellets differed from initial leaf communities and with anoxic and oxic conditioning. Bacterial communities developing on leaves were dominated by common leaf decomposers including Flavobacterium and Pseudomonas whereas faecal pellets harbored gut bacterial taxa including Acinetobacter and Carnobacterium. These results underline the importance of conditioning and shredder activity in shaping FPOM-attached bacterial communities, increasing bacterial diversity in stream ecosystems.