Systematic and applied microbiology最新文献

{"title":"N-glyceroyl alkylamine phosphoglycolipids dominate the lipidome of several Bacillota bacteria","authors":"Nicole J. Bale ,&nbsp;Michel Koenen ,&nbsp;Su Ding ,&nbsp;Jaap S. Sinninghe Damsté","doi":"10.1016/j.syapm.2025.126609","DOIUrl":"10.1016/j.syapm.2025.126609","url":null,"abstract":"<div><div>Elucidation of the membrane lipid composition of bacteria can help to better understand how bacterial cells interact with their surroundings, adapt to environmental stress, and resist antimicrobial agents. Here we describe for the first time the detection of a wide array of N-glyceroyl alkylamine phosphoglycolipids (NGAPs) in a range of <em>Bacillota</em> bacteria (formerly <em>Firmicutes</em>). <em>Bacillota</em> includes a diverse range of bacteria that are typically highly resistant to harsh conditions such as heat, radiation, and pH, allowing the bacteria to survive in unfavorable environments. In 9 out 18 investigated strains of <em>Bacillota</em>, spread across 5 orders (<em>Thermoanaerobacterales, Thermosediminibacterales, Eubacteriales, Halanaerobiales</em>, and <em>Sulfobacillia</em>) mild acid hydrolysis released N-glyceroyl alkylamines (NGAs), which were detectable by gas chromatography–mass spectrometry (GC–MS) during routine fatty acid analysis. One strain, <em>Moorella thermoacetica</em> was found to produce long-chain NGAs (C₃₀-C₃₂), which are postulated to have <em>iso</em>diabolic acid-like structures. A wide variety of intact polar NGAPs were identified using ultra-high pressure liquid chromatography high resolution multi-stage mass spectrometry (UHPLC-HRMSⁿ). These include many previously undescribed lipids with a variety of sugar moieties and glycerol-bound core lipid moieties, including ether-bound components and alkyl 1,2-diols. The NGAPs constituted the majority of the intact polar lipid composition of these strains and presumably contribute to their tough cell membranes. The presence of NGAs in <em>Bacillota</em> appears to be associated with thermophilia. Both the hydrolysis-derived NGAs and intact polar NGAPs have potential to be biomarkers for extremophilic and, in particular, thermophilic bacteria.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126609"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918523","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":"Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella","authors":"Juliana Botero ,&nbsp;Nikolas Basler ,&nbsp;Margo Cnockaert ,&nbsp;Charlotte Peeters ,&nbsp;Maria Schreiber ,&nbsp;Manja Marz ,&nbsp;Dirk C. de Graaf ,&nbsp;Jelle Matthijnssens ,&nbsp;Peter Vandamme","doi":"10.1016/j.syapm.2025.126625","DOIUrl":"10.1016/j.syapm.2025.126625","url":null,"abstract":"<div><div>We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 <em>Bartonella</em> isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as <em>Bartonella apihabitans</em> and three as <em>Bartonella choladocola</em> was straightforward, the identification of 25 <em>Bartonella apis</em>-like isolates was challenging. A taxonomic and functional analysis of four <em>B. apis</em>-like genomes and of publicly available <em>B. apis</em> genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of <em>B. apis</em> and <em>B. apis</em>-like genomes. Different phylogenomic analyses showed that <em>B. apis</em> and <em>B. apis</em>-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as <em>B. apis</em>. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of <em>Bartonella</em> species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the <em>Bartonella tamiae</em> clade into the novel genus <em>Attibartonella</em> gen. nov., with <em>Attibartonella tamiae</em> comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated <em>Bartonella</em> clade into the novel genus <em>Ditibartonella</em> gen. nov., with <em>Ditibartonella apis</em> comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional <em>Ditibartonella</em> species in honey bee samples, highlighted an evolutionary adaptation of <em>Ditibartonella</em> bacteria to bee hosts and suggested shared transmission routes.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126625"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144271231","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":"Unveiling the hidden microbiome: a microbiological exploration of untouched burial crypts in Krakow, Poland","authors":"Patrycja Tarnawska ,&nbsp;Aleksandra Burkowska-But ,&nbsp;Maria Swiontek Brzezińska ,&nbsp;Anna Drążkowska ,&nbsp;Adriana Osińska ,&nbsp;Maciej Walczak","doi":"10.1016/j.syapm.2025.126618","DOIUrl":"10.1016/j.syapm.2025.126618","url":null,"abstract":"<div><div>Cultural heritage objects provide valuable historical information, but can also harbour biological threats. Still, little is said about the potential risks that may await unaware researchers, conservators, and archaeologists. Our work discusses the study results from the crypts in Krakow, which were opened for the first time. The human and coffin remains were examined. The number of actinomycetes, other mesophilic bacteria, bacterial spores, and xerophilic and non-xerophilic fungi was determined. In general, a low number of microbes was observed. However, scanning electron microscope (SEM) images showed many bacterial conglomerates and confirmed that microbial activity affected the fibres covering cadavers in the crypts. The most abundant were mesophilic bacteria, followed by bacterial spores and actinomycetes. They reached up to 10⁷ CFU/g in fabric remains, 5.2 × 10⁶ CFU/g in burial remains, and 1.6 × 10⁶ CFU/g found under the coffin, and above 7.5 × 10⁵ CFU/g for xerophilic and non-xerophilic fungi. NGS (Next-Generation Sequencing) results suggested that the low presence of microorganisms may be due to the dominance of unculturable or long-growing bacteria belonging to <em>Mycobacterium</em>, such as <em>M. coloregonium</em>, <em>M. arupense</em>, and <em>M. pinnipedii.</em> Moreover, other obligatory/non-obligatory pathogens, <em>Bacteroides fragilis, Clostridium botulinum, Coxiella burnetii</em>, <em>Clostridium tetani</em>, <em>Corynebacterium diphtheriae</em>, <em>Enterobacter cloacae</em>, <em>Escherichia coli</em>, <em>Legionella pneumophila</em>, <em>Mycobacterium leprae</em>, <em>Rhodococcus equi</em>, and <em>Staphylococcus aureus</em> have been recorded in examined samples, with the dominance in bone samples. Results indicate the risk of dangerous pathogens present in historical objects, the impact on health may be severe, and the need to use personal protective equipment and proper measures to control the physical conditions of crypts.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126618"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168667","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":"Genomic and phylogenetic re-assessment of the genus Stenotrophomonas: Description of Stenotrophomonas thermophila sp. nov., and the proposal of Parastenotrophomonas gen. Nov., Pseudostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., and Allostenotrophomonas gen. Nov.","authors":"Amandine Chauviat,&nbsp;Danis Abrouk,&nbsp;Elisabeth Brothier,&nbsp;Daniel Muller,&nbsp;Thibault Meyer ,&nbsp;Sabine Favre-Bonté","doi":"10.1016/j.syapm.2025.126630","DOIUrl":"10.1016/j.syapm.2025.126630","url":null,"abstract":"<div><div>The <em>Stenotrophomonas maltophilia</em> species complex (Smc) currently comprises 19 genomospecies, known for their ecological versatility and role as opportunistic human pathogens. However, significant genomic variability among strains has complicated their classification, and only a few species within the Smc have been validly described. Despite successive taxonomic revisions, there remains no consensus on the naming of many genomospecies, largely due to the phenotypic heterogeneity across the complex.</div><div>In this study, we performed a comprehensive genomic and phylogenetic re-assessment to clarify the boundaries of the <em>Stenotrophomonas</em> genus and its species complex. Using whole-genome phylogeny and Overall Genome-Related Indices (OGRIs) such as digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANIb and ANIm), and Average Amino Acid Identity (AAI), we established precise cutoffs for defining the genus and the Smc. Our analysis led to the formal revision of the <em>Stenotrophomonas</em> genus, resulting in the delineation of four novel bacterial genera: <em>Allostenotrophomonas</em> gen. Nov., <em>Pedostenotrophomonas</em> gen. Nov., <em>Parastenotrophomonas</em> gen. Nov., and <em>Pseudostenotrophomonas</em> gen. Nov. Additionally, we standardized the nomenclature within the Smc by identifying reference strains for each genomospecies. Among these, we describe a novel species, <em>Stenotrophomonas thermophila</em> sp. nov. (type strain BurA1^T = LMG 33562^T = EML 1882^T). This study provides a robust framework for future taxonomic and ecological studies within the <em>Stenotrophomonas</em> genus.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126630"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144338327","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":"Classification of MAGs associated with trace gas metabolism in volcanic soils named following SeqCode rules","authors":"Shamik Roy ,&nbsp;Gary M. King ,&nbsp;Marcela Hernández","doi":"10.1016/j.syapm.2025.126622","DOIUrl":"10.1016/j.syapm.2025.126622","url":null,"abstract":"<div><div>Trace gas metabolism is important for nutrient flow in all ecosystems, particularly volcanic ecosystems. Microbes in volcanic ecosystems are among the early colonisers and can play key roles in ecological succession. Here, we describe the taxonomic and functional characteristics of two new metagenome-assembled genomes (MAGs), one belonging to <em>Bacteria</em> (MAG_1957-2.1) and one to <em>Archaea</em> (MAG_C2-3), retrieved from soils in volcanoes located in Chile (Llaima) and the USA (Kilauea), respectively. MAG_1957-2.1 has a genome size of 6.36<!--> <!-->Mb with 96.21 % completeness. MAG_C2-3 has a genome size of 3.02<!--> <!-->Mb with 97.57 % completeness. Phylogenetic analyses of the bacterial MAGs placed MAG_1957-2.1 in the class <em>Ktedonobacteria</em>, while the archaeal MAG_C2-3 was placed in the class <em>Nitrososphaeria</em>. Functional characterisation for potential trace gas metabolism showed that MAG_1957-2.1 contains a <em>coxL</em> gene encoding the large subunit of form I carbon monoxide dehydrogenase (CoxL), which is associated with the oxidation of carbon monoxide (CO). It also contains the form I <em>cox</em> gene cluster with a <em>coxMSL</em> arrangement. On the other hand, MAG_C2-3 contains gene subunit A (<em>amoA</em>) as well as subunit B (<em>amoB</em>), which encode for ammonia monooxygenase, the enzyme that catalyses the oxidation of ammonia. Based on the sequence characteristics and phylogenomic analyses we propose the names <em>Paraktedonobacter carboxidivorans sp.</em> nov for MAG_1957-2.1 and <em>Nitrososphaera maunauluensis sp.</em> nov for MAG_C2-3. The names are proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126622"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230868","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":"Corrigendum to: “Flavobacterium plantiphilum sp. nov., Flavobacterium rhizophilum sp. nov., Flavobacterium rhizosphaerae sp. nov., Chryseobacterium terrae sp. nov., and Sphingomonas plantiphila sp. nov. isolated from salty soil showing plant growth promoting potential” [Systematic and Applied Microbiology 48 (2025) 126588]","authors":"Peter Kämpfer ,&nbsp;André Lipski ,&nbsp;Kathy S. Lawrence ,&nbsp;Walker R. Olive ,&nbsp;Molli M. Newman ,&nbsp;John A. McInroy ,&nbsp;Tomeu Viver","doi":"10.1016/j.syapm.2025.126603","DOIUrl":"10.1016/j.syapm.2025.126603","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126603"},"PeriodicalIF":3.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671054","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":"Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov","authors":"Izzet Burcin Saticioglu ,&nbsp;Nihed Ajmi ,&nbsp;Orkid Coskuner-Weber ,&nbsp;Semih Alpsoy ,&nbsp;Hilal Ay ,&nbsp;Fuat Aydin ,&nbsp;Seçil Abay ,&nbsp;Emre Karakaya ,&nbsp;Tuba Kayman ,&nbsp;Cem Dalyan ,&nbsp;Fatih Doğan Koca ,&nbsp;Gorkem Tasci ,&nbsp;Doğancan Yarim ,&nbsp;Danny Morick ,&nbsp;Artun Yibar ,&nbsp;Serdar Erdogan ,&nbsp;Soner Altun ,&nbsp;Muhammed Duman","doi":"10.1016/j.syapm.2025.126600","DOIUrl":"10.1016/j.syapm.2025.126600","url":null,"abstract":"<div><div>Three bacterial strains, Mu-43^T, Mu-80^T, and Mu-86^T, were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus <em>Microbacterium</em>. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. <em>M. istanbulense</em> Mu-43^T showed 99.0 % 16S rRNA similarity to <em>M. bandirmense</em> Mu-80^T, with digital DNA–DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. <em>M. bandirmense</em> Mu-80^T exhibited 99.2 % similarity to <em>M. esteraromaticum</em> DSM 8609^T, with dDDH and ANIb values of 23.6 % and 80 %. <em>M. marmarense</em> Mu-86^T showed 97.4 % similarity to <em>M. arthrosphaerae</em> JCM 30492^T, with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: <em>M. istanbulense</em> sp. nov. Mu-43^T (LMG 33297^T = DSM 117065^T), <em>M. bandirmense</em> sp. nov. Mu-80^T (LMG 33295^T = DSM 117210^T), and <em>M. marmarense</em> sp. nov. Mu-86^T (LMG 33293^T = DSM 117066^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126600"},"PeriodicalIF":3.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550595","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":"Thiohalorhabdus methylotropha sp. nov., an extremely halophilic autotrophic methylotiotroph from hypersaline lakes","authors":"Dimitry Y. Sorokin ,&nbsp;Alexander Y. Merkel ,&nbsp;William Gebbe ,&nbsp;Marina G. Kalyuzhnaya","doi":"10.1016/j.syapm.2025.126602","DOIUrl":"10.1016/j.syapm.2025.126602","url":null,"abstract":"<div><div>So far, there have been no reports of trimethylamine (TMA)-utilizing extremely halophilic microorganisms in hypersaline habitats. Our aerobic enrichments at 4 M total Na⁺ with 5 mM TMA inoculated with surface sediments from hypersaline soda (at pH 9.5) or chloride-sulfate (at pH 7) lakes in southwestern Siberia were successful only for the latter. The initial enrichment included both bacteria and haloarchaea but only the bacterial component was able to grow as a pure culture with TMA. Strain Cl-TMA forms a new-species lineage within the genus <em>Thiohalorhabdus</em> which includes extremely halophilic and obligate lithoautotrophic sulfur-oxidizing gammaproteobacteria. Cl-TMA can grow methyloautotrophically utilizing TMA, dimethylamine (DMA) and methanol (MeOH) as the electron donors or chemolithoautotrophically with thiosulfate. Mixotrophic growth was also observed with the three methyl compounds and thiosulfate. Carbon is assimilated autotrophically via the Calvin-Benson-Basham pathway. Unlike the type species of <em>Thiohalorhabdus</em>, <em>T. denitrificans</em>, Cl-TMA was incapable of anaerobic growth via denitrification. The isolate belongs to extreme halophiles growing between 2.5 and 5 M NaCl with an optimum at 3–3.5 M. Genome analysis identified two gene clusters coding for PQQ-dependent methanol dehydrogenases (MxaFI and XoxF), four homologues of the formaldehyde activating enzymes (Faes), a TMA/DMA oxidation locus, and two cluster of genes encoding an <em>N</em>-methylglutamate dehydrogenase pathway (NMGP) for methylamine oxidation. The first steps of C₁-subtrate conversions are followed by the tetrahydrofolate (THF)-linked and tetrahydromethanopterin (H4MPT)-linked formaldehyde oxidation pathways and two formate dehydrogenases. All of those signatures of methylotrophy were absent in <em>T. denitrificans</em>. In contrast, genes for two key sulfur oxidation enzymes, thiosulfate dehydrogenase TsdAB and sulfide dehydrogenase FccAB, that are present in the type species are missing in Cl-TMA. Thiosulfate is oxidized to sulfate by a combination of an incomplete Sox cycle and an sHdr system. Strain Cl-TMA^T (JCM 35977 = UQM 41915) is proposed to be classified as <em>Thiohalorhabdus methylotrophus</em> sp. nov.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126602"},"PeriodicalIF":3.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636963","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":"Representatives of the Synergistaceae family, taxonomic description and genome sequence of Caenicola nitritireducens gen nov., sp. nov., a novel fermenting and amino-acid degrading bacterium isolated from a municipal anaerobic digester sludge","authors":"Abdelaziz El Houari ,&nbsp;Magali Ranchou-Peyruse ,&nbsp;Elisabeth Carlier ,&nbsp;Anthony Ranchou-Peyruse ,&nbsp;Agnès Hirschler-Réa ,&nbsp;Rhizlane Bennisse ,&nbsp;Radia Bouterfas ,&nbsp;James E. McDonald ,&nbsp;Rémy Guyoneaud ,&nbsp;Abdel-Illah Qatibi","doi":"10.1016/j.syapm.2025.126607","DOIUrl":"10.1016/j.syapm.2025.126607","url":null,"abstract":"<div><div>Members of the phylum <em>Synergistota</em> are important but understudied components of microbial communities during anaerobic digestion. In this study, their diversity was assessed in full-scale anaerobic digester sludge samples from Marrakesh wastewater treatment plant (Morocco), using <em>16S rRNA</em> gene community profiling, as well as targeted isolation, physiological characterization, and genome sequencing of novel <em>Synergistaceae</em> isolates<em>.</em> The <em>16S rRNA</em> gene analysis identified 23 operational taxonomic units (OTUs) belonging to the family of <em>Synergistaceae</em>, representing 8.8 % of the total microbial community. 17 of these OTUs belonged to previously uncultured taxa. A dominant OTU19, presumably a new representative of the family of <em>Synergistaceae</em> was isolated in pure culture (strain DS-S4^T) and subjected to both culture- and genome-based characterizations. Phylogenetic analysis revealed that strain DZ-S4^T was related to <em>Cloacibacillus porcorum</em> CL-84^T and <em>Cloacibacillus evryensis</em> 158^T but with low sequence similarity of 89.94 % and 88.60 %, respectively. Based on genome relatedness, including Average Nucleotide Identity (ANI) and Amino Acid Identity (AAI), strain DZ-S4^T is considered to represent a novel genus for which the name <em>Caenicola</em> gen.nov is proposed. Moreover, several phenotypic and eco-physiological properties differentiated the novel isolate from its related species, indicating that the strain represents a new species for which the name <em>Caenicola nitritireducens</em> sp. nov. is proposed, with strain DZ-S4^T (=DSM 104940^T = JCM 31897^T) being the type strain. Additionally, this study investigates the ecological role of strain DZ-S4^T, specifically the protein degradation, the bioconversion of carbohydrates, and the nitrite reduction during anaerobic digestion.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126607"},"PeriodicalIF":3.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877548","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":"Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1Ts sp. nov. from an acidic peatland","authors":"Pranami Goswami ,&nbsp;Runjia Ji ,&nbsp;Jianxun Shen ,&nbsp;Andrew P. Roberts ,&nbsp;Wei Lin","doi":"10.1016/j.syapm.2025.126605","DOIUrl":"10.1016/j.syapm.2025.126605","url":null,"abstract":"<div><div>Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe₃O₄) and/or greigite (Fe₃S₄) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the <em>Nitrospirota</em> phylum (previously known as the <em>Nitrospirae</em> phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce <em>Magnetominusculus dajiuhuensis</em> DJH-1^Ts, a newly discovered <em>Nitrospirota</em> MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus <em>Magnetominusculus</em>, family <em>Magnetobacteriaceae</em>, order <em>Thermodesulfovibrionales</em>, class <em>Thermodesulfovibrionia</em> according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name <em>Magnetominusculus dajiuhuensis</em> DJH-1^Ts sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of <em>Magnetominusculus dajiuhuensis</em> DJH-1^Ts provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126605"},"PeriodicalIF":3.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698021","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}