scholarly journals mdRNA-Seq analysis of marine microbial communities from the northern Red Sea

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Shengwei Hou ◽  
Ulrike Pfreundt ◽  
Dan Miller ◽  
Ilana Berman-Frank ◽  
Wolfgang R. Hess
Keyword(s):  
Microbial Communities ◽  
Red Sea ◽  
Marine Microbial Communities ◽  
Northern Red Sea

Enhanced CO2 concentrations change the structure of Antarctic marine microbial communities

2016 ◽  
Vol 552 ◽  
pp. 93-113 ◽  
Author(s):  
AT Davidson ◽  
J McKinlay ◽  
K Westwood ◽  
PG Thomson ◽  
R van den Enden ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Co2 Concentrations ◽  
Antarctic Marine ◽  
Marine Microbial Communities

scholarly journals Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Yoshitake ◽  
Gaku Kimura ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Pacific Coast ◽  
Three Dimensional ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Shotgun Metagenomics ◽  
Functional Features ◽  
Pacific Coast Of Japan ◽  
Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

scholarly journals Effects of Water Column Mixing and Stratification on Planktonic Primary Production and Dinitrogen Fixation on a Northern Red Sea Coral Reef

2018 ◽  
Vol 9 ◽  
Author(s):  
Arjen Tilstra ◽  
Nanne van Hoytema ◽  
Ulisse Cardini ◽  
Vanessa N. Bednarz ◽  
Laura Rix ◽  
...  
Keyword(s):  
Coral Reef ◽  
Primary Production ◽  
Water Column ◽  
Red Sea ◽  
Dinitrogen Fixation ◽  
Water Column Mixing ◽  
Northern Red Sea

Oceanization Starts at Depth During Continental Rupturing in the Northern Red Sea

2018 ◽  
pp. 131-157 ◽  
Author(s):  
Marco Ligi ◽  
Enrico Bonatti ◽  
William Bosworth ◽  
Sara Ronca
Keyword(s):  
Red Sea ◽  
Northern Red Sea
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