Arthrobacter Paludis Sp. Nov., Isolated from a Marsh
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S41598-018-29442-2 1
www.nature.com/scientificreports OPEN Actinobacteria associated with Chinaberry tree are diverse and show antimicrobial activity Received: 28 February 2018 Ke Zhao1, Jing Li1, Meiling Shen1, Qiang Chen1, Maoke Liu2, Xiaolin Ao1, Decong Liao1, Accepted: 10 July 2018 Yunfu Gu1, Kaiwei Xu1, Menggen Ma1, Xiumei Yu1, Quanju Xiang1, Ji Chen1, Xiaoping Zhang1 & Published: xx xx xxxx Petri Penttinen 3,4 Many actinobacteria produce secondary metabolites that include antimicrobial compounds. Since most of the actinobacteria cannot be cultivated, their antimicrobial potential awaits to be revealed. We hypothesized that the actinobacterial endophyte communities inside Melia toosendan (Chinaberry) tree are diverse, include strains with antimicrobial activity, and that antimicrobial activity can be detected using a cultivation independent approach and co-occurrence analysis. We isolated and identifed actinobacteria from Chinaberry, tested their antimicrobial activities, and characterized the communities using amplicon sequencing and denaturing gradient gel electrophoresis as cultivation independent methods. Most of the isolates were identifed as Streptomyces spp., whereas based on amplicon sequencing the most abundant OTU was assigned to Rhodococcus, and Tomitella was the most diverse genus. Out of the 135 isolates, 113 inhibited the growth of at least one indicator organism. Six out of the 7577 operational taxonomic units (OTUs) matched 46 cultivated isolates. Only three OTUs, Streptomyces OTU4, OTU11, and OTU26, and their corresponding isolate groups were available for comparing co-occurrences and antimicrobial activity. Streptomyces OTU4 correlated negatively with a high number of OTUs, and the isolates corresponding to Streptomyces OTU4 had high antimicrobial activity. However, for the other two OTUs and their corresponding isolate groups there was no clear relation between the numbers of negative correlations and antimicrobial activity. -
Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample
geosciences Article Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample Andrey A. Belov 1,*, Vladimir S. Cheptsov 1,2 , Elena A. Vorobyova 1,2, Natalia A. Manucharova 1 and Zakhar S. Ezhelev 1 1 Soil Science Faculty, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (V.S.C.); [email protected] (E.A.V.); [email protected] (N.A.M.); [email protected] (Z.S.E.) 2 Space Research Institute, Russian Academy of Sciences, Moscow 119991, Russia * Correspondence: [email protected]; Tel.: +7-917-584-44-07 Received: 28 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated. -
Taxonomy and Systematics of Plant Probiotic Bacteria in the Genomic Era
AIMS Microbiology, 3(3): 383-412. DOI: 10.3934/microbiol.2017.3.383 Received: 03 March 2017 Accepted: 22 May 2017 Published: 31 May 2017 http://www.aimspress.com/journal/microbiology Review Taxonomy and systematics of plant probiotic bacteria in the genomic era Lorena Carro * and Imen Nouioui School of Biology, Newcastle University, Newcastle upon Tyne, UK * Correspondence: Email: [email protected]. Abstract: Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics. Keywords: phylogeny; plant; probiotic; PGPR; IAA; ACC; genome; metagenomics Abbreviations: ACC 1-aminocyclopropane-1-carboxylate ANI average nucleotide identity FAO Food and Agriculture Organization DDH DNA-DNA hybridization IAA indol acetic acid JA jasmonic acid OTUs Operational taxonomic units NGS next generation sequencing PGP plant growth promoters WHO World Health Organization PGPR plant growth-promoting rhizobacteria 384 1. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Data of Read Analyses for All 20 Fecal Samples of the Egyptian Mongoose
Supplementary Table S1 – Data of read analyses for all 20 fecal samples of the Egyptian mongoose Number of Good's No-target Chimeric reads ID at ID Total reads Low-quality amplicons Min length Average length Max length Valid reads coverage of amplicons amplicons the species library (%) level 383 2083 33 0 281 1302 1407.0 1442 1769 1722 99.72 466 2373 50 1 212 1310 1409.2 1478 2110 1882 99.53 467 1856 53 3 187 1308 1404.2 1453 1613 1555 99.19 516 2397 36 0 147 1316 1412.2 1476 2214 2161 99.10 460 2657 297 0 246 1302 1416.4 1485 2114 1169 98.77 463 2023 34 0 189 1339 1411.4 1561 1800 1677 99.44 471 2290 41 0 359 1325 1430.1 1490 1890 1833 97.57 502 2565 31 0 227 1315 1411.4 1481 2307 2240 99.31 509 2664 62 0 325 1316 1414.5 1463 2277 2073 99.56 674 2130 34 0 197 1311 1436.3 1463 1899 1095 99.21 396 2246 38 0 106 1332 1407.0 1462 2102 1953 99.05 399 2317 45 1 47 1323 1420.0 1465 2224 2120 98.65 462 2349 47 0 394 1312 1417.5 1478 1908 1794 99.27 501 2246 22 0 253 1328 1442.9 1491 1971 1949 99.04 519 2062 51 0 297 1323 1414.5 1534 1714 1632 99.71 636 2402 35 0 100 1313 1409.7 1478 2267 2206 99.07 388 2454 78 1 78 1326 1406.6 1464 2297 1929 99.26 504 2312 29 0 284 1335 1409.3 1446 1999 1945 99.60 505 2702 45 0 48 1331 1415.2 1475 2609 2497 99.46 508 2380 30 1 210 1329 1436.5 1478 2139 2133 99.02 1 Supplementary Table S2 – PERMANOVA test results of the microbial community of Egyptian mongoose comparison between female and male and between non-adult and adult. -
Aestuariimicrobium Ganziense Sp. Nov., a New Gram-Positive Bacterium Isolated from Soil in the Ganzi Tibetan Autonomous Prefecture, China
Aestuariimicrobium ganziense sp. nov., a new Gram-positive bacterium isolated from soil in the Ganzi Tibetan Autonomous Prefecture, China Yu Geng Yunnan University Jiang-Yuan Zhao Yunnan University Hui-Ren Yuan Yunnan University Le-Le Li Yunnan University Meng-Liang Wen yunnan university Ming-Gang Li yunnan university Shu-Kun Tang ( [email protected] ) Yunnan Institute of Microbiology, Yunnan University https://orcid.org/0000-0001-9141-6244 Research Article Keywords: Aestuariimicrobium ganziense sp. nov., Chemotaxonomy, 16S rRNA sequence analysis Posted Date: February 11th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-215613/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Archives of Microbiology on March 12th, 2021. See the published version at https://doi.org/10.1007/s00203-021-02261-2. Page 1/11 Abstract A novel Gram-stain positive, oval shaped and non-agellated bacterium, designated YIM S02566T, was isolated from alpine soil in Shadui Towns, Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, PR China. Growth occurred at 23–35°C (optimum, 30°C) in the presence of 0.5-4 % (w/v) NaCl (optimum, 1%) and at pH 7.0–8.0 (optimum, pH 7.0). The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain YIM S02566T was most closely related to the genus Aestuariimicrobium, with Aestuariimicrobium kwangyangense R27T and Aestuariimicrobium soli D6T as its closest relative (sequence similarities were 96.3% and 95.4%, respectively). YIM S02566T contained LL-diaminopimelic acid in the cell wall. -
This Article Appeared in a Journal Published by Elsevier. the Attached
This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Pharmacological Research 69 (2013) 32–41 Contents lists available at SciVerse ScienceDirect Pharmacological Research journa l homepage: www.elsevier.com/locate/yphrs Invited review Microbiota of male genital tract: Impact on the health of man and his partner a,b,∗ Reet Mändar a Department of Microbiology, University of Tartu, Ravila 19, Tartu 50411, Estonia b Competence Centre on Reproductive Medicine and Biology, Tiigi 61b, Tartu 50410, Estonia a r t i c l e i n f o a b s t r a c t Article history: This manuscript describes the male genital tract microbiota and the significance of it on the host’s and Received 10 July 2012 his partner’s health. Microbiota exists in male lower genital tract, mostly in urethra and coronal sulcus Received in revised form 16 October 2012 while high inter-subject variability exists. Differences appear between sexually transmitted disease pos- Accepted 29 October 2012 itive and negative men as well as circumcised and uncircumcised men. -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method. -
Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products. -
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SUPPLEMENTARY DATA Characterization of microbial communities associated with ceramic raw materials as potential contributors for the improvement of ceramic rheological properties Angela M. Garcia-Sanchez 1, Bernardino Machado-Moreira 2, Mário Freire 3, Ricardo Santos 3, Sílvia Monteiro 3, Diamantino Dias 4, Orquídia Neves 2, Amélia Dionísio 2 and Ana Z. Miller 5* 1 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville. Profesor García González 2, 41012 Seville, Spain; 2 CERENA, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisboa, Portugal; 3 Laboratorio de Análises do Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; 4 Rauschert Portuguesa, SA., Estrada Nacional 249-4, Trajouce, 2785-653 São Domingos de Rana, Portugal; 5 Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain; 6 HERCULES Laboratory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal. * Correspondence: [email protected] The Supplementary data include: Figure S1. Rarefaction curves. Table S1. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 1A (74 sequences, 64 OTUs). Table S2. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 2B (69 sequences, 51 OTUs). Table S3. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 4D (80 sequences, 54 OTUs). Table S4. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 6F (86 sequences, 38 OTUs). Table S5. Phylogenetic affiliations of the 16S rRNA gene sequences of total bacteria obtained from sample 7G (79 sequences, 48 OTUs). -
Isolation of Arthrobacter Species from the Phyllosphere and Demonstration of Their Epiphytic fitness Tanja R
ORIGINAL RESEARCH Isolation of Arthrobacter species from the phyllosphere and demonstration of their epiphytic fitness Tanja R. Scheublin1 & Johan H. J. Leveau1,2 1Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands 2Department of Plant Pathology, University of California, One Shields Avenue, Davis, California 95616 Keywords Abstract Arthrobacter, biodegradation, phylloplane, phylloremediation, soil, triadimenol Bacteria of the genus Arthrobacter are common inhabitants of the soil environ- ment, but can also be recovered from leaf surfaces (the phyllosphere). Using Correspondence enrichment cultures on 4-chlorophenol, we succeeded in specifically isolating Johan Leveau, University of California, Arthrobacter bacteria from ground cover vegetation in an apple orchard. Based Department of Plant Pathology, One Shields on 16S rRNA gene sequencing, the isolates were found to belong to at least Avenue, Davis, CA 95616. three different species of Arthrobacter. Compared to the model bacterial epi- Tel: +1 (530) 752 5046; Fax: +1 (530) 752 5674; E-mail: [email protected] phyte Pantoea agglomerans, the Arthrobacter isolates performed as well or even better in a standardized laboratory test of phyllosphere fitness. A similar perfor- Funding Information mance was observed with the well-characterized soil isolate Arthrobacter chloro- This work was supported as part of the phenolicus A6. These findings suggest that the frequently reported presence of BACSIN project within -
Comparative Genomics and Physiological Investigation
Comparative Genomics and Physiological Investigation Supported Safety, Cold Adaptation, Ecient Hydrolytic and Plant Growth-promoting Potential of Psychrotrophic Glutamicibacter Arilaitensis LJH19, Isolated from Night-Soil Compost Shruti Borker Institute of Himalayan Bioresource Technology Aman Thakur Institute of Himalayan Bioresource Technology Sanjeet Kumar Institute of Himalayan Bioresource Technology Sareeka Kumari Institute of Himalayan Bioresource Technology Rakshak Kumar ( [email protected] ) Institute of Himalayan Bioresource Technology Sanjay Kumar Institute of Himalayan Bioresource Technology Research Article Keywords: Winter dry toilet, polysaccharide metabolism, indole acetic acid, siderophore, type III PKS Posted Date: December 10th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-122385/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on April 28th, 2021. See the published version at https://doi.org/10.1186/s12864-021-07632-z. Page 1/37 Abstract Background: Night-soil compost (NSC) has traditionally been conserving water and a source of organic manure in northwestern Himalaya. Lately, this traditional method is declining due to modernization, its unhygienic conditions, and social apprehensions. Reduction in the age-old traditional practice has led to excessive chemical fertilizers and water shortage in the eco-sensitive region. In the current study, a bacterium has been analysed for its safety, cold-adaptation, ecient degradation, and plant growth potential attributes for its possible application as a safe bioinoculant in psychrotrophic bacterial consortia for improved night-soil composting. Results: Glutamicibacter arilaitensis LJH19, a psychrotrophic bacterium, was isolated from the night-soil compost of Lahaul valley in northwestern Himalaya.