Applied and Environmental Microbiology最新文献

{"title":"An experimental test of the influence of microbial manipulation on sugar kelp (<i>Saccharina latissima</i>) supports the core influences host function hypothesis.","authors":"Jungsoo Park, Evan Kohn, Siobhan Schenk, Katherine M Davis, Jennifer S Clark, Laura Wegener Parfrey","doi":"10.1128/aem.00301-25","DOIUrl":"10.1128/aem.00301-25","url":null,"abstract":"<p><p>Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild <i>Saccharina latissima</i> and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.</p><p><strong>Importance: </strong>Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0030125"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172422","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":"Isolation of a <i>Stenotrophomonas</i> strain and identification of methyltransferase genes conferring the high arsenic volatilizing ability.","authors":"Diksha Singh, Nitish Sharma, Sheetal Agarwal, Sadaf Aiman Khan, Veena Jain, Sukhveer Singh, Somendu Roy, Kusum Yadav, Sudhir Pratap Singh, Vikas Srivastava","doi":"10.1128/aem.02467-24","DOIUrl":"10.1128/aem.02467-24","url":null,"abstract":"<p><p>Microbial arsenic (As) volatilization plays a significant role in the global As biogeochemical cycle and presents a promising approach for bioremediation. In this study, an autotrophic strain of <i>Stenotrophomonas maltophilia</i> was isolated from sewage water containing 75 ppb of arsenic, exhibiting a high arsenic metabolism and volatilization rate. This strain tolerated arsenic concentrations ranging from 10 to 500 ppm. Volatilization tests were conducted at an environmental median of 200 ppb (0.2 ppm) As. The strain eliminated 50% of the total arsenic within 48 h, and 0.1 ppm (101 ppb) of arsenic was reported to be trapped in the headspace of the culture tube, confirming its volatilization. After genome isolation, sequencing, and assembly, the existence of the As metabolizing operon (<i>ars</i>RABC), as well as other As-resistance conferring genes (<i>ars</i>M, <i>ars</i>I, <i>aio</i>A, <i>aox</i>B, and <i>arx</i>A), was identified using different annotation methodologies. The genes conferring resistance against different heavy metals and multiple drugs used as antimicrobials were also identified in the genome assembly of the isolate. Based on the gene expression measured using real-time polymerase chain reaction, complete gene sequences of four <i>ars</i>M genes were mined, cloned, and expressed in <i>Escherichia coli</i> BL21(DE3) cells. The cells harboring recombinant plasmid of each construct could volatilize As up to 86 ppb after 48 h incubation in arsenic-enriched media. The isolated strain of <i>Stenotrophomonas</i> and its heterologously expressed methyltransferase genes could be a potent tool for permanently removing arsenic from water samples by volatilization.IMPORTANCEArsenic contamination in water, soil, and air poses significant health and environmental risks, as inorganic arsenic compounds are highly toxic and carcinogenic. Microorganisms capable of transforming arsenic into volatile forms play a pivotal role in the biogeochemical cycling of this metalloid, reducing its bioavailability and toxicity in contaminated environments. In this work, a strain of <i>Stenotrophomonas</i> sp. was isolated from the sewage water and tested for its ability to survive in minimal arsenic media. The strain was found to be highly resistant to arsenic and volatilized more than 50% of the arsenic from the growth media. The putative methyltransferase genes from the isolated strain, when heterologously expressed in <i>Escherichia coli</i>, conferred an ability to volatilize arsenic in the recombinant host, too. Therefore, the isolated microorganism offers a natural, eco-friendly alternative to conventional chemical methods, making it an important tool for addressing arsenic biosafety issues in the environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0246724"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186337","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":"Molecular adaptations specific to extreme halophilic archaea could promote high perchlorate tolerance.","authors":"Jorge Díaz-Rullo, José Eduardo González-Pastor","doi":"10.1128/aem.00512-25","DOIUrl":"10.1128/aem.00512-25","url":null,"abstract":"<p><p>Perchlorate is a strong chaotropic agent that causes macromolecule denaturation, DNA damage, and oxidative stress. However, perchlorate deliquescence is thought to promote the formation of liquid salt brines, even at hyper-arid and cold environments, such as the Martian regolith. For that reason, the detection of high levels of perchlorate at different locations on the Martian surface led to hypotheses about the existence of Martian microenvironments compatible with life, especially with those organisms tolerant to hyper-salinity and perchlorate. Extreme halophilic archaea have been proposed as the best candidates to inhabit those environments not only due to their high tolerance to salinity and perchlorate, but also because of their resistance to a wide variety of stress conditions. Since specific perchlorate responses remain largely unknown, in this work, we have analyzed the molecular mechanisms of perchlorate tolerance exhibited by the model extreme halophilic archaeon <i>Haloferax volcanii</i> using a transcriptomic approach. We report that perchlorate produced transcriptional effects opposite to those of salinity, and we propose that the \"salt-in\" strategy could promote high perchlorate tolerance in extreme halophilic archaea due to the intracellular accumulation of KCl, which may shield the chaotropic activity of perchlorate. This natural adaptation would be enhanced by changes in other stress responses like DNA repair, refolding and turnover of damaged proteins, removal of oxidative species, and tRNA modifications, among others. These results may help to understand how life could survive on Mars, now or in the past, and highlight the importance of extreme halophiles in the development of <i>in situ</i> resource utilization systems.IMPORTANCEPerchlorate is a toxic chlorinated compound that promotes the formation of liquid salt brines, even at hyper-arid and cold environments. For the past two decades, different probes have reported high levels of perchlorate salts at multiple locations on the Martian surface, which could facilitate the presence of potentially habitable environments by specific microorganisms capable of tolerating both hyper-salinity and high perchlorate concentrations. Therefore, the significance of this research was to investigate the molecular mechanisms for perchlorate tolerance using the extreme haloarchaeon <i>Haloferax volcanii</i> as a model organism. This analysis leads to the identification of critical genes and pathways involved in perchlorate tolerance and supports that certain molecular adaptations specific to extreme haloarchaea may be responsible for the high levels of perchlorate tolerance exhibited by these microorganisms, serving as a valuable resource for Mars exploration.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0051225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966501","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":"Metabolic engineering of <i>Escherichia coli</i> for high-yield dopamine production via optimized fermentation strategies.","authors":"Xu Li, Yanghao Liu, Ling Ma, Wenjing Jiang, Tangen Shi, Lanxiao Li, Changgeng Li, Zhichao Chen, Xiaoguang Fan, Qingyang Xu","doi":"10.1128/aem.00159-25","DOIUrl":"10.1128/aem.00159-25","url":null,"abstract":"<p><p>Dopamine (DA) is a high-value metabolic product; however, its biosynthesis has multiple limitations due to metabolic regulation and fermentation strategies. This study aimed to construct a high-yield dopamine-producing <i>Escherichia coli</i> strain devoid of plasmids and defects using <i>E. coli</i> W3110 as the chassis strain. We constitutively expressed the <i>DmDdC</i> gene from <i>Drosophila melanogaster</i> in <i>E. coli</i>, which was combined with the <i>hpaBC</i> gene from <i>E. coli</i> BL21 (DE3), successfully constructed a dopamine biosynthesis module, and achieved preliminary dopamine synthesis in <i>E. coli</i>. By optimizing the promoters of the key enzyme genes, we achieved a coordinated balance between the generation and utilization of intermediate metabolites. Subsequently, we used metabolic engineering strategies, such as increasing the carbon flux through the dopamine synthesis pathway, elevating the gene copy number of key enzymes, and constructing an FADH₂-NADH supply module to create a high-yield strain, DA-29. In this study, a two-stage pH fermentation strategy was developed to enhance fermentation. The first stage ensures the normal growth of the strain, whereas the second stage reduces dopamine degradation by maintaining a low pH. Finally, using a combined Fe²⁺ and ascorbic acid feeding strategy, we obtained 22.58 g/L of dopamine in a 5 L bioreactor, demonstrating that the constructed strain DA-29 possesses high dopamine production capacity, providing strong support for the industrial-scale dopamine production.</p><p><strong>Importance: </strong>In this study, we developed a plasmid-free, defect-free <i>Escherichia coli</i> strain with high dopamine production. We further optimized the fermentation process for this strain by applying the dual-stage pH fermentation strategy developed in this research, combined with an Fe²⁺-ascorbic acid co-feeding strategy. This approach significantly increased dopamine yield and addressed the issue of dopamine oxidation during fermentation. The yield reached 22.58 g/L, marking the highest known yield to date and laying a solid foundation for future scale-up production. This research explores the metabolic pathway of dopamine and the efficient fermentation methods for its production, providing a novel fermentation strategy. It offers new insights into microbial production of aromatic amino acid derivatives, advancing research in this field.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0015925"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967261","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":"Strong antimicrobial activity and unique physicochemical characteristics in honey from Australian stingless bees <i>Tetragonula carbonaria</i>, <i>Tetragonula hockingsi</i>, and <i>Austroplebeia australis</i>.","authors":"Kenya E Fernandes, Aviva Levina, Nural N Cokcetin, Dean Haley, Jasmin Li, Peter Brooks, Rosalyn Gloag, Dee A Carter","doi":"10.1128/aem.02523-24","DOIUrl":"10.1128/aem.02523-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Natural products have evolved antimicrobial properties that can be exploited in our search for new ways of treating infectious diseases. This study evaluates the antimicrobial properties and chemical profiles of honey produced by the Australian stingless bee species &lt;i&gt;Tetragonula carbonaria&lt;/i&gt;, &lt;i&gt;Tetragonula hockingsi&lt;/i&gt;, and &lt;i&gt;Austroplebeia australis&lt;/i&gt; against selected human pathogens. Using broth microdilution methods, we found that all tested honey samples had antimicrobial activity. The fungal dermatophyte species &lt;i&gt;Trichophyton interdigitale&lt;/i&gt; displayed the highest susceptibility (average MICs: 4%-9% [wt/wt]), followed by &lt;i&gt;Staphylococcus aureus&lt;/i&gt; (9%-11%), &lt;i&gt;Escherichia coli&lt;/i&gt; (10%-13%), and &lt;i&gt;Cryptococcus neoformans&lt;/i&gt; (24%-34%). &lt;i&gt;T. carbonaria&lt;/i&gt; honey had the highest overall activity, while &lt;i&gt;A. australis&lt;/i&gt; honey was the weakest. After heat treatment at 80°C for 30 min to remove hydrogen peroxide (H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;)-based activity, &lt;i&gt;T. carbonaria&lt;/i&gt; and &lt;i&gt;T. hockingsi&lt;/i&gt; honey retained significant non-peroxide activity against &lt;i&gt;E. coli&lt;/i&gt; (14% and 17%, respectively) and &lt;i&gt;S. aureus&lt;/i&gt; (17% and 18%, respectively), although their efficacy against the fungal pathogens diminished. Chemical analysis revealed distinct differences in H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; production, color intensity, phenolic and antioxidant content, density, and pH among the honey types. The dynamic generation of H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; in stingless bee honey was remarkably prolonged, with some samples producing H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; for more than 6 days. Proteomic analysis identified diverse proteins that may contribute to antimicrobial efficacy. Phenolic extracts had antimicrobial activity, with flavonoids identified as potential contributors. &lt;i&gt;T. carbonaria&lt;/i&gt; honey re-tested after 18 years of storage retained substantial non-peroxide-based activity. Overall, this study highlights the unique properties of stingless bee honeys and their potential as natural antimicrobial agents.IMPORTANCEAntimicrobial resistance poses a critical global health challenge. Various natural products have evolved as a defense against microbial attack and can be exploited as novel therapeutic agents. While honey from the European honey bee (&lt;i&gt;Apis mellifera&lt;/i&gt;) is well studied, the medicinal potential of Australian stingless bee honey remains underexplored. This study demonstrates that honeys produced by the stingless bee species &lt;i&gt;Tetragonula carbonaria&lt;/i&gt;, &lt;i&gt;Tetragonula hockingsi&lt;/i&gt;, and &lt;i&gt;Austroplebeia australis&lt;/i&gt; possess unique antimicrobial properties that persist after heat treatment and following long-term storage and are distinct from the antimicrobial properties of honey bee honey. Diverse bioactive compounds, including phenolics and proteins, were seen, underscoring the complexity of these honeys as antimicrobial agents. These honeys have potential as sustainable, natural solutions for combating drug-resistant infec","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0252324"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109516","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":"Expression of xylanase XynB is synergistically controlled by two two-component systems in <i>Ruminiclostridium cellulolyticum</i>.","authors":"Wenhao Zhang, Zili Qiu, Qiuyun Zhao, Ziyi Liu, Xiaorong Zhang, Houhui Song, Chenggang Xu","doi":"10.1128/aem.00062-25","DOIUrl":"10.1128/aem.00062-25","url":null,"abstract":"<p><p>Xylan, a major component of hemicellulose, is crucially targeted by xylanases for its breakdown. This study focuses on the free xylanase XynB from <i>Ruminiclostridium cellulolyticum</i> to elucidate its expression and regulatory mechanisms. We successfully achieved heterologous expression and purification of recombinant XynB, verifying its enzymatic activity specifically against xylan. The mutation of <i>xynB</i> confirmed its essential role in xylan degradation by <i>R. cellulolyticum</i>. We further explored the transcription of <i>xynB</i> under various carbon sources and uncovered its regulatory mechanisms mediated by two-component systems (TCSs). We found that <i>xynB</i> transcription is activated by the xylan-sensing TCS (XuaDRS) and repressed by the cellobiose-sensing TCS (CuaDRS). This research enriches our understanding of the regulatory mechanisms governing the activity and expression of free xylanases like XynB from <i>R. cellulolyticum</i>, offering potential targets for the genetic engineering and process optimization of cellulolysis.IMPORTANCE<i>Ruminiclostridium cellulolyticum</i>, an anaerobic, mesophilic, and cellulolytic gram-positive bacterium, is a model organism for the microbial degradation of plant cell wall polysaccharides and a promising host for biofuel production from lignocelluloses. The degradation process of lignocellulosic materials is complex due to their intricate structure and interlocking complexity. XynB, a GH11 family xylanase, plays a significant role in the breakdown of xylan, a major constituent of hemicelluloses. Our study reveals the molecular mechanisms that link the specific adaptation of xylan utilization with the general stress response in the regulatory network of <i>R. cellulolyticum</i>, particularly by detailing the synergistic effects of two two-component systems on the transcriptional regulation of <i>xynB</i>. This knowledge is essential for harnessing the full potential of <i>R. cellulolyticum</i> in the production of biofuels from lignocellulosic biomass.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0006225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186335","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>Chlorobaculum tepidum</i> outer membrane vesicles may transport biogenic elemental sulfur.","authors":"Vadesse L Noundou, Amalie Levy, Shannon Modla, Yanbao Yu, Jing Qu, Thomas E Hanson","doi":"10.1128/aem.01019-25","DOIUrl":"10.1128/aem.01019-25","url":null,"abstract":"<p><p>Outer membrane-derived vesicles (OMVs) have been studied in different phyla of gram-negative bacteria, most extensively in the Pseudomonadota, where they have been shown to participate in diverse biological and environmental processes. To date, the production of OMVs has not been reported in the Chlorobiaceae within the phylum Chlorobiota. <i>Chlorobaculum tepidum</i> is the model organism for the Chlorobiaceae that synthesizes and consumes insoluble extracellular sulfur (S(0)) globules by an unknown mechanism. Here, we report evidence implicating outer membrane vesicles in biogenic S(0) globule synthesis. We demonstrate that <i>Cba. tepidum</i> secretes OMVs in the extracellular milieu and that OMV concentration and size vary with growth conditions, particularly sulfide concentration. A core of 31 proteins involved in diverse biological processes such as cell wall biogenesis, inorganic ion transport, and metabolism was found to be shared between OMVs, extracellular S(0) globules, and <i>Cba. tepidum</i>-intact cells. Multiple analytical methods indicated that OMVs contain S(0) and that OMVs and biogenic S(0) globules share protein and polysaccharide signatures, including lipooligosaccharides. Together, these lines of evidence indicate that <i>Cba. tepidum</i>'s OMVs are one component of sulfur transport between cells and extracellular sulfur globules.IMPORTANCEAll living cells must exchange material with their environment while maintaining cellular integrity. This is a particular challenge for materials that are not water-soluble; however, many bacteria utilize insoluble materials for energy conservation and as nutrients for growth. Here, we show that <i>Cba. tepidum</i> makes outer membrane vesicles, and these vesicles are likely involved in the exchange of material with extracellular elemental sulfur globules formed and consumed by <i>Cba. tepidum</i> as part of its energy metabolism based on oxidizing reduced sulfur compounds like hydrogen sulfide. These data expand our basic understanding of <i>Cba. tepidum</i>'s metabolism. As elemental sulfur is an industrial by-product with a limited number of uses, the information here may help enable the use of additional sulfur compounds by <i>Cba. tepidum</i> to drive the synthesis of biomass and/or specialty biochemicals from waste elemental sulfur by this autotrophic bacterium.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0101925"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324325","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 protozoan perspective on climate change and biosafety threats: differences in testate amoebae in lakes in forest-swamp and forest-steppe zones in Western Siberia.","authors":"Olga N Zagumyonnaya, Dmitry G Zagumyonnyi, Elena A Gerasimova, Denis V Tikhonenkov","doi":"10.1128/aem.00330-25","DOIUrl":"10.1128/aem.00330-25","url":null,"abstract":"<p><p>The problem of increasing salinity and mineralization in natural and artificial freshwater bodies with climate warming is very relevant nowadays, as it leads to changes in the species composition of planktonic organisms. Testate amoebae are one of the responsive bioindicators that are sensitive to even minor changes in environmental conditions. In this study, a comparative analysis of the species diversity of planktonic testate amoebae was carried out in a number of lakes in the forest-steppe and forest-swamp natural zones of Western Siberia using microscopy and metabarcoding. One new species, <i>Pseudodifflugia siemensmai</i> sp. nov., was described. The detection frequency and the number of reads of amplicon sequence variants of potentially pathogenic testate amoebae belonging to the genera <i>Rhogostoma</i> and <i>Fisculla</i> were higher in forest-steppe lakes. Universal eukaryotic primers for the 18S rRNA gene are well suited for identifying testate amoebae from the supergroup Cercozoa but are practically not applicable for identifying Amoebozoa testaceans. The plankton of the lakes with the highest mineralization and salinity was characterized by the most specific species composition. These results should be taken into account when predicting changes in aquatic communities with further climate warming, which may also be associated with an increase in the occurrence of pathogenic testaceans that pose biosafety threats.IMPORTANCEMicroscopic and metabarcoding analyses reveal important differences in testate amoebae communities in lakes in two natural and climatic zones of Western Siberia that should be taken into account when predicting changes in aquatic communities with further climate warming, which may also be associated with an increase in the occurrence of pathogenic testaceans that pose biosafety threats.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0033025"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175505/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952833","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":"Spatiotemporal patterns of soil myxomycetes in subtropical managed forests and their potential interactions with bacteria.","authors":"Wen-Long Song, Di Lin, Xia Chen, Qun Dai, Gu Rao, Ya-Jing Chen, Shuang-Lin Chen","doi":"10.1128/aem.00479-25","DOIUrl":"10.1128/aem.00479-25","url":null,"abstract":"<p><p>Soil myxomycetes are crucial soil protists with important ecological functions. Yet, our understanding of their diversity patterns in managed forests and the interactions with their food is far behind other taxa. This study investigates the spatiotemporal patterns of soil myxomycetes in four northern subtropical managed forest types across seasons and aims to identify assembly processes, main predictors of myxomycete communities, and the potential interactions between myxomycetes and bacteria. Results showed that no significant difference in α diversity of myxomycete communities among forest types was observed, but a significant difference was observed in community structures. Significant differences were observed in α diversity and community structures of myxomycetes among seasons. Deterministic processes in each forest type and season dominated myxomycete community assemblies. Soil physicochemical properties and bacterial communities have a significant direct impact on the myxomycete community, while forest types, seasons, and enzyme activities have an indirect effect. There is a significant synergistic covariation between the soil myxomycete community and bacterial community. The genera of the phyla Acidobacteriota, Actinobacteriota, and Bacteroidota have a strong correlation with the richness of myxomycete genera. Overall, this study provides new insight into the diversity of soil myxomycetes and their influence by bacteria, crucial for myxomycetes ecology.IMPORTANCESoil myxomycetes are an important component of soil protists. Our study revealed for the first time the community structure of soil myxomycetes in managed forests of the northern subtropical regions and systematically investigated the seasonal variation patterns of soil myxomycetes. Meanwhile, we further investigated the potential interactions between soil myxomycetes and bacteria. This study will greatly enhance our understanding of the ecology of soil myxomycetes and their biological roles.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0047925"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957990","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":"Deciphering the ammonia transformation mechanism of a novel marine multi-stress-tolerant yeast, <i>Pichia kudriavzevii</i> HJ2, as revealed by integrated omics analysis.","authors":"Kunmei Huang, Huashan Bai, Can Meng, Muhammad Kashif, Zhiling Wei, Zaihang Tang, Shu He, Shanguang Wu, Sheng He, Chengjian Jiang","doi":"10.1128/aem.02211-24","DOIUrl":"10.1128/aem.02211-24","url":null,"abstract":"<p><p>Ammonia nitrogen posed a significant threat to aquatic animals in aquaculture environments, and the substantial potential of microorganisms in removing ammonia nitrogen had garnered considerable attention. This study identified a marine yeast, <i>Pichia kudriavzevii</i> HJ2, which effectively removed ammonia nitrogen. By combining transcriptomics and metabolomics, the ammonia nitrogen transformation mechanism of HJ2 was elucidated. HJ2 achieved 100% ammonia nitrogen removal efficiency within 1 day of fermentation at 35°C with 300 mg/L ammonia nitrogen and 73.56% removal efficiency within 36 h with 600 mg/L ammonia nitrogen. Transcriptomics revealed that exposure to 600 mg/L ammonia nitrogen resulted in 541 up-regulated genes and 567 down-regulated genes in the HJ2 strain. Differentially expressed genes (DEGs) were primarily involved in the tricarboxylic acid (TCA) cycle and amino acid metabolism. Metabolomics revealed that HJ2 facilitated the production of 383 up-regulated metabolites and suppressed 137 down-regulated metabolites when exposed to 600 mg/L ammonia nitrogen. Integrating transcriptomics and metabolomics analyses showed that HJ2 removed ammonia nitrogen by sensing its presence in the extracellular environment, activating the TCA cycle, enhancing amino acid metabolism and nucleotide metabolism, and promoting its robust growth and reproduction. Amino acid metabolism played an important role in the ammonia transformation mechanism of HJ2. The result was confirmed by the increased activity of glutamate dehydrogenase (GDH) and aspartate aminotransferase (GOT). Up-regulated nitrogen metabolites such as L-glutamate, L-aspartic acid, spermidine, and trigonelline were produced. The results of enzyme activity tests, construction of overexpressing strains, and adding exogenous amino acid experiments demonstrated that HJ2 could utilize GDH and GOT ammonia assimilation pathways.<b>IMPORTANCE</b>Ammonia nitrogen removal ability was a universal characteristic among the ammonia-oxidizing bacteria or archaea. Recently, yeast strains from the genus <i>Pichia</i> were found to have ammonia nitrogen removal ability. However, the mechanism of ammonia nitrogen removal in <i>Pichia</i> had not been reported. In the study, the ammonia nitrogen removal efficiency of <i>Pichia kudriavzevii</i> HJ2 was identified, and the mechanisms by which HJ2 transformed ammonia nitrogen into non-toxic organic nitrogen were elucidated, offering potential solutions to pollution challenges in aquaculture and helping minimize resource waste. The study offered new insights into the transformation mechanism of microbial ammonia nitrogen removal and its environmentally friendly application.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0221124"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960619","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}