Applied and Environmental Microbiology最新文献

{"title":"<i>Leptospira</i> biofilms: implications for survival, transmission, and disease management.","authors":"Carla Silva Dias, Melissa Hanzen Pinna","doi":"10.1128/aem.01914-24","DOIUrl":"10.1128/aem.01914-24","url":null,"abstract":"<p><p>Leptospirosis is a zoonotic disease caused by <i>Leptospira</i> bacteria, affecting humans and a broad range of wild and domestic animals in diverse epidemiological settings (rural, urban, and wild). The disease's pathogenesis and epidemiology are complex networks not fully elucidated. Epidemiology reflects the One Health integrated approach of environment-animal-human interaction, causing severe illness in humans and animals, with consequent public health burdens. Saprophytic and pathogenic leptospires have been shown to form biofilms <i>in vivo</i>, <i>in vitro,</i> and in environmental samples. Biofilms are characterized by a polymeric matrix that confers protection against hostile environments (both inside and outside of the host), favoring bacterial survival and dissemination. Despite its significance, the role of this bacterial growth mode in leptospiral survival, transmission, and decreased antibiotic susceptibility remains poorly understood and underexplored. Even so, the literature indicates that biofilms might be correlated with lower antimicrobial susceptibility and chronicity in leptospirosis. In this minireview, we discuss the aspects of biofilm formation by <i>Leptospira</i> and their significance for epidemiology and therapeutic management. Understanding the current scenario provides insight into the future prospects for biofilm diagnosis, prevention, and treatment of leptospirosis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0191424"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942934","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}

{"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":"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":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837538/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Newly identified SpoVAF/FigP complex: the role in <i>Bacillus subtilis</i> spore germination at moderate high pressure and influencing factors.","authors":"Fengzhi Lyu, Ziqi Gong, Tianyu Zhang, Dong Yang, Lei Rao, Xiaojun Liao","doi":"10.1128/aem.02047-24","DOIUrl":"10.1128/aem.02047-24","url":null,"abstract":"<p><p>The SpoVAF/FigP complex, a newly identified dormant spore ion channel, has been shown to amplify the response of germinant receptors (GRs) to nutrient germinants. However, its contribution to high-pressure-induced germination remains unexplored. In this study, we discovered that the 5AF/FigP complex played an important role in the GR-dependent germination of <i>Bacillus subtilis</i> spores under moderate high pressure (MHP) by facilitating the release of ions, such as potassium (K⁺), a mechanism in parallel with its role in nutrient-induced germination. Despite its predicted function as an ion channel, the 5AF/FigP complex failed to be activated by MHP in the absence of GerA-type GRs. We quantitatively examined the factors that influence the 5AF/FigP complex's function in MHP-induced germination using modeling and fitting techniques. Our results indicated that the complex's amplification effect was both enhanced and accelerated as pressure levels increase from 50 to 200 MPa. However, raising the MHP treatment temperature from 22°C to 30°C only speeded up the complex's function without enhancing its effectiveness. Moreover, extreme conditions of higher pressure (300 MPa) and temperature (34°C-37°C) could diminish the complex's functionality. Additionally, the amplification effect was weakened in spores produced at both elevated and reduced sporulation temperatures. Taken together, our findings highlight the essential role of the 5AF/FigP complex in boosting the efficiency of MHP-induced germination. This revelation has enriched our understanding of the intricate mechanisms underlying GR-dependent germination in <i>Bacillus</i> spores, offering valuable insights that can be utilized to refine the germination-inactivation strategies within the food industry.</p><p><strong>Importance: </strong>High-pressure-induced spore germination has been discovered for more than half a century, but the signal transduction pathway of the process still needs to be refined. In this study, for the first time, we revealed the role of the newly identified SpoVAF/FigP complex in high-pressure-induced spore germination, as well as the factors influencing its function in this process. The new findings in this work not only enhance the theoretical understanding of spore germination mechanisms under high pressure but also pave the way for developing novel strategies to inactivate spores during high-pressure food processing, a technology that is gaining popularity in the food industry as a promising non-thermal preservation method.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0204724"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837508/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998467","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}

{"title":"Physico-chemical properties and substrate specificity of α-(1→3)-d-glucan degrading recombinant mutanase from <i>Trichoderma harzianum</i> expressed in <i>Penicillium verruculosum</i>.","authors":"Olga A Sinitsyna, Pavel V Volkov, Ivan N Zorov, Alexandra M Rozhkova, Oleg V Emshanov, Yulia M Romanova, Bozhena S Komarova, Natalia S Novikova, Nikolay E Nifantiev, Arkady P Sinitsyn","doi":"10.1128/aem.00226-24","DOIUrl":"10.1128/aem.00226-24","url":null,"abstract":"<p><p>The gene <i>mutAW</i> encoding <i>Trichoderma harzianum</i> fungus mutanase (MutA, GH71 family, α-1,3-glucanase, EC 3.2.1.59) was cloned and heterologously expressed by the highly productive <i>Penicillium verruculosum</i> fungus. <i>P. verruculosum MutA</i> strain secreted crude enzyme preparations with the recombinant MutA content of 40% of the total secreted protein, and the specific activity increased 150 folds compared to that of enzyme preparation obtained by the host strain. Homogeneous MutA had molecular mass of 70 kDa and displayed maximum of the activity on mutan at pH 5.0 and 50°C, with <i>K</i>_m and <i>k</i>_cat being 1.0 g/L and 30 s^-1, respectively. At 40-50°C, the MutA was stable for at least 3 h. Glucose was the main product of long-term mutan hydrolysis. HPLC analysis of hydrolysis product of oligo-α-(1→3)-D-glucosides bearing UV-detectable <i>N</i>-<i>trans</i>-cinnamoyl residue in the aglycon clearly indicated that MutA has an endo-processive hydrolytic mode of action. It was demonstrated that MutA can destroy the polysaccharide matrix of both gram-positive and gram-negative pathogenic bacteria biofilms.</p><p><strong>Importance: </strong>The manuscript describes the properties of a novel recombinant GH71 mutanase Mut A from <i>Trichoderma harzianum</i>. Gene <i>mutAW</i> encoding mutanase was heterologously expressed in the host strain <i>Penicillium verruculosum</i> B1-537 (ΔniaD). The recipient strain has a high secretory ability and allowed to obtain preparations containing the target recombinant enzyme up to 80% of the total protein pool. MutA exhibited a high activity against mutan and negligible or zero activity toward other types of glucans including α-(1→4)-, β-(1→3)-, β-(1→4)-, and β-(1→6)-glucans. By using a series of synthetic oligo-α-(1→3)-D-glucosides, we demonstrated that MutA is an endo-processive enzyme, which hydrolyzes the internal glucosidic bonds and releases glucose from the reducing end sliding into the non-reducing end. MutA recognizes tetrasaccharide as a minimal substrate and hydrolyzes it to trisaccharide and glucose. The effectiveness of the use of MutA for the destruction of clinical isolates of gram-positive and gram-negative bacteria is also described.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0022624"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021856","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}

{"title":"A cytochrome <i>bd</i> repressed by a MarR family regulator confers resistance to metals, nitric oxide, sulfide, and cyanide in <i>Chromobacterium violaceum</i>.","authors":"Bianca B Batista, Vinicius M de Lima, W Ryan Will, Ferric C Fang, José F da Silva Neto","doi":"10.1128/aem.02360-24","DOIUrl":"10.1128/aem.02360-24","url":null,"abstract":"<p><p><i>Chromobacterium violaceum</i> is a ubiquitous environmental pathogen. Despite its remarkable adaptability, little is known about the mechanisms of stress resistance in this bacterium. Here, in a screen for iron-susceptible transposon mutants, we identified a cytochrome <i>bd</i> that protects <i>C. violaceum</i> against multiple stresses. The two subunits of this cytochrome <i>bd</i> (CioAB) are encoded by the <i>cioRAB</i> operon, which also encodes a GbsR-type MarR family transcription factor (CioR). A ∆<i>cioAB</i> mutant strain was sensitive to iron and the iron-requiring antibiotic streptonigrin and showed a decrease in siderophore production. Growth curves and survival assays revealed that the ∆<i>cioAB</i> strain was also sensitive to zinc, hydrogen peroxide, nitric oxide, sulfide, and cyanide. Expression analysis showed that the promoter activity of the <i>cioRAB</i> operon and the transcript levels of the <i>cioAB</i> genes were increased in a ∆<i>cioR</i> mutant. CioR bound the promoter region of the <i>cio</i> operon <i>in vitro</i>, indicating that CioR is a direct repressor of its own operon. Expression of the <i>cio</i> operon increased at high cell density and was dependent on the quorum-sensing regulator CviR. As cyanide is also a signal for <i>cio</i> expression, and production of endogenous cyanide is known to be a quorum sensing-regulated trait in <i>C. violaceum</i>, we suggest that CioAB is a cyanide-insensitive terminal oxidase that allows respiration under cyanogenic growth conditions. Our findings indicate that the cytochrome <i>bd</i> CioAB protects <i>C. violaceum</i> against multiple stress agents that are potentially produced endogenously or during interactions with a host.</p><p><strong>Importance: </strong>The terminal oxidases of bacterial respiratory chains rely on heme-copper (heme-copper oxidases) or heme (cytochrome <i>bd</i>) to catalyze the reduction of molecular oxygen to water. <i>Chromobacterium violaceum</i> is a facultative anaerobic bacterium that uses oxygen and other electron acceptors for respiration under conditions of varying oxygen availability. The <i>C. violaceum</i> genome encodes multiple respiratory terminal oxidases, but their role and regulation remain unexplored. Here, we demonstrate that CioAB, the single cytochrome <i>bd</i> from <i>C. violaceum</i>, protects this bacterium against multiple stressors that are inhibitors of heme-copper oxidases, including nitric oxide, sulfide, and cyanide. CioAB also confers <i>C. violaceum</i> resistance to iron, zinc, and hydrogen peroxide. This cytochrome <i>bd</i> is encoded by the <i>cioRAB</i> operon, which is under direct repression by the MarR-type regulator CioR. In addition, the <i>cioRAB</i> operon responds to quorum sensing and to cyanide, suggesting a protective mechanism of increasing CioAB in the setting of high endogenous cyanide production.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0236024"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031628","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}

{"title":"<i>Shewanella</i> is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm <i>Eisenia fetida</i>.","authors":"Jan-Philpp Wittlinger, Natalia Castejón, Bela Hausmann, David Berry, Stephanie L Schnorr","doi":"10.1128/aem.02069-24","DOIUrl":"10.1128/aem.02069-24","url":null,"abstract":"<p><p>Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (<i>pfa</i>), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of <i>Eisenia fetida</i>, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including <i>Shewanellaceae</i>, and Planctomycetota, including <i>Gemmataceae</i> within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to <i>Shewanella</i>. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that <i>Shewanella</i> can explain PUFA enrichment in the gut environment because of the <i>pfa</i> gene presence detected <i>via</i> PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially <i>Shewanella,</i> activated through the gut ecosystem.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0206924"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998946","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}

{"title":"Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.","authors":"Kayla Cross, Noelle Beckman, Benjamin Jahnes, Zakee L Sabree","doi":"10.1128/aem.02368-24","DOIUrl":"10.1128/aem.02368-24","url":null,"abstract":"<p><p>Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous <i>Periplaneta americana</i> over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome \"service outages\" due to functional redundancy.</p><p><strong>Importance: </strong>Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0236824"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063287","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}

{"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":"&lt;p&gt;&lt;p&gt;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. &lt;i&gt;Dolichospermum&lt;/i&gt; was the dominant bloom-forming cyanobacterium, co-occurring with &lt;i&gt;Microcystis&lt;/i&gt; at most sites. &lt;i&gt;Microcystis&lt;/i&gt; and &lt;i&gt;Planktothrix&lt;/i&gt; were more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) of &lt;i&gt;Dolichospermum&lt;/i&gt; harbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation of &lt;i&gt;Dolichospermum&lt;/i&gt; 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. &lt;i&gt;Microcystis&lt;/i&gt; MAGs contained &lt;i&gt;mcy&lt;/i&gt; 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.IMPORTANCEThe Winam Gulf (Kenya) is a vital resource that experiences prolific cyanobacterial harmful algal blooms (cyanoHABs). Bloom-forming cyanobacteria produce cyanotoxins, threatening human and environmental health, recreation, and fishing. However, cyanotoxin production in the gulf has not been linked to a specific type of cyanobacteria. We used DNA sequencing of whole microbial communities to track the species of cyanobacteria present across the gulf and investigate the genes responsible for synthesis of known and novel toxins. Our results reveal &lt;i&gt;Dolichospermum&lt;/i&gt; as the main bloom-forming cyanobacteria in the gulf, often co-occurring with high abundance of toxigenic &lt;i&gt;Microcystis.&lt;/i&gt; Over 300 unique gene clusters were found, with most predicted to encode the synthesis of uncharacterized molecules. These results provide initial insights into the diverse biosynthetic potential encoded by cyanobacteria in the Winam Gulf and underscore the need to further elucidate and investigate the effects of known and novel molecules produced in cyanoHABs in this region","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0150724"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837572/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel FadL family outer membrane transporter is involved in the uptake of polycyclic aromatic hydrocarbons.","authors":"Qiu Meng, Yuxuan Liang, Yinming Xu, Saiyue Li, Haiyan Huang, Yuanyou Xu, Feifei Cao, Jianhua Yin, Tingheng Zhu, Haichun Gao, Zhiliang Yu","doi":"10.1128/aem.00827-24","DOIUrl":"10.1128/aem.00827-24","url":null,"abstract":"<p><p>Gram-negative bacteria play a pivotal role in the bioremediation of persistent organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs). Because the outer membrane (OM) of these bacteria hinders the direct permeation of hydrophobic substances into the cells, trans-OM proteins are required for the uptake of PAHs. However, neither the characteristics of PAH transporters nor the specific transport mechanism has been well interpreted. In this study, we revealed the participation of a novel FadL family transporter, PadL, in the biodegradation of the representative PAH phenanthrene in <i>Novosphingobium pentaromativorans</i> US6-1, an efficient PAH-degrading bacterium. PadL facilitates the cross-OM transport of phenanthrene, thus upregulating the expression of the gene <i>ahdA1e</i> that is critical to the PAH catabolism. We then showed that hydrophobic amino acid residues in the substrate binding pockets of PadL are essential for the binding of PAHs, such as phenanthrene and benzo[<i>a</i>]pyrene. PadL homologs commonly exist in most of the PAH-degrading species from <i>Sphingomonas</i> and <i>Novosphingobium</i>. The characterization of PadL provided in this study holds significant potential for improving the PAH biodegradation efficiency.</p><p><strong>Importance: </strong>Persistent organic pollutants, including polycyclic aromatic hydrocarbons (PAHs), pose serious threats to human health, and biodegradation has been applied as an efficient strategy for PAH removal. However, due to the high hydrophobicity of PAHs, their uptake is hindered by the bacterial outer membrane, restraining degradation efficiency. The present study reveals the critical roles of a novel FadL family protein (PadL) in the biodegradation of PAHs. PadL specifically transports PAHs such as phenanthrene and benzo[a]pyrene and PadL homologs generally exist in PAH-degrading bacteria of Sphingomonas and Novosphingobium. Our findings fill the knowledge gap in the bacterial trans-membrane uptake process of PAHs and provide a future direction for enhancing the bacterial PAH bioremediation capacity.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0082724"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031632","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}

{"title":"CRISPR-guided base editor enables efficient and multiplex genome editing in bacterial cellulose-producing <i>Komagataeibacter</i> species.","authors":"Bo Xin, Jiaheng Liu, Jinyang Li, Zhaojun Peng, Xinyue Gan, Yuxi Zhang, Cheng Zhong","doi":"10.1128/aem.02455-24","DOIUrl":"10.1128/aem.02455-24","url":null,"abstract":"<p><p>Bacterial cellulose (BC) is an extracellular polysaccharide produced by bacteria that has wide applications in the food industry, tissue engineering, and battery manufacturing. Genome editing of BC-producing <i>Komagataeibacter</i> species is expected to optimize BC production and its properties. However, the available technology can target only one gene at a time and requires foreign DNA templates, which may present a regulatory hurdle for genetically modified organisms. In this study, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-guided base editing method for <i>Komagataeibacter</i> species using Cas9 nickase and cytidine deaminase. Without foreign DNA templates, C-to-T conversions were performed within an 8 bp editing window with 90% efficiency. Double- and triple-gene editing was achieved with 80%-90% efficiency. Fusing uracil-DNA glycosylase with the base editor enabled C-to-G editing. The base editor worked efficiently with various <i>Komagataeibacter</i> species. Finally, mannitol metabolic genes were investigated using base-editing-mediated gene inactivation. This study provides a powerful tool for multiplex genome editing of <i>Komagataeibacter</i> species.</p><p><strong>Importance: </strong><i>Komagataeibacter</i>, a bacterial genus belonging to the family <i>Acetobacteraceae</i>, has important applications in food and material biosynthesis. However, the genome editing of <i>Komagataeibacter</i> relies on traditional homologous recombination methods. Therefore, only one gene can be manipulated in each round using foreign DNA templates, which may present a regulatory hurdle for genetically modified organisms when microorganisms are used in the food industry. In this study, a powerful base editing technology was developed for <i>Komagataeibacter</i> species. C-to-T and C-to-G base conversions were efficiently implemented at up to three loci in the <i>Komagataeibacter</i> genome. This base editing system is expected to accelerate basic and applied research on <i>Komagataeibacter</i> species.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0245524"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063266","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}