Systematic and applied microbiology最新文献

{"title":"Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds","authors":"Kohli Pragya ,&nbsp;Pannikurungottu Sreya ,&nbsp;Lakshmanan Vighnesh ,&nbsp;Dhurka Mahima ,&nbsp;Mallick Sushmita ,&nbsp;Chintalapati Sasikala ,&nbsp;Chintalapati Venkata Ramana","doi":"10.1016/j.syapm.2024.126502","DOIUrl":"10.1016/j.syapm.2024.126502","url":null,"abstract":"<div><p>Six metagenome-assembled genomes (JB008^Ts, JB007, JB015, JB003, JB004, and JB002) belonging to the order <em>Spirochaetales</em> were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008^Ts and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2–93.4 %, respectively with uncultivated <em>Spirochaetaceae</em> family members, and &lt; 90 % identity with <em>Marispirochaeta aestuari</em> JC444^T. While, the bin JB015 showed 99.1 % identity with <em>Pleomorphochaeta naphthae</em> SEBR 4209^T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008^Ts confirmed that these members belong to the family <em>Spirochaetaceae</em> and bins JB015, JB002, JB003, and JB004 belong to the genus <em>Pleomorphochaeta</em> within the family <em>Sphaerochaetaceae</em>. The AAI values of the binned genomes JB007 and JB008^Ts compared to other members of the <em>Spirochaetaceae</em> family were between 53.9- 56.8 % and 53.8–57.1 %, respectively. Furthermore, the comparison of ANI, <em>d</em>DDH, and POCP metrics of the binned genomes JB007 and JB008^Ts, both among themselves and with the members of <em>Spirochaetaceae,</em> was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008^Ts is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name <em>Thalassospirochaeta sargassi</em> gen. nov. sp. nov., in the family <em>Spirochaetaceae</em> while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other <em>Pleomorphochaeta</em> members.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126502"},"PeriodicalIF":3.4,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140044344","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":"Halomontanus rarus gen. nov., sp. nov., a novel halophilic archaeon of the family Natrialbaceae from salt lakes on the Qinghai-Xizang Plateau","authors":"Ya-Ling Mao,&nbsp;Bei-Bei Wang,&nbsp;Xue-Meng Yin,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1016/j.syapm.2024.126500","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126500","url":null,"abstract":"<div><p>Two halophilic archaeal strains TS33^T and KZCA124 were isolated from two distant salt lakes on the Qinghai-Xizang Plateau, respectively. Culture-independent analysis indicated that these two strains were original inhabitants but low abundant taxa in respective salt lakes. Strains TS33^T and KZCA124 were able to grow at 20–60 °C (optimum were 42 and 35 °C, respectively), with 0.9–4.8 M NaCl (optimum were 3.0 and 2.6 M, respectively), with 0–0.7 M MgCl₂ (optimum, 0.3 M) and at pH 5.0–9.5 (optimum were pH 7.5 and pH 7, respectively). The 16S rRNA and <em>rpoB'</em> gene similarities between these two strains were 99.7% and 99.4%, and these two similarities among strains TS33^T, KZCA124, and existing species of the family <em>Natrialbaceae</em> were 90.6–95.5% and 84.4–89.3%, respectively. Phylogenetic and phylogenomic analyses indicated that strains TS33^T and KZCA124 formed an independent branch separated from neighboring genera, <em>Saliphagus</em>, <em>Natronosalvus</em>, and <em>Natronobiforma</em>. The average<!--> <!-->nucleotide<!--> <!-->identity (ANI), digital DNA-DNA<!--> <!-->hybridization (dDDH), and average amino acid identity (AAI) values between strains TS33^T and KZCA124 were 96.4%, 73.1%, and 96.7%, respectively, higher than the thresholds for species demarcation. The overall genome-related indexes between these two strains and existing species of family <em>Natrialbaceae</em> were 73–77%, 21–25%, and 63–70%, respectively, significantly lower than the species boundary thresholds. Strains TS33^T and KZCA124 may represent a novel species of a new genus within the family <em>Natrialbaceae</em> judged by the cutoff value of AAI (≤76%) proposed to differentiate genera within the family <em>Natrialbaceae</em>. The major polar lipids of strains TS33^T and KZCA124 were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated mannosyl glucosyl diether, and sulfated galactosyl mannosyl glucosyl diether. These two strains could be distinguished from the related genera according to differential phenotypic characteristics. These phenotypic, phylogenetic, and genomic analyses revealed that strains TS33^T (=KCTC 4310^T = MCCC 4K00132^T) and KZCA124 (=CGMCC 1.17432 = JCM 34316) represent a novel species of a new genus of the family <em>Natrialbaceae</em> and were named <em>Halomontanus rarus</em> gen. nov., sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126500"},"PeriodicalIF":3.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139975705","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":"Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode","authors":"Iain C. Sutcliffe ,&nbsp;Luis M. Rodriguez-R ,&nbsp;Stephanus N. Venter ,&nbsp;William B. Whitman","doi":"10.1016/j.syapm.2024.126498","DOIUrl":"10.1016/j.syapm.2024.126498","url":null,"abstract":"<div><p>Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of <em>Archaea</em> and <em>Bacteria</em> using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126498"},"PeriodicalIF":3.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000122/pdfft?md5=762a11d283f0db1e74c77527e4520630&pid=1-s2.0-S0723202024000122-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140007964","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":"Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus","authors":"Megha Malhotra ,&nbsp;Sarah Bello ,&nbsp;Radhey S. Gupta","doi":"10.1016/j.syapm.2024.126499","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126499","url":null,"abstract":"<div><p>To clarify the evolutionary relationships among <em>Peptoniphilus</em> species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, <em>Peptoniphilus</em> species formed eight distinct clades, with <em>Aedoeadaptatus</em> and <em>Anaerosphaera</em> species branching between them. The observed clades designated as <em>Peptoniphilus sensu stricto</em> (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several <em>Peptoniphilus</em> species (viz. <em>P. coxii</em>, <em>P</em>. <em>ivorii</em>, <em>P</em>. <em>nemausensis</em> and some non-validly published species) grouped reliably with the type species of <em>Aedoeadaptatus</em> (<em>A. acetigenes</em>) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence<em>,</em> we are proposing the transfer of these species into the emended genus <em>Aedoeadaptatus</em>. Our analyses on protein sequences from <em>Peptoniphilus</em> genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different <em>Peptoniphilus</em> species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized <em>Peptoniphilus</em> spp. (cultured and uncultured), their affiliations to the specific <em>Peptoniphilus</em> clades can be accurately predicted. These results should prove useful in understanding the potential involvement of <em>Peptoniphilus</em>-related species in diseases.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126499"},"PeriodicalIF":3.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139999227","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":"Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov","authors":"Nicole Hugouvieux-Cotte-Pattat ,&nbsp;Jean-Pierre Flandrois ,&nbsp;Jérôme Briolay ,&nbsp;Sylvie Reverchon ,&nbsp;Céline Brochier-Armanet","doi":"10.1016/j.syapm.2024.126497","DOIUrl":"10.1016/j.syapm.2024.126497","url":null,"abstract":"<div><p>The <em>Pectobacteriaceae</em> family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their diversity, a survey of pectinolytic bacteria was performed in brackish lakes of the French region La Camargue near the Mediterranean Sea. The genome of six atypical isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains form a new clade of <em>Pectobacteriaceae</em> that branches at the basis of the group encompassing the genera <em>Lonsdalea</em>, <em>Musicola</em>, and <em>Dickeya</em>. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name <em>Prodigiosinella</em> gen. nov<em>.</em> Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups, G1 and G2. The type strain LS101^T (CFBP 8826^T = LMG 32072^T) and strain CE70 (CFBP 9054 = LMG 32867) are representative G1 and G2 members, respectively. Three genomic methods were used to analyze DNA–DNA relatedness: digital DNA–DNA hybridization (isDDH), average nucleotide identity (ANI), and genome alignment fraction (AF). They revealed a close relationship between genomes of the two groups, supporting their appurtenance to a same species for which we propose the name <em>Prodigiosinella aquatilis</em> sp. nov. Four strains previously designated as <em>Serratia</em> sp. (ATCC 39006), <em>Brenneria</em> “<em>ulupoensis”</em> (K61) or <em>Erwinia</em> sp. (MK01 and MK09) belong to the new genus <em>Prodigiosinella</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126497"},"PeriodicalIF":3.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000110/pdfft?md5=80fdafebb6872b34e10a36ad1568139f&pid=1-s2.0-S0723202024000110-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139919668","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":"Description of the first cultured representative of “Candidatus Synoicihabitans” genus, isolated from deep-sea sediment of South China Sea","authors":"Tariq Ahmad ,&nbsp;Sidra Erum Ishaq ,&nbsp;Lewen Liang ,&nbsp;Jialin Hou ,&nbsp;Ruize Xie ,&nbsp;Yijing Dong ,&nbsp;Tiantian Yu ,&nbsp;Fengping Wang","doi":"10.1016/j.syapm.2024.126490","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126490","url":null,"abstract":"<div><p>In this study we describe the first cultured representative of <em>Candidatus</em> Synoicihabitans genus, a novel strain designated as LMO-M01^T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01^T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family <em>Opitutaceae</em>, Phylum <em>Verrucomicrobiota</em>. The genomic analysis of strain LMO-M01^T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain’s physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01^T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01^T represents a novel genus (previously <em>Candidatus</em>) within the family <em>Opitutaceae</em> of phylum <em>Verrucomicrobiota</em>, for which the name <em>Synoicihabitans lomoniglobus</em> gen. nov., sp. nov. was proposed. The type of strain is LMO-M01^T (= CGMCC 1.61593^T = KCTC 92913^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126490"},"PeriodicalIF":3.4,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139700113","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":"Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum","authors":"Ebrahim Osdaghi ,&nbsp;S. Mohsen Taghavi ,&nbsp;Mozhde Hamidizade ,&nbsp;Mehdi Kariminejhad ,&nbsp;Amal Fazliarab ,&nbsp;Habibeh Hajian Maleki ,&nbsp;Steve Baeyen ,&nbsp;Geraldine Taghouti ,&nbsp;Marie-Agnes Jacques ,&nbsp;Johan Van Vaerenbergh ,&nbsp;Perrine Portier","doi":"10.1016/j.syapm.2024.126489","DOIUrl":"10.1016/j.syapm.2024.126489","url":null,"abstract":"<div><p><em>Curtobacterium flaccumfaciens</em> (<em>Microbacteriaceae</em>), a plant-pathogenic coryneform species includes five pathovars with valid names and a number of proposed – but unvalidated – new members. In this study, phenotypic features and DNA similarity indexes were investigated among all <em>C. flaccumfaciens</em> members. Results showed that the <em>C. flaccumfaciens</em> pv. <em>poinsettiae</em> strains causing bacterial canker of <em>Euphorbia pulcherrima</em> in the USA as well as the orange-/red-pigmented strains of <em>C. flaccumfaciens</em> pv. <em>flaccumfaciens</em> pathogenic on dry beans in Iran are too distinct from each other and from the type strain of the species to be considered members of <em>C. flaccumfaciens</em>. Hence, the latter two groups were elevated at the species level as <em>C. poinsettiae</em> sp. nov. (ATCC 9682^T = CFBP 2403^T = ICMP 2566^T = LMG 3715^T = NCPPB 854^T as type strain), and <em>C. aurantiacum</em> sp. nov. (50R^T = CFBP 8819^T = ICMP 22071^T as type strain). Within the emended species <em>C. flaccumfaciens</em> comb. nov., yellow-pigmented strains causing bacterial wilt of dry beans and those causing bacterial canker of <em>Euphorbia pulcherrima</em> in Europe were retained as <em>C. flaccumfaciens</em> pv. <em>flaccumfaciens</em> and <em>C. flaccumfaciens</em> pv<em>. poinsettiae,</em> respectively; while taxonomic position of the sugar beet pathogen <em>C. flaccumfaciens</em> pv. <em>beticola</em> ATCC BAA144^PT was confirmed. The newly described onion pathogen <em>C. allii</em> was also reclassified as <em>C. flaccumfaciens</em> pv<em>. allii</em> with the pathotype strain LMG 32517^PT. Furthermore, <em>C. flaccumfaciens</em> pv. <em>basellae</em> causing bacterial leaf spot of malabar spinach (<em>Basella rubra</em>) was transferred to <em>C. citreum</em> pv. <em>basellae</em> with ATCC BAA143^PT as pathotype.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126489"},"PeriodicalIF":3.4,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139679730","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":"Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes","authors":"Laura Díaz-García ,&nbsp;Maria Chuvochina ,&nbsp;Golo Feuerriegel ,&nbsp;Boyke Bunk ,&nbsp;Cathrin Spröer ,&nbsp;Wolfgang R. Streit ,&nbsp;Luis M. Rodriguez-R ,&nbsp;Jörg Overmann ,&nbsp;Diego Javier Jiménez","doi":"10.1016/j.syapm.2023.126485","DOIUrl":"10.1016/j.syapm.2023.126485","url":null,"abstract":"<div><p><span><span>An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures<span> containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as </span></span>inoculum<span><span> and lignocellulose<span> as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and </span></span>phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to </span></span><em>Caenibius</em> spp. (<span><em>Sphingomonadaceae</em></span>). Following the rules and requirements of the SeqCode, we propose the name <em>Andeanibacterium colombiense</em> gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (<em>Pseudobacter hemicellulosilyticus</em><span> sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the </span><span><em>Sphingobacteriaceae</em></span><span> family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by </span><em>A. colombiense</em><span>. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.</span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 1","pages":"Article 126485"},"PeriodicalIF":3.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138561074","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":"Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil","authors":"Lian Xu ,&nbsp;Hua-Mei Wei ,&nbsp;Ye-Nan Sun ,&nbsp;Qi Wu ,&nbsp;Xiao-Yan Gao ,&nbsp;Biao Shen ,&nbsp;Ji-Quan Sun","doi":"10.1016/j.syapm.2024.126488","DOIUrl":"10.1016/j.syapm.2024.126488","url":null,"abstract":"<div><p><span>Four vanillic acid-degrading bacterial strains, named LR5S13</span>^T, LR5S20, and M4R5S39^T and LN1S58, were isolated from <em>Kalidium cuspidatum</em><span><span><span> rhizosphere and bulk soils, respectively. </span>Phylogenetic analysis based on 16S </span>rRNA gene as well as core genome revealed that LR5S13</span>^T and LR5S20 clustered closely with each other and with <span><em>Halomonas</em><em> ventosae</em></span> Al12^T, and that the two strains shared the highest similarities (both 99.3 %) with <em>H. ventosae</em> Al12^T, in contrast, M4R5S39^T and LN1S58 clustered together and with <em>Halomonas heilongjiangensis</em> 9–2^T, and the two strains shared the highest similarities (99.4 and 99.2 %, respectively) with <em>H. heilongjiangensis</em> 9–2^T. The average nucleotides identities based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) values of strains LR5S13^T to LR5S20, and M4R5S39^T<span> to LN1S58, were both higher than the threshold values for delineation of a species. The ANIb and dDDH values of the four strains to their closely relatives were lower than the threshold values. All four strains take phosphatidylethanolamine<span>, phosphatidylglycerol<span>, and diphosphatidylglycerol as the major polar lipids, Summed Feature 8, Summed Feature 3, and C</span></span></span>_16:0 as the major fatty acids. Based on the phylogenetic and phenotypic results, the four strains should be classified as two novel <em>Halomonas</em> species. Therefore, <em>Halomonas rhizosphaerae</em> sp. nov. (type strain LR5S13^T = KCTC 8016^T = CGMCC 1.62049^T) and <em>Halomonas kalidii</em> (type strain M4R5S39^T = KCTC 8015^T = CGMCC 1.62047^T<span>) are proposed. The geographical distribution analysis based on 16S rRNA gene revealed that the two novel species are widely distributed across the globe, specifically in highly saline habits, especially in Central and Eastern Asia.</span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 1","pages":"Article 126488"},"PeriodicalIF":3.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139517363","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":"First single-strain enrichments of Electrothrix cable bacteria, description of E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., and proposal of a cable bacteria taxonomy following the rules of the SeqCode","authors":"Lea E. Plum-Jensen,&nbsp;Andreas Schramm,&nbsp;Ian P.G. Marshall","doi":"10.1016/j.syapm.2024.126487","DOIUrl":"10.1016/j.syapm.2024.126487","url":null,"abstract":"<div><p>Cable bacteria are electrically conductive, filamentous Desulfobulbaceae, which are morphologically, functionally, and phylogenetically distinct from the other members of this family. Cable bacteria have not been obtained in pure culture and were therefore previously described as candidate genera, <em>Candidatus</em> Electrothrix and <em>Ca.</em> Electronema; a representative of the latter is available as single-strain sediment enrichment. Here we present an improved workflow to obtain the first single-strain enrichments of <em>Ca.</em> Electrothrix and report their metagenome-assembled genomes (MAGs) and morphology. Based on these results and on previously published high-quality MAGs and morphological data of cable bacteria from both candidate genera, we propose to adopt the genus names <em>Electrothrix</em> and <em>Electronema</em> following the rules of the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), with <em>Electrothrix communis</em> RB^TS and <em>Electronema aureum</em> GS^TS, respectively, as the nomenclatural types of the genera. Furthermore, based on average nucleotide identity (ANI) values &lt; 95 % with any described species, we propose two of our three single-strain enrichment cultures as novel species of the genus <em>Electrothrix</em>, with the names <em>E. aestuarii</em> sp. nov. and <em>E. rattekaaiensis</em> sp. nov., according to the SeqCode.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 1","pages":"Article 126487"},"PeriodicalIF":3.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000018/pdfft?md5=bf0854542f33b2bd8f04b55b6069e5f4&pid=1-s2.0-S0723202024000018-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139583548","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}