Plastid 16S rRNA Gene Diversity among Eukaryotic Picophytoplankton Sorted by Flow Cytometry from the South Pacific Ocean

A Gram-stain-positive, strictly aerobic, coccus-shaped, non-motile, yellow-pigmented bacterium, designated strain XH208T, was isolated from a deep subseafloor sediment sample collected from the South Pacific Gyre (41° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH208T belonged to the genus Luteococcus and showed the highest 16S rRNA gene sequence similarities with Luteococcus peritonei CCUG 38120T (96.9 %), Luteococcus japonicus DSM 10546T (95.4 %) and Luteococcus sanguinis CCUG 33897T (95.2 %). The DNA G+C content of strain XH208T was 66.9 mol%. The cell wall of strain XH208T possessed a type A3γ peptidoglycan (ll-diaminopimelic acid–glycine), and ribose, glucose and galactose as the major whole-cell sugars. The major fatty acids were C17 : 1ω8c, C17 : 1ω6c, and C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3). The major respiratory quinone was menaquinone MK-9(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. On the basis of data from the polyphasic analysis, strain XH208T is considered to represent a novel species in the genus Luteococcus , for which the name Luteococcus sediminum sp. nov. is proposed. The type strain is XH208T ( = DSM 27277T = JCM 19259T).

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Carbon Dioxide, Hydrographic, and Chemical Data Obtained in the South Pacific Ocean (WOCE Section P16A/P17A, P17E/P19S, and P19C, R/V Knorr, October 1992-April 1993)

Carbon Dioxide Information Analysis Center (CDIAC) Datasets ◽

10.3334/cdiac/otg.ndp065 ◽

1998 ◽

Cited By ~ 4

Author(s):

S. Rubin, ◽

J.G. Goddard, ◽

D.W. Chipman, ◽

T. Takahashi, ◽

S.C. Sutherland, ◽

...

Keyword(s):

Carbon Dioxide ◽

Pacific Ocean ◽

South Pacific ◽

Chemical Data ◽

The South ◽

South Pacific Ocean

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Carbon monoxide in the South Pacific Ocean

Tellus ◽

10.3402/tellusa.v26i1-2.9744 ◽

1974 ◽

Vol 26 (1-2) ◽

pp. 136-142 ◽

Cited By ~ 15

Author(s):

J. W. Swinnerton ◽

R. A. Lamontagne

Keyword(s):

Carbon Monoxide ◽

Pacific Ocean ◽

South Pacific ◽

The South ◽

South Pacific Ocean

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Daily accumulation rates of marine litter on the shores of Rapa Nui (Easter Island) in the South Pacific Ocean

Marine Pollution Bulletin ◽

10.1016/j.marpolbul.2021.112535 ◽

2021 ◽

Vol 169 ◽

pp. 112535

Author(s):

Martin Thiel ◽

Bárbara Barrera Lorca ◽

Luis Bravo ◽

Iván A. Hinojosa ◽

Hugo Zeballos Meneses

Keyword(s):

Pacific Ocean ◽

South Pacific ◽

Easter Island ◽

Accumulation Rates ◽

The South ◽

Rapa Nui ◽

Marine Litter ◽

South Pacific Ocean

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Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries

Nature Communications ◽

10.1038/s41467-021-22409-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Eric J. Raes ◽

Kristen Karsh ◽

Swan L. S. Sow ◽

Martin Ostrowski ◽

Mark V. Brown ◽

...

Keyword(s):

16S Rrna ◽

Metabolic Pathways ◽

Low Cost ◽

Marker Gene ◽

South Pacific ◽

Rrna Gene ◽

South Pacific Ocean ◽

Bacterial Marker ◽

Gene 16S Rrna ◽

Gene Data

AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.

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Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64658-0 ◽

2007 ◽

Vol 57 (2) ◽

pp. 219-222 ◽

Cited By ~ 31

Author(s):

Jiao-Yan Ying ◽

Zhi-Pei Liu ◽

Bao-Jun Wang ◽

Xin Dai ◽

Su-Sheng Yang ◽

...

Keyword(s):

Fatty Acids ◽

South China Sea ◽

16S Rrna ◽

16S Rrna Gene ◽

South China ◽

The South China Sea ◽

Rrna Gene ◽

The South ◽

China Sea ◽

Emended Description

A novel marine bacterial strain, HY1T, was isolated from sediment of the South China Sea. The strain was aerobic and heterotrophic and formed saffron yellow-pigmented colonies on marine agar 2216. Cells were non-motile, Gram-negative rods, frequently occurring in chains. blastn searches revealed that the 16S rRNA gene sequence of strain HY1T showed high similarity with those of members of the genera Gillisia (91.7–93.8 %) and Salegentibacter (92.6–93.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain clustered with members of both Salegentibacter and Gillisia and phylogenetic trees constructed using three different methods (neighbour-joining, maximum-parsimony and minimum-evolution) indicated that strain HY1T clustered more frequently with members of the genus Salegentibacter. The DNA G+C content of strain HY1T was 44.4 mol% and its major cellular fatty acids (⩾5 % of the total fatty acids) were iso-15 : 1 (5.0 %), iso-15 : 0 (6.8 %), anteiso-15 : 0 (6.4 %), 15 : 0 (10.4 %), iso-16 : 0 (13.5 %), summed feature 3 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c; 6.3 %), iso-17 : 0 3-OH (5.2 %) and 17 : 0 2-OH (5.0 %). Cells contained menaquinone 6. Based on the phylogenetic and phenotypic analyses, strain HY1T should be classified as representing a novel species within the genus Salegentibacter, for which the name Salegentibacter catena sp. nov. is proposed. The type strain is HY1T (=CGMCC 1.6101T=JCM 14015T). Based on this study and on previously described Salegentibacter species, an emended description of the genus Salegentibacter is given.

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Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽

10.1099/mic.0.038224-0 ◽

2010 ◽

Vol 156 (7) ◽

pp. 2080-2091 ◽

Cited By ~ 28

Author(s):

Anne-Laure Michon ◽

Fabien Aujoulat ◽

Laurent Roudière ◽

Olivier Soulier ◽

Isabelle Zorgniotti ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Diversity ◽

Natural Populations ◽

Variable Region ◽

Housekeeping Gene ◽

Single Copy ◽

Population Based ◽

Rrna Gene ◽

Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

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