Screening, Production, and Characterization of Dextranase from Catenovulum Sp
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Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment
Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen. -
Alishewanella Jeotgali Sp. Nov., Isolated from Traditional Fermented Food, and Emended Description of the Genus Alishewanella
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2313–2316 DOI 10.1099/ijs.0.007260-0 Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella Min-Soo Kim,1,2 Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,1 Kyoung-Ho Kim,1 Mi-Ja Jung,1 Jung-Hye Choi,1 Eun-Jin Park1 and Jin-Woo Bae1,2 Correspondence 1Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee Jin-Woo Bae University, Seoul 130-701, Republic of Korea [email protected] 2University of Science and Technology, Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea A novel Gram-negative and facultative anaerobic strain, designated MS1T, was isolated from gajami sikhae, a traditional fermented food in Korea made from flatfish. Strain MS1T was motile, rod-shaped and oxidase- and catalase-positive, and required 1–2 % (w/v) NaCl for growth. Growth occurred at temperatures ranging from 4 to 40 6C and the pH range for optimal growth was pH 6.5–9.0. Strain MS1T was capable of reducing trimethylamine oxide, nitrate and thiosulfate. Phylogenetic analysis placed strain MS1T within the genus Alishewanella. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MS1T was related closely to Alishewanella aestuarii B11T (98.67 % similarity) and Alishewanella fetalis CCUG 30811T (98.04 % similarity). However, DNA–DNA reassociation experiments between strain MS1T and reference strains showed relatedness values ,70 % (42.6 and 14.8 % with A. -
Bacterial Succession Within an Ephemeral Hypereutrophic Mojave Desert Playa Lake
Microb Ecol (2009) 57:307–320 DOI 10.1007/s00248-008-9426-3 MICROBIOLOGY OF AQUATIC SYSTEMS Bacterial Succession within an Ephemeral Hypereutrophic Mojave Desert Playa Lake Jason B. Navarro & Duane P. Moser & Andrea Flores & Christian Ross & Michael R. Rosen & Hailiang Dong & Gengxin Zhang & Brian P. Hedlund Received: 4 February 2008 /Accepted: 3 July 2008 /Published online: 30 August 2008 # Springer Science + Business Media, LLC 2008 Abstract Ephemerally wet playas are conspicuous features RNA gene sequencing of bacterial isolates and uncultivated of arid landscapes worldwide; however, they have not been clones. Isolates from the early-phase flooded playa were well studied as habitats for microorganisms. We tracked the primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet geochemistry and microbial community in Silver Lake clone libraries were dominated by Betaproteobacteria and yet playa, California, over one flooding/desiccation cycle uncultivated Actinobacteria. Isolates from the late-flooded following the unusually wet winter of 2004–2005. Over phase ecosystem were predominantly Proteobacteria, partic- the course of the study, total dissolved solids increased by ularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, ∽10-fold and pH increased by nearly one unit. As the lake Hydrogenophaga, Alishwenella, and relatives of Thauera; contracted and temperatures increased over the summer, a however, clone libraries were composed almost entirely of moderately dense planktonic population of ∽1×106 cells ml−1 Synechococcus (Cyanobacteria). A sample taken after the of culturable heterotrophs was replaced by a dense popula- playa surface was completely desiccated contained diverse tion of more than 1×109 cells ml−1, which appears to be the culturable Actinobacteria typically isolated from soils. -
Genes for Degradation and Utilization of Uronic Acid-Containing Polysaccharides of a Marine Bacterium Catenovulum Sp
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 Go Furusawa, Nor Azura Azami and Aik-Hong Teh Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia ABSTRACT Background. Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods. To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results. The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in Submitted 5 August 2020 the QB4 genome based on the CAZy database. -
Alishewanella Aestuarii Sp. Nov., Isolated from Tidal Flat Sediment, and Emended Description of the Genus Alishewanella
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 421–424 DOI 10.1099/ijs.0.65643-0 Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,2 Kyoung-Ho Kim,2 Min-Soo Kim,1,2 Hee-Mock Oh2 and Jin-Woo Bae1,2,3 Correspondence 1University of Science & Technology, 52, Eoeun-dong, Daejeon 305-333, Republic of Korea Jin-Woo Bae 2Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea [email protected] 3Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea A Gram-negative strain, B11T, was isolated from tidal flat sediment in Yeosu, Republic of Korea. Strain B11T did not require NaCl for growth and grew between 18 and 44 6C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B11T was associated with the genus Alishewanella and was closely related to the type strain of Alishewanella fetalis (98.3 % similarity). Within the phylogenetic tree, the novel isolate shared a branching point with A. fetalis. Analysis of 16S rRNA gene sequences and DNA–DNA relatedness, as well as physiological and biochemical tests, indicated genotypic and phenotypic differences between strain B11T and the type strain of A. fetalis. Thus, strain B11T is proposed as a representative of a novel species, Alishewanella aestuarii sp. nov.; the type strain is B11T (5KCTC 22051T 5DSM 19476T). The genus Alishewanella, proposed by Fonnesbech Vogel et description; Table 1 shows a comparison between the al. -
Succession and Cazyme Expression of Marine Bacterial
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; this version posted December 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Sweet and magnetic: Succession and CAZyme expression of marine bacterial communities encountering a mix of alginate and pectin particles Carina Bunse1,2,*, Hanna Koch3,4,*, Sven Breider3, Meinhard Simon1,3 and Matthias Wietz2,3# 1Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Germany 2Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Germany 3Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany 4Department of Microbiology, Radboud University Nijmegen, The Netherlands *These authors contributed equally to this work. #Corresponding author HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Am Handelshafen 12 27570 Bremerhaven Germany Email: [email protected] Telephone +49-471-48311454 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; this version posted December 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT Polysaccharide particles are an important nutrient source and microhabitat for marine bacteria. However, substrate-specific bacterial dynamics in a mixture of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. -
Draft Genomic Sequence of a Chromate- and Sulfate-Reducing
Xia et al. Standards in Genomic Sciences (2016) 11:48 DOI 10.1186/s40793-016-0169-3 SHORT GENOME REPORT Open Access Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination Xian Xia1, Jiahong Li1, Shuijiao Liao1,2, Gaoting Zhou1,2, Hui Wang1, Liqiong Li1, Biao Xu1 and Gejiao Wang1* Abstract Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative, rod-shaped bacterium isolated from soil of a copper and iron mine. This strain efficiently reduces chromate (Cr6+) to the much 3+ 2− 2− 2− 2+ less toxic Cr . In addition, it reduces sulfate (SO4 )toS . The S could react with Cd to generate precipitated CdS. Thus, strain WH16-1 shows a great potential to bioremediate Cr and Cd contaimination. Here we describe the features of this organism, together with the draft genome and comparative genomic results among strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp, 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative chromate- and sulfate-reducing genes are identified. Keywords: Alishewanella, Chromate-reducing bacterium, Sulfate-reducing bacterium, Cadmium, Chromium Abbreviation: PGAP, Prokaryotic Genome Annotation Pipeline Introduction Alishewanella sp. WH16-1 was isolated from mining The genus Alishewanella was established by Vogel et al., soil in 2009. This strain could resist to multiple heavy in 2000 with Alishewanella fetalis as the type species. It metals. During cultivation, it could efficiently reduce the belongs to the family Alteromonadaceae of the class toxic chromate (Cr6+) to the much less toxic and less 3+ 2− Gammaproteobacteria [1]. -
Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas Joobiniege Gen, Nov, Sp
J. Microbiol. Biotechnol. (2013), 23(11), 1509–1518 http://dx.doi.org/10.4014/jmb.1308.08007 Research Article jmb Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea Won-Jae Chi1, Jae-Seon Park1, Min-Jung Kwak2, Jihyun F. Kim3, Yong-Keun Chang4, and Soon-Kwang Hong1* 1Division of Biological Science and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea 2Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Republic of Korea 3Department of Systems Biology, Yonsei University, Seoul 120-749, Republic of Korea 4Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea Received: August 2, 2013 Revised: August 14, 2013 An agar-degrading bacterium, designated as strain G7T, was isolated from a coastal seawater Accepted: August 20, 2013 sample from Gaya Island (Gayado in Korean), Republic of Korea. The isolated strain G7T is gram-negative, rod shaped, aerobic, non-motile, and non-pigmented. A similarity search based on its 16S rRNA gene sequence revealed that it shares 95.5%, 90.6%, and 90.0% T First published online similarity with the 16S rRNA gene sequences of Catenovulum agarivorans YM01, Algicola August 22, 2013 sagamiensis, and Bowmanella pacifica W3-3AT, respectively. Phylogenetic analyses demonstrated T *Corresponding author that strain G7 formed a distinct monophyletic clade closely related to species of the family Phone: +82-31-330-6198; Alteromonadaceae in the Alteromonas-like Gammaproteobacteria. The G+C content of strain Fax: +82-31-335-8249; G7T was 41.12 mol%. -
Metagenomics Unveils the Attributes of the Alginolytic Guilds of Sediments from Four Distant Cold Coastal Environments
Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments Marina N Matos1, Mariana Lozada1, Luciano E Anselmino1, Matías A Musumeci1, Bernard Henrissat2,3,4, Janet K Jansson5, Walter P Mac Cormack6,7, JoLynn Carroll8,9, Sara Sjöling10, Leif Lundgren11 and Hebe M Dionisi1* 1Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina 2Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France 3INRA, USC 1408 AFMB, F-13288 Marseille, France 4Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia 5Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA 6Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, C1064ABR, Argentina 7Instituto Nanobiotec, CONICET- Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1113AAC, Argentina 8Akvaplan-niva, Fram – High North Research Centre for Climate and the Environment, NO- 9296 Tromsø, Norway 9CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, N-9037 Tromsø, Norway 10School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden 11Stockholm University, SE-106 91 Stockholm, Sweden This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an ‘Accepted Article’, doi: 10.1111/1462-2920.13433 This article is protected by copyright. All rights reserved. Page 2 of 41 Running title: Alginolytic guilds from cold sediments *Correspondence: Hebe M. -
Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2010 Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi South Dakota School of Mines and Technology Shariff Osman Lawrence Berkeley National Laboratory Ravi K. Kukkadapu Pacific Northwest National Laboratory, [email protected] Mark Engelhard Pacific Northwest National Laboratory Parag A. Vaishampayan California Institute of Technology See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub Part of the Bioresource and Agricultural Engineering Commons Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi K.; Engelhard, Mark; Vaishampayan, Parag A.; Andersen, Gary L.; and Sani, Rajesh K., "Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota" (2010). US Department of Energy Publications. 170. https://digitalcommons.unl.edu/usdoepub/170 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Gurdeep Rastogi, Shariff Osman, Ravi K. Kukkadapu, Mark Engelhard, Parag A. Vaishampayan, Gary L. Andersen, and Rajesh K. Sani This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdoepub/170 Microb Ecol (2010) 60:539–550 DOI 10.1007/s00248-010-9657-y SOIL MICROBIOLOGY Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi & Shariff Osman & Ravi Kukkadapu & Mark Engelhard & Parag A. -
Selfish, Sharing and Scavenging Bacteria in the Atlantic Ocean: A
The ISME Journal (2019) 13:1119–1132 https://doi.org/10.1038/s41396-018-0326-3 ARTICLE Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation 1 2 1 1 Greta Reintjes ● Carol Arnosti ● B. Fuchs ● Rudolf Amann Received: 13 May 2018 / Revised: 6 November 2018 / Accepted: 23 November 2018 / Published online: 7 December 2018 © The Author(s) 2018. This article is published with open access Abstract Identifying the roles played by individual heterotrophic bacteria in the degradation of high molecular weight (HMW) substrates is critical to understanding the constraints on carbon cycling in the ocean. At five sites in the Atlantic Ocean, we investigated the processing of organic matter by tracking changes in microbial community composition as HMW polysaccharides were enzymatically hydrolysed over time. During this investigation, we discovered that a considerable fraction of heterotrophic bacteria uses a newly-identified ‘selfish’ mode of substrate processing. We therefore additionally examined the balance of individual substrate utilisation mechanisms at different locations by linking individual microorganisms to distinct substrate utilisation mechanisms. Through FISH and uptake of fluorescently-labelled ‘ fi ’ fi 1234567890();,: 1234567890();,: polysaccharides, sel sh organisms were identi ed as belonging to the Bacteroidetes, Planctomycetes and Gammapro- teobacteria. ‘Sharing’ (extracellular enzyme producing) and ‘scavenging’ (non-enzyme producing) organisms predomi- nantly belonged to the Alteromonadaceae and SAR11 clades, respectively. The extent to which individual mechanisms prevail depended on the initial population structure of the bacterial community at a given location and time, as well as the growth rate of specific bacteria. Furthermore, the same substrate was processed in different ways by different members of a pelagic microbial community, pointing to significant follow-on effects for carbon cycling. -
TPP Riboswitch Characterization in Alishewanella Tabrizica And
Erschienen in: Microbiological Research ; 195 (2017). - S. 71-80 https://dx.doi.org/10.1016/j.micres.2016.11.003 TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches a,b,c d a e,f Elnaz Mehdizadeh Aghdam , Malte Sinn , Vahideh Tarhriz , Abolfazl Barzegar , d,∗∗ a,b,∗ Jörg S. Hartig , Mohammad Saeid Hejazi a Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran b Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran c Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran d Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany e Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran f The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran a b s t r a c t Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environ- mental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5 UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized. Moreover, affinity analysis of TPP binding to the TPP aptamer domains originated from A. tabrizica, A. aestuarii, E.coli, and B. subtilis were studied and compared using In-line probing and Sur- face Plasmon Resonance (SPR).