Environmental microbiology最新文献

Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Through amplicon sequencing of soil samples collected from 54 stands in six forest sites across the eastern United States, we identified 29 distinct Amplicon Sequence Variants (ASVs) representing Tetracladium, with large differences in relative abundance and small changes in ASV community composition among sites. Tetracladium richness was positively related to soil pH, soil temperature, total sulphur and silt content, and negatively related to plant litter quality, such as the lignin-to-nitrogen ratio and the lignocellulose index. Co-occurrence network analysis indicated negative relationships between Tetracladium and other abundant fungal groups, including ectomycorrhizal and arbuscular mycorrhizal fungi. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.

Cobalamin influences marine microbial communities because an exogenous source is required by most eukaryotic phytoplankton, and demand can exceed supply. Pseudocobalamin is a cobalamin analogue produced and used by most cyanobacteria but is not directly available to eukaryotic phytoplankton. Some microbes can remodel pseudocobalamin into cobalamin, but a scarcity of pseudocobalamin measurements impedes our ability to evaluate its importance for marine cobalamin production. Here, we perform simultaneous measurements of pseudocobalamin and methionine synthase (MetH), the key protein that uses it as a co-factor, in Synechococcus cultures and communities. In Synechococcus sp. WH8102, pseudocobalamin quota decreases in low temperature (17°C) and low nitrogen to phosphorus ratio, while MetH did not. Pseudocobalamin and MetH quotas were influenced by culture methods and growth phase. Despite the variability present in cultures, we found a comparably consistent quota of 300 ± 100 pseudocobalamin molecules per cyanobacterial cell in the Northwest Atlantic Ocean, suggesting that cyanobacterial cell counts may be sufficient to estimate pseudocobalamin inventories in this region. This work offers insights into cellular pseudocobalamin metabolism, environmental and physiological conditions that may influence it, and provides environmental measurements to further our understanding of when and how pseudocobalamin can influence marine microbial communities.

The Arctic Ocean is an oligotrophic ecosystem facing escalating threats of oil spills as ship traffic increases owing to climate change-induced sea ice retreat. Biostimulation is an oil spill mitigation strategy that involves introducing bioavailable nutrients to enhance crude oil biodegradation by endemic oil-degrading microbes. For bioremediation to offer a viable response for future oil spill mitigation in extreme Arctic conditions, a better understanding of the effects of nutrient addition on Arctic marine microorganisms is needed. Controlled experiments tracking microbial populations revealed a significant decline in community diversity along with changes in microbial community composition. Notably, differential abundance analysis highlighted the significant enrichment of the unexpected genera Lacinutrix, Halarcobacter and Candidatus Pseudothioglobus. These groups are not normally associated with hydrocarbon biodegradation, despite closer inspection of genomes from closely related isolates confirming the potential for hydrocarbon metabolism. Co-occurrence analysis further revealed significant associations between these genera and well-known hydrocarbon-degrading bacteria, suggesting potential synergistic interactions during oil biodegradation. While these findings broaden our understanding of how biostimulation promotes enrichment of endemic hydrocarbon-degrading genera, further research is needed to fully assess the suitability of nutrient addition as a stand-alone oil spill mitigation strategy in this sensitive and remote polar marine ecosystem.

The impact of Borrelia miyamotoi on human health, facilitated by the expanding geographical distribution and increasing population of Ixodes ticks, remains obscure in the context of global climate change. We employed multiple models to evaluate the effect of global climate change on the risk of B. miyamotoi worldwide across various scenarios. The habitat suitability index of four primary vector tick species for B. miyamotoi, including Ixodes persulcatus, Ixodes ricinus, Ixodes pacificus and Ixodes scapularis, was projected using a boosted regression tree model, considering multiple shared socio-economic pathway scenarios over various time periods. The modelling analysis reveals that, apart from I. scapularis, future global warming will result in a northward shift in the other three vector tick species and a gradual reduction in suitable habitats. Random forest models indicate consistent changes in B. miyamotoi and its primary tick species, with potential risk areas shrinking and shifting northward, particularly in the eastern USA, northeastern and northern Europe and northeast Asia. These findings highlight the urgent need for enhanced active surveillance of B. miyamotoi infection in primary vector tick species across projected potential risk areas. The effect of climate change on B. miyamotoi distribution might have significant implications for public health decision-making regarding tick-borne pathogens.

Cable bacteria exhibit a unique metabolism involving long-distance electron transport, significantly impacting elemental cycling in various sediments. These long filamentous bacteria are distributed circumglobally, suggesting an effective mode of dispersal. However, oxygen strongly inhibits their activity, posing a challenge to their dispersal through the water column. We investigated the effective dispersal of marine cable bacteria in a compartmentalised microcosm experiment. Cable bacteria were grown in natural ‘source’ sediment, and their metabolic activity was recorded in autoclaved ‘destination’ cores, which were only accessible through oxygenated seawater. Colonisation occurred over weeks, and destination cores contained only one cable bacterium strain. Filament ‘snippets’ (fragments with a median size of ~15 cells) accumulated in the microcosm water, with about 30% of snippets attached to sediment particles. Snippet release was also observed in situ in a salt marsh creek. This provides a model for the dispersal of cable bacteria through oxygenated water: snippets are formed by filament breakage in the sediment, released into the overlying water and transported with sediment particles that likely offer protection. These insights are informative for broader theories on microbial community assembly and prokaryotic biogeography in marine sediments.

Recently, there has been increased attention to hydrocarbonoclastic bacteria in the plastisphere. One particular genus, Alcanivorax, is reported in the biodegradation of several polymers in the literature. In this study, we further explored the role of Alcanivorax in the early colonization of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH), nylon 6/69, and a novel plastic B4PF01. Starting from enrichments of a one-year experiment with a maximum relative abundance of 58.8% of Alcanivorax, two parallel experiments were set up. One experiment followed growth and activity during the first 21 days of plastic incubations, and the other followed the same parameters on the different material fractions of the plastics, such as leachables and pure polymer. For all plastic types, the highest microbial growth was associated with the total plastics compared to the other material fractions. A relative abundance of 62.7% of Alcanivorax in the nylon 6/69-enriched community was observed. This, combined with data on activity, suggests that nylon 6/69 is potentially degraded by this genus. Two isolates were obtained, closely related to A. borkumensis SK2 and Alcanivorax sp. DG881. The activity and growth of the isolates as axenic cultures resemble their abundance in the community. In conclusion, this study contributes to the knowledge of the role of Alcanivorax in plastic-enriched communities.

Microbial biostalactites and streamers commonly grow at iron seepages in abandoned mines worldwide. This study addresses the diversity and composition of these simple prokaryotic communities, which thrive in pH ranges from 2.4 to 6.6 across six different mines. Our analysis of 85 communities reveals that a pH of approximately 3.2 is a critical threshold where alpha and beta diversity change discretely. Below this pH, the average number of ASVs per sample is 2.91 times lower than above this boundary. Autotrophs, heterotrophs, and symbionts of eukaryotes originate from nearly non-overlapping species pools in the two habitat types that differ only in pH. Communities below pH 3.2 further divide into two distinct groups, differing in diversity, taxonomic, and functional composition. Both types of communities coexist within the same stalactites, likely corresponding to zones where the capillary structure of the stalactite is either perfused or clogged. These findings indicate that microbial community structure can be significantly influenced by the intricate spatial organization of the ecosystem, rather than solely by measurable environmental parameters.

Flowers serve as hubs for biotic interactions with pollinators and microbes, which can significantly impact plant reproduction and health. Previous studies have shown that the flower microbiota undergoes dynamic assembly processes during anthesis. However, the influence of foraging pollinators on the assembly and dispersal of the flower microbiota and the transmission of plant pathogens remains poorly understood. In this study, we used insect exclusion netting to investigate the role of pollinators in the assembly of the microbiota on apple stigma and the transmission of the fire blight pathogen Erwinia amylovora. We found that excluding pollinators had a minor impact on the community diversity and composition of the apple stigma microbiota, while the flower's developmental stage had a strong influence. Additionally, pollinator exclusion altered bacterial dispersal and the relative abundance of different bacterial species, including E. amylovora, suggesting that pollinators play a role in transmitting plant pathogens. Using a reporter system, we demonstrated that bumble bees can transmit the fire blight pathogen from an infected flower under controlled growth conditions. Our study highlights the importance of intrinsic and pollinator-independent microbes as sources of inoculum for the stigma microbiota and underscores the role of foraging pollinators in vectoring plant pathogens.

Lichens can withstand fluctuating environmental conditions such as hydration-desiccation cycles. Many species distribute across climate zones, suggesting population-level adaptations to conditions such as freezing and drought. Here, we aim to understand how climate affects population genomic patterns in lichenized fungi. We analysed population structure along elevational gradients in closely related Umbilicaria phaea (North American; two gradients) and Umbilicaria pustulata (European; three gradients). All gradients showed clear genomic breaks splitting populations into low-elevation (Mediterranean zone) and high-elevation (cold temperate zone). A total of 3301 SNPs in U. phaea and 138 SNPs in U. pustulata were driven to fixation between the two ends of the gradients. The difference between the species is likely due to differences in recombination rate: the sexually reproducing U. phaea has a higher recombination rate than the primarily asexually reproducing U. pustulata. Cline analysis revealed allele frequency transitions along all gradients at approximately 0°C, coinciding with the transition between the Mediterranean and cold temperate zones, suggesting freezing is a strong driver of population differentiation. Genomic scans further confirmed temperature-related selection targets. Both species showed similar differentiation patterns overall, but different selected alleles indicate convergent adaptation to freezing. Our results enrich our knowledge of fungal genomic functions related to temperature and climate, fungal population genomics, and species responses to environmental heterogeneity.

Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.