Applied and Environmental Microbiology最新文献

{"title":"Closed genomes of commercial inoculant rhizobia provide a blueprint for management of legume inoculation.","authors":"MacLean G Kohlmeier, Graham W O'Hara, Joshua P Ramsay, Jason J Terpolilli","doi":"10.1128/aem.02213-24","DOIUrl":"https://doi.org/10.1128/aem.02213-24","url":null,"abstract":"<p><p>Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N₂ into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N₂-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera, <i>Bradyrhizobium</i>, <i>Mesorhizobium</i>, <i>Methylobacterium</i>, <i>Rhizobium</i>, and <i>Sinorhizobium</i>, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for <i>Rhizobium</i> sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.</p><p><strong>Importance: </strong>Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia's legume inoculation program.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0221324"},"PeriodicalIF":3.9,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cultivation and mating of the truffle <i>Tuber japonicum</i> in plantations of ectomycorrhizal <i>Quercus serrata</i> seedlings.","authors":"Noritaka Nakamura, Akihiko Kinoshita, Shota Nakano, Hitomi Furusawa, Keisuke Obase, Muneyoshi Yamaguchi, Kyotaro Noguchi, Yuki Kitade, Takashi Yamanaka","doi":"10.1128/aem.02362-24","DOIUrl":"https://doi.org/10.1128/aem.02362-24","url":null,"abstract":"<p><p><i>Tuber japonicum</i>, a white-colored truffle that is endemic to Japan, is promising for culinary purposes due to its unique aroma. We were able to cultivate <i>T. japonicum</i> in plantations of inoculated <i>Quercus serrata</i> seedlings for the first time. Ascocarps were found after 43 months at one site and after 61 months at another. We developed simple sequence repeat markers for multilocus genotyping of glebal tissue and ascospores and confirmed that the harvested ascocarps were derived from inocula. All paternal individuals matched the multilocus genotypes of neighboring maternal individuals, indicating frequent hermaphroditism and the absence of externally introduced individuals. Our findings provide important clues to understanding the reproductive biology of <i>T. japonicum</i> during the early period after the truffle plantation establishment.</p><p><strong>Importance: </strong>Truffles are highly prized as a delicacy, but only a select few species have been successfully cultivated. In our study, we succeeded for the first time in cultivating <i>Tuber japonicum</i>. Two out of four plantations produced ascocarps shortly after planting, with one of them yielding a comparable weight to other cultivated truffle species. This promising productivity suggests that the fungus has potential when cultivated. Our analysis of the ascocarps' maternal and paternal genotypes, using simple sequence repeat markers, revealed hermaphroditic behavior in the fungus at our planting site. Our findings provide crucial insights into the truffle mating events.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0236224"},"PeriodicalIF":3.9,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methylation of foreign DNA overcomes the restriction barrier of <i>Flavobacterium psychrophilum</i> and allows efficient genetic manipulation.","authors":"Seada Sloboda, Xinwei Ge, Daqing Jiang, Lin Su, Gregory D Wiens, Carly A Beveridge, Eric Duchaud, Mark J McBride, Tatiana Rochat, Yongtao Zhu","doi":"10.1128/aem.01448-24","DOIUrl":"https://doi.org/10.1128/aem.01448-24","url":null,"abstract":"<p><p><i>Flavobacterium psychrophilum</i> causes bacterial cold-water disease (BCWD) in salmonids and other fish, resulting in substantial economic losses in aquaculture worldwide. The mechanisms <i>F. psychrophilum</i> uses to cause disease are poorly understood. Despite considerable effort, most strains of <i>F. psychrophilum</i> have resisted attempts at genetic manipulation. <i>F. psychrophilum</i> restriction-modification (R-M) systems may contribute to this resistance. Restriction endonucleases (REases) rapidly degrade nonself DNA if it is not properly methylated by their cognate DNA methyltransferases (MTases). We used comparative genomics to show that R-M systems are abundant in <i>F. psychrophilum</i> and that strain-specific variations partially align with phylogeny. We identified two critical type II R-M systems, HpaII-like (FpsJI) and ScrFI-like (FpsJVI), that are conserved in most of the sequenced strains. Protection of foreign DNA against HpaII and ScrFI was achieved by expression of the MTases M.FpsJI and M.FpsJVI in <i>Escherichia coli</i>. Furthermore, deleting the two REase genes from <i>F. psychrophilum</i> resulted in efficient conjugative DNA transfer from <i>E. coli</i> into the otherwise genetically intractable <i>F. psychrophilum</i> strain CSF259-93. This allowed us to construct a CSF259-93 mutant lacking <i>gldN</i>, a core component of the type IX protein secretion system. The pre-methylation system developed in this study functions in all tested <i>F. psychrophilum</i> strains harboring HpaII-like and ScrFI-like REases. These newly developed genetic tools may allow the identification of key virulence factors and facilitate the development of live attenuated vaccines or other measures to control BCWD.</p><p><strong>Importance: </strong>Bacterial cold-water disease (BCWD) caused by <i>Flavobacterium psychrophilum</i> is a problem for salmonid aquaculture worldwide, and current control measures are inadequate. An obstacle in understanding and controlling BCWD is that most <i>F. psychrophilum</i> strains resist DNA transfer, thus limiting genetic studies of their virulence mechanisms. <i>F. psychrophilum</i> restriction enzymes that destroy foreign DNA were suspected to contribute to this problem. Here, we used <i>F. psychrophilum</i> DNA methyltransferases to modify and protect foreign DNA from digestion. This allowed efficient conjugative DNA transfer into nine diverse <i>F. psychrophilum</i> strains that had previously resisted DNA transfer. Using this approach, we constructed a gene deletion mutant that failed to cause disease in rainbow trout. Further genetic studies could help determine the molecular factors involved in pathogenesis and may aid development of innovative BCWD control strategies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0144824"},"PeriodicalIF":3.9,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A modified iChip for <i>in situ</i> cultivation of bacteria in arid environments.","authors":"Seven Nazipi Bushi, Marie B Lund, Tobias Sandfeld, Sanne Sadolin Nørskov, Simon Fruergaard, Marianne Glasius, Trine Bilde, Andreas Schramm","doi":"10.1128/aem.01325-24","DOIUrl":"https://doi.org/10.1128/aem.01325-24","url":null,"abstract":"<p><p>Antimicrobial resistance is an ever-increasing problem for human health, and with only a few novel antimicrobials discovered in recent decades, an extraordinary effort is needed to circumvent this crisis. A promising source of new microbial-derived antimicrobial compounds resides in the large fraction of microbes that are not readily cultured by standard cultivation. It has previously been shown that nests of the social spider <i>Stegodyphus dumicola</i> contain a diverse bacterial community, where only a small fraction of the microbes could be recovered by standard cultivation. To improve the recovery of the bacterial diversity cultured from nests, we modified the previously described isolation chip (iChip) to fit the natural arid environment of <i>S. dumicola</i> nests. Here we provide a comprehensive analysis of the modified iChip's performance. We found that the modified iChip improved the overall culturability, performed equally or better at recovering the bacterial diversity from individual nests, and improved the recovery of rare isolates compared to standard cultivation. Furthermore, we show that the modified iChip can be used in the field. In addition, we observed that the nests contain volatile organic compounds (VOCs) that could serve as substrate for the selective enrichment of rare and iChip-specific isolates. Our modified iChip can be applied for <i>in situ</i> cultivation in a broad range of arid habitats that can be exploited for future drug discovery.IMPORTANCEThe demand for novel antimicrobial compounds is an ever-increasing problem due to the rapid spread of antibiotic-resistant microbes. Therefore, exploring new habitats for microbial-derived antimicrobial compounds is crucial. The nest microbiome of <i>Stegodyphus dumicola</i> remains largely unexplored and could potentially serve as a new source of antimicrobial compounds. To access the nest's microbial diversity, we designed a modified iChip for <i>in situ</i> cultivation inside spider nests and tested its applications in both field and laboratory settings. Our study shows that the iChip's ability to recover <i>in situ</i> abundant genera was comparable or superior to standard cultivation, while the recovery of rare (low-abundant genera) was higher. We argue that these low-abundant and iChip-specific isolates are enriched from naturally occurring nest volatile organic compounds (VOCs) during iChip incubation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0132524"},"PeriodicalIF":3.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-resolved adaptation strategies of <i>Rhodobacterales</i> to changing conditions in the Chesapeake and Delaware Bays.","authors":"Mir Alvee Ahmed, Barbara J Campbell","doi":"10.1128/aem.02357-24","DOIUrl":"https://doi.org/10.1128/aem.02357-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The abundant and metabolically versatile aquatic bacterial order, &lt;i&gt;Rhodobacterales&lt;/i&gt;, influences marine biogeochemical cycles. We assessed &lt;i&gt;Rhodobacterales&lt;/i&gt; metagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closed &lt;i&gt;Rhodobacterales&lt;/i&gt; genomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. &lt;i&gt;Rhodobacterales&lt;/i&gt; genera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity. &lt;i&gt;Planktomarina&lt;/i&gt; genomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. These &lt;i&gt;Rhodobacterales&lt;/i&gt; also differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarine &lt;i&gt;Rhodobacterales&lt;/i&gt; within and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;In the complex web of global biogeochemical nutrient cycling, the &lt;i&gt;Rhodobacterales&lt;/i&gt; emerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range of &lt;i&gt;Rhodobacterales&lt;/i&gt; genera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarine &lt;i&gt;Rhodobacterales&lt;/i&gt;, revealing their various energy production pathways and diverse resource management, especially duri","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0235724"},"PeriodicalIF":3.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya.","authors":"Lauren N Hart, Brittany N Zepernick, Kaela E Natwora, Katelyn M Brown, Julia Akinyi Obuya, Davide Lomeo, Malcolm A Barnard, Eric O Okech, E Anders Kiledal, Paul A Den Uyl, Mark Olokotum, Steven W Wilhelm, R Michael McKay, Ken G Drouillard, David H Sherman, Lewis Sitoki, James Achiya, Albert Getabu, Kefa M Otiso, George S Bullerjahn, Gregory J Dick","doi":"10.1128/aem.01507-24","DOIUrl":"10.1128/aem.01507-24","url":null,"abstract":"<p><p>The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf's cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf's cyanobacterial composition, function, and biosynthetic potential. <i>Dolichospermum</i> was the dominant bloom-forming cyanobacterium, co-occurring with <i>Microcystis</i> at most sites. <i>Microcystis</i> and <i>Planktothrix</i> were more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) of <i>Dolichospermum</i> harbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation of <i>Dolichospermum</i> in the nitrogen-limited gulf. Over 300 biosynthetic gene clusters (BGCs) putatively encoding the synthesis of toxins and other secondary metabolites were identified across the gulf, even at sites where there were no visible cyanoHAB events. Almost all BGCs identified had no known synthesis product, indicating a diverse and novel biosynthetic repertoire capable of synthesizing harmful or potentially therapeutic metabolites. <i>Microcystis</i> MAGs contained <i>mcy</i> genes encoding the synthesis of hepatotoxic microcystins which are a concern for drinking water safety. These findings illustrate the spatial variation of bloom-forming cyanobacteria in the Winam Gulf and their available strategies to dominate different ecological niches. This study underscores the need for further use of genomic techniques to elucidate the dynamics and mitigate the potentially harmful effects of cyanoHABs and their associated toxins on human, environmental, and economic health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0150724"},"PeriodicalIF":3.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitrogen source type modulates heat stress response in coral symbiont (<i>Cladocopium goreaui</i>).","authors":"Yulin Huang, Jiamin He, Yujie Wang, Ling Li, Senjie Lin","doi":"10.1128/aem.00591-24","DOIUrl":"https://doi.org/10.1128/aem.00591-24","url":null,"abstract":"<p><p>Ocean warming due to climate change endangers coral reefs, and regional nitrogen overloading exacerbates the vulnerability of reef-building corals as the dual stress disrupts coral-Symbiodiniaceae mutualism. Different forms of nitrogen may create different interactive effects with thermal stress, but the underlying mechanisms remain elusive. To address the gap, we measured and compared the physiological and transcriptional responses of the Symbiodiniaceae <i>Cladocopium goreaui</i> to heat stress (31°C) when supplied with different types of nitrogen (nitrate, ammonium, or urea). Under heat stress (HS), cell proliferation and photosynthesis of <i>C. goreaui</i> declined, while cell size, lipid storage, and total antioxidant capacity increased, both to varied extents depending on the nitrogen type. Nitrate-cultured cells exhibited the most robust acclimation to HS, as evidenced by the fewest differentially expressed genes (DEGs) and less ROS accumulation, possibly due to activated nitrate reduction and enhanced ascorbate biogenesis. Ammonium-grown cultures exhibited higher algal proliferation and ROS scavenging capacity due to enhanced carotenoid and ascorbate quenching, but potentially reduced host recognizability due to the downregulation of N-glycan biosynthesis genes. Urea utilization led to the greatest ROS accumulation as genes involved in photorespiration, plant respiratory burst oxidase (RBOH), and protein refolding were markedly upregulated, but the greatest cutdown in photosynthate potentially available to corals as evidenced by photoinhibition and selfish lipid storage, indicating detrimental effects of urea overloading. The differential warming nitrogen-type interactive effects documented here has significant implication in coral-Symbiodiniaceae mutualism, which requires further research.IMPORTANCERegional nitrogen pollution exacerbates coral vulnerability to globally rising sea-surface temperature, with different nitrogen types exerting different interactive effects. How this occurs is poorly understood and understudied. This study explored the underlying mechanism by comparing physiological and transcriptional responses of a coral symbiont to heat stress under different nitrogen supplies (nitrate, ammonium, and urea). The results showed some common, significant responses to heat stress as well as some unique, N-source dependent responses. These findings underscore that nitrogen eutrophication is not all the same, the form of nitrogen pollution should be considered in coral conservation, and special attention should be given to urea pollution.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0059124"},"PeriodicalIF":3.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AAV-based gene delivery of antimicrobial peptides to combat drug-resistant pathogens.","authors":"Piyush Baindara, Dinata Roy, Chandra S Boosani, Santi M Mandal, Jonathan A Green","doi":"10.1128/aem.01702-24","DOIUrl":"https://doi.org/10.1128/aem.01702-24","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) have emerged as potential alternatives to conventional antibiotics due to their novelty and multiple mechanisms of action. Because they are peptides, AMPs are amenable to bioengineering and suitable for cloning and expression at large production scales. However, the efficient delivery of AMPs is an unaddressed issue, particularly due to their large size, possible toxicities, and the development of adverse immune responses. Here, we have reviewed the possibilities of adeno-associated virus (AAV)-based localized gene delivery of AMPs for the treatment of infectious diseases with a special focus on respiratory infections. By discussing the gene delivery mechanism of AAV and the accompanying technical and therapeutic challenges with AMPs, we describe a foundation that emphasizes the use of viral vector-based gene delivery of AMPs for disease treatment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0170224"},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A powerful but frequently overlooked role of thermodynamics in environmental microbiology: inspirations from anammox.","authors":"Zibin Li, Mingda Zhou, Xiaochuan Ran, Weigang Wang, Han Wang, Tong Wang, Yayi Wang","doi":"10.1128/aem.01668-24","DOIUrl":"https://doi.org/10.1128/aem.01668-24","url":null,"abstract":"<p><p>Thermodynamics has long been applied in predicting undiscovered microorganisms or analyzing energy flows in microbial metabolism, as well as evaluating microbial impacts on global element distributions. However, further development and refinement in this interdisciplinary field are still needed. This work endeavors to develop a whole-cycle framework integrating thermodynamics with microbiological studies, focusing on representative nitrogen-transforming microorganisms. Three crucial concepts (reaction favorability, energy balance, and reaction directionality) are discussed in relation to nitrogen-transforming reactions. Specifically, reaction favorability, which sheds lights on understanding the diversity of nitrogen-transforming microorganisms, has also provided guidance for novel bioprocess development. Energy balance, enabling the quantitative comparison of microbial energy efficiency, unravels the competitiveness of nitrogen-transforming microorganisms under substrate-limiting conditions. Reaction directionality, revealing the niche-differentiating patterns of nitrogen-transforming microorganisms, provides a foundation for predicting biogeochemical reactions under various environmental conditions. This review highlights the need for a more comprehensive integration of thermodynamics in environmental microbiology, aiming to comprehensively understand microbial impacts on the global environment from micro to macro scales.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0166824"},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel virus potentially evolved from the N4-like viruses represents a unique viral family: <i>Poorviridae</i>.","authors":"Wei Wang, Hongmin Wang, Xiao Zou, Yundan Liu, Kaiyang Zheng, Xin Chen, Xinyi Wang, Shujuan Sun, Yang Yang, Min Wang, Hongbing Shao, Yantao Liang","doi":"10.1128/aem.01559-24","DOIUrl":"10.1128/aem.01559-24","url":null,"abstract":"<p><p><i>Pseudoalteromonas</i> are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect <i>Pseudoalteromonas</i> remains limited. This study isolated a virus infecting <i>Pseudoalteromonas nigrifaciens</i> from Xiaogang in Qingdao, China. vB_PunP_Y3 comprises a linear, double-strand DNA genome with a length of 48,854 bp, encoding 52 putative open reading frames. Transmission electron microscopy demonstrates the short-tailed morphology of vB_PunP_Y3. Phylogenetic and genome-content-based analysis indicate that vB_PunP_Y3 represents a novel virus family named as <i>Poorviridae</i>, along with three high-quality uncultivated viral genomes. Biogeographical analyses show that <i>Poorviridae</i> is distributed across five viral ecological zones, and is predominantly detected in the Antarctic, Arctic, and bathypelagic zones. Comparative genomics analyses identified three of the seven hallmark proteins of N4-like viruses (DNA polymerase, major capsid protein, and virion-encapsulated RNA polymerase) from vB_PunP_Y3, combing with the protein tertiary structures of the major capsid protein, suggesting that vB_PunP_Y3 might evolve from the N4-like viruses.</p><p><strong>Importance: </strong>vB_PunP_Y3 is a unique strain containing three of the seven hallmark proteins of N4-like viruses, but is grouped into a novel family-level viral cluster with three uncultured viruses from metagenomics, named <i>Poorviridae</i>. This study enhanced the understanding about the genetic diversity, evolution, and distribution of <i>Pseudoalteromonas</i> viruses and provided insights into the novel evolution mechanism of marine viruses.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0155924"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11654794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}