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Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism 走进微生物黑箱：以氧化还原为中心的微生物代谢解密框架
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 DOI: 10.1016/j.tim.2024.05.003
John A. Bouranis, Malak M. Tfaily
{"title":"Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism","authors":"John A. Bouranis, Malak M. Tfaily","doi":"10.1016/j.tim.2024.05.003","DOIUrl":"https://doi.org/10.1016/j.tim.2024.05.003","url":null,"abstract":"<p>Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD<sup>+</sup> through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":"101 1","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141192430","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
Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past. 微生物固氮作用的神秘演化：从地球过去的角度看问题。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2023-04-13 DOI: 10.1016/j.tim.2023.03.011
Holly R Rucker, Betül Kaçar
{"title":"Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past.","authors":"Holly R Rucker, Betül Kaçar","doi":"10.1016/j.tim.2023.03.011","DOIUrl":"10.1016/j.tim.2023.03.011","url":null,"abstract":"<p><p>The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"554-564"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9306041","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
Diversity and ecology of NrfA-dependent ammonifying microorganisms. 依赖 NrfA 的氨化微生物的多样性和生态学。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2024-03-09 DOI: 10.1016/j.tim.2024.02.007
Aurélien Saghaï, Sara Hallin
{"title":"Diversity and ecology of NrfA-dependent ammonifying microorganisms.","authors":"Aurélien Saghaï, Sara Hallin","doi":"10.1016/j.tim.2024.02.007","DOIUrl":"10.1016/j.tim.2024.02.007","url":null,"abstract":"<p><p>Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N<sub>2</sub>O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"602-613"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140094628","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
Colorful windows to the dark rhizosphere. 通向黑暗根瘤菌群的多彩窗户
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2024-03-14 DOI: 10.1016/j.tim.2024.03.005
Hamed Azarbad
{"title":"Colorful windows to the dark rhizosphere.","authors":"Hamed Azarbad","doi":"10.1016/j.tim.2024.03.005","DOIUrl":"10.1016/j.tim.2024.03.005","url":null,"abstract":"<p><p>The dynamic and complex interactions between plant and microbiomes in the rhizosphere play a major role in the plant's health and productivities. Using interdisciplinary approaches, Behr et al. studied how farming practices can influence the rhizosphere process, offering an exciting direction for microbial manipulation to enhance agricultural productivity.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"529-531"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137272","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
Unsolved mysteries in marine nitrogen fixation. 海洋固氮的未解之谜。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2023-08-30 DOI: 10.1016/j.tim.2023.08.004
Jonathan P Zehr, Douglas G Capone
{"title":"Unsolved mysteries in marine nitrogen fixation.","authors":"Jonathan P Zehr, Douglas G Capone","doi":"10.1016/j.tim.2023.08.004","DOIUrl":"10.1016/j.tim.2023.08.004","url":null,"abstract":"<p><p>Biological nitrogen (N<sub>2</sub>) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N<sub>2</sub>-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N<sub>2</sub> fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"532-545"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10492433","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
Scripting a new dialogue between diazotrophs and crops. 编写重氮菌和作物之间的新对话。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2023-09-26 DOI: 10.1016/j.tim.2023.08.007
Sanhita Chakraborty, Maya Venkataraman, Valentina Infante, Brian F Pfleger, Jean-Michel Ané
{"title":"Scripting a new dialogue between diazotrophs and crops.","authors":"Sanhita Chakraborty, Maya Venkataraman, Valentina Infante, Brian F Pfleger, Jean-Michel Ané","doi":"10.1016/j.tim.2023.08.007","DOIUrl":"10.1016/j.tim.2023.08.007","url":null,"abstract":"<p><p>Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N<sub>2</sub>) into ammonium. Plant-diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant-diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant-diazotroph interactions. We discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"577-589"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10950843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41171104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Microbial nitrogen transformation processes across environments: more than just a cycle. 跨环境的微生物氮转化过程：不仅仅是一个循环。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2024-05-07 DOI: 10.1016/j.tim.2024.04.006
Jennifer B Glass, Kathrin Rousk
{"title":"Microbial nitrogen transformation processes across environments: more than just a cycle.","authors":"Jennifer B Glass, Kathrin Rousk","doi":"10.1016/j.tim.2024.04.006","DOIUrl":"10.1016/j.tim.2024.04.006","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"519-521"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140892668","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
Microbial nitrogen transformation processes: a collaborative network. 微生物氮转化过程：协作网络。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2024-05-09 DOI: 10.1016/j.tim.2024.04.005
Jennifer B Glass, Kathrin Rousk
{"title":"Microbial nitrogen transformation processes: a collaborative network.","authors":"Jennifer B Glass, Kathrin Rousk","doi":"10.1016/j.tim.2024.04.005","DOIUrl":"10.1016/j.tim.2024.04.005","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"522-525"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140903879","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
Salt marsh nitrogen cycling: where land meets sea. 盐沼氮循环：陆地与海洋交汇的地方。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-06-01 Epub Date: 2023-10-10 DOI: 10.1016/j.tim.2023.09.010
Jennifer L Bowen, Amanda C Spivak, Anne E Bernhard, Robinson W Fulweiler, Anne E Giblin
{"title":"Salt marsh nitrogen cycling: where land meets sea.","authors":"Jennifer L Bowen, Amanda C Spivak, Anne E Bernhard, Robinson W Fulweiler, Anne E Giblin","doi":"10.1016/j.tim.2023.09.010","DOIUrl":"10.1016/j.tim.2023.09.010","url":null,"abstract":"<p><p>Salt marshes sit at the terrestrial-aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"565-576"},"PeriodicalIF":15.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41214011","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
Gene transfer agents: structural and functional properties of domesticated viruses. 基因转移剂：驯化病毒的结构和功能特性。
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-05-27 DOI: 10.1016/j.tim.2024.05.002
Matthew W Craske, Jason S Wilson, Paul C M Fogg
{"title":"Gene transfer agents: structural and functional properties of domesticated viruses.","authors":"Matthew W Craske, Jason S Wilson, Paul C M Fogg","doi":"10.1016/j.tim.2024.05.002","DOIUrl":"https://doi.org/10.1016/j.tim.2024.05.002","url":null,"abstract":"<p><p>Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162259","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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