Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses

A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.

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Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea

Ocean and Polar Research ◽

10.4217/opr.2010.32.3.309 ◽

2010 ◽

Vol 32 (3) ◽

pp. 309-319 ◽

Cited By ~ 5

Author(s):

Bo-Bae Kim ◽

Hye-Youn Cho ◽

Jung-Ho Hyun

Keyword(s):

Community Structure ◽

16S Rrna ◽

16S Rrna Gene ◽

Vertical Distribution ◽

Deep Sea ◽

Gene Analysis ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Deep Sea Sediment ◽

Structure Diversity

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Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity

Applied and Environmental Microbiology ◽

10.1128/aem.00137-09 ◽

2009 ◽

Vol 75 (12) ◽

pp. 4139-4148 ◽

Cited By ~ 33

Author(s):

James P. Davis ◽

Noha H. Youssef ◽

Mostafa S. Elshahed

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Clone Library ◽

Phylogenetic Diversity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Qpcr Analysis ◽

Freshwater Pond ◽

Candidate Division

ABSTRACT We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55°C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.

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Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis

International Endodontic Journal ◽

10.1111/iej.12361 ◽

2014 ◽

Vol 48 (8) ◽

pp. 717-728 ◽

Cited By ~ 17

Author(s):

M. N. Zakaria ◽

T. Takeshita ◽

Y. Shibata ◽

H. Maeda ◽

N. Wada ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Clone Library ◽

Apical Periodontitis ◽

Gene Clone ◽

Rrna Gene ◽

Clone Library Analysis

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Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods

Applied and Environmental Microbiology ◽

10.1128/aem.67.7.3077-3085.2001 ◽

2001 ◽

Vol 67 (7) ◽

pp. 3077-3085 ◽

Cited By ~ 102

Author(s):

Wolfgang Eder ◽

Linda L. Jahnke ◽

Mark Schmidt ◽

Robert Huber

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Red Sea ◽

Deep Sea ◽

Rrna Gene ◽

Strictly Anaerobic ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Cultivation Methods

ABSTRACT The brine-seawater interface of the Kebrit Deep, northern Red Sea, was investigated for the presence of microorganisms using phylogenetic analysis combined with cultivation methods. Under strictly anaerobic culture conditions, novel halophiles were isolated. The new rod-shaped isolates belong to the halophilic genus Halanaerobiumand are the first representatives of the genus obtained from deep-sea, anaerobic brine pools. Within the genus Halanaerobium, they represent new species which grow chemoorganotrophically at NaCl concentrations ranging from 5 to 34%. The cellular fatty acid compositions are consistent with those of otherHalanaerobium representatives, showing unusually large amounts of Δ7 and Δ11 16:1 fatty acids. Phylogenetic analysis of the brine-seawater interface sample revealed the presence of various bacterial 16S rRNA gene sequences dominated by cultivated members of the bacterial domain, with the majority affiliated with the genusHalanaerobium. The new Halanaerobium 16S rRNA clone sequences showed the highest similarity (99.9%) to the sequence of isolate KT-8-13 from the Kebrit Deep brine. In this initial survey, our polyphasic approach demonstrates that novel halophiles thrive in the anaerobic, deep-sea brine pool of the Kebrit Deep, Red Sea. They may contribute significantly to the anaerobic degradation of organic matter enriched at the brine-seawater interface.

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Bacterial Communities of Traditional Salted and Fermented Seafoods from Jeju Island of Korea Using 16S rRNA Gene Clone Library Analysis

Journal of Food Science ◽

10.1111/1750-3841.12431 ◽

2014 ◽

Vol 79 (5) ◽

pp. M927-M934 ◽

Cited By ~ 23

Author(s):

Min-Soo Kim ◽

Eun-Jin Park

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Clone Library ◽

Bacterial Communities ◽

Jeju Island ◽

Gene Clone ◽

Rrna Gene ◽

Clone Library Analysis

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Insights into Bacterial Community Structure of a Commercial Copper Bioheapleaching Plant: Growth of Heterotrophic Bacteria in the System

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.825.50 ◽

2013 ◽

Vol 825 ◽

pp. 50-53 ◽

Cited By ~ 3

Author(s):

Xing Yu Liu ◽

Bo Wei Chen ◽

Jian Kang Wen

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Clone Library ◽

Heterotrophic Bacteria ◽

Outer Part ◽

Gene Clone ◽

Rrna Gene ◽

Liquid Samples ◽

Lower Depth

The distribution and diversity of bacterial community in Zijinshan commercial non-aeration copper bioheapleaching system operated at pH 0.8 for three years were investigated. The 24 meters high heap was cut off by mechanical digger. On the trapezoidal cross-section of the heap, 9 ore samples were taken from different vertical and horizontal locations and investigated by 16S rRNA gene clone library. Another 3 liquid samples from raffinate solution pond, spray solution pond and pregnant solution pond were also applied to 16S rRNA gene clone library analysis. The retrieved 1166 clone sequences from 12 samples were mainly related to genus Acidithiobacillus (42.36%), genus Leptospirillum (37.73%) and genus Sulfobacillus (6.52%). Relative high amount of heterotrophic bacteria were distributed at the ore surface in the internal part of the heap and in the liquid samples respectively. The retrieved heterotrophic bacterial sequences were mainly related to genus Acidiphilium (accounting 11.11% to 32.00% percent in the liquid samples), genus Acidovorax (accounting 12.37% in A1 sample), genus Pelomonas (accounting 4.17% to 10.31% in several ore samples) and genus Aquabacterium (accounting 10.31% in C2 sample). Bacterial diversity in the heap was increased from the surfcae layer to the interior of the heap. The proportion of genus Leptospirillum horizontally increased from the inner to the outer part while vertically decreased from lower depth (2-3 years leaching time) to higher depth(3-6 month leaching time), and reverse correlation of genus Acidithiobacillus was found in the heap. Our finding indicated that heterotrophic bacteria may play very important roles in the commercial bioheapleaching system, and revealed high distribution of genus Leptospirillum in the outer part of this non-aerated heap.

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Luteimonas abyssi sp. nov., isolated from deep-sea sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.056010-0 ◽

2014 ◽

Vol 64 (Pt_2) ◽

pp. 668-674 ◽

Cited By ~ 26

Author(s):

Xiaoyang Fan ◽

Tong Yu ◽

Zhao Li ◽

Xiao-Hua Zhang

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Deep Sea ◽

Type Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Strictly Aerobic ◽

Content Type ◽

Deep Sea Sediment ◽

Link Type

Three Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031T, XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51′ S 153° 6′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9T (96.95 %), Luteimonas huabeiensis HB2T (96.93 %) and Xanthomonas cucurbitae LMG 690T (96.92 %). The DNA G+C contents of the three isolates were 70.2–73.9 mol%. The major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C11 : 0 and C16 : 010-methyl and/or iso-C17 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas , for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031T ( = DSM 25880T = CGMCC 1.12611T).

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Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques

Applied and Environmental Microbiology ◽

10.1128/aem.71.4.2162-2169.2005 ◽

2005 ◽

Vol 71 (4) ◽

pp. 2162-2169 ◽

Cited By ~ 176

Author(s):

Hideyuki Tamaki ◽

Yuji Sekiguchi ◽

Satoshi Hanada ◽

Kazunori Nakamura ◽

Nakao Nomura ◽

...

Keyword(s):

Comparative Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Clone Library ◽

Eutrophic Lake ◽

Freshwater Sediment ◽

Gene Clone ◽

Rrna Gene ◽

Shallow Eutrophic Lake

ABSTRACT Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.

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