Environmental microbiology最新文献

Synthetic microbial communities (SynComs) hold great promise for enhancing plant health and productivity, yet their field performance is often inconsistent due to challenges in establishing stable populations within complex rhizosphere environments. Predation by microbial grazers, including protists, nematodes, and bacterial predators, plays a significant role in regulating SynCom engraftment, population dynamics, and functional outcomes, but remains largely overlooked in SynCom design. Here we review the ecological processes governing predator–prey interactions in the rhizosphere, microbial traits conferring resistance to predation, and suggest strategies to incorporate these defences into SynCom assembly. By integrating predator resistance as a design criterion, we argue that SynComs can achieve greater resilience and persistence under natural biotic pressures, reducing variability in SynCom performance and improving their functional reliability in agricultural applications.

Once regarded primarily as a healthcare-associated pathogen, Clostridioides difficile has increasingly been reported as a cause of community-acquired infection, raising questions about the contribution of animal and environmental reservoirs to persistence and transmission. Ribotype 033 (RT033) is predominantly associated with animal and environmental reservoirs, yet key traits underlying its ecology are poorly defined. Here we show that RT033 strains produce spores with enhanced germination sensitivity and expanded germinant specificity, enabling germination at low concentrations of bile-salts and in response to bile-salts that are typically inhibitory, including those more typical of animal hosts. Genetic analysis identified a single amino acid substitution (R1036I) in CspA, a component of the CspBAC germination apparatus, as the determinant of this phenotype. Expression of the RT033 cspBAC operon in a laboratory strain was sufficient to confer increased sensitivity and expanded bile-salt responsiveness. The R1036I substitution disrupts a conserved salt bridge at the CspA:CspC interface while not causing major destabilisation of the complex in the absence or presence of germinants and co-germinants. Together, our findings reveal a naturally occurring rewiring of bile-salt sensing in spores of RT033 strains that likely reflects adaptation to animal-associated bile-acid environments and may influence persistence, transmission, and zoonotic potential of this lineage.

Microbial communities have evolved interactions to support growth and essential ecosystem functions. For example, marine cyanobacteria like Prochlorococcus lack the catalase genes (katE, katG and manganese catalase) required for detoxifying freely-diffusible hydrogen peroxide, relying on co-occurring catalase-carrying ‘helper’ microbes for this function. However, the eco-evolutionary forces shaping catalase distribution are not well understood. We examined genomes, metagenome-assembled genomes (MAGs), and metagenomes to assess catalase gene distributions across diverse marine prokaryotes—including within the known ‘helper’ genus Alteromonas—and across surface ocean ecosystems. Within Alteromonas, most genomes contain two katE copies, while katG copy number varies across species. Across ecosystems, the Altermonadaceae family is the predominant katE carrier. Some taxa (e.g., SAR202) lack all catalases, highlighting their dependence on ‘helpers’. Overall, streamlined genomes, including from SAR11, generally have one katG copy and lack katE, while larger genomes with higher GC content characteristic of copiotrophs have more copies of both catalases. Finally, in free-living communities, katG gene frequency increases with decreased particulate organic carbon (POC) concentrations, whereas in particle-associated communities, katE gene frequency increases with elevated POC. Together, these observations suggest that hydrogen peroxide detoxification capabilities are widespread and shaped by the contributions of particle-associated microbes to total community metabolism.