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Salman-Carvalho V, Fadeev E, Joye SB, Teske A. How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a "Candidatus Marithrix sp." Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico. Front Microbiol 2016; 7:1173. [PMID: 27536274 PMCID: PMC4971068 DOI: 10.3389/fmicb.2016.01173] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/15/2016] [Indexed: 11/13/2022] Open
Abstract
“Candidatus Marithrix” is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria). This genus of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 μm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, “Candidatus Marithrix” was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the “Candidatus Marithrix” genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98 and 100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes—the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs) between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or “intrasegmental sequence heterogeneity” (ISH) events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.
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Affiliation(s)
- Verena Salman-Carvalho
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Eduard Fadeev
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia Athens, GA, USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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Aranda CP, Valenzuela C, Matamala Y, Godoy FA, Aranda N. Sulphur-cycling bacteria and ciliated protozoans in a Beggiatoaceae mat covering organically enriched sediments beneath a salmon farm in a southern Chilean fjord. MARINE POLLUTION BULLETIN 2015; 100:270-278. [PMID: 26359117 DOI: 10.1016/j.marpolbul.2015.08.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 08/23/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
The colourless mat covering organically enriched sediments underlying an intensive salmon farm in Estero Pichicolo, southern Chile, was surveyed by combined 454 PyroTag and conventional Sanger sequencing of 16S/18S ribosomal RNA genes for Bacteria and Eukarya. The mat was dominated by the sulphide-oxidizing bacteria (SOB) Candidatus Isobeggiatoa, Candidatus Parabeggiatoa and Arcobacter. By order of their abundances, sulphate-reducing bacteria (SRB) were represented by diverse deltaproteobacterial Desulfobacteraceae, but also within Desulfobulbaceae, Desulfuromonadaceae and Desulfovibrionaceae. The eukaryotic PyroTags were dominated by polychaetes, copepods and nematodes, however, ciliated protozoans were highly abundant in microscopy observations, and were represented by the genera Condylostoma, Loxophyllum and Peritromus. Finally, the abundant Sulfurimonas/Sulfurovum also suggest the occurrence of zero-valence sulphur oxidation, probably derived from Beggiatoaceae as a result of bacteriovorus infaunal activity or generated as free S(0) by the Arcobacter bacteria. The survey suggests an intense and complex sulphur cycle within the surface of salmon-farm impacted sediments.
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Affiliation(s)
- Carlos P Aranda
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue Km. 6, Puerto Montt, Chile.
| | - Cristian Valenzuela
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue Km. 6, Puerto Montt, Chile
| | - Yessica Matamala
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue Km. 6, Puerto Montt, Chile
| | - Félix A Godoy
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue Km. 6, Puerto Montt, Chile
| | - Nicol Aranda
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue Km. 6, Puerto Montt, Chile
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Flood BE, Bailey JV, Biddle JF. Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments. GEOBIOLOGY 2014; 12:119-132. [PMID: 24382125 DOI: 10.1111/gbi.12072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 11/27/2013] [Indexed: 06/03/2023]
Abstract
Wrinkle structures are sedimentary features that are produced primarily through the trapping and binding of siliciclastic sediments by mat-forming micro-organisms. Wrinkle structures and related sedimentary structures in the rock record are commonly interpreted to represent the stabilizing influence of cyanobacteria on sediments because cyanobacteria are known to produce similar textures and structures in modern tidal flat settings. However, other extant bacteria such as filamentous representatives of the family Beggiatoaceae can also interact with sediments to produce sedimentary features that morphologically resemble many of those associated with cyanobacteria-dominated mats. While Beggiatoa spp. and cyanobacteria are metabolically and phylogenetically distant, genomic analyses show that the two groups share hundreds of homologous genes, likely as the result of horizontal gene transfer. The comparative genomics results described here suggest that some horizontally transferred genes may code for phenotypic traits such as filament formation, chemotaxis, and the production of extracellular polymeric substances that potentially underlie the similar biostabilizing influences of these organisms on sediments. We suggest that the ecological utility of certain basic life modes such as the construction of mats and biofilms, coupled with the lateral mobility of genes in the microbial world, introduces an element of uncertainty into the inference of specific phylogenetic origins from gross morphological features preserved in the ancient rock record.
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Affiliation(s)
- B E Flood
- Department of Earth Sciences, University of Minnesota- Twin Cities, Minneapolis, MN, USA
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Salman V, Bailey JV, Teske A. Phylogenetic and morphologic complexity of giant sulphur bacteria. Antonie van Leeuwenhoek 2013; 104:169-86. [PMID: 23793621 DOI: 10.1007/s10482-013-9952-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
The large sulphur bacteria, first discovered in the early nineteenth century, include some of the largest bacteria identified to date. Individual cells are often visible to the unaided eye and can reach 750 μm in diameter. The cells usually feature light-refracting inclusions of elemental sulphur and a large internal aqueous vacuole, which restricts the cytoplasm to the outermost periphery. In some taxa, it has been demonstrated that the vacuole can also serve for the storage of high millimolar concentrations of nitrate. Over the course of the past two centuries, a wide range of morphological variation within the family Beggiatoaceae has been found. However, representatives of this clade are frequently recalcitrant to current standard microbiological techniques, including 16S rRNA gene sequencing and culturing, and a reliable classification of these bacteria is often complicated. Here we present a summary of the efforts made and achievements accomplished in the past years, and give perspectives for investigating the heterogeneity and possible evolutionary developments in this extraordinary group of bacteria.
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Affiliation(s)
- Verena Salman
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3300, USA.
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Li X, Vanner S, Wang W, Li Y, Gallardo VA, Magarvey NA. Macplocimine A, a new 18-membered macrolide isolated from the filamentous sulfur bacteria Thioploca sp. J Antibiot (Tokyo) 2013; 66:443-6. [PMID: 23778115 DOI: 10.1038/ja.2013.52] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/08/2013] [Accepted: 04/12/2013] [Indexed: 11/09/2022]
Abstract
Macplocimine A (1), a rare naturally occurring 18-membered macrolide, was isolated from the marine-derived filamentous sulfur bacteria Thioploca sp. The structure was determined by a combination of spectroscopic techniques, including HRESIMS, 1D and 2D NMR analyses. 1 features a thymine group, which is attached to an aromatic fused 18-membered macrolide ring structure derived from a polyketide synthase biosynthetic pathway.
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Affiliation(s)
- Xiang Li
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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Enrichment and identification of large filamentous sulfur bacteria related to Beggiatoa species from brackishwater ecosystems of Tamil Nadu along the southeast coast of India. Syst Appl Microbiol 2012; 35:396-403. [DOI: 10.1016/j.syapm.2012.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 05/30/2012] [Accepted: 05/31/2012] [Indexed: 11/20/2022]
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Salman V, Amann R, Girnth AC, Polerecky L, Bailey JV, Høgslund S, Jessen G, Pantoja S, Schulz-Vogt HN. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. Syst Appl Microbiol 2011; 34:243-59. [PMID: 21498017 DOI: 10.1016/j.syapm.2011.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 02/20/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.
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Affiliation(s)
- Verena Salman
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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8
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Comparative analysis of Beggiatoa from hypersaline and marine environments. Micron 2010; 41:507-17. [DOI: 10.1016/j.micron.2010.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 01/28/2010] [Accepted: 01/29/2010] [Indexed: 11/22/2022]
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Jørgensen BB, Dunker R, Grünke S, Røy H. Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 degrees N). FEMS Microbiol Ecol 2010; 73:500-13. [PMID: 20608982 DOI: 10.1111/j.1574-6941.2010.00918.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Fjord sediments on the west coast of the arctic archipelago Svalbard were surveyed to understand whether large filamentous sulfur bacteria of the genus Beggiatoa thrive at seawater temperatures permanently near freezing. Two sediments had abundant populations of Beggiatoa, while at six sites, only sporadic occurrences were observed. We conclude that Beggiatoa, although previously unnoticed, are widespread in these arctic fjord sediments. Beggiatoa ranged in diameter from 2 to 52 microm and, by those tested, stored nitrate in vacuoles at up to 260 mM. The 16S rRNA gene sequence of a 20-microm-wide filament is closely associated with other large, marine, nitrate-storing Beggiatoa. The Beggiatoa mostly occurred in the upper 2-5 cm of oxidized surface sediment between oxygen and the deeper sulfidic zone. In spite of a very low or an undetectable sulfide concentration, sulfate reduction provided abundant H(2)S in this zone. The total living biomass of Beggiatoa filaments at one study site varied over 3 years between 1.13 and 3.36 g m(-2). Because of their large size, Beggiatoa accounted for up to 15% of the total prokaryotic biomass, even though the filament counts at this site were rather low, comprising <1/10,000 of the bacterial numbers on a cell basis.
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Bacterial and β-proteobacterial diversity in Olea europaea var. mastoidis- and O. europaea var. koroneiki-generated olive mill wastewaters: influence of cultivation and harvesting practice on bacterial community structure. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0426-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hinck S, Neu TR, Lavik G, Mussmann M, de Beer D, Jonkers HM. Physiological adaptation of a nitrate-storing Beggiatoa sp. to diel cycling in a phototrophic hypersaline mat. Appl Environ Microbiol 2007; 73:7013-22. [PMID: 17766448 PMCID: PMC2074952 DOI: 10.1128/aem.00548-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to investigate the supposed vertical diel migration and the accompanying physiology of Beggiatoa bacteria from hypersaline microbial mats. We combined microsensor, stable-isotope, and molecular techniques to clarify the phylogeny and physiology of the most dominant species inhabiting mats of the natural hypersaline Lake Chiprana, Spain. The most dominant morphotype had a filament diameter of 6 to 8 microm and a length varying from 1 to >10 mm. Phylogenetic analysis by 16S rRNA gene comparison revealed that this type appeared to be most closely related (91% sequence identity) to the narrow (4-microm diameter) nonvacuolated marine strain MS-81-6. Stable-isotope analysis showed that the Lake Chiprana species could store nitrate intracellularly to 40 mM. The presence of large intracellular vacuoles was confirmed by fluorescein isothiocyanate staining and subsequent confocal microscopy. In illuminated mats, their highest abundance was found at a depth of 8 mm, where oxygen and sulfide co-occurred. However, in the dark, the highest Beggiatoa densities occurred at 7 mm, and the whole population was present in the anoxic zone of the mat. Our findings suggest that hypersaline Beggiatoa bacteria oxidize sulfide with oxygen under light conditions and with internally stored nitrate under dark conditions. It was concluded that nitrate storage by Beggiatoa is an optimal strategy to both occupy the suboxic zones in sulfidic sediments and survive the dark periods in phototrophic mats.
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Affiliation(s)
- Susanne Hinck
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany.
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12
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Kojima H, Nakajima T, Fukui M. Carbon source utilization and accumulation of respiration-related substances by freshwater Thioploca species. FEMS Microbiol Ecol 2006; 59:23-31. [PMID: 16989657 DOI: 10.1111/j.1574-6941.2006.00201.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Carbon source utilization of Thioploca species from freshwater and brackish lakes in Japan was investigated. Microautoradiography demonstrated that freshwater and brackish Thioploca samples assimilate acetate. In addition, vertical nitrate transportation by freshwater Thioploca was examined by measuring substances accumulated in Thioploca filaments. The filaments of Thioploca sp. from Lake Biwa, a Japanese mesotrophic lake, contained nitrate at concentrations higher than ambient by two to three orders of magnitude. They also accumulated high concentrations of sulfate and abundant elemental sulfur. The results suggest that the Thioploca-specific strategy for sulfur oxidation, migration with accumulated nitrate, is effective even in freshwater habitats of lower sulfide supply.
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Affiliation(s)
- Hisaya Kojima
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan.
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Ahmad A, Kalanetra KM, Nelson DC. Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria. Can J Microbiol 2006; 52:591-8. [PMID: 16788728 DOI: 10.1139/w05-154] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Within the last 10 years, numerous SSU rRNA sequences have been collected from natural populations of conspicuous, vacuolate, colorless sulfur bacteria, which form a phylogenetically cohesive cluster (large-vacuolate sulfur bacteria clade) in the gamma-Proteobacteria. Currently, this clade is composed of four named or de facto genera: all known Thioploca and Thiomargarita strains, all vacuolate Beggiatoa strains, and several strains of vacuolate, attached filaments, which bear a superficial similarity to Thiothrix. Some of these vacuolate bacteria accumulate nitrate for respiratory purposes. This clade encompasses the largest known prokaryotic cells (Thiomargarita namibiensis) and several strains that are important in the global marine sulfur cycle. Here, we report additional sequences from five pure culture strains of Beggiatoa spp., including the only two cultured marine strains (nonvacuolate), which firmly establish the root of this vacuolate clade. Each of several diverse metabolic motifs, including obligate and facultative chemolithoautotrophy, probable mixotrophy, and seemingly strict organoheterotrophy, is represented in at least one of the nonvacuolate strains that root the vacuolate clade. Because the genus designation Beggiatoa is interspersed throughout the vacuolate clade along with other recognized or de facto genera, the need for taxonomic revision is clear.
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Affiliation(s)
- Azeem Ahmad
- Section of Microbiology, University of California, Davis, 95616, USA
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Kalanetra KM, Joye SB, Sunseri NR, Nelson DC. Novel vacuolate sulfur bacteria from the Gulf of Mexico reproduce by reductive division in three dimensions. Environ Microbiol 2005; 7:1451-60. [PMID: 16104867 DOI: 10.1111/j.1462-2920.2005.00832.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Large spherical sulfur bacteria, 180-375 microm in diameter, were found regularly and in abundance in surface sediments collected from hydrocarbon seeps (water depth 525-640 m) in the Gulf of Mexico. These bacteria were characterized by a thin 'shell' of sulfur globule-filled cytoplasm that surrounded a central vacuole (roughly 80% of biovolume) containing high concentrations of nitrate (average 460 mM). Approximately 800 base pairs of 16S rRNA gene sequence data, linked to this bacterium by fluorescent in situ hybridization, showed 99% identity with Thiomargarita namibiensis, previously described only from sediments collected off the coast of Namibia (Western Africa). Unlike T. namibiensis, where cells form a linear chain within a common sheath, the Gulf of Mexico strain occurred as single cells and clusters of two, four and eight cells, which were clearly the product of division in one to three planes. In sediment cores maintained at 4 degrees C, which undoubtedly experienced a diminishing flux of hydrogen sulfide over time, the Thiomargarita-like bacterium remained viable for up to 2 years. During that long period, each cell appeared to undergo (as judged by change in biovolume) one to three reductive divisions, perhaps as a dispersal strategy in the face of diminished availability of its putative electron donor.
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Affiliation(s)
- Karen M Kalanetra
- Section of Microbiology, 357 Briggs Hall, University of California, Davis, CA 95616, USA
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Zhang CL, Huang Z, Cantu J, Pancost RD, Brigmon RL, Lyons TW, Sassen R. Lipid biomarkers and carbon isotope signatures of a microbial (Beggiatoa) mat associated with gas hydrates in the gulf of Mexico. Appl Environ Microbiol 2005; 71:2106-12. [PMID: 15812044 PMCID: PMC1082508 DOI: 10.1128/aem.71.4.2106-2112.2005] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 10/29/2004] [Indexed: 11/20/2022] Open
Abstract
White and orange mats are ubiquitous on surface sediments associated with gas hydrates and cold seeps in the Gulf of Mexico. The goal of this study was to determine the predominant pathways for carbon cycling within an orange mat in Green Canyon (GC) block GC 234 in the Gulf of Mexico. Our approach incorporated laser-scanning confocal microscopy, lipid biomarkers, stable carbon isotopes, and 16S rRNA gene sequencing. Confocal microscopy showed the predominance of filamentous microorganisms (4 to 5 mum in diameter) in the mat sample, which are characteristic of Beggiatoa. The phospholipid fatty acids extracted from the mat sample were dominated by 16:1omega7c/t (67%), 18:1omega7c (17%), and 16:0 (8%), which are consistent with lipid profiles of known sulfur-oxidizing bacteria, including Beggiatoa. These results are supported by the 16S rRNA gene analysis of the mat material, which yielded sequences that are all related to the vacuolated sulfur-oxidizing bacteria, including Beggiatoa, Thioploca, and Thiomargarita. The delta13C value of total biomass was -28.6 per thousand; those of individual fatty acids were -29.4 to -33.7 per thousand. These values suggested heterotrophic growth of Beggiatoa on organic substrates that may have delta13C values characteristic of crude oil or on their by-products from microbial degradation. This study demonstrated that integrating lipid biomarkers, stable isotopes, and molecular DNA could enhance our understanding of the metabolic functions of Beggiatoa mats in sulfide-rich marine sediments associated with gas hydrates in the Gulf of Mexico and other locations.
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Affiliation(s)
- Chuanlun L Zhang
- Department of Marine Sciences and Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29802, USA.
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Kalanetra KM, Huston SL, Nelson DC. Novel, attached, sulfur-oxidizing bacteria at shallow hydrothermal vents possess vacuoles not involved in respiratory nitrate accumulation. Appl Environ Microbiol 2005; 70:7487-96. [PMID: 15574952 PMCID: PMC535177 DOI: 10.1128/aem.70.12.7487-7496.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel, vacuolate sulfur bacteria occur at shallow hydrothermal vents near White Point, Calif. There, these filaments are attached densely to diverse biotic and abiotic substrates and extend one to several centimeters into the surrounding environment, where they are alternately exposed to sulfidic and oxygenated seawater. Characterizations of native filaments collected from this location indicate that these filaments possess novel morphological and physiological properties compared to all other vacuolate bacteria characterized to date. Attached filaments, ranging in diameter from 4 to 100 microm or more, were composed of cylindrical cells, each containing a thin annulus of sulfur globule-filled cytoplasm surrounding a large central vacuole. A near-complete 16S rRNA gene sequence was obtained and confirmed by fluorescent in situ hybridization to be associated only with filaments having a diameter of 10 microm or more. Phylogenetic analysis indicates that these wider, attached filaments form within the gamma proteobacteria a monophyletic group that includes all previously described vacuolate sulfur bacteria (the genera Beggiatoa, Thioploca, and Thiomargarita) and no nonvacuolate genera. However, unlike for all previously described vacuolate bacteria, repeated measurements of cell lysates from samples collected over 2 years indicate that the attached White Point filaments do not store internal nitrate. It is possible that these vacuoles are involved in transient storage of oxygen or contribute to the relative buoyancy of these filaments.
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Affiliation(s)
- Karen M Kalanetra
- Section of Microbiology, University of California, Davis, CA 95616, USA
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Koizumi Y, Takii S, Fukui M. Depth-related change in archaeal community structure in a freshwater lake sediment as determined with denaturing gradient gel electrophoresis of amplified 16S rRNA genes and reversely transcribed rRNA fragments. FEMS Microbiol Ecol 2004; 48:285-92. [DOI: 10.1016/j.femsec.2004.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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