Environmental microbiology最新文献

Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.

Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.

Given that most microbes experience spatially structured environments, examining how such environments affect microbial growth and functions is paramount. Previous studies have shown that a spatially structured environment can impact microbial growth and interactions, and that microbial growth can create or magnify spatial structure. Here, we review some of these instances of past studies to develop a consistent framework that highlights the interplay between microbial interactions, spatial structure of the environment and spatial organisation of microbes. We re-examine the level, degree and scale of spatial structure with regard to the phenomena and biological processes of interest. We then discuss how mathematical models can reveal the contribution of the spatial structure to community assembly and coexistence. Lastly, we offer an outlook on important steps for the progress of this field.

N₂O emissions by nitrifiers are often estimated using selective inhibitors, such as 1-alkynes. However, the effects of these inhibitors on anaerobic ammonium-oxidising (anammox) bacteria are largely unknown. In this study, we assessed the inhibitory effect of linear and aromatic alkynes on anammox activity and identified their target enzyme. ‘Candidatus Kuenenia stuttgartiensis’ biomass and constructed wetland soil samples were incubated with 10 μM of C₂–C₈ linear alkynes or phenylacetylene for 10 days. Anammox activity was determined using the isotopic tracer ¹⁵N-nitrite and ²⁹N₂ production. Anammox activity was suppressed by C₂–C₅ alkynes, whereas the larger or aromatic alkynes caused no inhibition. However, hydrazine oxidation activity was not affected, indicating that C₂–C₅ alkynes inactivated enzymes upstream of hydrazine dehydrogenase. In incubations using an NO donor and ¹⁵N-ammonium, ²⁹N₂ production stopped, suggesting that hydrazine synthase was the target of these alkynes. A comparable trend was observed in the wetland samples, but with a less pronounced reduction in ²⁹N₂ production. Since alkynes >C₅ did not affect anammox, these findings demonstrate the suitability of using 1-octyne as a selective inhibitor to quantify N₂O contributions from ammonia-oxidising bacteria (AOB) versus ammonia-oxidising archaea (AOA) in oxic/anoxic interface environments.

The broad metabolic capacity of Shewanella species allows them to colonise a wide range of aquatic niches. Their ability to convert sulphur compounds, including tetrathionate, has been reported. This may seem surprising, as this ability has long been considered restricted to human gut pathogens such as Enterobacteria and tetrathionate is considered unstable in the external environment. The molecular basis of Shewanella growth on tetrathionate had never been analysed. By combining the construction and metabolic characterisation of deletion mutants and complementary biochemical analyses, we determined that Shewanella sp. ANA-3 uses two enzymes, homologous to the tetrathionate reductase Ttr and the polysulphide reductase Psr, respectively, to respire tetrathionate. This study provides the first evidence that a Psr homologue can catalyse this reaction. Neither the octahaem tetrathionate reductase OTR nor the thiosulfate dehydrogenase Tsd, which were also examined, participate in this respiration. Although reduction of tetrathionate is the known physiological function of the Ttr, this work represents the first rigorous establishment of this role in an environmental microorganism. Based on the relatively high redox potential of the tetrathionate/thiosulphate redox couple and the wide distribution of ttr genes, we discuss the hypothesis of widespread distribution of Ttr-based tetrathionate respiration in the external environment.

The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits—α-niche traits involved in partitioning resources (e.g., broadened resource consumption) and β-niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co-evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.

Psychrophilic and psychrotolerant microorganisms have the unique ability to grow below 0°C, which makes them ideal candidates for studying how life could survive on the icy moons of the solar system. The renewed interest, in view of the JUICE and Europe Clipper missions, to explore these locations has pushed for the identification of organisms which could survive on the icy moons. In this study we selected the extremophilic yeast Rhodotorula frigidalcoholis given its innate ability to grow between 30°C and −10°C and to survive a range of extreme conditions including x-ray, UV-C and polychromatic UV radiation, desiccation at different temperatures, and freeze–thaw cycles. We report the survival of R. frigidalcoholis under conditions analogous to those found on icy moons. Using transcriptomic approaches, we present novel insights into differential gene expression before, during, and after exposure to combined icy moon conditions. We also identified the rapid activation of genes involved in catalytic activity and DNA repair during exposure. Our results contribute to a better understanding of the survival mechanisms of psychrotolerant microorganisms in extreme environments and can inform future life-detection missions on moons such as Enceladus and Europa, also highlighting the need to consider yeasts in planetary protection efforts.

Marine sediments host diverse benthic prokaryotic communities that are integral to global biogeochemical cycles. However, the spatial distribution and environmental drivers of these communities, particularly in unique environments like the Red Sea, remain largely underexplored. In this study, we examine benthic prokaryotic communities sampled during the Red Sea Decade Expedition (RSDE) using 16S rRNA gene sequencing across five major regions along the Red Sea's latitudinal gradient and three depth strata. Our findings reveal distinct biogeographical patterns shaped by depth, latitude, and oxygen availability, with clear shifts in microbial community composition across the epibenthic, mesobenthic and bathybenthic zones. Bathybenthic communities exhibited consistently low levels of OTU richness throughout the Red Sea, likely due to uniform niche environmental conditions at depth, while shallower communities showed higher OTU richness towards the Southern Red Sea. The southern region harboured higher relative abundances of Chloroflexi and reduced relative abundances of Proteobacteria and Acidobacteriota relative to the northern regions. Extreme environments, such as the Atlantis II brine pool, supported specialised microbial communities likely adapted to extreme conditions like hypersalinity. This study established a critical baseline for understanding the responses of marine microbial communities to climate change and their roles in biogeochemical processes.