Bacterial Diversity in the Bottom Boundary Layer of the Inner Continental Shelf of Oregon, USA
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Description of Ectothiorhodospira Salini Sp. Nov
J. Gen. Appl. Microbiol., 56, 313‒319 (2010) Full Paper Description of Ectothiorhodospira salini sp. nov. Vemuluri Venkata Ramana,1 Chintalapati Sasikala,1,* Eedara Veera Venkata Ramaprasad,2 and Chintalapati Venkata Ramana2 1 Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukakatpally, Hyderabad 500 085, India 2 Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India (Received October 26, 2009; Accepted April 28, 2010) Strain JA430T is a Gram-negative, vibrioid to spiral shaped phototrophic purple sulfur bacterium isolated from anoxic sediment of a saltern at Kanyakumari in a mineral salts medium that con- tained 2% NaCl (w/v). Strain JA430T grows optimally at 5‒6% NaCl and tolerates up to 12% NaCl. Intracellular photosynthetic membranes were of the lamellar type. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series are present as photosynthetic pigments. Major cellular T fatty acids are C18:1ω7c, C16:0, C19:0cycloω8c and C16:1ω7c/C16:1ω6c. Strain JA430 exhibits pho- toorganoheterotrophy and chemoorganoheterotrophy and requires para-aminobenzoic acid, pantothenate and pyridoxal phosphate for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequence analysis showed that strain JA430T forms monophyletic group in the genus Ectothiorhodospira. The highest sequence similarity for strain JA430T was found with the type strains of Ectothiorhodospira variabilis DSM 21381T (96.1%) and Ectothiorhodospira haloalka- liphila ATCC 51935T (96.2%). Morphological and physiological characteristics discriminate strain JA430T from other species of the genus Ectothiorhodospira, for which we describe this as a novel species, Ectothiorhodospira salini sp. -
1 Anoxygenic Phototrophic Chloroflexota Member Uses a Type
Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center Supplementary Materials J. M. Tsuji, N. A. Shaw, S. Nagashima, J. J. Venkiteswaran, S. L. Schiff, S. Hanada, M. Tank, J. D. Neufeld Correspondence to: [email protected]; [email protected]; [email protected] This PDF file includes: Materials and Methods Supplementary Text, Sections S1 to S4 Figs. S1 to S9 Tables S1 to S3 1 Materials and Methods Enrichment cultivation of ‘Ca. Chx. allophototropha’ To culture novel anoxygenic phototrophs, we sampled Lake 227, a seasonally anoxic and ferruginous Boreal Shield lake at the International Institute for Sustainable Development Experimental Lakes Area (IISD-ELA; near Kenora, Canada). Lake 227 develops up to ~100 μM concentrations of dissolved ferrous iron in its anoxic water column (31), and anoxia is more pronounced than expected naturally due to the long-term experimental eutrophication of the lake (32). The lake’s physico-chemistry has been described in detail previously (31). We collected water from the illuminated portion of the upper anoxic zone of Lake 227 in September 2017, at 3.875 and 5 m depth, and transported this water anoxically and chilled in 120 mL glass serum bottles, sealed with black rubber stoppers (Geo-Microbial Technology Company; Ochelata, Oklahoma, USA), to the laboratory. Water was supplemented with 2% v/v of a freshwater medium containing 8 mM ferrous chloride (33) and was distributed anoxically into 120 mL glass serum bottles, also sealed with black rubber stoppers (Geo-Microbial Technology Company), that had a headspace of dinitrogen gas at 1.5 atm final pressure. -
Photosynthesis Is Widely Distributed Among Proteobacteria As Demonstrated by the Phylogeny of Puflm Reaction Center Proteins
fmicb-08-02679 January 20, 2018 Time: 16:46 # 1 ORIGINAL RESEARCH published: 23 January 2018 doi: 10.3389/fmicb.2017.02679 Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Johannes F. Imhoff1*, Tanja Rahn1, Sven Künzel2 and Sven C. Neulinger3 1 Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 Max Planck Institute for Evolutionary Biology, Plön, Germany, 3 omics2view.consulting GbR, Kiel, Germany Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Edited by: Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the Marina G. Kalyuzhanaya, phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria San Diego State University, United States employing this photosystem in nature. Almost complete pufLM gene sequences and Reviewed by: the derived protein sequences from 152 type strains and 45 additional strains of Nikolai Ravin, phototrophic Proteobacteria employing photosystem II were compared. The results Research Center for Biotechnology (RAS), Russia give interesting and comprehensive insights into the phylogeny of the photosynthetic Ivan A. Berg, apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as Universität Münster, Germany major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from *Correspondence: Caulobacterales (Brevundimonas subvibrioides). -
Thiobacillus Prosperus’ Huber and Stetter 1989 As Acidihalobacter Prosperus Gen
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 3641–3644 DOI 10.1099/ijsem.0.000468 Reclassification of ‘Thiobacillus prosperus’ Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae Juan Pablo Ca´rdenas,1,2,3 Rodrigo Ortiz,1,3 Paul R. Norris,4 Elizabeth Watkin5 and David S. Holmes1,2 Correspondence 1Departamento de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, David S. Holmes Santiago, Chile [email protected] 2Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Santiago, Chile 3Laboratorio de Ecofisiologı´a Microbiana, Fundacion Ciencia & Vida, Santiago, Chile 4Environment and Sustainability Institute, University of Exeter, UK 5School of Biomedical Sciences, Curtin University, Perth, Australia Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile ‘Thiobacillus prosperus’ DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that ‘Thiobacillus prosperus’ DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130T (5JCM 30709T) and that it becomes the type strain of the type species of this genus. ‘Thiobacillus prosperus’ DSM 5130, is a halotolerant 2000) and the genus Acidithiobacillus was moved out of (growth with up to 0.6 M NaCl) acidophile (,pH 3) the class Gammaproteobacteria into the class Acidithiobacil- that was isolated from a geothermally heated seafloor at lia (Williams & Kelly, 2013). -
Genome-Based Classification of Two
TAXONOMIC DESCRIPTION Khaleque et al., Int J Syst Evol Microbiol DOI 10.1099/ijsem.0.003313 Genome-based classification of two halotolerant extreme acidophiles, Acidihalobacter prosperus V6 (=DSM 14174 =JCM 32253) and ’Acidihalobacter ferrooxidans’ V8 (=DSM 14175 =JCM 32254) as two new species, Acidihalobacter aeolianus sp. nov. and Acidihalobacter ferrooxydans sp. nov., respectively Himel N. Khaleque,1,2† Carolina Gonzalez, 3† Anna H. Kaksonen,2 Naomi J. Boxall,2 David S. Holmes3,* and Elizabeth L. J. Watkin1,* Abstract Phylogenomic analysis of recently released high-quality draft genome sequences of the halotolerant acidophiles, Acidihalobacter prosperus V6 (=DSM 14174=JCM 32253) and ‘Acidihalobacter ferrooxidans’ V8 (=DSM 14175=JCM 32254), was undertaken in order to clarify their taxonomic relationship. Sequence based phylogenomic approaches included 16S rRNA gene phylogeny, multi-gene phylogeny from the concatenated alignment of nine selected housekeeping genes and multiprotein phylogeny using clusters of orthologous groups of proteins from ribosomal protein families as well as those from complete sets of markers based on concatenated alignments of universal protein families. Non-sequence based approaches for species circumscription were based on analyses of average nucleotide identity, which was further reinforced by the correlation indices of tetra-nucleotide signatures as well as genome-to-genome distance (digital DNA–DNA hybridization) calculations. The different approaches undertaken in this study for species tree reconstruction resulted in a tree that was phylogenetically congruent, revealing that both micro-organisms are members of separate species of the genus Acidihalobacter. In accordance, it is proposed that A. prosperus V6T (=DSM 14174 T=JCM 32253 T) be formally classified as Acidihalobacter aeolianus sp. -
Thiorhodospira Sibirica Gen. Nov., Sp. Nov., a New Alkaliphilic Purple Sulfur Bacterium from a Siberian Soda Lake
International Journal of Systematic Bacteriology (1 999),49, 697-703 Printed in Great Britain Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake kina Bryantseva,’ Vladimir M. Gorlenko,’ Elena 1. Kompantseva,’ Johannes F. Imhoff,2 Jdrg Suling’ and Lubov’ Mityushina’ Author for correspondence : Johannes F. Imhoff. Tel : + 49 43 1 697 3850. Fax : + 49 43 1 565 876. e-mail : [email protected] 1 Institute of Microbiology, A new purple sulfur bacterium was isolated from microbial films on decaying Russian Academy of plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 95,02% Sciences, pr. 60-letiya Oktyabrya 7 k. 2, Moscow salinity) located in the steppe of the Chita region of south-east Siberia. Single 11781 1, Russia cells were vibrioid- or spiral-shaped (34 pm wide and 7-20 pm long) and motile * lnstitut fur Meereskunde, by means of a polar tuft of flagella. Internal photosynthetic membranes were Abt. Marine of the lamellar type. Lamellae almost filled the whole cell, forming strands Mikro biolog ie, and coils. Photosynthetic pigments were bacteriochlorophyll a and carotenoids Dusternbrooker Weg 20, 24105 Kiel, Germany of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, f umarate and malate were utilized as carbon sources. -
Chemosynthetic Symbionts of Marine Invertebrate Animals Are Capable of Nitrogen fixation Jillian M
ARTICLES PUBLISHED: 24 OCTOBER 2016 | VOLUME: 2 | ARTICLE NUMBER: 16195 OPEN Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation Jillian M. Petersen1,2*, Anna Kemper2, Harald Gruber-Vodicka2,UlisseCardini1, Matthijs van der Geest3,4, Manuel Kleiner5, Silvia Bulgheresi6, Marc Mußmann1,CraigHerbold1, Brandon K.B. Seah2, Chakkiath Paul Antony2, Dan Liu5, Alexandra Belitz1 and Miriam Weber7 Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host’s nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity. ymbioses between animals and chemosynthetic bacteria are 400 living species, occupying a range of habitats including mangrove widespread in -
Bchn GCA 000020645.1 Asm2064v1 Protein ACF42657.1 Light-Independent Protochlorophyllide Reductase N Subunit Pelodictyon Phaeocl
bchY d Bacteria p Eremiobacterota c Eremiobacteria o UBP12 f UBA5184 g Bog-1527 s Bog-1527 sp003155175 WGS ID PMFP01 1/6-406 1.00 bchY d Bacteria p Eremiobacterota c Eremiobacteria o UBP12 f UBA5184 g BOG-1502 s BOG-1502 sp003134035 WGS ID PLAE01 1/1-392 bchY GCA 000019165.1 ASM1916v1 protein ABZ83898.1 chlorophyllide reductase 52.5 kda chain subunit y Heliobacterium modesticaldum Ice1 /4-399 0.78 bchY d Bacteria p Acidobacteriota c Blastocatellia o Chloracidobacteriales f Chloracidobacteriaceae g Chloracidobacterium s Chloracidobacterium thermophilum A WGS ID LMXM01 1/5-406 0.99 bchY GCA 000226295.1 ASM22629v1 protein AEP12321.1 chlorophyllide reductase subunit Y Chloracidobacterium thermophilum B /1-393 bchY GCA 000016665.1 ASM1666v1 protein ABQ91618.1 chlorophyllide reductase subunit Y Roseiflexus sp. RS-1 /8-398 1.00 bchY GCA 000017805.1 ASM1780v1 protein ABU59784.1 chlorophyllide reductase subunit Y Roseiflexus castenholzii DSM 13941 /8-403 0.95 bchY d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Chloroflexaceae g UBA1466 s UBA1466 sp002325605 WGS ID DCSM01 1/1-395 0.89 bchY d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Chloroflexaceae g Chloroploca s Chloroploca asiatica WGS ID LYXE01 1/18-408 1.000.85 bchY d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Chloroflexaceae g Oscillochloris s Oscillochloris trichoides WGS ID ADVR01 1/17-412 0.97 bchY GCA 000152145.1 ASM15214v1 protein EFO79680.1 chlorophyllide reductase subunit Y Oscillochloris trichoides DG6 /22-417 0.98 bchY d Bacteria p Chloroflexota c Chloroflexia o Chloroflexales f Chloroflexaceae g Chloroflexus s Chloroflexus islandicus WGS ID LWQS01 1/17-417 0.71bchY GCA 000021945.1 ASM2194v1 protein ACL23771.1 chlorophyllide reductase subunit Y Chloroflexus aggregans DSM 9485 /22-423 0.91 0.54bchY GCA 000022185.1 ASM2218v1 protein ACM55468.1 chlorophyllide reductase subunit Y Chloroflexus sp. -
Recommended Standards for the Description of New Species of Anoxygenic Phototrophic Bacteria
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by OceanRep International Journal of Systematic and Evolutionary Microbiology (2004), 54, 1415–1421 DOI 10.1099/ijs.0.03002-0 Recommended standards for the description of new species of anoxygenic phototrophic bacteria Johannes F. Imhoff1 and Pierre Caumette2 Correspondence 1Institut fu¨r Meereswissenschaften, Du¨sternbrooker Weg 20, D-24105 Kiel, Germany Johannes F. Imhoff 2Laboratoire d’Ecologie Mole´culaire, Microbiologie, EA 3525, Universite´ de Pau, F-64000 Pau, [email protected] France Recommended standards for the description of new species of the anoxygenic phototrophic bacteria are proposed in accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria. These standards include information on the natural habitat, ecology and phenotypic properties including morphology, physiology and pigments and on genetic information and nucleic acid data. The recommended standards were supported by the Subcommittee on the taxonomy of phototrophic bacteria of the International Committee on Systematics of Prokaryotes. They are considered as guidelines for authors to prepare descriptions of new species. Introduction complete database of 16S rDNA sequences of available type Four major phenotypically and phylogenetically well- strains (and additional other strains) of the species of distinguished groups of bacteria are able to perform Chlorobiaceae (Overmann & Tuschack, 1997; Alexander anoxygenic photosynthesis and to grow phototrophically -
Lipoate-Binding Proteins and Specific Lipoate-Protein Ligases in Microbial
RESEARCH ARTICLE Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor Xinyun Cao1†‡, Tobias Koch2†, Lydia Steffens2, Julia Finkensieper2, Renate Zigann2, John E Cronan1,3, Christiane Dahl2* 1Department of Biochemistry, University of Illinois, Urbana, United States; 2Institut fu¨ r Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universita¨ t Bonn, Bonn, Germany; 3Department of Microbiology, University of Illinois, Urbana, United States Abstract Many Bacteria and Archaea employ the heterodisulfide reductase (Hdr)-like sulfur oxidation pathway. The relevant genes are inevitably associated with genes encoding lipoate- binding proteins (LbpA). Here, deletion of the gene identified LbpA as an essential component of the Hdr-like sulfur-oxidizing system in the Alphaproteobacterium Hyphomicrobium denitrificans. *For correspondence: Thus, a biological function was established for the universally conserved cofactor lipoate that is [email protected] markedly different from its canonical roles in central metabolism. LbpAs likely function as sulfur- binding entities presenting substrate to different catalytic sites of the Hdr-like complex, similar to †These authors contributed the substrate-channeling function of lipoate in carbon-metabolizing multienzyme complexes, for equally to this work example pyruvate dehydrogenase. LbpAs serve a specific function in sulfur oxidation, cannot ‡ Present address: Department functionally replace the related GcvH protein in Bacillus subtilis and are not modified by the of Biochemistry, University of canonical E. coli and B. subtilis lipoyl attachment machineries. Instead, LplA-like lipoate-protein Wisconsin-Madison, Madison, ligases encoded in or in immediate vicinity of hdr-lpbA gene clusters act specifically on these United States proteins. Competing interests: The DOI: https://doi.org/10.7554/eLife.37439.001 authors declare that no competing interests exist. -
Thiorhodospira Sibirica Gen. Nov., Sp. Nov., a New Alkaliphilic Purple Sulfur Bacterium from a Siberian Soda Lake
International Journal of Systematic Bacteriology (1 999),49, 697-703 Printed in Great Britain Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake kina Bryantseva,’ Vladimir M. Gorlenko,’ Elena 1. Kompantseva,’ Johannes F. Imhoff,2 Jdrg Suling’ and Lubov’ Mityushina’ Author for correspondence : Johannes F. Imhoff. Tel : + 49 43 1 697 3850. Fax : + 49 43 1 565 876. e-mail : [email protected] 1 Institute of Microbiology, A new purple sulfur bacterium was isolated from microbial films on decaying Russian Academy of plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 95,02% Sciences, pr. 60-letiya Oktyabrya 7 k. 2, Moscow salinity) located in the steppe of the Chita region of south-east Siberia. Single 11781 1, Russia cells were vibrioid- or spiral-shaped (34 pm wide and 7-20 pm long) and motile * lnstitut fur Meereskunde, by means of a polar tuft of flagella. Internal photosynthetic membranes were Abt. Marine of the lamellar type. Lamellae almost filled the whole cell, forming strands Mikro biolog ie, and coils. Photosynthetic pigments were bacteriochlorophyll a and carotenoids Dusternbrooker Weg 20, 24105 Kiel, Germany of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, f umarate and malate were utilized as carbon sources. -
Isolation and Characterization of Spirilloid Purple Phototrophic
International Journal of Systematic and Evolutionary Microbiology (2003), 53, 153–163 DOI 10.1099/ijs.0.02226-0 Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns: description of Halorhodospira neutriphila sp. nov. and emendation of the genus Halorhodospira Agne`s Hirschler-Re´a,1 Robert Matheron,1 Christine Riffaud,1 Sophie Moune´,2,4 Claire Eatock,3 Rodney A. Herbert,3 John C. Willison2 and Pierre Caumette4 Correspondence 1Laboratoire de Microbiologie, IMEP, Faculte´ des Sciences et Techniques de Saint Je´roˆme, Pierre Caumette 13397 Marseille cedex 20, France [email protected] 2Laboratoire de Biochimie et Biophysique des Syste`mes Inte´gre´s, DBMS/BBSI, CEA Grenoble, 38054 Grenoble, France 3Division of Environmental and Applied Biology, Biological Sciences Institute, University of Dundee, Dundee DD1 4HN, UK 4Laboratoire d’Ecologie Mole´culaire-Microbiologie, IBEAS, BP 1155, Universite´ de Pau, F 64013 Pau cedex, France Microbial mats developing in the hypersaline lagoons of a commercial saltern in the Salin-de-Giraud (Rhoˆ ne delta) were found to contain a red layer fully dominated by spirilloid phototrophic purple bacteria underlying a cyanobacterial layer. From this layer four strains of spirilloid purple bacteria were isolated, all of which were extremely halophilic. All strains were isolated by using the same medium under halophilic photolithoheterotrophic conditions. One of them, strain SG 3105 was a purple non-sulfur bacterial strain closely related to Rhodovibrio sodomensis with a 16S rDNA sequence similarity of 98?8 %. The three other isolated strains, SG 3301T, SG 3302 and SG 3304, were purple sulfur bacteria and were found to be very similar.