FEMS microbiology ecology最新文献_第4页

Environmental factors and potential probiotic lineages shape the active prokaryotic communities associated with healthy Penaeus stylirostris larvae and their rearing water. 环境因素和潜在的益生菌系形成了与健康的青花鱼幼体及其饲养水相关的活性原核生物群落。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae156

Carolane Giraud, Nelly Wabete, Célia Lemeu, Nazha Selmaoui-Folcher, Dominique Pham, Viviane Boulo, Nolwenn Callac

{"title":"Environmental factors and potential probiotic lineages shape the active prokaryotic communities associated with healthy Penaeus stylirostris larvae and their rearing water.","authors":"Carolane Giraud, Nelly Wabete, Célia Lemeu, Nazha Selmaoui-Folcher, Dominique Pham, Viviane Boulo, Nolwenn Callac","doi":"10.1093/femsec/fiae156","DOIUrl":"10.1093/femsec/fiae156","url":null,"abstract":"Microbial dysbiosis is hypothesized to cause larval mass mortalities in New Caledonian shrimp hatcheries. In order to confirm this hypothesis and allow further microbial comparisons, we studied the active prokaryotic communities of healthy Penaeus stylirostris larvae and their surrounding environment during the first 10 days of larval rearing. Using daily nutrient concentration quantitative analyses and spectrophotometric organic matter analyses, we highlighted a global eutrophication of the rearing environment. We also evidenced drastic bacterial community modifications in the water and the larvae samples using Illumina HiSeq sequencing of the V4 region of the 16S rRNA gene. We confirmed that Alteromonadales, Rhodobacterales, Flavobacteriales, Oceanospirillales, and Vibrionales members formed the core bacteriota of shrimp larvae. We also identified, in the water and the larvae samples, several potential probiotic bacterial strains that could lead to rethink probiotic use in aquaculture (AEGEAN 169 marine group, OM27 clade, Ruegeria, Leisingera, Pseudoalteromonas, and Roseobacter). Finally, investigating the existing correlations between the environmental factors and the major bacterial taxa of the water and the larvae samples, we suggested that deterministic and stochastic processes were involved in the assembly of prokaryotic communities during the larval rearing of P. stylirostris. Overall, our results showed that drastic changes mostly occurred during the zoea stages suggesting that this larval phase is crucial during shrimp larval development.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microfluidics for studying the deep underground biosphere: from applications to fundamentals. 研究地下深层生物圈的微流体技术：从应用到基础。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae151

Sandy Morais, Emeline Vidal, Anaïs Cario, Samuel Marre, Anthony Ranchou-Peyruse

{"title":"Microfluidics for studying the deep underground biosphere: from applications to fundamentals.","authors":"Sandy Morais, Emeline Vidal, Anaïs Cario, Samuel Marre, Anthony Ranchou-Peyruse","doi":"10.1093/femsec/fiae151","DOIUrl":"10.1093/femsec/fiae151","url":null,"abstract":"In this review, selected examples are presented to demonstrate how microfluidic approaches can be utilized for investigating microbial life from deep geological environments, both from practical and fundamental perspectives. Beginning with the definition of the deep underground biosphere and the conventional experimental techniques employed for these studies, the use of microfluidic systems for accessing critical parameters of deep life in geological environments at the microscale is subsequently addressed (high pressure, high temperature, low volume). Microfluidics can simulate a range of environmental conditions on a chip, enabling rapid and comprehensive studies of microbial behavior and interactions in subsurface ecosystems, such as simulations of porous systems, interactions among microbes/microbes/minerals, and gradient cultivation. Transparent microreactors allow real-time, noninvasive analysis of microbial activities (microscopy, Raman spectroscopy, FTIR microspectroscopy, etc.), providing detailed insights into biogeochemical processes and facilitating pore-scale analysis. Finally, the current challenges and opportunities to expand the use of microfluidic methodologies for studying and monitoring the deep biosphere in real time under deep underground conditions are discussed.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbiome analysis of monarch butterflies reveals effects of development and diet. 帝王斑蝶的微生物组分析揭示了发育和饮食的影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae143

Ehsan Sanaei, Joselyne Chavez, Erica V Harris, Tiffanie Y Alcaide, Keisha Baffour-Addo, Mahal J Bugay, Kandis L Adams, Anna Zelaya, Jacobus C de Roode, Nicole M Gerardo

{"title":"Microbiome analysis of monarch butterflies reveals effects of development and diet.","authors":"Ehsan Sanaei, Joselyne Chavez, Erica V Harris, Tiffanie Y Alcaide, Keisha Baffour-Addo, Mahal J Bugay, Kandis L Adams, Anna Zelaya, Jacobus C de Roode, Nicole M Gerardo","doi":"10.1093/femsec/fiae143","DOIUrl":"10.1093/femsec/fiae143","url":null,"abstract":"Diet profoundly influences the composition of an animal's microbiome, especially in holometabolous insects, offering a valuable model to explore the impact of diet on gut microbiome dynamics throughout metamorphosis. Here, we use monarch butterflies (Danaus plexippus), specialist herbivores that feed as larvae on many species of chemically well-defined milkweed plants (Asclepias sp.), to investigate the impacts of development and diet on the composition of the gut microbial community. While a few microbial taxa are conserved across life stages of monarchs, the microbiome appears to be highly dynamic throughout the life cycle. Microbial diversity gradually diminishes throughout the larval instars, ultimately reaching its lowest point during the pupal stage and then recovering again in the adult stage. The microbial composition then undergoes a substantial shift upon the transition from pupa to adult, with female adults having significantly different microbial communities than the eggs that they lay, indicating limited evidence for vertical transmission of gut microbiota. While diet did not significantly impact overall microbial composition, our results suggest that fourth instar larvae exhibit higher microbial diversity when consuming milkweed with high concentrations of toxic cardenolide phytochemicals. This study underscores how diet and developmental stage collectively shape the monarch's gut microbiota.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metatranscriptomics provide insights into the role of the symbiont Midichloria mitochondrii in Ixodes ticks. 元转录组学揭示了线粒体共生体敌敌畏在蜱中的作用。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae133

Laurene Leclerc, John Mattick, Brendan P Burns, Davide Sassera, Julie Dunning Hotopp, Nathan Lo

{"title":"Metatranscriptomics provide insights into the role of the symbiont Midichloria mitochondrii in Ixodes ticks.","authors":"Laurene Leclerc, John Mattick, Brendan P Burns, Davide Sassera, Julie Dunning Hotopp, Nathan Lo","doi":"10.1093/femsec/fiae133","DOIUrl":"10.1093/femsec/fiae133","url":null,"abstract":"Ticks are important vectors of bacterial, viral, and protozoan pathogens of humans and animals worldwide. Candidatus Midichloria mitochondrii is a highly abundant bacterial endosymbiont found in many tick species, including two medically important ticks respectively found in Europe and Australia, Ixodes ricinus and Ixodes holocyclus. The present study aimed to determine the symbiont's biological role by identifying lateral gene transfer (LGT) events, characterizing the transcriptome, and performing differential expression analyses. Metatranscriptomic data revealed that M. mitochondrii species in I. ricinus and I. holocyclus were equipped with the metabolic potential and were actively transcribing the genes for several important roles including heme, biotin and folate synthesis, oxidative stress response, osmotic regulation, and ATP production in microaerobic conditions. Differential expression analyses additionally showed an upregulation in stringent response and DNA repair genes in M. mitochondrii of I. holocyclus nymphs compared to adults. Low rates of differential expression suggest the symbiont may lack global gene regulation, as observed in other endosymbionts. Moreover, the identification of an LGT event and the proposed specialization of the M. mitochondrii strains, mIxholo1 and mIxholo2, for different I. holocyclus life stages highlight the complex interactions between M. mitochondrii and their tick hosts.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Regulators of aerobic and anaerobic methane oxidation in two pristine temperate peatland types. 两种原始温带泥炭地中需氧和厌氧甲烷氧化的调节因子。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae153

Justus Amuche Nweze, Vojtěch Tláskal, Magdalena Wutkowska, Travis B Meador, Tomáš Picek, Zuzana Urbanová, Anne Daebeler

{"title":"Regulators of aerobic and anaerobic methane oxidation in two pristine temperate peatland types.","authors":"Justus Amuche Nweze, Vojtěch Tláskal, Magdalena Wutkowska, Travis B Meador, Tomáš Picek, Zuzana Urbanová, Anne Daebeler","doi":"10.1093/femsec/fiae153","DOIUrl":"10.1093/femsec/fiae153","url":null,"abstract":"Despite covering <5% of Earth's terrestrial area, peatlands are crucial for global carbon storage and are hot spots of methane cycling. This study examined the dynamics of aerobic and anaerobic methane oxidation in two undisturbed peatlands: a fen and a spruce swamp forest. Using microcosm incubations, we investigated the effect of ammonium addition, at a level similar to current N pollution processes, on aerobic methane oxidation. Our findings revealed higher methane consumption rates in fen compared to swamp peat, but no effect of ammonium amendment on methane consumption was found. Members of Methylocystis and Methylocella were the predominant methanotrophs in both peatlands. Furthermore, we explored the role of ferric iron and sulfate as electron acceptors for the anaerobic oxidation of methane (AOM). AOM occurred without the addition of an external electron acceptor in the fen, but not in the swamp peat. AOM was stimulated by sulfate and ferric iron addition in the swamp peat and inhibited by ferric iron in the fen. Our findings suggest that aerobic methane oxidizers are not N-limited in these peatlands and that there is an intrinsic potential for AOM in these environments, partially facilitated by ferric iron and sulfate acting as electron acceptors.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members. 从基因组学角度了解嗜酸性耐卤酸杆菌属成员碳、氮和磷酸盐同化的关键机制。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae145

Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H Kaksonen, Jorge Valdés, Eva Vergara, David S Holmes, Elizabeth L J Watkin

{"title":"Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.","authors":"Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H Kaksonen, Jorge Valdés, Eva Vergara, David S Holmes, Elizabeth L J Watkin","doi":"10.1093/femsec/fiae145","DOIUrl":"10.1093/femsec/fiae145","url":null,"abstract":"In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface. 沉积物-水界面及以下铁质条件下的绿藻群的分类和功能分区。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae140

Aurèle Vuillemin, Fatima Ruiz-Blas, Sizhong Yang, Alexander Bartholomäus, Cynthia Henny, Jens Kallmeyer

{"title":"Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.","authors":"Aurèle Vuillemin, Fatima Ruiz-Blas, Sizhong Yang, Alexander Bartholomäus, Cynthia Henny, Jens Kallmeyer","doi":"10.1093/femsec/fiae140","DOIUrl":"10.1093/femsec/fiae140","url":null,"abstract":"The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum. 荚膜酸杆菌在纳米缺氧条件下的呼吸发酵生存策略

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae152

Daniela Trojan, Emilio García-Robledo, Bela Hausmann, Niels Peter Revsbech, Dagmar Woebken, Stephanie A Eichorst

{"title":"A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum.","authors":"Daniela Trojan, Emilio García-Robledo, Bela Hausmann, Niels Peter Revsbech, Dagmar Woebken, Stephanie A Eichorst","doi":"10.1093/femsec/fiae152","DOIUrl":"10.1093/femsec/fiae152","url":null,"abstract":"Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1 µM oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MetaCompare 2.0: differential ranking of ecological and human health resistome risks. MetaCompare 2.0：生态和人类健康抗蚀体风险的差异排序。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae155

Monjura Afrin Rumi, Min Oh, Benjamin C Davis, Connor L Brown, Adheesh Juvekar, Peter J Vikesland, Amy Pruden, Liqing Zhang

{"title":"MetaCompare 2.0: differential ranking of ecological and human health resistome risks.","authors":"Monjura Afrin Rumi, Min Oh, Benjamin C Davis, Connor L Brown, Adheesh Juvekar, Peter J Vikesland, Amy Pruden, Liqing Zhang","doi":"10.1093/femsec/fiae155","DOIUrl":"10.1093/femsec/fiae155","url":null,"abstract":"While numerous environmental factors contribute to the spread of antibiotic resistance genes (ARGs), quantifying their relative contributions remains a fundamental challenge. Similarly, it is important to differentiate acute human health risks from environmental exposure, versus broader ecological risk of ARG evolution and spread across microbial taxa. Recent studies have proposed various methods for achieving such aims. Here, we introduce MetaCompare 2.0, which improves upon original MetaCompare pipeline by differentiating indicators of human health resistome risk (potential for human pathogens of acute resistance concern to acquire ARGs) from ecological resistome risk (overall mobility of ARGs and potential for pathogen acquisition). The updated pipeline's sensitivity was demonstrated by analyzing diverse publicly-available metagenomes from wastewater, surface water, soil, sediment, human gut, and synthetic microbial communities. MetaCompare 2.0 provided distinct rankings of the metagenomes according to both human health resistome risk and ecological resistome risk, with both scores trending higher when influenced by anthropogenic impact or other stress. We evaluated the robustness of the pipeline to sequence assembly methods, sequencing depth, contig count, and metagenomic library coverage bias. The risk scores were remarkably consistent despite variations in these technological aspects. We packaged the improved pipeline into a publicly-available web service (http://metacompare.cs.vt.edu/) that provides an easy-to-use interface for computing resistome risk scores and visualizing results.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss. 弗兰科菌[NiFe]摄取氢化酶和基因组减少：损失的不同系列。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae147

Katharina Pawlowski, Daniel Wibberg, Sara Mehrabi, Nadia Binte Obaid, András Patyi, Fede Berckx, Han Nguyen, Michelle Hagen, Daniel Lundin, Andreas Brachmann, Jochen Blom, Aude Herrera-Belaroussi, Danis Abrouk, Petar Pujic, Ann-Sofi Hahlin, Jörn Kalinowski, Philippe Normand, Anita Sellstedt

{"title":"Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss.","authors":"Katharina Pawlowski, Daniel Wibberg, Sara Mehrabi, Nadia Binte Obaid, András Patyi, Fede Berckx, Han Nguyen, Michelle Hagen, Daniel Lundin, Andreas Brachmann, Jochen Blom, Aude Herrera-Belaroussi, Danis Abrouk, Petar Pujic, Ann-Sofi Hahlin, Jörn Kalinowski, Philippe Normand, Anita Sellstedt","doi":"10.1093/femsec/fiae147","DOIUrl":"10.1093/femsec/fiae147","url":null,"abstract":"Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup-, while only one Hup- Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0