Applied and Environmental Microbiology最新文献

{"title":"Exploring auxotrophy and engineering vitamin B₆ prototrophy in the acetogen <i>Clostridium</i> sp. AWRP.","authors":"Soo Jae Kwon, Joungmin Lee, Hyun Sook Lee","doi":"10.1128/aem.01160-24","DOIUrl":"10.1128/aem.01160-24","url":null,"abstract":"<p><p>Gas fermentation using acetogenic bacteria requires a chemically defined minimal medium to be established. This approach not only helps in creating a cost-effective medium but also allows for a thorough exploration of their metabolic potential. In this study, the auxotrophy of the acetogen <i>Clostridium</i> sp. AWRP was investigated through genomic analysis and growth performance in formulated media. It was found that the strain needs pantothenate and biotin and that substituting vitamin B₆ from pyridoxine to pyridoxamine or pyridoxal-5'-phosphate is crucial for growth. The determined chemically defined minimal medium supported both heterotrophic (using fructose as a substrate) and autotrophic (using syngas as a substrate) growth of the AWRP strain. To overcome the vitamin B₆ auxotrophy, the <i>pdxST</i> genes responsible for vitamin B₆ biosynthesis were introduced into the AWRP strain using plasmid-based gene expression system and CRISPR/Cas12a genome-editing technology. As a result, the genetically engineered strains were able to grow successfully without vitamin B₆. This chemically defined minimal medium will enhance the fermentation performance of AWRP.</p><p><strong>Importance: </strong>The identification of auxotrophy in <i>Clostridium</i> sp. AWRP underpins subsequent investigations into its physiology and metabolism. Additionally, the development of a chemically defined minimal medium specific to this acetogenic bacterium will enable reproducible industrial processes. This innovation is particularly significant for the bioconversion of carbon monoxide and/or dioxide into commercially valuable chemicals through the process of gas fermentation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0116024"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602788","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":"Identifying potential introduced and natural sources of pollution in Delaware watersheds.","authors":"Malique Bowen, Christopher R Main, Ibrahim F Farag, Jennifer F Biddle","doi":"10.1128/aem.01958-24","DOIUrl":"10.1128/aem.01958-24","url":null,"abstract":"<p><p>Managing water quality with microbial impairment caused by <i>Enterococcus</i> poses unique challenges regarding the determination of fecal host origin. Most water monitoring is performed based on <i>Enterococcus</i> counts that neither detect the location of the introduction of pollution nor identify the type of contaminating <i>Enterococcus</i>. The use of sequenced-based microbial source tracking could allow for identification of fecal origin and potential remediation of pollution. The state of Delaware has numerous waterways with high microbial impairment from unknown sources, so we used sequence-based microbial source tracking to investigate potential microbial pollution in three watersheds with significant variation in land use and population density. In this study, we use a 16S rRNA sequence reference library of microbial communities from relevant fecal sources (wild animal, domestic animal, sediment, and septic/wastewater) to determine the most likely sources of microbial impairment in three Delaware watersheds. This study assigned sources of microbial contamination to mostly human-related sources (septic and wastewater) or unknown sources indicating that waste infrastructure may have a larger influence on microbial community structure in Delaware watersheds than previously considered. Our results suggest that long-term source tracking is valuable for ruling out native or domesticated animals as contributors to water pollution.IMPORTANCETraditional microbial pollution monitoring utilizes specific fecal indicator bacteria that need to grow in the laboratory for detection. Here, we show the use of sequence information from whole microbial communities and an expanded reference library in microbial source tracking. Expanding the host detection range by including the whole microbial community may allow for a wider range of potential fecal origin identification even when specific fecal indicators are absent or in low concentration. We show that many Delaware waterways bear the signature of human influence compared to natural sources. In addition, the robust reference library built in this study can be used to conduct source tracking studies in the mid-Atlantic USA.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0195824"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613488","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":"Inside the Atacama Desert: uncovering the living microbiome of an extreme environment.","authors":"Alexander Bartholomäus, Steffi Genderjahn, Kai Mangelsdorf, Beate Schneider, Pedro Zamorano, Samuel P Kounaves, Dirk Schulze-Makuch, Dirk Wagner","doi":"10.1128/aem.01443-24","DOIUrl":"10.1128/aem.01443-24","url":null,"abstract":"<p><p>The Atacama Desert in Chile is one of the driest and most inhospitable places on Earth. To analyze the diversity and distribution of microbial communities in such an environment, one of the most important and challenging steps is DNA extraction. Using commercial environmental DNA extraction protocols, a mixture of living, dormant, and dead cells of microorganisms is extracted, but separation of the different DNA pools is almost impossible. To overcome this problem, we applied a novel method on soils across a west-east moisture transect in the Atacama Desert to distinguish between extracellular DNA (eDNA) and intracellular DNA (iDNA) at the cell extraction level. Here, we show that a large number of living and potentially active microorganisms, such as <i>Acidimicrobiia</i>, <i>Geodermatophilaceae</i>, <i>Frankiales</i>, and <i>Burkholderiaceae,</i> occur in the hyperarid areas. We observed viable microorganisms involved as pioneers in initial soil formation processes, such as carbon and nitrogen fixation, as well as mineral-weathering processes. In response to various environmental stressors, microbes coexist as generalists or specialists in the desert soil environment. Our results show that specialists compete in a limited range of niches, while generalists tolerate a wider range of environmental conditions. Use of the DNA separation approach can provide new insights into different roles within viable microbial communities, especially in low-biomass environments where RNA-based analyses often fail.IMPORTANCEThe novel e- and iDNA separation technique offers insights into the living community at the cell extraction level in the hyperarid Atacama Desert. This approach provides a new framework for analyzing the composition and structure of the potentially active part of the microbial communities as well as their specialization, ecological network and community assembly process. Our findings underscore the significance of utilizing alternative genomic techniques in low-biomass environments where traditional DNA- and RNA-based analyses may not be feasible. The results demonstrate the viability of the proposed study framework and show that specialized microorganisms are important in initial soil formation processes, including microbial-driven mineral weathering, as well as the fixation of carbon and nitrogen.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0144324"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613489","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":"Growth substrate limitation enhances anaerobic arsenic methylation by <i>Paraclostridium bifermentans</i> strain EML.","authors":"Jiangtao Qiao, Hugo Sallet, Karin Lederballe Meibom, Rizlan Bernier-Latmani","doi":"10.1128/aem.00961-24","DOIUrl":"10.1128/aem.00961-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Microbial arsenic methylation is established as a detoxification process under aerobic conditions (converting arsenite to monomethylated arsenate) but is proposed to be a microbial warfare strategy under anoxic conditions due to the toxicity of its main product, monomethylarsonous acid (MMAs(III)). Here we leveraged a paddy soil-derived anaerobic arsenic methylator, &lt;i&gt;Paraclostridium bifermentans&lt;/i&gt; strain EML, to gain insights into this process. Strain EML was inoculated into a series of media involving systematic dilutions of Reinforced Clostridial Broth (RCB) with 25 µM arsenite to assess the impact of growth substrate concentration on arsenic methylation. Growth curves evidenced the sensitivity of strain EML to arsenite, and arsenic speciation analysis revealed the production of MMAs(III). Concentrations of MMAs(III) and arsenic methylation gene (&lt;i&gt;arsM&lt;/i&gt;) transcription were found to be positively correlated with RCB dilution, suggesting that substrate limitation enhances &lt;i&gt;arsM&lt;/i&gt; gene expression and associated anaerobic arsenic methylation. We propose that growth substrate competition among microorganisms may also contribute to an increase in anaerobic arsenic methylation. This hypothesis was further evaluated in an anaerobic co-culture system involving strain EML and either wild-type &lt;i&gt;Escherichia coli&lt;/i&gt; K-12 MG1655 (WT) or &lt;i&gt;E. coli&lt;/i&gt; expressing the MMAs(III)-resistance gene (&lt;i&gt;arsP&lt;/i&gt;) (ArsP &lt;i&gt;E. coli&lt;/i&gt;). We observed increased MMAs(III) production in the presence of &lt;i&gt;E. coli&lt;/i&gt; than its absence and growth inhibition of WT &lt;i&gt;E. coli&lt;/i&gt; to a greater extent than ArsP &lt;i&gt;E. coli&lt;/i&gt;, presumably due to the MMAs(III) produced by strain EML. Collectively, our findings suggest an ecological role for anaerobic arsenic methylation, highlighting the significance of microbe-microbe competition and interaction in this process.IMPORTANCEMicrobial arsenic methylation is highly active in rice paddy fields under flooded conditions, leading to increased accumulation of methylated arsenic in rice grains. In contrast to the known detoxification process for aerobic arsenic methylation, the ecological role of anaerobic arsenic methylation remains elusive and is proposed to be an antibiotic-producing process involved in microbial warfare. In this study, we interrogated a rice paddy soil-derived anaerobic arsenic-methylating bacterium, &lt;i&gt;Paraclostridium bifermentans&lt;/i&gt; strain EML, to explore the effect of growth substrate limitation on arsenic methylation in the context of the microbial warfare hypothesis. We provide direct evidence for the role of growth substrate competition in anaerobic arsenic methylation &lt;i&gt;via&lt;/i&gt; anaerobic prey-predator co-culture experiments. Moreover, we demonstrate a feedback loop, in which a bacterium resistant to MMAs(III) enhances its production, presumably through enhanced expression of &lt;i&gt;arsM&lt;/i&gt; resulting from substrate limitation. Our work uncovers the complex interactions between an anaerobic ar","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0096124"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602797","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":"Adaptive immunity in <i>Mus musculus</i> influences the acquisition and abundance of <i>Borrelia burgdorferi</i> in <i>Ixodes scapularis</i> ticks.","authors":"Cody W Koloski, Hesham Adam, Georgia Hurry, Alexandra Foley-Eby, Christopher B Zinck, Haomiao Wei, Satyender Hansra, Jenny Wachter, Maarten J Voordouw","doi":"10.1128/aem.01299-24","DOIUrl":"10.1128/aem.01299-24","url":null,"abstract":"<p><p>The Lyme disease spirochete <i>Borrelia burgdorferi</i> cycles between immature black-legged ticks (<i>Ixodes scapularis</i>) and vertebrate reservoir hosts, such as rodents. Larval ticks acquire spirochetes from infected hosts, and the resultant nymphs transmit the spirochetes to naïve hosts. This study investigated the impact of immunocompetence and host tissue spirochete load on host-to-tick transmission (HTT) of <i>B. burgdorferi</i> and the spirochete load inside immature <i>I. scapularis</i> ticks. Wild-type (WT) C57BL/6J mice and mice with severe combined immunodeficiency (SCID) were experimentally infected with <i>B. burgdorferi</i>. To measure HTT, WT and SCID mice were repeatedly infested with <i>I. scapularis</i> larvae, and ticks were sacrificed at three different developmental stages: engorged larvae, 1-month-old, and 12-month-old nymphs. The spirochete loads in immature ticks and mouse tissues were estimated using qPCR. In WT mice, HTT decreased from 90% to 65% over the course of the infection, whereas in the SCID mice, HTT was always 100%. Larvae that fed on SCID mice acquired a much larger dose of spirochetes compared to larvae that fed on WT mice. This difference in spirochete load persisted over tick development where nymphs that fed as larvae on SCID mice had significantly higher spirochete loads compared to their WT counterparts. HTT and the tick spirochete loads were strongly correlated with the mouse tissue spirochete loads. Our study shows that the host immune system (e.g., the presence of antibodies) influences HTT of <i>B. burgdorferi</i> and the spirochete load in immature <i>I. scapularis</i> ticks.IMPORTANCEThe tick-borne spirochete <i>Borrelia burgdorferi</i> causes Lyme disease in humans. This pathogen is maintained in nature by cycles involving black-legged ticks and wildlife hosts. The present study investigated the host factors that influence the transmission of <i>B. burgdorferi</i> from infected hosts to feeding ticks. We infected immunocompetent mice and immunocompromised mice (that cannot develop antibodies) with <i>B. burgdorferi</i> and repeatedly infested these mice with ticks. We determined the percentage of infected ticks and their spirochete loads. This percentage was 100% for immunocompromised mice but decreased from 90% to 65% over time (8 weeks) for immunocompetent mice. The tick spirochete load was much higher in ticks fed on immunocompromised mice compared to ticks fed on immunocompetent mice. In summary, the host immune system influences the transmission of <i>B. burgdorferi</i> from infected hosts to ticks and the spirochete loads in those ticks, which, in turn, determines the risk of Lyme disease for people.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0129924"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581930","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":"Design of ancestral mammalian alkaline phosphatase bearing high stability and productivity.","authors":"Yusuke Hagiwara, Yasuhiro Mihara, Tomoharu Motoyama, Sohei Ito, Shogo Nakano","doi":"10.1128/aem.01831-24","DOIUrl":"10.1128/aem.01831-24","url":null,"abstract":"<p><p>Mammalian alkaline phosphatase (AP) is widely used in diagnostics and molecular biology but its widespread use is impaired because it is difficult to express in <i>Escherichia coli</i> and has low thermostability. To overcome these challenges, we employed sequence-based protein redesign methods, specifically full consensus design (FCD) and ancestral sequence reconstruction (ASR), to create APs with enhanced properties. Biochemical analyses revealed that these newly designed APs exhibited improved levels of expression in their active form and increased thermostability compared to bovine intestinal AP isozyme II (bIAPII), without impeding enzymatic activity. Notably, the activity in culture broth of the designed APs was an order of magnitude higher than that of bIAPII, and their thermal stability increased by 13°C-17°C (measured as <i>T</i>₅₀). We also assessed 28 single-point mutants of bIAPII to identify regions influencing thermostability and expression level; these mutations were common in the engineered APs but not in bIAPII. Specific mutations, such as T413E and G402S, enhanced thermostability, whereas increasing the expression level required multiple mutations. This suggests that a synergistic effect is required to enhance the expression level. Mutations enhancing thermostability were located in the crown domain, while those improving expression were close to the dimer interface, indicating distinct mechanisms underpinning these enhancements.</p><p><strong>Importance: </strong>Sequence-based protein redesign methods, such as full consensus design (FCD) and ancestral sequence reconstruction (ASR), have the potential to construct new enzymes utilizing protein sequence data registered in a rapidly expanding sequence database. The high thermostability of these enzymes would expand their application in diagnostics and molecular biology. These enzymes have also demonstrated a high level of active expression by <i>Escherichia coli</i>. These characteristics make these APs attractive candidates for industrial application. In addition, different amino acid residues are primarily responsible for thermal stability and active expression, suggesting important implications for strategies for designing enzymes by FCD and ASR.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0183124"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638568","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":"Cu- and Ag-mediated inactivation of <i>L. pneumophila</i> in bench- and pilot-scale drinking water systems.","authors":"Chelsea L Hintz, Brian Morris, Sue Witt, Nicole Sojda, Helen Y Buse","doi":"10.1128/aem.01073-24","DOIUrl":"https://doi.org/10.1128/aem.01073-24","url":null,"abstract":"<p><p><i>Legionella pneumophila</i> (Lp) is an opportunistic drinking water pathogen that can cause infections through the inhalation of Lp-containing aerosols and can occur in premise plumbing systems. In this work, the use of copper (Cu) and silver (Ag) ions was evaluated at the bench and pilot scale to determine (i) the effective independent concentrations of copper and silver that are efficacious in inactivating Lp, (ii) the impact of various water quality parameters on the efficaciousness of copper and silver ions, and (iii) the effectiveness and practicality of using dissociation to produce ions at the pilot scale. At the bench scale, it was determined that 0.3 ppm and 0.03 ppm of Cu and Ag, respectively, achieved 6-log inactivation of Lp in 5 h in experimental buffer. But, in dechlorinated filter-sterilized tap water, the same concentrations of Cu were not effective, and the effectiveness of Ag was slower. pH and dissolved inorganic carbon content were found to be important parameters in determining if the use of Cu and Ag ions is appropriate. At the pilot scale, dissociation was successfully used to produce Cu and Ag ions. Target levels of ions were met at the pilot scale but were difficult to achieve, and no impact was observed on Lp concentrations. Results from this study suggest that there are important caveats in the application of this technology when applied in a drinking water matrix and prior understanding of a system's water chemistry may be important to determine the effectiveness of Lp disinfection using Cu and Ag.IMPORTANCEThis work sheds light on the effectiveness of using Cu and Ag ions to inactivate (or kill) <i>Legionella pneumophila. Legionella</i> is an opportunistic drinking water pathogen of public health concern. This work demonstrates that there are important caveats in the application of using Cu and Ag ions to inactivate <i>Legionella pneumophila</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0107324"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845653","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":"Investigation on L-rhamnose metabolism of <i>Loigolactobacillus coryniformis</i> subsp. <i>coryniformis</i> DSM 20001 and its propionate-containing fermentates.","authors":"Mensure Elvan Gezer, Kathrine Gravlund Fønss, Maria Florencia Bambace, Angeliki Marietou, Sanne Sandberg Overby, Ulrik Sundekilde, Clarissa Schwab","doi":"10.1128/aem.01613-24","DOIUrl":"https://doi.org/10.1128/aem.01613-24","url":null,"abstract":"<p><p>Propionate is an important short-chain carboxylic acid (SCCA) that serves as an effective antimicrobial agent for food preservation. Previous research has highlighted that few <i>Lactobacillaceae</i> can synthesize propionate by metabolizing deoxyhexoses via the fermentation intermediate 1,2-propanediol (1,2-PD). In this study, we investigated propionate production by <i>Loigolactobacillus coryniformis</i> subsp. <i>coryniformis</i> DSM 20001 while utilizing L-rhamnose as the primary carbon source. We cultivated <i>L. coryniformis</i> in small-scale anaerobic bioreactors at 30°C and pH 6.5 for 72 h and monitored the expression of key genes associated with deoxyhexose metabolism using quantitative PCR. In addition, we assessed the contribution of individual SCCA to the antimicrobial activity of the fermentate against common foodborne pathogens, including <i>Escherichia coli</i>, <i>Salmonella enterica</i>, <i>Klebsiella oxytoca</i>, <i>Staphylococcus aureus</i>, <i>Candida albicans</i>, <i>Aspergillus niger</i>, <i>Penicillium roqueforti</i>, and <i>Penicillium purpurogenum</i> using broth dilution assays. During cultivation, we observed the production of up to 16 mM propionate, alongside other metabolites such as lactate (26 mM), formate (2 mM), and acetate (4 mM), derived from 32 mM L-rhamnose. Genes related to L-rhamnose utilization were upregulated within the initial 48 h, while genes involved in 1,2-PD utilization remained highly transcribed throughout fermentation. Comparing the antimicrobial efficacy of the fermentates to synthetic SCCA mixtures, bacterial indicator strains were more sensitive than molds and yeast. Propionate was the primary SCCA responsible for inhibitory activity; inhibition was reduced if indicator strains were able to use lactate.IMPORTANCEWorldwide, approximately 30% of food produced is lost. Despite the application of complementary treatment methods, microbial food spoilage can occur along the entire value chain. The rising concern about food waste has led to increasing interest in natural preservation approaches. <i>Lactobacillaceae</i> fermentative systems produce a variety of short-chain carboxylic acid (SCCA) with antimicrobial potential, and we present here fundamental insight into the only recently discovered deoxyhexose metabolism of <i>Loigolactobacillus coryniformis</i> producing the antimicrobial SCCA propionate. We developed a bioprocess to produce propionate from L-rhamnose under controlled conditions as a first step toward the exploitation of L-rhamnose metabolism in the production of antimicrobial fermentates for use in the food industry, potentially replacing chemical alternatives. Our investigations highlight the major contribution of propionate in antimicrobial activity but also indicate the issue of co-occurring fermentable metabolites, which can affect the efficiency of fermentates.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0161324"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845654","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":"Acidification-based mineral weathering mechanism involves a glucose/methanol/choline oxidoreductase in <i>Caballeronia mineralivorans</i> PML1(12).","authors":"Cintia Blanco Nouche, Laura Picard, Carine Cochet, Cedric Paris, Philippe Oger, Marie-Pierre Turpault, Stéphane Uroz","doi":"10.1128/aem.01221-24","DOIUrl":"10.1128/aem.01221-24","url":null,"abstract":"<p><p>While mineral weathering (MWe) plays a key role in plant growth promotion and soil fertility, the molecular mechanisms and the genes used by bacteria to weather minerals remain poorly characterized. Acidification-based dissolution is considered the primary mechanism used by bacteria. This mechanism is historically associated with the conversion of glucose to protons and gluconic acid through the action of particular glucose dehydrogenases (GDH) dependent on the pyrroquinoline quinone (PQQ) cofactor. Recently, bacteria lacking the GDH-PQQ system have been shown to perform the same enzymatic conversion with a glucose/methanol/choline (GMC) FAD-dependent oxidoreductase. Determining whether this particular enzyme is specific or widespread is especially important in terms of ecology and evolution. Genome analysis of the effective MWe strain <i>Caballeronia mineralivorans</i> PML1(12) revealed the presence of both systems (<i>i.e</i>., GDH-PQQ and several GMC oxidoreductases). The combination of mutagenesis, functional assays, and geochemical analyses demonstrated the key role of one of these GMC oxidoreductases in the mineral weathering ability of strain PML1(12) and the importance of the carbon source metabolized. Mass spectrometry confirmed the conversion of glucose to gluconic acid. Phylogenetic analyses highlighted a good relatedness of this new GMC oxidoreductase with GMC oxidoreductases presenting a GDH activity in <i>Burkholderia cepacia</i> and <i>Collimonas pratensis</i> and conferring its mineral weathering ability to the last one. Together, our analyses expand the number of bacteria capable of weathering minerals using GMC oxidoreductases, showing that such enzymes are not restricted to <i>Collimonas</i>.</p><p><strong>Importance: </strong>This work deciphers the molecular and genetic bases used by strain PML1(12) of <i>Caballeronia mineralivorans</i> to weather minerals. Through bioinformatics analyses, we identified a total of four GMC-FAD oxidoreductases in the genome of strain PML1(12) and a putative PQQ-dependent glucose dehydrogenase. Through a combination of physiological and geochemical analyses, we revealed that one of them (i.e., GMC3) was the enzyme responsible for the acidification-based mineral weathering mechanism used by strain PML1(12). To date, a single representative of this enzyme family has been identified in the effective mineral-weathering bacterial strain <i>Collimonas pratensis</i> PMB3(1). Phylogenetic analyses revealed that this new system appeared conserved in the <i>Collimonas</i> genus. The new findings presented in this work demonstrate that GMC oxidoreductases can have an active role in other effective MWe bacteria outside of collimonads and that <i>Caballeronia</i> are capable of weathering minerals using this type of enzyme. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, evolutionary biology, and soil sciences.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0122124"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581929","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":"Potential role of alginate in marine bacteria-yeast interactions.","authors":"Shota Nakata, Ryuichi Takase, Shigeyuki Kawai, Kohei Ogura, Wataru Hashimoto","doi":"10.1128/aem.01683-24","DOIUrl":"10.1128/aem.01683-24","url":null,"abstract":"<p><p>The ability of microorganisms to decompose brown algae has attracted attention. This study aims to clarify the characteristics of marine microbial communities in which prokaryotic and eukaryotic microorganisms interact via the metabolism of brown algae carbohydrates. Amplicon-based microbiome analysis revealed the predominance of the genera <i>Marinomonas</i> and <i>Vibrio</i> in seawater and seaweed samples mixed with alginate and mannitol, which are the primary carbohydrates in brown algae. Three <i>Vibrio</i> species and <i>Candida intermedia</i> were isolated via alginate enrichment culture. Although <i>C. intermedia</i> did not utilize alginate as a nutrient source, the yeast grew in the spent alginate medium in which <i>Vibrio algivorus</i> had been cultured. Coculture with <i>C. intermedia</i> and the <i>Vibrio</i> isolates, especially <i>V. algivorus</i>, also enhanced the growth of the yeast on alginate. These results suggested that <i>C. intermedia</i> grew because of the supply of nutrients via alginate metabolism by <i>Vibrio</i> species. In the coculture medium, the amount of phosphatidylserine increased in the early phase but decreased with the growth of <i>C. intermedia</i>, indicating that phosphatidylserine secreted by <i>Vibrio</i> is involved in the putative mutualistic interaction. We examined whether such interaction is applicable to the production of useful substances and succeeded in lipid production by oleaginous marine yeast <i>Yarrowia lipolytica</i> through coculture with <i>V. algivorus</i>. Our study suggested the potential of mutualistic interaction via degradation of alginate by marine <i>Vibrio</i> for production of industrially useful substances in yeast cells.IMPORTANCEIn this study, we analyzed the microbiome of seawater and seaweed in the presence of brown algae carbohydrates and reconstructed the putative mutualistic relationship of marine <i>Vibrio</i> and <i>Candida intermedia</i> mediated by metabolism of brown algae in the ocean.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0168324"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602803","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}