scholarly journals A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jaeho Song ◽  
Juchan Hwang ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Novel Species ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Novel Genus ◽  
Sulfate Reducing ◽  
Tidal Flat Sediments ◽  
Reducing Bacteria

AbstractTidal-flat sediments harbor a diverse array of sulfate-reducing bacteria. To isolate novel sulfate-reducing bacteria and determine their abundance, a tidal-flat sediment sample collected off Ganghwa Island (Korea) was investigated using cultivation-based and culture-independent approaches. Two Gram-stain-negative, strictly anaerobic, rod-shaped, sulfate-reducing bacteria, designated IMCC35004T and IMCC35005T, were isolated from the sample. The two strains reduced sulfate, sulfite, elemental sulfur, thiosulfate, Fe(III) citrate, and Mn(IV) oxide by utilizing several carbon sources, including acetate. The 16S rRNA gene amplicon sequencing revealed that the tidal-flat sediment contained diverse members of the phylum Desulfobacterota, and the phylotypes related to IMCC35004T and IMCC35005T were < 1%. The two strains shared 97.6% similarity in 16S rRNA gene sequence and were closely related to Desulfopila aestuarii DSM 18488T (96.1–96.5%). The average nucleotide identity, level of digital DNA–DNA hybridization, average amino acid identity, and percentages of conserved proteins determined analyzing the whole-genome sequences, as well as the chemotaxonomic data showed that the two strains belong to two novel species of a novel genus. Additionally, genes related to dissimilatory sulfate reduction were detected in the genomes of the two strains. Unlike the genera Desulfopila and Desulfotalea, IMCC35004T and IMCC35005T contained menaquinone-5 as the major respiratory quinone. Collectively, IMCC35004T and IMCC35005T were concluded to represent two novel species of a novel genus within the family Desulfocapsaceae, for which the names Desulfosediminicola ganghwensis gen. nov., sp. nov. (IMCC35004T = KCTC 15826T = NBRC 114003T) and Desulfosediminicola flagellatus sp. nov. (IMCC35005T = KCTC 15827T = NBRC 114004T) are proposed.

scholarly journals Production of biogas: relationship between methanogenic and sulfate-reducing microorganisms

2017 ◽  
Vol 12 (1) ◽  
pp. 82-91 ◽  
Author(s):  
Ivan Kushkevych ◽  
Monika Vítězová ◽  
Tomáš Vítěz ◽  
Milan Bartoš
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Biogas Production ◽  
Sulfate Reducing Bacteria ◽  
Quantitative Composition ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Relationship Of ◽  
Reducing Bacteria

AbstractThe production of high-quality methane depends on many factors, including temperature, pH, substrate, composition and relationship of the microorganisms. The qualitative and quantitative composition of methanogenic and sulfate-reducing microorganisms and their relationship in the experimental bioreactors has never been studied. The aim of this research was to characterize, for the first time, the diversity of the methanogenic microorganisms and sulfate-reducing bacteria, and study their relationship and biogas production in experimental bioreactors. Amplification of 16S rRNA gene fragments was carried out. Purified amplicons were paired-end sequenced on an Illumina Mi-Seq platform. The dominant morphotypes of these microorganisms in the bioreactor were homologous (99%) by the sequences of 16S rRNA gene to theMethanosarcina,Thermogymnomonas,Methanoculleusgenera andArchaeondeposited in GenBank. Three dominant genera of sulfate-reducing bacteria,Desulfomicrobium,DesulfobulbusandDesulfovibrio, were detected in the bioreactor. The phylogenetic trees showing their genetic relationship were constructed. The diversity and number of the genera, production of methane, hydrogen sulfide and hydrogen in the bioreactor was investigated. This research is important for understanding the relationship between methanogenic microbial populations and other bacterial physiological groups, their substrate competition and, in turn, can be helpful for controlling methanogenesis in bioreactors.

scholarly journals Chromium Precipitation Activity and Molecular Characterization of Sulfate-Reducing Bacteria

2019 ◽  
Vol 4 (1) ◽  
pp. 15
Author(s):  
Dwiana Muflihah Yulianti ◽  
Endah Retnaningrum ◽  
Wahyu Wilopo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Sulfate Reducing ◽  
Sulfate Reducing Bioreactor ◽  
Reducing Bacteria

Chromium is one of the metals used in many areas of industry., However, chromium is toxic to organisms when present in large quantities in the environment. One of the method for treatment of hazardous waste containing chromium in the aquatic environment can be removed by bioremediation using sulfate-reducing bacteria (SRB). Therefore, the purpose of this research were to analyze the chromium precipitation activity of sulfate-reducing bacteria isolated from sulfate reducing bioreactor and its molecular identification using 16S rRNA gene sequences. The result observed that the isolate of sulfate-reducing bacteria (KGP1 strain) has chromium tolerancy ability up to 5 ppm. It also showed that the strain KGP1 could precipitate chromium up to 0.141 ppm (79 %) on 5 days incubation. Based on 16S rRNA gene sequences, this strain identified as Desulfovibrio aerotolerans.

scholarly journals Overestimation of the Abundance of Sulfate-Reducing Bacteria in Human Feces by Quantitative PCR Targeting the Desulfovibrio 16S rRNA Gene

2011 ◽  
Vol 77 (10) ◽  
pp. 3544-3546 ◽  
Author(s):  
C. T. Christophersen ◽  
M. Morrison ◽  
M. A. Conlon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Gene Assay ◽  
Reducing Bacteria ◽  
Pcr Targeting ◽  
The 16S Rrna Gene

ABSTRACTThe dominant genus of sulfate-reducing bacteria (SRB) in humans isDesulfovibrio, and quantitative PCR (QPCR) targeting the 16S rRNA gene is often used in assays. We show that the 16S rRNA gene assay overestimated SRB abundance in feces from 24 adults compared to QPCR assays using primers targeting two genes involved in SRB energy metabolism.

scholarly journals Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1913 ◽  
Author(s):  
Elizabeth Trembath-Reichert ◽  
David H. Case ◽  
Victoria J. Orphan
Keyword(s):  
Network Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sulfate Reducing Bacteria ◽  
Gene Clone ◽  
Rrna Gene ◽  
Methane Seep ◽  
Sulfate Reducing ◽  
Card Fish ◽  
Reducing Bacteria

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1,Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involvingEpsilon-,Delta-, andGammaproteobacteriain methane seep ecosystems.

Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 761-765 ◽  
Author(s):  
Yuriko Higashioka ◽  
Hisaya Kojima ◽  
Miho Watanabe ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Sulfate Reducing ◽  
Tidal Flat Sediment

A novel sulfate-reducing bacterium, strain S28bFT, was isolated from tidal flat sediment from Tokyo Bay, Japan. Cells of strain S28bFT were rod-shaped (0.5–0.6×1.7–3.8 µm), motile and Gram-stain-negative. For growth, the optimum pH was pH 6.8–7.3 and the optimum temperature was 34–42 °C. Strain S28bFT used sulfate and thiosulfate as electron acceptors, but not nitrate. The G+C content of the genomic DNA was 56.6 mol%. The fatty acid profile of strain S28bFT was characterized by the presence of anteiso-C15 : 0 and C16 : 0 as the major components. Phylogenetic analyses based on genes for 16S rRNA, the alpha subunit of dissimilatory sulfite reductase (dsrA) and adenosine-5′-phosphosulfate reductase (aprA) revealed that the isolated strain belonged to the class Deltaproteobacteria . Its closest relative was Desulfosarcina cetonica DSM 7267T with a 16S rRNA gene sequence similarity of 93.3 %. Two other strains, S28OL1 and S28OL2 were also isolated from the same sediment. These strains were closely related to S28bFT with 16S rRNA gene sequence similarities of 99 %, and the same physiological characteristics were shared with strain S28bFT. On the basis of phylogenetic and phenotypic characterization, a novel species in a new genus, Desulfatitalea tepidiphila gen. nov., sp. nov., is proposed to accommodate the strains obtained in this study. The type strain is S28bFT ( = NBRC 107166T = DSM 23472T).

Microbial Diversity in Acidic Anaerobic Sediments at the Geothermal Caviahue-Copahue System, Argentina

2013 ◽  
Vol 825 ◽  
pp. 7-10 ◽  
Author(s):  
Graciana Willis ◽  
Sabrina Hedrich ◽  
Ivan Nancucheo ◽  
D. Barrie Johnson ◽  
Edgardo R. Donati
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hot Spring ◽  
Rrna Gene ◽  
Sulfate Reducer ◽  
Sulfate Reducing ◽  
Culture Independent ◽  
Cultivation Techniques ◽  
Reducing Bacteria ◽  
The 16S Rrna Gene

In this work we have examined the bacterial diversity from the hot spring sediment Agua del Limón (AL1) present at the geothermal Caviahue-Copahue system using a combination of molecular and cultivation techniques, with particular emphasis on indigenous anaerobic prokaryotes. Microorganisms involved in the iron (Acidithiobacillus ferrooxidansandLeptospirillumspp.) and sulphur (Acidithiobacillusspp., Thermotogales-like bacteria,Thiomonassp., andDesulfurellasp.) cycles were identified in the clone library. Although no obvious sulfate-reducing bacteria were detected by culture-independent techniques, several isolates related to the mesophilic, spore-forming sulfate-reducer"Desulfobacillus acidavidus"strain CL4 were isolated at 30°C and 40°C. The 16S rRNA gene of another isolate showed 94% similarity toDesulfotomaculum thermobenzoicum. Sulfate-reducing enrichment cultures of the Copahue samples were also dominated by"Dsb. acidavidus"CL4.

Affinibrenneria salicis gen. nov. sp. nov. isolated from Salix matsudana bark canker

2021 ◽  
Author(s):  
Dan-ran Bian ◽  
Han Xue ◽  
Guang-ming Wang ◽  
Chun-gen Piao ◽  
Yong Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Novel Genus ◽  
Separate Branch ◽  
The Family ◽  
Salix Matsudana

Abstract L3-3HAT, a Gram-negative-staining, facultatively anaerobic, motile bacterial strain, was isolated from the symptomatic bark of Salix matsudana canker in China. 16S rRNA gene analysis revealed that the novel strain shares the highest sequence similarity with Brenneria goodwinii FRB141T (95.5 %). In phylogenetic trees based on four housekeeping genes (gyrB, rpoB, atpD and infB) and the 16S rRNA gene sequence, the novel strain formed a separate branch from the five genera of the family Pectobacteriaceae (Lonsdalea, Brenneria, Dickeya, Pectobacterium and Sodalis), suggesting that the novel strain should belong to a novel species of a novel genus within the family Pectobacteriaceae. The result was also supported by phylogenomics, amino acid identity and average nucleotide identity. The major fatty acids were C14:0, C16:0, C17:0 cyclo, and C19:0 cyclo ɷ8c. Genome analysis showed that the novel strain has a large genome (5.89 Mb) with 5,052 coding genes, including 181 virulence genes by searching the pathogen-host interactions database (PHI-base), indicating that the novel strain is a potential pathogen of plants and animals. Based on phenotypic and genotypic characteristics, the L3-3HAT strain represents a novel species of a novel genus in the Pectobacteriaceae family, for which the name Affinibrenneria salicis gen nov. sp. nov. is proposed. The strain type is L3-3HAT (= CFCC 15588T = LMG 31209T).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

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