Environmental microbiology最新文献

Understanding the extraordinary environmental adaptability of prokaryotes is crucial for manipulating microbial communities, as their adaptive mechanisms drive community dynamics, resilience and functional responses to interventions like bioremediation. Microbial adaptation to the environment is shaped not only by their intrinsic characteristics but also by interactions with other microorganisms. Among them, temperate phages, which reside alongside cellular microorganisms across diverse ecosystems, are emerging as key players in microbial adaptation. This review delves into the contribution of temperate phages to microbial adaptation across multiple levels. It begins with a survey of culture-dependent studies that reveal the complex mechanisms by which temperate phages facilitate adaptation at the individual and population levels. The review then explores how temperate phage–host symbioses interact with selection pressures in complex environments, assessing both the influence of these pressures on lysogeny at the community level and how prophages respond. Finally, building on established concepts and recent scientific advances, this review outlines the potential for harnessing temperate phages to help address major societal challenges. This synthesis underscores the importance of temperate phages and encourages further exploration in phage ecology.

Many fungi have a dimorphic life cycle, alternating between unicellular yeast and multicellular filamentous phases. Although dimorphism is assumed for many lichen-associated basidiomycetes, the existence of a yeast stage has rarely been confirmed. Using taxon-specific PCR and FISH-CLSM, we studied Tremella hypogymniae and T. tubulosae Tremellomycetes), two presumably dimorphic species previously known only from their filamentous phase in galls on the lichens Hypogymnia physodes and H. tubulosa, respectively. We investigated their presence and frequency, lichen ranges and within-thallus distribution of life-cycle stages. We also explored the co-occurrence of both species with Cystobasidiomycetes—one of the most widespread lichen-associated yeast lineages—in the same lichen thalli. The filamentous phase of Tremella hypogymniae and T. tubulosae was confined to a single lichen species each, whereas the yeast phase occurred in several closely related lichens. Both phases co-occurred with various Cystobasidiomycete lineages. Filamentous structures were restricted to galls, whereas gall-free thalli contained Tremella yeasts in the cortex, soredia and medulla, and pseudohyphae in the cortex. The presence of yeasts in soredia suggests co-dispersal with other lichen symbionts. These findings reveal narrow specificity in the filamentous phase but broader associations in the yeast phase, pointing to complex interactions within the lichen symbiosis.

The dairy starter Lactococcus lactis shifts its metabolism from mixed-acid fermentation to homolactic fermentation under anaerobic conditions as growth rates increase. Although its metabolism at acidic and neutral pH values is well-researched, knowledge about lactococcal physiology under alkaline conditions remains limited. Here, we investigated how L. lactis subsp. lactis biovar diacetylactis FM03 adapts its metabolism and morphology at alkaline pH using lactose-limited chemostat cultures at pH 6, 7 and 8. At alkaline pH, L. lactis FM03 shifted from energetically more favourable mixed-acid fermentation towards homolactic fermentation at lower growth rates compared to pH 6, resulting in a 20% lower biomass yield despite an unchanged maintenance coefficient and maximum biomass yield per ATP. Proteome analysis revealed a 1.5 to 13.5-fold downregulation of enzymes in the mixed-acid fermentation pathway at alkaline pH, thereby reducing its metabolic capacity. Morphologically, L. lactis became more spherical at alkaline pH, reducing the surface-to-volume ratio and did not enlarge upon higher dilution rates. This morphological shift potentially limits substrate uptake, contributing to the lower maximum growth rate at pH 8. Our findings reveal new insights into pH-driven metabolic plasticity and resource allocation in L. lactis and highlight opportunities for optimising fermentation processes under varying pH conditions.

Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H₂/CO₂, TMA, and H₂/CO₂-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.

Small photosynthetic eukaryotes are a productive and dynamic component of marine planktonic communities. Here, we investigate how seasonal changes in the abundance of these primary producers relate to changes in their community composition at a coastal site on the Northeast US Shelf. We present a 9-year time series of 18S rRNA sequencing data and identify gradual transitions within the pico- and nanoplankton community that occur repeatedly over the annual cycle. We compare these compositional changes to concurrent high-resolution in situ flow cytometry measurements of eukaryotic phytoplankton abundance and division rate. We find that the Chlorophyta contribute a large proportion of the sequences in our samples and drive much of the seasonal variability within the small phytoplankton community. Across the time series, Bathycoccus, Micromonas and Picochlorum are the dominant genera, with the first being present year-round, while Micromonas bravo and Picochlorum are representative of the summer community. We also find a strong winter Phaeocystis signal which might be leading to flow cytometry measurements of relatively large cells in the early spring. Our results provide fundamental knowledge of the taxonomic composition of the phytoplankton community on the Northeast US Shelf, improving our understanding of the region's diversity and compositional variability over time.

Limonene is a natural monoterpene omnipresent in human environments. It enters wastewater and is also metabolised in methanogenic digesters. A stable limonene-degrading methanogenic enrichment culture was investigated by metagenomic, metatranscriptomic and metaproteomic data sets to characterise the microbial community and identify the limonene degradation pathway. Thirty-two metagenome-assembled genomes revealed a complex community of bacteria and methanogenic archaea dominated by Candidatus Velamenicoccus archaeovorus as the top predator, contributing two-thirds of the reads in the metagenome. The presence of several fermenting bacteria (Anaerolineaceae, Aminidesulfovibrio, Smithellaceae, Lentimicrobium) indicated the recycling of necromass in a microbial loop. Only one hydrocarbon-activating enzyme system was expressed, a member of the alkyl- and arylsuccinate synthase family which is a glycine radical enzyme that adds fumarate to hydrocarbons. The limonenylsuccinate synthase gene encodes a modified substrate binding pocket with two smaller amino acids, suggesting an adaptation for the larger structure of limonene. The limonenylsuccinate synthase operon and a ring cleavage operon, as well as genes for the final syntrophic fermentation to acetate, hydrogen and formate were encoded in a Syntrophobacteraceae genome. Almost all genes for this degradation pathway were highly transcribed and expressed, demonstrating a catalytic role for glycine radical enzymes in methanogenic systems degrading limonene.