Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

{"title":"The genus Coelastrella (Chlorophyceae, Chlorophyta): molecular species delimitation, biotechnological potential, and description of a new species Coelastrella affinis sp. nov., based on an integrative taxonomic approach","authors":"E. Krivina,&nbsp;M. Sinetova,&nbsp;E. Zadneprovskaya,&nbsp;M. Ivanova,&nbsp;A. Starikov,&nbsp;K. Shibzukhova,&nbsp;E. Lobakova,&nbsp;Yu. Bukin,&nbsp;A. Portnov,&nbsp;A. Temraleeva","doi":"10.1007/s10482-024-02008-1","DOIUrl":"10.1007/s10482-024-02008-1","url":null,"abstract":"<div><p>Despite the long research history on the genus <i>Coelastrella</i>, its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship. It the light of it, the taxonomic status of species can reliably be determined using specific DNA region, such as 18S–ITS1–5.8S–ITS2. The V4 and V9 regions of gene 18S rRNA are relatively conservative fragments which are not suitable for species identification. The ITS2 can be used as a “short barcode”. Among the advanced machine methods for delimitation species, the most effective algorithm for distinguishing <i>Coelastrella</i> species was the Generalized Mixed Yule Coalescent (GMYC) method. This paper represented for the first time our comprehensive review of the works devoted to the analysis of the biotechnological potential of representatives of the genus <i>Coelastrella</i> and shows that fatty acid composition of the three main chemogroups within the studied genus differs. In the future, this may form the basis for predicting the composition of the fatty acid profile of new strains, which is important while searching for organisms with specified biotechnological properties. In conclusion, an integrative approach was employed to describe <i>Coelastrella affinis</i> sp. nov., a new species of the genus <i>Coelastrella</i> with high biotechnological potential. Also, a new description of <i>C. thermophila</i> var. <i>astaxanthina</i> comb. nov. was proposed.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001264","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}

{"title":"Peteryoungia algae sp. nov. isolated from seaweeds of Gouqi Island, China, and its unique genetic features among Peteryoungia strains","authors":"Jun Yin,&nbsp;Min He,&nbsp;Xiao-Xiao Liu,&nbsp;Chang-Bin Ren,&nbsp;Hou-Hong Liu,&nbsp;Hai Luo,&nbsp;Gen Chen,&nbsp;Ze-Fei Wang,&nbsp;Sanjit Chandra Debnath,&nbsp;Pin-Mei Wang,&nbsp;Hai-Xin Chen,&nbsp;Dao-Qiong Zheng","doi":"10.1007/s10482-024-02010-7","DOIUrl":"10.1007/s10482-024-02010-7","url":null,"abstract":"<div><p>A Gram-stain-negative, light khaki, strictly aerobic, rod-shaped, motile via multiple flagella, and catalase- and oxidase-positive bacterium, designated as SSM4.3^T, was isolated from the seaweed of Gouqi Island in the East China Sea. The novel isolate grows at 0–5.0% NaCl concentrations (w/v) (optimum 1%), pH 5.0–9.0 (optimum pH 7.0), and 15–37 °C (optimum 30 °C). The 16S rRNA gene sequences-based phylogeny indicates that the novel marine isolate belongs to the family <i>Rhizobiaceae</i> and that it shared the greatest sequence similarity (98.9%) with <i>Peteryoungia rhizophila</i> CGMCC 1.15691^T. This classification was also supported by phylogenetic analysis using core genes. The predominant fatty acids (≥ 10%) of the strain were identified as C_18:1 ω7c/C_18:1 ω6c. Q-10 was identified as the major isoprenoid quinone, with trace levels of Q-9 present. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The complete genome size of strain SSM4.3^T is 4.39 Mb with a DNA G+C content of 61.3%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain SSM4.3^T and its closely related representatives were 74.80–86.93%, 20.00–32.30%, and 70.30–91.52%, respectively. Phylogenetic analysis, grounded on the core genes, reveals the evolutionary relationship between SSM4.3^T and other <i>Peteryoungia</i> strains. Pan-genomics analysis of 8 previously classified <i>Peteryoungia</i> species and SSM4.3^T revealed their unique genetic features and functions. Overall, strain SSM4.3^T was considered to be a new species of the <i>Peteryoungia</i> genus; the name <i>Peteryoungia algae</i> sp. nov. has been proposed, with type strain SSM4.3^T (= LMG 32561 = MCCC 1K07170).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917989","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}

{"title":"Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan","authors":"Sadia Manzoor,&nbsp;Saira Abbas,&nbsp;Sobia Zulfiqar,&nbsp;Hong-Chuan Wang,&nbsp;Min Xiao,&nbsp;Wen-Jun Li,&nbsp;Muhammad Arshad,&nbsp;Iftikhar Ahmed","doi":"10.1007/s10482-024-02006-3","DOIUrl":"10.1007/s10482-024-02006-3","url":null,"abstract":"<div><p>The strain designated NCCP-602^T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602^T within genus <i>Brevibacterium</i> and showed that it was closely related to <i>Brevibacterium ammoniilyticum</i> JCM 17537^T. Strain NCCP-602^T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602^T provided additional evidence supporting the classification of strain NCCP-602^T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C_15:0, iso-C_15:0, iso-C_16:0, iso-C_17:0, and anteiso-C_17:0 were identified as the predominant cellular fatty acids (&gt; 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602^T be classified as a distinct species <i>Brevibacterium metallidurans</i> sp. nov. within genus <i>Brevibacterium</i> with type strain NCCP-602^T (JCM 18882^T = CGMCC1.62055^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894812","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}

{"title":"Additional new species of Xenodidymella from pasture-medicinal plants in Iran","authors":"Maryam Karimi,&nbsp;Mehdi Mehrabi-Koushki,&nbsp;Reza Farokhinejad,&nbsp;Siamak Beigi","doi":"10.1007/s10482-024-02007-2","DOIUrl":"10.1007/s10482-024-02007-2","url":null,"abstract":"<div><p><i>Xenodidymella</i> species have a wide range of hosts and can be found as pathogens and saprobes. In this study, two new species of <i>Xenodidymella</i> were found from leaf diseases of three pasture-medicinal plants in Ilam Province, in the west of Iran, and proposed here as <i>X. ilamica</i> and <i>X. scandicis</i> spp. nov. These species were identified based on morphological features and phylogenetic analyses of the internal transcribed spacer regions 1 &amp; 2 and 5.8S nrDNA (ITS), partial beta-tubulin gene (<i>tub2</i>), and partial RNA polymerase II second largest subunit (<i>rpb2</i>) gene. The four <i>Xenodidymella</i> strains isolated in this study were delimited into two sister clades, with the two isolates of <i>X. ilamica</i> from the leaf spot of <i>Colchicum speciosum</i> and <i>Ficaria kochii</i> and two isolates of <i>X. scandicis</i> from leaf blight of <i>Scandix pecten-veneris</i>. Morphologically, <i>X. scandicis</i> produces larger, ostiolate or poroid pycnidia in vitro, while pycnidia in the cultures of <i>X. ilamica</i> are non-ostiolate and smaller. Some pycnidia in old cultures of <i>X. scandicis</i> produce a neck, but a distinct neck in <i>X. ilamica</i> has not been observed. Moreover, three plants under study are new hosts for the genus <i>Xenodidymella</i>.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861500","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}

{"title":"Phylogenetic and morphological re-evaluation of Camptophora","authors":"Akira Hashimoto,&nbsp;Saho Shibata,&nbsp;Yuuri Hirooka,&nbsp;Moriya Ohkuma","doi":"10.1007/s10482-024-01990-w","DOIUrl":"10.1007/s10482-024-01990-w","url":null,"abstract":"<div><p>The genetic variety and habitats of <i>Camptophora</i> species, generally known as black yeast, have not been clarified. In this study, we re-evaluated <i>Camptophora</i> based on morphological observations and phylogenetic analyses. Because prior investigations on <i>Camptophora</i> only included a few strains/specimens, 24 <i>Camptophora</i>-related strains were newly obtained from 13 leaf samples of various plant species to redefine the genetic and species concepts of <i>Camptophora</i>. Their molecular phylogenetic relationships were examined using small subunit nuclear ribosomal DNA (nSSU, 18S rDNA), the internal transcribed spacer (ITS) rDNA operon, the large subunit nuclear ribosomal DNA (LSU, 28S rDNA), β-tubulin, the second largest subunit of RNA polymerase II (<i>rpb2</i>), and mitochondrial small subunit DNA (mtSSU). Single- and multi-locus analyses using nSSU-ITS-LSU-<i>rpb2</i>-mtSSU revealed a robust phylogenetic relationship among <i>Camptophora</i> species within <i>Chaetothyriaceae</i>. <i>Camptophora</i> species could be distinguished from other chaetothyriaceous genera by their snake-shaped conidia with microcyclic conidiation and loosely interwoven mycelial masses. Based on the results of phylogenetic analyses, two undescribed lineages were recognized, and <i>Ca. schimae</i> was excluded from the genus. ITS sequence comparison with environmental DNA sequences revealed that the distribution of the genus is restricted to the Asia–Pacific region. <i>Camptophora</i> has been isolated or detected from abrupt sources, and this was attributed to its microcycle. The mechanisms driving genetic diversity within species are discussed with respect to their phyllosphere habitats.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857046","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}

{"title":"Desertibaculum subflavum gen. nov., sp. nov., a novel member of the family Sneathiellaceae isolated from the Kumtag Desert soil","authors":"Chu-Ying Feng,&nbsp;Huan-Huan He,&nbsp;Shuai Li,&nbsp;Zhuo-Huan Zheng,&nbsp;Yi-Jun Mo,&nbsp;Wen-Hui Lian,&nbsp;Chun-Yan Lu,&nbsp;Dong-Ya Zhang,&nbsp;Wen-Jun Li,&nbsp;Lei Dong","doi":"10.1007/s10482-024-02003-6","DOIUrl":"10.1007/s10482-024-02003-6","url":null,"abstract":"<div><p>A novel rod-shaped bacterium, designated as strain SYSU D60015^T that formed yellowish colonies was isolated from a sandy soil collected from the Kumtag Desert in Xinjiang, China. Cells were Gram-stain-negative, oxidase-positive, catalase-negative and motile with a single polar flagellum. Growth optimum occurred between 28 and 37 °C, pH 7.0 and with 0–0.5% (W/V) NaCl. The predominant cellular fatty acids (&gt; 5%) were summed feature 8 (C_18:1 <i>ω</i>7<i>c</i> and/or C_18:1 <i>ω</i>6<i>c</i>), C_19:0 cyclo <i>ω</i>8<i>c</i>, C_18:1 <i>ω</i>7<i>c</i> 11-methyl and C_16:0. The polar lipid profile contained one phosphatidylethanolamine, one diphosphatidylglycerol, one phosphatidylglycerol, one unidentified phospholipid, three unidentified aminolipids, two unidentified aminophospholipids and seven unidentified lipids. The only respiratory quinone was ubiquinone-10. Based on 16S rRNA gene sequence phylogenetic analysis, strain SYSU D60015^T was found to form a distinct linage within the family <i>Sneathiellaceae</i>, and had 16S rRNA gene sequence similarities of 90.8% to <i>Taonella mepensis</i> H1^T, and 90.2% to <i>Ferrovibrio denitrificans</i> S3^T. The genome of SYSU D60015^T was 5.66 Mb in size with 68.2% of DNA G + C content. The low digital DNA-DNA hybridization (dDDH, 18.0%), average nucleotide identity (ANI, 77.5%) and amino acid identity (AAI, 56.0%) values between SYSU D60015^T and <i>Ferrovibrio terrae</i> K5^T indicated that SYSU D60015^T might represent a distinct genus. Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose <i>Desertibaculum subflavum</i> gen. nov., sp. nov. as a novel species of a new genus within the family <i>Sneathiellaceae</i>. The type strain is SYSU D60015^T (= NBRC 112952^T = CGMCC 1.16256^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857045","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}

{"title":"Chengkuizengella axinellae sp. nov., a symbiotic bacterium isolated from a marine sponge of the genus Axinella","authors":"Yea-Lin Moon,&nbsp;Kyung Hyun Kim,&nbsp;Jin-Sook Park","doi":"10.1007/s10482-024-01998-2","DOIUrl":"10.1007/s10482-024-01998-2","url":null,"abstract":"<div><p>A Gram-stain-positive, strictly aerobic, creamy-white colored, endospore-forming and non-motile rods strain, designated as strain 2205SS18-9^T, was isolated from a marine sponge, <i>Axinella</i> sp. collected from Seopseom Island, Republic of Korea. Optimal growth of strain 2205SS18-9^T was observed at 25–30 °C, pH 6.5–7.0, and in the presence of 3.0% (w/v) NaCl. Cells were oxidase-positive and catalase-negative. Negative for nitrate reduction and indole production. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2205SS18-9^T formed a distinct phyletic lineage in the genus <i>Chengkuizengella</i>, and it was most closely related to <i>Chengkuizengella marina</i> YPA3-1-1^T and <i>Chengkuizengella sediminis</i> J15A17^T with 97.1 and 96.6% 16S rRNA gene sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2205SS18-9^T and <i>Chengkuizengella marina</i> YPA3-1-1^T were 79.0 and 21.6%, respectively. The genomic DNA G + C content was 34.1%. The genome harbors a number of host-adhesion and transporter genes, suggested that strain 2205SS18-9^T may interact with its sponge host as a symbiont. Menaquinone-7 was the sole isoprenoid quinone and antieiso-C_15:0 (28.5%), iso-C_16:0 (25.8%), C_16:1 <i>ω</i>7c alcohol (15.0%), and iso-C_15:0 (11.2%) were detected as the major fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and an unidentified lipid. The cell-wall peptidoglycan contained lysine, alanine, glutamate, and aspartate. Based on these analyses, strain 2205SS18-9^T represents a novel species of the genus <i>Chengkuizengella</i>, for which the name <i>Chengkuizengella axinellae</i> sp. nov. is proposed. The type strain is 2205SS18-9^T (= KACC 23238^T = LMG 33063^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141767920","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}

{"title":"Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest","authors":"Mikitoshi Harada,&nbsp;Atsuya Endo,&nbsp;Shuji Wada,&nbsp;Takeshi Watanabe,&nbsp;Daniel Epron,&nbsp;Susumu Asakawa","doi":"10.1007/s10482-024-02004-5","DOIUrl":"10.1007/s10482-024-02004-5","url":null,"abstract":"<div><p>Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, <i>Cryptomeria japonica</i>, <i>Quercus crispula</i>, <i>Fraxinus mandshurica</i>, <i>Acer pictum</i>, <i>Aesculus turbinata</i>, <i>Magnolia obovata</i>, and <i>Populus tremula</i>. Amplicon sequencing analysis of 16S rRNA genes showed that <i>Methanobacteriaceae</i> predominated the archaeal communities and <i>Methanomassiliicoccaceae</i> also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal <i>mcrA</i> genes from all the tree species, with a maximum of 10⁷ copies g⁻¹ dry wood. Digital PCR analysis also detected <i>mcrA</i> genes derived from <i>Methanobacterium</i> spp. and <i>Methanobrevibacter</i> spp. from several samples, with a maximum of 10⁵ and 10⁴ copies g⁻¹ dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 10⁶ cells g⁻¹ dry wood was enumerated from a heartwood sample of <i>C. japonica</i>. Methanogenic archaea related to <i>Methanobacterium beijingense</i> were cultivated from a heartwood sample of <i>Q. crispula</i> and <i>F. mandshurica</i>. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141767921","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}

{"title":"Genomics and taxonomy of the glyphosate-degrading, copper-tolerant rhizospheric bacterium Achromobacter insolitus LCu2","authors":"Yelena V. Kryuchkova,&nbsp;Alexandra A. Neshko,&nbsp;Natalia E. Gogoleva,&nbsp;Alexander S. Balkin,&nbsp;Vera I. Safronova,&nbsp;Kristina Yu. Kargapolova,&nbsp;Elena I. Shagimardanova,&nbsp;Yuri V. Gogolev,&nbsp;Gennady L. Burygin","doi":"10.1007/s10482-024-01989-3","DOIUrl":"10.1007/s10482-024-01989-3","url":null,"abstract":"<div><p>A rhizosphere strain, <i>Achromobacter insolitus</i> LCu2, was isolated from alfalfa (<i>Medicago sativa</i> L.) roots. It was able to degrade of 50% glyphosate as the sole phosphorus source, and was found resistant to 10 mM copper (II) chloride, and 5 mM glyphosate–copper complexes. Inoculation of alfalfa seedlings and potato microplants with strain LCu2 promoted plant growth by 30–50%. In inoculated plants, the toxicity of the glyphosate–copper complexes to alfalfa seedlings was decreased, as compared with the noninoculated controls. The genome of <i>A. insolitus</i> LCu2 consisted of one circular chromosome (6,428,890 bp) and encoded 5843 protein genes and 76 RNA genes. Polyphasic taxonomic analysis showed that <i>A. insolitus</i> LCu2 was closely related to <i>A. insolitus</i> DSM23807^T on the basis of the average nucleotide identity of the genomes of 22 type strains and the multilocus sequence analysis. Genome analysis revealed genes putatively responsible for (1) plant growth promotion (osmolyte, siderophore, and 1-aminocyclopropane-1-carboxylate deaminase biosynthesis and auxin metabolism); (2) degradation of organophosphonates (glyphosate oxidoreductase and multiple <i>phn</i> clusters responsible for the transport, regulation and C–P lyase cleavage of phosphonates); and (3) tolerance to copper and other heavy metals, effected by the CopAB–CueO system, responsible for the oxidation of copper (I) in the periplasm, and by the efflux Cus system. The putative catabolic pathways involved in the breakdown of phosphonates are predicted. <i>A. insolitus</i> LCu2 is promising in the production of crops and the remediation of soils contaminated with organophosphonates and heavy metals.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753277","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}

{"title":"Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria","authors":"Wouter B. Lenferink,&nbsp;Theo A. van Alen,&nbsp;Mike S. M. Jetten,&nbsp;Huub J. M. Op den Camp,&nbsp;Maartje A. H. J. van Kessel,&nbsp;Sebastian Lücker","doi":"10.1007/s10482-024-02002-7","DOIUrl":"10.1007/s10482-024-02002-7","url":null,"abstract":"<div><p>Bacteria of the phylum <i>Planctomycetota</i> have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class <i>Phycisphaerae</i> have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality <i>Phycisphaerae</i> genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird’s eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any <i>Phycisphaerae</i> genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by <i>Phycisphaerae</i> families.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753276","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}