Applied and Environmental Microbiology最新文献

{"title":"The healthy human gut can take it all: vancomycin-variable, linezolid-resistant strains and specific bacteriocin-species interplay in <i>Enterococcus</i> spp.","authors":"Ana C Almeida-Santos, Bárbara Duarte, Ana P Tedim, Maria J Teixeira, Joana C Prata, Rui M S Azevedo, Carla Novais, Luísa Peixe, Ana R Freitas","doi":"10.1128/aem.01699-24","DOIUrl":"https://doi.org/10.1128/aem.01699-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Enterococcus&lt;/i&gt; spp. are opportunistic human pathogens colonizing the human gut and a significant reservoir for the continuous adaptation of hospital clones. However, studies on the features of enterococci species co-colonizing healthy individuals are scarce. We investigated the prevalence, antibiotic resistance, and bacteriocin profiles of &lt;i&gt;Enterococcus&lt;/i&gt; species in fecal samples from healthy adults in Portugal using culture-based methods, WGS, and bacteriocin inhibition assays. Results were compared with data from a 2001 study in the same region. &lt;i&gt;Enterococcus&lt;/i&gt; spp. (&lt;i&gt;n&lt;/i&gt; = 315; 24% MDR) were recovered from all volunteers. &lt;i&gt;Enterococcus lactis&lt;/i&gt; was the prevalent species (75%), followed by &lt;i&gt;Enterococcus faecalis&lt;/i&gt; (65%) and &lt;i&gt;Enterococcus faecium&lt;/i&gt; (47%). &lt;i&gt;E. lactis&lt;/i&gt; prevalence increased 2.5-fold since 2001. Linezolid resistance genes (&lt;i&gt;optrA/poxtA&lt;/i&gt;) were detected in &lt;i&gt;E. faecium&lt;/i&gt; and &lt;i&gt;Enterococcus thailandicus&lt;/i&gt; isolates, while a vancomycin-variable &lt;i&gt;E. faecium&lt;/i&gt; was also identified. Virulence and plasmid profiles were diverse across species, with evidence of exchange of virulence markers and plasmid replicons between &lt;i&gt;E. faecium&lt;/i&gt; and &lt;i&gt;E. lactis&lt;/i&gt;. Bacteriocin gene repertoires were extensive and species-specific. Higher numbers of bacteriocin genes were associated with stronger inhibition profiles, and 25% of &lt;i&gt;E. faecium&lt;/i&gt; and &lt;i&gt;E. lactis&lt;/i&gt; isolates were capable of inhibiting relevant VRE clones. This study unveils the co-occurrence and ecological dynamics of &lt;i&gt;Enterococcus&lt;/i&gt; species in the healthy human gut, reinforcing its role as a reservoir for key antibiotic resistance genes and potentially pathogenic strains. The shift toward &lt;i&gt;E. lactis&lt;/i&gt; prevalence and the detection of linezolid resistance genes in healthy individuals underscore the need for ongoing surveillance of the gut microbiome to guide public health strategies and antibiotic stewardship efforts.IMPORTANCEThis study highlights the role of &lt;i&gt;Enterococcus&lt;/i&gt; species in the healthy human gut, revealing important insights into their prevalence and antibiotic resistance. It emphasizes that the human gut serves as a significant reservoir for antibiotic-resistant strains and shows a notable increase and prevalence of &lt;i&gt;Enterococcus lactis,&lt;/i&gt; which has been underappreciated due to identification challenges. The research also underscores the bacteriocins' role in microbial competition, where commensal strains inhibit clinical VRE, potentially aiding the restoration of the gut microbiota, after antibiotic treatment. The findings accentuate the need for ongoing surveillance to track changes in gut bacteria, especially with the emergence of resistance genes to last resort antibiotics. Such monitoring is crucial for shaping public health strategies and managing the growing threat of antibiotic-resistant infections. Profiling bacteriocins at the species and strain level can identify ecological adaptation factors","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0169924"},"PeriodicalIF":3.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852081","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":"Rational design and characterization of enhanced alcohol-inducible synthetic promoters in <i>Pichia pastoris</i>.","authors":"Qi Liu, Yun-Hao Li, Liu-Fei Tao, Jia-Yi Yang, Yi-Lun Zhang, Meng-Hao Cai","doi":"10.1128/aem.02191-24","DOIUrl":"https://doi.org/10.1128/aem.02191-24","url":null,"abstract":"<p><p>The C1 and C2 alcohols hold great promise as substrates for biomanufacturing due to their low cost and rich resources. <i>Pichia pastoris</i> is considered a preferred host for methanol and ethanol bioconversion due to its natural utilization of methanol and ethanol. However, the scarcity of strong and tightly regulated alcohol-inducible promoters limits its extended use. This study aimed to develop enhanced methanol- and ethanol-inducible promoters capable of improving gene expression in <i>P. pastoris</i>. Rational design strategies were employed to rewire the upstream regulatory sequence of the methanol-inducible P<i>_AOX1</i>, generating several high-strength methanol-inducible promoters with a stringent regulatory pattern. Eleven strong promoters were identified from 36 endogenous ethanol-inducible candidates recognized from transcriptome analysis. Core promoter regions, the crucial element influencing transcriptional strength, were also characterized. Five high-activity core promoters were then combined with four upstream regulatory sequences of high-strength promoters, resulting in four groups of synthetic promoters. Ultimately, the highly active methanol-inducible P<i>_A13</i> and ethanol-inducible P<i>₀₆₈₈</i> and P<i>_synIV-5</i> were selected for the expression of an α-amylase and yielded enzyme activity 1.6, 2.6, and 4.5 times higher as compared to that of P<i>_AOX1</i>. This work expands the genetic toolkit available for <i>P. pastoris</i>, providing more precise and efficient options for regulating gene expression. It benefits the use of <i>P. pastoris</i> as an efficient platform for the C1 and C2 alcohol-based biotransformation in industrial biotechnology.IMPORTANCE<i>P. pastoris</i> represents a preferred microbial host for the bio-utilization of C1 and C2 alcohols that are regarded as renewable carbon sources based on clean energy. However, lack of efficient and regulated expression tools highly limits the C1 and C2 alcohols based bioproduction. By exploring high-strength and strictly regulated alcohol-inducible promoters, this study expands the expression toolkit for <i>P. pastoris</i> on C1 and C2 alcohols. The newly developed methanol-inducible P<i>_A13</i> and ethanol-inducible P<i>_synIV-5</i> demonstrate significantly higher expression levels than the commercial P<i>_AOX1</i> system. The endogenous and synthetic promoter series established in this study provides new construction references and alternative tools for expression control in <i>P. pastoris</i> for C1 and C2 alcohols based biomanufacturing.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0219124"},"PeriodicalIF":3.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851961","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":"Does strain-level persistence of lactobacilli in long-term back-slopped sourdoughs inform on domestication of food-fermenting lactic acid bacteria?","authors":"Vi D Pham, Zhaohui S Xu, David J Simpson, Justina S Zhang, Michael G Gänzle","doi":"10.1128/aem.01892-24","DOIUrl":"10.1128/aem.01892-24","url":null,"abstract":"<p><p>Sourdoughs are maintained by back-slopping over long time periods. To determine strain-level persistence of bacteria, we characterized four sourdoughs from bakeries over a period of 3.3, 11.0, 18.0, and 19.0 years. One sourdough included isolates of <i>Levilactobacillus</i> spp. and <i>Fructilactobacillus</i> spp. that differed by fewer than 10 single-nucleotide polymorphisms (SNPs) from the isolates obtained 3.3 years earlier and thus likely represent the same strain. Isolates of <i>Levilactobacillus parabrevis</i> differed by 200-300 SNPs; their genomes were under positive selection, indicating transmission from an external source. In two other sourdoughs, isolates of <i>Fructilactobacillus sanfranciscensis</i> that were obtained 11 and 18 years apart differed by 19 and 29 SNPs, respectively, again indicating repeated isolation of the same strain. The isolate of <i>Fl. sanfranciscensis</i> from the fourth sourdough differed by 45 SNPs from the isolate obtained 19 years previously. We thus identified strain-level persistence in three out of four long-term back-slopped sourdoughs, making it possible that strains persisted over periods that are long enough to allow bacterial speciation and domestication.IMPORTANCEThe assembly of microbial communities in sourdough is shaped by dispersal and selection. Speciation and domestication of fermentation microbes in back-slopped food fermentations have been documented for food-fermenting fungi including sourdough yeasts but not for bacteria, which evolve at a slower rate. Bacterial speciation in food fermentations requires strain-level persistence of fermentation microbes over hundreds or thousands of years. By documenting strain-level persistence in three out of four sourdoughs over a period of up to 18 years, we demonstrate that persistence over hundreds or thousands of years is possible, if not likely. We thus not only open a new perspective on fermentation control in bakeries but also support the possibility that all humans, despite their cultural diversity, share the same fermentation microbes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0189224"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581933","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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection and quantification of human immunodeficiency virus-1 (HIV-1) total nucleic acids in wastewater settled solids from two California communities.","authors":"Marlene K Wolfe, Meri R J Varkila, Alessandro Zulli, Julie Parsonnet, Alexandria B Boehm","doi":"10.1128/aem.01477-24","DOIUrl":"10.1128/aem.01477-24","url":null,"abstract":"<p><p>Wastewater surveillance for infectious agents has proved useful in identifying the circulation of viruses within populations. We investigated the presence and concentration of human immunodeficiency virus (HIV)-1 total nucleic acids (including both viral RNA and proviral DNA) in wastewater solids. We retrospectively measured HIV-1 nucleic acids in two samples per week for 26 months at two wastewater treatment plants serving populations with different prevalences of HIV infections in San Francisco and Santa Clara County, California, USA. We detected HIV nucleic acids in a majority of samples with concentrations ranging from non-detect to 3.9 × 10⁵ cp/g (<i>N</i> = 459 samples total). Concentrations of HIV-1 were significantly higher in samples from the wastewater treatment plant serving a population with a higher prevalence of people living with HIV than in the plant serving a population with a lower prevalence. The HIV-1 nucleic acids amplified were primarily DNA and thus represented proviral DNA shedding into wastewater. Additionally, we found that HIV-1 nucleic acid concentrations in wastewater solids were orders of magnitude higher than those in liquid wastewater indicating that the HIV-1 target preferentially sorbs to solids. Whether concentrations of HIV-1 in wastewater solids can be used to identify the number of incident cases remains unknown. Additional work on HIV-1 shedding from individuals with viremia and people living with HIV is needed to translate wastewater measurements into quantitative information on infections. Additional work may also be needed to document non-human sources of HIV-1 nucleic acids in wastewater.</p><p><strong>Importance: </strong>Human immunodeficiency virus (HIV)-1 has infected nearly 100 million people since it emerged in the 1980s. Antiretroviral therapy prevents transmission of HIV and also allows infected individuals to live healthy lives with normal life expectancy. Consequently, identifying unrecognized cases of HIV is of paramount importance. Since wastewater represents a composite biological sample from a community, it may provide valuable information on HIV-1 prevalence that can be used to inform HIV testing and outreach.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0147724"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613486","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":"Tracing <i>Staphylococcus capitis</i> and <i>Staphylococcus epidermidis</i> strains causing septicemia in extremely preterm infants to the skin, mouth, and gut microbiota.","authors":"Forough L Nowrouzian, Kirth Lumingkit, Monica Gio-Batta, Daniel Jaén-Luchoro, Thordur Thordarson, Anders Elfvin, Agnes E Wold, Ingegerd Adlerberth","doi":"10.1128/aem.00980-24","DOIUrl":"https://doi.org/10.1128/aem.00980-24","url":null,"abstract":"<p><p>Coagulase-negative staphylococci (CoNS) comprise about 50 species, some of which cause septicemia in preterm neonates. CoNS establish early on the skin and in the oral and gut microbiota, from where they may spread to the bloodstream. The colonization pattern preceding septicemia is not well-defined. Forty-two extremely preterm neonates (≤28 + 0 gestational weeks) were followed from birth to 2 months with regular sampling and culturing of the skin and oral and gut microbiota. Blood samples were drawn upon clinical suspicion of septicemia and cultured. CoNS species were identified using matrix-assisted laser-desorption ionization time of flight mass spectrometry (MALDI-TOF). Random amplified polymorphic DNA was used for strain typing, and strains were characterized regarding biofilm production and virulence gene carriage. CoNS blood isolates underwent whole genome sequencing. <i>Staphylococcus epidermidis</i> represented 72% of the CoNS isolates on skin or mucous membranes, followed by <i>Staphylococcus capitis</i> (13%) and <i>Staphylococcus haemolyticus</i> (7%). CoNS septicemia was diagnosed in nine infants, yielding 11 septicemia isolates: seven <i>S</i>. <i>capitis</i> and four <i>S</i>. <i>epidermidis,</i> of which nine were further analyzed. The <i>S. capitis</i> septicemia isolates belonged to the NRCS-A clone. Two-thirds of the septicemia strains were traced back to the commensal microbiota. Colonization of the oral cavity by <i>S. capitis</i> was significantly associated with CoNS septicemia development, although the blood-borne <i>S. capitis</i> strains were more commonly found on the skin than in the mouth prior to invasion. Biofilm production was not associated with septicemia. Our results implicate CoNS colonization as a step that precedes septicemia in preterm neonates. Early colonization of the oral cavity by <i>S. capitis</i> may represent a particular risk.</p><p><strong>Importance: </strong>Septicemia is a major cause of morbidity in preterm infants. Coagulase-negative staphylococci (CoNS) can colonize skin, oral cavity, and intestines and are a common cause of septicemia in this group. The relation between CoNS colonization pattern at the species and strain level and septicemia has scarcely been studied. We mapped colonization of the skin, oral cavity, and intestines by CoNS species in extremely preterm infants and speciated and strain-typed the skin, mucosal, and blood isolates. Two-thirds of the CoNS septicemia blood strains, including a majority of <i>S. capitis</i> strains belonging to the NRCS-A clone, were tracked to the commensal microbiota. We demonstrated that CoNS species differ in their colonization patterns, whereby <i>S. capitis</i> was primarily a skin colonizer. However, its colonization of the oral cavity was enhanced among infants developing septicemia. Our study provides a starting point for further explorations of the relationship between CoNS colonization and septicemia in preterm infants.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0098024"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845655","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":"Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.","authors":"Valerie C Schiml, Juline M Walter, Live H Hagen, Aniko Varnai, Linda L Bergaust, Arturo Vera Ponce De Leon, Lars Elsgaard, Lars R Bakken, Magnus Ø Arntzen","doi":"10.1128/aem.01742-24","DOIUrl":"10.1128/aem.01742-24","url":null,"abstract":"<p><p>Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa <i>Giesbergeria</i>, <i>Cellulomonas</i>, <i>Azonexus,</i> and UBA5070 (<i>Fibrobacterota</i>). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.</p><p><strong>Importance: </strong>Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including <i>Giesbergeria</i>, <i>Cellulomonas</i>, <i>Azonexus</i>, and UBA5070 (<i>Fibrobacterota</i>) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0174224"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613490","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":"Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.","authors":"Vincent V Nowak, Peng Hou, Jeremy G Owen","doi":"10.1128/aem.00726-24","DOIUrl":"10.1128/aem.00726-24","url":null,"abstract":"<p><p>Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0072624"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674986","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":"<i>Azotobacter vinelandii</i> N₂ fixation increases in co-culture with the PGPR <i>Bacillus subtilis</i> in a nitrogen concentration-dependent manner.","authors":"Julie Leroux, Pascale B Beauregard, Jean-Philippe Bellenger","doi":"10.1128/aem.01528-24","DOIUrl":"10.1128/aem.01528-24","url":null,"abstract":"<p><p>Biological nitrogen fixation (BNF) is an essential source of new nitrogen (N) for terrestrial ecosystems. The abiotic factors regulating BNF have been extensively studied in various ecosystems and laboratory settings. Despite this, our understanding of the impact of neighboring bacteria on N₂ fixer activity remains limited. Here, we explored this question using a co-culture of the two model species: the free-living diazotroph <i>Azotobacter vinelandii</i> and the non-fixing plant growth-promoting rhizobacteria <i>Bacillus subtilis</i>. We observed that the interaction between the two bacteria was modulated by N availability. Under N-replete conditions, <i>B. subtilis</i> outcompeted <i>A. vinelandii</i> in the co-culture. Under N-limiting conditions, BNF activity by <i>A. vinelandii</i> was enhanced in the presence of <i>B. subtilis</i>. Reciprocally, the presence of <i>A. vinelandii</i> repressed sporulation by <i>B. subtilis</i> and supported its growth likely through N transfer. N inputs by <i>A. vinelandii</i> were doubled in the presence of <i>B. subtilis</i> compared to the monoculture, primarily due to the retention of a robust N₂ fixation activity in the stationary phase. A proteomic analysis revealed that <i>A. vinelandii</i> N metabolism, particularly the molybdenum nitrogenase isoform protein levels (NifK and NifD), was upregulated during the stationary growth phase in the presence of <i>B. subtilis</i>. This study revealed that N stress drives bacterial interactions and activity in a two-species community, especially in the stationary phase.</p><p><strong>Importance: </strong>Reducing inputs of chemical N fertilizers is essential to develop a more sustainable agriculture. The stimulation of biological nitrogen fixation by N2 fixers in multispecies cultures, here the plant growth-promoting rhizobacteria <i>Azotobacter vinelandii</i> and <i>Bacillus subtilis</i>, opens opportunities for the formulation of biofertilizers consortia. While most research on N2 fixation historically focussed on the exponential growth phase of microorganisms, we observed that <i>Bacillus subtilis</i> stimulated <i>Azotobacter vinelandii</i> N2 fixation mostly during the stationary phase. This result highlights that more research on the factors controlling N2 fixation repression during the stationary growth phase, especially bacteria-bacteria interactions, is eagerly needed.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0152824"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613485","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":"Spatio-temporal distribution and biotechnological potential of culturable yeasts in the intertidal sediments and seawater of Aoshan Bay, China.","authors":"Si-Jia Xue, Jie Liu, Fang-Yuan Zhao, Xin-Tong Zhang, Zhi-Qiang Zhu, Jin-Yong Zhang","doi":"10.1128/aem.01570-24","DOIUrl":"10.1128/aem.01570-24","url":null,"abstract":"<p><p>Marine yeasts play a crucial role in marine microbial ecology, facilitating the biogeochemical cycling of carbon and nitrogen in marine ecosystems, while also serving as important reservoirs of bioactive compounds with extensive applications in pharmaceuticals, agriculture, and various industries. Intertidal flats, characterized by their complex ecological dynamics, are postulated to harbor a wealth of yeast resources. This study employed a culture-dependent approach to assess the diversity, spatio-temporal distribution, and biotechnological potential of yeast communities residing within the intertidal sediments and seawater of Aoshan Bay. A total of 392 yeast strains were identified from 20 distinct genera, encompassing 43 recognized species and four candidate novel species. Notably, 17 of these species were identified as novel occurrences in marine environments, underscoring the rich yeast biodiversity of the Aoshan Bay ecosystem, with <i>Candida</i> emerging as the dominant genus in both sedimentary and aqueous habitats. Yeast community composition exhibited significant spatial and temporal variation, with peak diversity and abundance observed in autumn, the subtidal zone, and the surface soil layer. No clear pattern, however, emerged linking these shifts to specific changes in community composition, highlighting the complex interactions between microbial communities, environmental variables, and anthropogenic disturbance. Although several yeast species isolated here have been previously recognized for their biotechnological potential, their diverse and abundant extracellular enzyme profiles were characterized, further highlighting their crucial role in organic matter decomposition and nutrient cycling within the tidal ecosystem, as well as their potential applicability in the food, fine chemical, textile, and pharmaceutical industries.IMPORTANCEThis study presents groundbreaking insights into the yeast diversity of Aoshan Bay, offering invaluable information on their spatial and temporal distribution patterns, as well as their biotechnological potential in the tidal environment. The findings reveal that the eutrophic intertidal flat is a rich repository of yeasts with abundant extracellular enzymatic activity and an important role in nutrient cycling and decomposition processes. Also, these yeasts serve as crucial indicators of ecosystem health and function and are excellent candidates for biotechnological and industrial applications. Collectively, this study not only expands our knowledge of the diversity and distribution of intertidal yeasts but also highlights their promising potential for biotechnological applications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0157024"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602738","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}