scholarly journals Desulfoglaeba alkanexedens gen. nov., sp. nov., an n-alkane-degrading, sulfate-reducing bacterium

2006 ◽  
Vol 56 (12) ◽  
pp. 2737-2742 ◽  
Author(s):  
Irene A. Davidova ◽  
Kathleen E. Duncan ◽  
Ok Kyoung Choi ◽  
Joseph M. Suflita
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sulfate Reducing Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Oily Wastewater ◽  
Sulfate Reducing ◽  
Production Water ◽  
Large Clusters ◽  
Reducing Bacteria

Two novel sulfate-reducing bacteria, strains ALDCT and Lake, which were able to oxidize n-alkanes, were isolated from a naval oily wastewater-storage facility (VA, USA) and from oilfield production water (OK, USA), respectively. The type strain (ALDCT) had a narrow substrate specificity and could grow only with n-alkanes (from C6 to C12), pyruvate, butyrate, hexanoic acid and 4-methyloctanoic acid. Cells of strain ALDCT stained Gram-negative and were slightly curved, short rods with oval ends (2.5–3.0×1.0–1.4 μm), often occurring in pairs. Cells tended to form aggregates or large clusters and were non-motile and did not form endospores. Optimum growth occurred between 31 and 37 °C and at pH 6.5–7.2. NaCl was not required for growth, but salt concentrations up to 55 g l−1 could be tolerated. The DNA G+C content was 53.6 mol%. Phylogenetic analysis of the 16S rRNA genes revealed that strains ALDCT and Lake were closely related, but not identical (99.9 % similarity). The two strains were not closely related to other known alkane-degrading, sulfate-reducing bacteria or to other genera of the Deltaproteobacteria. Therefore, it is proposed that strain ALDCT (=JCM 13588T=ATCC BAA-1302T) represents the type strain of a novel species and genus, with the name Desulfoglaeba alkanexedens gen. nov., sp. nov.

scholarly journals ANME-1 archaea drive methane accumulation and removal in estuarine sediments

2020 ◽  
Author(s):  
Richard Kevorkian ◽  
Sean Callahan ◽  
Rachel Winstead ◽  
Karen G. Lloyd
Keyword(s):  
16S Rrna ◽  
Sulfate Reducing Bacteria ◽  
Low Energy ◽  
Estuarine Sediments ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sulfate Reducing ◽  
Hydrogenotrophic Methanogenesis ◽  
Natural Settings ◽  
Reducing Bacteria

AbstractUncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide.Abstract ImportanceLife may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.

scholarly journals Isolation of sulfate-reducing bacteria from Tunisian marine sediments and description of Desulfovibrio bizertensis sp. nov.

2006 ◽  
Vol 56 (12) ◽  
pp. 2909-2913 ◽  
Author(s):  
Olfa Haouari ◽  
Marie-Laure Fardeau ◽  
Laurence Casalot ◽  
Jean-Luc Tholozan ◽  
Moktar Hamdi ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Type Strain ◽  
Elemental Sulfur ◽  
Novel Species ◽  
Sulfate Reducing Bacteria ◽  
Electron Donors ◽  
Sulfate Reducing ◽  
Growth Optimum ◽  
Optimum Ph ◽  
Reducing Bacteria

Several strains of sulfate-reducing bacteria were isolated from marine sediments recovered near Tunis, Korbous and Bizerte, Tunisia. They all showed characteristics consistent with members of the genus Desulfovibrio. One of these strains, designated MB3T, was characterized further. Cells of strain MB3T were slender, curved, vibrio-shaped, motile, Gram-negative, non-spore-forming rods. They were positive for desulfoviridin as bisulfite reductase. Strain MB3T grew at temperatures of 15–45 °C (optimum 40 °C) and at pH 6.0–8.1 (optimum pH 7.0). NaCl was required for growth (optimum 20 g NaCl l−1). Strain MB3T utilized H2 in the presence of acetate with sulfate as electron acceptor. It also utilized lactate, ethanol, pyruvate, malate, fumarate, succinate, butanol and propanol as electron donors. Lactate was oxidized incompletely to acetate. Strain MB3T fermented pyruvate and fumarate (poorly). Electron acceptors utilized included sulfate, sulfite, thiosulfate, elemental sulfur and fumarate, but not nitrate or nitrite. The G+C content of the genomic DNA was 51 mol%. On the basis of genotypic, phenotypic and phylogenetic characteristics, strain MB3T (=DSM 18034T=NCIMB 14199T) is proposed as the type strain of a novel species, Desulfovibrio bizertensis sp. nov.

scholarly journals Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin

2003 ◽  
Vol 69 (5) ◽  
pp. 2765-2772 ◽  
Author(s):  
Ashita Dhillon ◽  
Andreas Teske ◽  
Jesse Dillon ◽  
David A. Stahl ◽  
Mitchell L. Sogin
Keyword(s):  
16S Rrna ◽  
Gulf Of California ◽  
Sulfate Reducing Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Terrestrial Organic Matter ◽  
Guaymas Basin ◽  
Sulfate Reducers ◽  
Sulfate Reducing ◽  
Reducing Bacteria

ABSTRACT The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

scholarly journals Anaerobic Oxidation of o -Xylene, m -Xylene, and Homologous Alkylbenzenes by New Types of Sulfate-Reducing Bacteria

1999 ◽  
Vol 65 (3) ◽  
pp. 999-1004 ◽  
Author(s):  
Gerda Harms ◽  
Karsten Zengler ◽  
Ralf Rabus ◽  
Frank Aeckersberg ◽  
Dror Minz ◽  
...  
Keyword(s):  
Crude Oil ◽  
Enrichment Culture ◽  
Sulfate Reducing Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Organic Substrates ◽  
Sulfate Reducing ◽  
Concomitant Reduction ◽  
Reducing Bacteria ◽  
Growth Experiments

ABSTRACT Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with o-xylene and m-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the δ subclass of the classProteobacteria. Strain oXyS1 showed the highest similarities to Desulfobacterium cetonicum andDesulfosarcina variabilis (similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being Desulfococcus multivorans (similarity value, 86.9%). Complete mineralization of o-xylene and m-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene, o-ethyltoluene, benzoate, ando-methylbenzoate in addition to o-xylene. Strain mXyS1 oxidized toluene, m-ethyltoluene,m-isoproyltoluene, benzoate, andm-methylbenzoate in addition to m-xylene. Strain oXyS1 did not utilize m-alkyltoluenes, whereas strain mXyS1 did not utilize o-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide.

scholarly journals Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water

2004 ◽  
Vol 54 (5) ◽  
pp. 1693-1697 ◽  
Author(s):  
Michel Magot ◽  
Odile Basso ◽  
Christèle Tardy-Jacquenod ◽  
Pierre Caumette
Keyword(s):  
Type Strain ◽  
Optimal Growth ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Moderately Halophilic ◽  
Sulfate Reducing ◽  
Production Water ◽  
Acidophilic Bacterium ◽  
Oilfield Water ◽  
Reducing Bacteria

Two moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from Emeraude Oilfield, Congo. Motile, vibrioid cells of SRL4225T grew optimally at a concentration of 4 % NaCl, at pH 5·8–6·2, with a minimal pH for growth of 5·2, showing that it is a moderately acidophilic bacterium. Cells of SRL6146T were motile, curved or vibrioid, long and thin rods. Optimal growth was obtained at a concentration of 5–6 % NaCl, at pH 6·8–7·2. The nutritional requirements showed that many of the characteristics of these strains overlap with those of known Desulfovibrio species. On the basis of 16S rRNA gene sequence analysis and DNA–DNA hybridization studies, both strains are members of the genus Desulfovibrio. However, they are not closely related to any species of the genus that have validly published names. It is therefore proposed that the two strains are members of two novel species of the genus Desulfovibrio with the names Desulfovibrio bastinii sp. nov. (type strain SRL4225T=DSM 16055T=ATCC BAA-903T) and Desulfovibrio gracilis sp. nov. (type strain SRL6146T=DSM 16080T=ATCC BAA-904T).

scholarly journals Detection and Quantification of Functional Genes of Cellulose- Degrading, Fermentative, and Sulfate-Reducing Bacteria and Methanogenic Archaea

2010 ◽  
Vol 76 (7) ◽  
pp. 2192-2202 ◽  
Author(s):  
L. P. Pereyra ◽  
S. R. Hiibel ◽  
M. V. Prieto Riquelme ◽  
K. F. Reardon ◽  
A. Pruden
Keyword(s):  
Cellulose Degradation ◽  
Methanogenic Archaea ◽  
Sulfate Reducing Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Significant Advance ◽  
Sulfate Reducing ◽  
Degrading Bacteria ◽  
Fermentative Bacteria ◽  
Reducing Bacteria

ABSTRACT Cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. Compared to the study of 16S rRNA genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. However, no methods are available for the broad quantification of these genes from uncultured microbes characteristic of complex environments. In this study, consensus degenerate hybrid oligonucleotide primers were designed and validated to amplify both sequenced and unsequenced glycoside hydrolase genes of cellulose-degrading bacteria, hydA genes of fermentative bacteria, dsrA genes of sulfate-reducing bacteria, and mcrA genes of methanogenic archaea. Specificity was verified in silico and by cloning and sequencing of PCR products obtained from an environmental sample characterized by the target functions. The primer pairs were further adapted to quantitative PCR (Q-PCR), and the method was demonstrated on samples obtained from two sulfate-reducing bioreactors treating mine drainage, one lignocellulose based and the other ethanol fed. As expected, the Q-PCR analysis revealed that the lignocellulose-based bioreactor contained higher numbers of cellulose degraders, fermenters, and methanogens, while the ethanol-fed bioreactor was enriched in sulfate reducers. The suite of primers developed represents a significant advance over prior work, which, for the most part, has targeted only pure cultures or has suffered from low specificity. Furthermore, ensuring the suitability of the primers for Q-PCR provided broad quantitative access to genes that drive critical anaerobic catalytic processes.

scholarly journals Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

A thermophilic nitrate-reducing bacterium isolated from production water of a high temperature oil reservoir and its inhibition on sulfate-reducing bacteria

2016 ◽  
Vol 1 (2) ◽  
pp. 35 ◽  
Author(s):  
Jin-Feng Liu ◽  
Wei-Lin Wu ◽  
Feng Yao ◽  
Biao Wang ◽  
Bing-Liang Zhang ◽  
...  
Keyword(s):  
High Temperature ◽  
Anaerobic Bacterium ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Oil Reservoir ◽  
Sulfate Reducing ◽  
Production Water ◽  
Facultative Anaerobic ◽  
Reducing Bacteria ◽  
H2s Production

A thermophilic spore-forming facultative anaerobic bacterium, designated as Njiang2, was isolated from the production water of a high temperature oil reservoir (87°C). The physiological, biochemical and 16S rRNA gene based phylogenetic analysis indicated that Njiang2 belonged to the genus Anoxybacillus. Njiang2 could significantly inhibit H2S production when co-cultured with Desulfotomaculum sp under laboratory conditions, which implied its great potential in mitigation of brine souring in the oil reservoir and in control of biocorrosion caused by sulfate-reducing bacteria. As far as we know, this might be the first report of Anoxybacillus sp. isolated from high temperature oilfield

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