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Anaerobic oxidation of short-chain volatile alkanes. 短链挥发性烷烃的厌氧氧化。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-10 DOI: 10.1016/j.tim.2025.06.013
Florin Musat, Song-Can Chen, Niculina Musat, Kasper Urup Kjeldsen
{"title":"Anaerobic oxidation of short-chain volatile alkanes.","authors":"Florin Musat, Song-Can Chen, Niculina Musat, Kasper Urup Kjeldsen","doi":"10.1016/j.tim.2025.06.013","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.013","url":null,"abstract":"<p><p>The short-chain volatile alkanes ethane, propane, and butane are major components of natural gas. Released from deep-seated subsurface reservoirs through natural seepage or gas extraction, they percolate through anoxic and oxic environments before reaching the atmosphere, where they contribute to tropospheric chemistry and act as greenhouse gases. While their aerobic biological oxidation is well established, their fate in anoxic environments has only recently come into focus. Here we review their oxidation in anoxic settings - from subsurface reservoirs and deep-sea seep sediments to terrestrial hot springs and wastewater treatment plants. We discuss the phylogenetic diversity, biochemical mechanisms, and physiology of microorganisms mediating anaerobic oxidation of volatile alkanes, including nitrate- and sulfate-reducing bacteria (SRB) and the recently discovered alkane-oxidizing archaea. We also highlight advances in diagnostic tools, such as stable isotope analyses and single-cell chemical imaging. Finally, we outline major unresolved research questions, including the unique biochemistry of anaerobes and the extent to which they act as natural biofilters by reducing atmospheric emissions of volatile alkanes.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144620736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scientific mobility in microbiology - 2. 微生物学的科学流动性- 2。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-08 DOI: 10.1016/j.tim.2025.06.007
Leonardo Castanedo
{"title":"Scientific mobility in microbiology - 2.","authors":"Leonardo Castanedo","doi":"10.1016/j.tim.2025.06.007","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.007","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scientific mobility in microbiology. 微生物学的科学流动性。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-07 DOI: 10.1016/j.tim.2025.06.016
Shankar Iyer
{"title":"Scientific mobility in microbiology.","authors":"Shankar Iyer","doi":"10.1016/j.tim.2025.06.016","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.016","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Low biomass bacterial transcriptomics takes shape. 低生物量细菌转录组学形成。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-07 DOI: 10.1016/j.tim.2025.06.015
Qinnan Yang, Eric C Martens
{"title":"Low biomass bacterial transcriptomics takes shape.","authors":"Qinnan Yang, Eric C Martens","doi":"10.1016/j.tim.2025.06.015","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.015","url":null,"abstract":"<p><p>Bornet et al. apply a low-input bacterial RNA-seq pipeline to transcriptionally profile small, medium, and large cell populations of the human gut symbiont Bacteroides thetaiotaomicron separated by fluorescence activated cell sorting (FACS). Their approach opens paths to measure transcriptional changes in individual cells of genetically identical bacteria that vary in morphology or other FACS-sortable features like antibody staining.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scientific mobility in microbiology - 1. 微生物学的科学流动性- 1。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-05 DOI: 10.1016/j.tim.2025.06.008
Juliana Almario
{"title":"Scientific mobility in microbiology - 1.","authors":"Juliana Almario","doi":"10.1016/j.tim.2025.06.008","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.008","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scientific mobility in microbiology - 3. 微生物学的科学流动性- 3。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-05 DOI: 10.1016/j.tim.2025.06.009
Sitara S R Ajjampur
{"title":"Scientific mobility in microbiology - 3.","authors":"Sitara S R Ajjampur","doi":"10.1016/j.tim.2025.06.009","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.009","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144650684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scientific mobility in microbiology - 4. 微生物学的科学流动性- 4。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-04 DOI: 10.1016/j.tim.2025.06.010
Leanid Laganenka
{"title":"Scientific mobility in microbiology - 4.","authors":"Leanid Laganenka","doi":"10.1016/j.tim.2025.06.010","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.010","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144650685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Culturing the uncultured anaerobes from the perspective of microbial growth curves. 从微生物生长曲线的角度对未培养的厌氧菌进行培养。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-03 DOI: 10.1016/j.tim.2025.06.006
Kejia Wu, Shichun Ma, Jiang Li, Diana Z Sousa, Lei Cheng
{"title":"Culturing the uncultured anaerobes from the perspective of microbial growth curves.","authors":"Kejia Wu, Shichun Ma, Jiang Li, Diana Z Sousa, Lei Cheng","doi":"10.1016/j.tim.2025.06.006","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.006","url":null,"abstract":"<p><p>Anaerobic microorganisms inhabit diverse anoxic environments and play a fundamental role in global biogeochemical cycles. Expanding our knowledge of these organisms offers the potential to transform our understanding of ecological and evolutionary processes and to uncover new biotechnological applications. Recent advances in DNA sequencing have revealed a striking gap between the vast microbial diversity found in anoxic environments and the small number of anaerobes - fewer than 0.1% of the estimated millions of anaerobic species in nature - that have been cultivated in the laboratory. This challenge reflects the 'great plate count anomaly', in which most microorganisms observed in nature fail to grow in laboratory conditions, and aligns with the 'scout' model, which suggests that only a few opportunistic species thrive under standard cultivation approaches. Overcoming these limitations requires a shift in cultivation strategies. Here, we review recent advances in the cultivation and isolation of novel anaerobes. Specifically, we introduce a growth-curve-guided strategy that uses real-time monitoring of microbial growth (primarily at the species level) to inform approaches that leverage relative growth advantages and improve the recovery of target microorganisms. By prioritizing growth performance over abundance and selectively removing non-target microbes, this approach offers a more predictable and adaptable framework for isolating anaerobes from complex communities.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Composing a microbial symphony: synthetic communities for promoting plant growth. 谱写微生物交响曲：促进植物生长的合成群落。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-01 Epub Date: 2025-02-17 DOI: 10.1016/j.tim.2025.01.006
Xinming Xu, Caja Dinesen, Adele Pioppi, Ákos T Kovács, Carlos N Lozano-Andrade
{"title":"Composing a microbial symphony: synthetic communities for promoting plant growth.","authors":"Xinming Xu, Caja Dinesen, Adele Pioppi, Ákos T Kovács, Carlos N Lozano-Andrade","doi":"10.1016/j.tim.2025.01.006","DOIUrl":"10.1016/j.tim.2025.01.006","url":null,"abstract":"<p><p>Plant microbiomes are pivotal for host development, influencing growth, health, fitness, and evolution, and have emerged as promising resources for sustainable agriculture. However, leveraging these microbiomes to improve crop yield and resilience is challenging due to the huge diversity of plant-associated and soil microorganisms and their intricate interactions. Recently, synthetic microbial communities (SynComs) have been exploited as a reductionist approach to harness microbial benefits and to understand multispecies interactions. Additionally, the advanced functionality of SynComs promises to surpass classic single-strain-based biosolutions. Nevertheless, challenges remain in designing customized, robust, and predictable SynComs for agronomic use. Here, we synthesize and discuss the logical and implemented approaches used to design and assemble SynComs, highlighting important principles, challenges, and trends in utilizing SynComs as alternatives to agrochemicals.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"738-751"},"PeriodicalIF":14.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Post-transcriptional regulation in archaea. 古细菌的转录后调控。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-07-01 Epub Date: 2025-03-05 DOI: 10.1016/j.tim.2025.02.004
Jie Li, Yueting Liang, Xiuzhu Dong
{"title":"Post-transcriptional regulation in archaea.","authors":"Jie Li, Yueting Liang, Xiuzhu Dong","doi":"10.1016/j.tim.2025.02.004","DOIUrl":"10.1016/j.tim.2025.02.004","url":null,"abstract":"<p><p>During genetic information transfer from DNA to protein, gene expression is strictly controlled at several key stages. Post-transcriptional regulation provides a plethora of mechanisms for precise and rapid control of gene expression, ensuring cellular survival and environmental adaptation. Emerging evidence shows that Archaea, the third domain of life, employ diverse post-transcriptional regulation strategies, including distinct RNA-associated proteins and small noncoding RNAs (sRNAs), to control gene expression. This review summarizes recent advances in understanding archaeal post-transcriptional regulation, focusing on processes, mechanisms, and physiological significances, and key elements including sRNAs, 5'- or 3'-untranslated regions (5'-UTRs or 3'-UTRs), RNA-binding proteins (RBPs) or chaperones, and ribonucleases, underscoring their crucial roles in optimizing archaeal gene expression for survival and environmental responsiveness.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"765-781"},"PeriodicalIF":14.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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