Environmental microbiology最新文献

Wine industry has faced pressure to innovate its products. Saccharomyces cerevisiae has been the traditional yeast for producing alcoholic beverages, but interest has shifted from the conventional S. cerevisiae to non-Saccharomyces yeasts for their biotechnological potential. Among these, Torulaspora delbrueckii is particularly notable for its ability to enrich wine with novel flavours. During winemaking, sulphites are added to suppress spoilage microorganisms, making sulphite tolerance a valuable characteristic of wine yeasts. Adaptive laboratory evolution in liquid and solid media improved sulphite resistance in two T. delbrueckii strains, achieving, in the best case, a fourfold increase from 0.50 to 2.00 mM of sodium metabisulphite, highlighting the potential of these evolve strains for winemaking applications. Genomic analysis revealed SNPs/InDels in all the strains, including a novel unique missense mutation common to the four evolved isolates, but absent from the parental strains, located in chromosome VIII (protein TDEL0H03170, homologue of S. cerevisiae MPH1). These genes code for a protein catalogued as an ATP-dependent DNA helicase, known for its role in maintaining genome stability by participating in DNA repair pathways. We propose that this valine-to-serine mutation, common to all the evolved isolates, helps the evolved strains repair sulphite-induced DNA damage more effectively.

Corals associate with a diverse community of prokaryotic symbionts that provide nutrition, antioxidants and other protective compounds to their host. However, the influence of microbes on coral thermotolerance remains understudied. Here, we examined the prokaryotic microbial communities associated with colonies of Acropora cf. tenuis that exhibit high or low thermotolerance upon exposure to 33°C (heated) relative to 29°C (control). Using 16S rRNA sequencing, we show that the microbial community structure of all A. cf. tenuis colonies was similar to each other at control temperature. Thermotolerant colonies, however, had relatively greater abundance of Endozoicomonas, Arcobacter, Bifidobacterium and Lactobacillus. At elevated temperature, only thermosensitive colonies showed a distinct shift in their microbiome, with an increase in Flavobacteriales, Rhodobacteraceae and Vibrio, accompanying a marked bleaching response. Functional prediction indicated that prokaryotic communities associated with thermotolerant corals were enriched for genes related to metabolism, while microbiomes of thermosensitive colonies were enriched for cell motility and antibiotic compound synthesis. These differences may contribute to the variable performance of thermotolerant and thermosensitive corals under thermal stress. Identification of microbial taxa correlated with thermotolerance provides insights into beneficial bacterial groups that could be used for microbiome engineering to support reef health in a changing climate.

Human activities such as agriculture and urban development are linked to water quality degradation. Canada represents a large and heterogeneous landscape of freshwater lakes, where variations in climate, geography and geology interact with land cover alteration to influence water quality differently across regions. In this study, we investigated the influence of water quality and land use on bacterial communities across 12 ecozones. At the pan-Canadian scale, total phosphorus (TP) was the most significant water quality variable influencing community structure, and the most pronounced shift was observed at 110 μg/L of TP, corresponding to the transition from eutrophic to hypereutrophic conditions. At the regional scale, water quality significantly explained bacterial community structure in all ecozones. In terms of land use effect, at the pan-Canadian scale, agriculture and, to a lesser extent, urbanisation were significant land use variables influencing community structure. Regionally, in ecozones characterised by extensive agriculture, this land cover variable was consistently significant in explaining community structure. Likewise, in extensively urbanised ecozones, urbanisation was consistently significant in explaining community structure. Overall, these results demonstrate that bacterial richness and community structure are influenced by water quality and shaped by agriculture and urban development in different ways.

Anaerobic digestion (AD) of organic wastes relies on the interaction and cooperation of various microorganisms. Phages are crucial components of the microbial community in AD systems, but their diversity and interactions with the prokaryotic populations are still inadequately comprehended. In this study, 2121 viral operational taxonomic units (vOTUs) were recovered from 12 anaerobic fatty acid–fed reactors. Notably, 63.1% of these vOTUs could not be assigned to any known family, revealing a substantial presence of uncharted phages specifically associated with AD environments. Over half of the vOTUs associated with hosts had the capability to infect multiple hosts, ranging from 2 to 49, with a prevalent tendency to infect 2–5 hosts. In silico predictions of phage-host linkages uncovered that only a small fraction of vOTUs were shared across different functional groups, including fermentative bacteria, syntrophic fatty acid–oxidising bacteria (SFOB) and methanogens. Phages linked to hosts in all three groups primarily consisted of generalists and temperate species, especially those linked to SFOB. Additionally, metabolic reconstruction identified auxiliary metabolic genes participating in fatty acid degradation, methanogenesis and energy conservation. The present study provides insights into phage characteristics and their in situ interactions with prokaryotic hosts, highlighting their ecological role in AD systems.

Evolutionary novelty has been one of the central themes in the field of evolutionary biology for many years. Structural and functional innovations such as scales in the reptiles, fins in the fishes and mammary glands in the mammals have been the focus of the studies. Insights obtained from these studies have shaped the criterion for the identification of novelty as well as provide the framework for studying novelty. In this article, I argue that unicellular organisms present an excellent opportunity for the investigation of evolutionary novelty. Even though bacteria share some fundamental aspects of novelty with higher organisms, there are definite departures. Here, I outline these departures in four different contexts: criterion for the identification of novelty, types of evolutionary novelties, level of biological complexity that bacteria embody and, most importantly, the role of the environment. Identifying the role of the environment allows the categorisation of novelty as probable or improbable and adaptive or latent. This categorisation of novel traits, based on the role of the environment, can facilitate the study of novelty in bacteria. Insights obtained from such studies are crucial for understanding the fundamental aspects of evolutionary novelty.