scholarly journals Successional Development of Sulfate-Reducing Bacterial Populations and Their Activities in a Wastewater Biofilm Growing under Microaerophilic Conditions

2002 ◽  
Vol 68 (3) ◽  
pp. 1392-1402 ◽  
Author(s):  
Tsukasa Ito ◽  
Satoshi Okabe ◽  
Hisashi Satoh ◽  
Yoshimasa Watanabe
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Cloning ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Sulfide Production ◽  
Microaerophilic Conditions ◽  
Successional Development

ABSTRACT A combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA fragments, and 16S rRNA gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 μM) and in the presence of nitrate. Microelectrode measurements showed that oxygen penetrated 200 μm from the surface during all stages of biofilm development. The first sulfide production of 0.32 μmol of H2S m−2 s−1 was detected below ca. 500 μm in the 3rd week and then gradually increased to 0.70 μmol H2S m−2 s−1 in the 8th week. The most active sulfide production zone moved upward to the oxic-anoxic interface and intensified with time. This result coincided with an increase in SRB populations in the surface layer of the biofilm. The numbers of the probe SRB385- and 660-hybridized SRB populations significantly increased to 7.9 × 109 cells cm−3 and 3.6 × 109 cells cm−3, respectively, in the surface 400 μm during an 8-week cultivation, while those populations were relatively unchanged in the deeper part of the biofilm, probably due to substrate transport limitation. Based on 16S rRNA gene cloning analysis data, clone sequences that related to Desulfomicrobium hypogeium (99% sequence similarity) and Desulfobulbus elongatus (95% sequence similarity) were most frequently found. Different molecular analyses confirmed that Desulfobulbus, Desulfovibrio, and Desulfomicrobium were found to be the numerically important members of SRB in this wastewater biofilm.

scholarly journals Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Meromictic Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Sulfate Reducing ◽  
The Family ◽  
The 16S Rrna Gene

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

scholarly journals Desulfovibrio arcticus sp. nov., a psychrotolerant sulfate-reducing bacterium from a cryopeg

2012 ◽  
Vol 62 (1) ◽  
pp. 33-37 ◽  
Author(s):  
Svetlana A. Pecheritsyna ◽  
Elizaveta M. Rivkina ◽  
Vladimir N. Akimov ◽  
Viktoria A. Shcherbakova
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Barents Sea ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sulfate Reducing ◽  
The 16S Rrna Gene

A psychrotolerant sulfate-reducing bacterium, designated B15T, was isolated from supercooled water brine from within permafrost of the Varandey Peninsula, on the southern coast of the Barents Sea. Cells were Gram-negative, motile vibrions (3.0–4.0×0.4–0.5 µm) with a single polar flagellum. The isolate was positive for desulfoviridin as a bisulfite reductase. Strain B15T grew at −2 to 28 °C (optimum 24 °C) and with 0–2.0 % NaCl (optimum 0.2 %). The isolate used H2 plus acetate, formate, ethanol, lactate, pyruvate and choline as electron donors and used sulfate, sulfite, thiosulfate, elemental sulfur, DMSO and Fe3+ as electron acceptors. Pyruvate and lactate were not fermented in the absence of sulfate. The G+C content of genomic DNA was 55.2 mol%. Analysis of the 16S rRNA gene sequence showed that the isolate belonged to the genus Desulfovibrio. Its closest relatives were Desulfovibrio idahonensis CY1T (98.8 % 16S rRNA gene sequence similarity) and Desulfovibrio mexicanus Lup1T (96.5 %). On the basis of genotypic, phenotypic and phylogenetic characteristics, the isolate represents a novel species, for which the name Desulfovibrio arcticus sp. nov. is proposed; the type strain is B15T ( = VKM B-2367T = DSM 21064T).

scholarly journals Influence of Biostimulation Treatment Using Composted Plant Biomass on Bacterial Diversity of an Aged Petroleum Contaminated Soil as Determined by Culture-dependent and 16S rRNA Gene PCR-DGGE Based Identification Methods

2018 ◽  
pp. 1-16 ◽  
Author(s):  
Leera Solomon ◽  
Chimezie Jason Ogugbue ◽  
Gideon Chijioke Okpokwasili
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Contaminated Soil ◽  
Plant Biomass ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Identification Methods ◽  
Culture Dependent

Influence of biostimulation treatment using composted plant biomass on bacterial diversity of an aged crude oil contaminated soil (ACOCS) was determined using culture-dependent and 16S rRNA gene PCR-DGGE based identification methods. Seven treatment plots were designed and included treatments A (TPA) through G (TPG). Samples were collected bi-weekly from 7 treatment plots designed in situ during a 70-day study period that spanned 10 weeks. Composted (2,500 g each) Water hyacinth (EC), Mexican sunflower (TD) and Bermuda grass (CD) were used as nutrient supplements in 4,000 g of ACOCS in situ. TPA was un-amended while TPB, TPC, and TPD had EC, TD and CD added singly. TPE had EC and TD while TPF contained EC and CD in combination. TPG consisted of EC, TD and CD combined. Bacterial isolates were obtained on mineral salts medium and identified based on their morphological and biochemical characteristics. DGGE fingerprints of PCR-amplified 16S rRNA bacterial gene fragments were also determined using the universal primer set: 7F: 5’-GAGTTTGATCCTGGCTCAG-3’ and 1492R:5’-GGTTACCTTGTTACGACT-3’that corresponded to positions 968 and 1401 of Escherichia coli 16S rRNA gene sequence. DGGE bands fell into corresponding operational taxonomic units based on a threshold of 91-100% sequence similarity. Dendrogram showed dominant DGGE bands in TPB though TPG over time with TPA having no band. The isolates are known crude oil utilizers and are closely related to Gordonia sp. BS261404 with 98% sequence similarity, Aquitalea magnusonii KG26145 (96%), Sphingobacterium sp. K1261411 (97%) and Achromobacter sp. HQ261417 (100%). Data indicated that pseudomonads are the dominant bacteria involved in hydrocarbon biodegradation after biostimulation with the composted plant materials. Cultural and molecular methods of cultivation of microorganisms are neither contradictory nor excluding and should be considered as complementary to interrogate the bacterial diversity in the natural soil environment.

Desulfotomaculum defluvii sp. nov., a sulfate-reducing bacterium isolated from the subsurface environment of a landfill

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2290-2295 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
Stefan Spring ◽  
Pinnaka Anil Kumar ◽  
Shanmugam Mayilraj ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel sulfate-reducing, strictly anaerobic and endospore-forming bacterium, designated strain A5LFS102T, was isolated from a subsurface landfill sample. The strain was characterized using a polyphasic approach. Optimal growth was observed at 37 °C and pH 7.5 with sulfate as an electron acceptor. Sulfite and thiosulfate were utilized as electron acceptors. The respiratory isoprenoid quinone was menaquinone MK-7. 16S rRNA gene sequence analysis assigned strain A5LFS102T to the genus Desulfotomaculum . Both 16S rRNA and dissimilatory sulfate reductase (dsr) genes were compared with those of representative members of the genus Desulfotomaculum . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A5LFS102T was closely related to Desulfotomaculum aeronauticum DSM 10349T (94.6 % sequence similarity). The G+C content of the DNA was 45.4 mol%. The total cellular fatty acid profile was dominated by C16 fatty acids. These phenotypic and genotypic data showed that strain A5LFS102T should be recognized as representative of a novel species of the genus Desulfotomaculum , for which the name Desulfotomaculum defluvii sp. nov. is proposed. The type strain is A5LFS102T ( = DSM 23699T = JCM 14036T = MTCC 7767T).

scholarly journals Desulfohalobium utahense sp. nov., a moderately halophilic, sulfate-reducing bacterium isolated from Great Salt Lake

2006 ◽  
Vol 56 (9) ◽  
pp. 2063-2069 ◽  
Author(s):  
Trine Fredlund Jakobsen ◽  
Kasper Urup Kjeldsen ◽  
Kjeld Ingvorsen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Salt Lake ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sulfate Reducing

A novel moderately halophilic, sulfate-reducing bacterium, strain EtOH3T, was isolated from anoxic hypersaline (270 g NaCl l−1) sediment of the northern arm of the Great Salt Lake, Utah, USA. Cells of strain EtOH3T were oval to rod-shaped, non-motile, non-sporulating and stained Gram-negative. The strain required sodium and magnesium ions for growth and grew at salinities of up to 240 g NaCl l−1 and 121 g MgCl2.6H2O l−1. The optimum NaCl concentration was 80–100 g l−1. Strain EtOH3T grew at temperatures ranging from 15 to 44 °C (optimum 37 °C). The pH range for growth was 6.5–8.3 (optimum around pH 6.8). Only sulfate and thiosulfate served as electron acceptors for a broad range of electron donors including various short-chain fatty acids and primary (C1–5) alcohols, amino acids, H2/acetate and H2/yeast extract. The G+C content of the genomic DNA was 51.4 mol%. Phylogenetic analysis of dsrAB [genes encoding the major subunits of dissimilatory (bi)sulfite reductase] and 16S rRNA gene sequence data placed strain EtOH3T within the deltaproteobacterial family Desulfohalobiaceae. Strain EtOH3T shared 76 and 91 % dsrAB and 16S rRNA gene sequence similarity, respectively, with the type strain of the phylogenetically most closely related species with a validly published name, Desulfohalobium retbaense DSM 5692T. High 16S rRNA gene sequence similarity (~97 %) was shared with the recently described strain ‘Desulfovermiculus halophilus’ VKM B-2364. Strain EtOH3T, however, clearly differed from this strain in both genomic G+C content and in several of its phenotypic properties. On the basis of phenotypic and genotypic characteristics, the novel species Desulfohalobium utahense sp. nov. is proposed, with strain EtOH3T (=VKM B-2384T=DSM 17720T) as the type strain.

scholarly journals Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 959-964 ◽  
Author(s):  
Martin Könneke ◽  
Jan Kuever ◽  
Alexander Galushko ◽  
Bo Barker Jørgensen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Sulfate Reducing ◽  
Link Type

A sulfate-reducing bacterium, designated JHA1T, was isolated from a permanently cold marine sediment sampled in an Artic fjord on the north-west coast of Svalbard. The isolate was originally enriched at 4 °C in a highly diluted liquid culture amended with hydrogen and sulfate. Strain JHA1T was a psychrophile, growing fastest between 14 and 16 °C and not growing above 20 °C. Fastest growth was found at neutral pH (pH 7.2–7.4) and at marine concentrations of NaCl (20–30 g l−1). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain JHA1T was a member of the family Desulfobacteraceae in the Deltaproteobacteria . The isolate shared 99 % 16S rRNA gene sequence similarity with an environmental sequence obtained from permanently cold Antarctic sediment. The closest recognized relatives were Desulfobacula phenolica DSM 3384T and Desulfobacula toluolica DSM 7467T (both <95 % sequence similarity). In contrast to its closest phylogenetic relatives, strain JHA1T grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity indicated the operation of the reductive acetyl-CoA pathway for inorganic carbon assimilation. Beside differences in physiology and morphology, strain JHA1T could be distinguished chemotaxonomically from the genus Desulfobacula by the absence of the cellular fatty acid C16 : 0 10-methyl. Phylogenetic differentiation from other genera was further supported by DsrAB and AprBA sequence analysis. Based on the described phylogenetic and phenotypic differences between strain JHA1T and its closest relatives, the establishment of a novel genus and a novel species, Desulfoconvexum algidum gen. nov., sp. nov. is proposed. The type strain is JHA1T ( = DSM 21856T  = JCM 16085T).

scholarly journals Filamentous “Epsilonproteobacteria” Dominate Microbial Mats from Sulfidic Cave Springs

2003 ◽  
Vol 69 (9) ◽  
pp. 5503-5511 ◽  
Author(s):  
Annette Summers Engel ◽  
Natuschka Lee ◽  
Megan L. Porter ◽  
Libby A. Stern ◽  
Philip C. Bennett ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Class Group ◽  
Sequence Similarity ◽  
Extreme Environments ◽  
Rrna Gene ◽  
Group I ◽  
Group Ii

ABSTRACT Hydrogen sulfide-rich groundwater discharges from springs into Lower Kane Cave, Wyoming, where microbial mats dominated by filamentous morphotypes are found. The full-cycle rRNA approach, including 16S rRNA gene retrieval and fluorescence in situ hybridization (FISH), was used to identify these filaments. The majority of the obtained 16S rRNA gene clones from the mats were affiliated with the “Epsilonproteobacteria” and formed two distinct clusters, designated LKC group I and LKC group II, within this class. Group I was closely related to uncultured environmental clones from petroleum-contaminated groundwater, sulfidic springs, and sulfidic caves (97 to 99% sequence similarity), while group II formed a novel clade moderately related to deep-sea hydrothermal vent symbionts (90 to 94% sequence similarity). FISH with newly designed probes for both groups specifically stained filamentous bacteria within the mats. FISH-based quantification of the two filament groups in six different microbial mat samples from Lower Kane Cave showed that LKC group II dominated five of the six mat communities. This study further expands our perceptions of the diversity and geographic distribution of “Epsilonproteobacteria” in extreme environments and demonstrates their biogeochemical importance in subterranean ecosystems.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

2021 ◽  
Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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