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Huo Y.-Y.,State Oceanic Administration | Li Z.-Y.,State Oceanic Administration | You H.,State Oceanic Administration | Wang C.-S.,State Oceanic Administration | And 3 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

Two Gram-stain-negative, aerobic, moderately halophilic, rod-shaped bacteria (strains Ar-45T and DY470T) were isolated from seawater collected from the Southern Ocean and the Pacific Ocean, respectively. Growth of strain Ar-45T was observed with between 0.5 and 10.0% (w/v) NaCl (optimally with 0.5–3.0%) and between pH 5.5 and 9.5. Strain DY470T grew in the presence of 0.5–7.5% (w/v) NaCl (optimally with 2.0%) and at pH 5.5–8.5. Chemotaxonomic analysis showed Q-10 as the respiratory quinone for both strains. The major fatty acids (.5%) of strain Ar-45T were C16: 0, C19: 0 cyclo ɷ8c and C18: 1ɷ7c, while those of strain DY470T were C18: 1ɷ7c, C16: 0 and 11-methyl C18: 1ɷ7c. The DNA G+C contents of the two strains were 62.0 and 61.8 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains Ar-45T and DY470T were related most closely to the genus Oceanicola, with sequence similarities of 97.4–94.0 and 97.7–94.7%, respectively. The DNA–DNA hybridization value between strain Ar-45T and Oceanicola marinus LMG 23705T was 22.0%. Levels of DNA-DNA relatedness between strain DY470T and Oceanicola nitratireducens LMG 24663T and Oceanicola batsensis DSM 15984T were 32.5 and 26.1%, respectively. Based on phylogenetic, chemotaxonomic and phenotypic data, strains Ar-45T and DY470T are considered to represent two novel species of the genus Oceanicola, for which the names Oceanicola antarcticus (type strain Ar-45T=CGMCC 1.12662T=LMG 27868T) and Oceanicola flagellatus (type strain DY470T=CGMCC 1.12664T=LMG 27871T) are proposed. © 2014 IUMS. Source

Pawlowski J.,University of Geneva | Christen R.,University of Nice Sophia Antipolis | Lecroq B.,Japan Agency for Marine - Earth Science and Technology | Bachar D.,University of Nice Sophia Antipolis | And 3 more authors.
PLoS ONE | Year: 2011

Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes. © 2011 Pawlowski et al. Source

Lie A.A.Y.,University of Southern California | Liu Z.,University of Southern California | Hu S.K.,University of Southern California | Jones A.C.,University of Southern California | And 10 more authors.
Applied and Environmental Microbiology | Year: 2014

Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages. © 2014, American Society for Microbiology. Source

Kamennaya N.A.,Hebrew University of Jerusalem | Kamennaya N.A.,Lawrence Berkeley National Laboratory | Post A.F.,Hebrew University of Jerusalem | Post A.F.,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Limnology and Oceanography | Year: 2013

We assessed the significance of cyanate utilization in marine primary productivity from the distribution of a dedicated transporter (encoded by cynABD) in different ocean environments. Several lines of evidence indicate that the cyanate utilization potential is associated mainly with surface populations of Prochlorococcus. Spatial and temporal dimensions of cynA, cynS, and ntcA expression by picocyanobacteria in the northern Red Sea supported our previous finding that cynA transcripts accumulate under more stringent N-limiting conditions. At the same time, cyanate utilization appeared to be more complex than suggested in our earlier publication, as we showed that picocyanobacteria also express their cyanate utilization potential under conditions where labile organic N compounds, such as urea, accumulate. These include N-sufficient transient conditions that result from nutrient upwelling during early mixing events in autumn as well as during spring bloom conditions that follow deep mixing events. Our finding that cynA occurrence is common in diverse marine environments suggests that cyanate utilization may be of a more fundamental importance to picophytoplankton productivity than previously considered.© 2013, by the Association for the Sciences of Limnology and Oceanography, Inc. Source

Mackey K.R.M.,Stanford University | Mackey K.R.M.,University of California at Santa Cruz | Bristow L.,University of Massachusetts Dartmouth | Parks D.R.,Stanford University | And 3 more authors.
Progress in Oceanography | Year: 2011

In the seasonally stratified Gulf of Aqaba Red Sea, both NO2- release by phytoplankton and NH4+ oxidation by nitrifying microbes contributed to the formation of a primary nitrite maximum (PNM) over different seasons and depths in the water column. In the winter and during the days immediately following spring stratification, NO2- formation was strongly correlated (R 2=0.99) with decreasing irradiance and chlorophyll, suggesting that incomplete NO3- reduction by light limited phytoplankton was a major source of NO2-. However, as stratification progressed, NO2- continued to be generated below the euphotic depth by microbial NH4+ oxidation, likely due to differential photoinhibition of NH4+ and NO2- oxidizing populations. Natural abundance stable nitrogen isotope analyses revealed a decoupling of the δ 15N and δ 18O in the combined NO3- and NO2- pool, suggesting that assimilation and nitrification were co-occurring in surface waters. As stratification progressed, the δ 15N of particulate N below the euphotic depth increased from -5‰ to up to +20‰.N uptake rates were also influenced by light; based on 15N tracer experiments, assimilation of NO3-, NO2-, and urea was more rapid in the light (434±24, 94±17, and 1194±48nmolNL -1day -1 respectively) than in the dark (58±14, 29±14, and 476±31nmolNL -1day -1 respectively). Dark NH4+ assimilation was 314±31nmolNL -1day -1, while light NH4+ assimilation was much faster, resulting in complete consumption of the 15N spike in less than 7h from spike addition. The overall rate of coupled urea mineralization and NH4+ oxidation (14.1±7.6nmolNL -1day -1) was similar to that of NH4+ oxidation alone (16.4±8.1nmolNL -1day -1), suggesting that mineralization of labile dissolved organic N compounds like urea was not a rate limiting step for nitrification. Our results suggest that assimilation and nitrification compete for NH4+ and that N transformation rates throughout the water column are influenced by light over diel and seasonal cycles, allowing phytoplankton and nitrifying microbes to contribute jointly to PNM formation. We identify important factors that influence the N cycle throughout the year, including light intensity, substrate availability, and microbial community structure. These processes could be relevant to other regions worldwide where seasonal variability in mixing depth and stratification influence the contributions of phytoplankton and non-photosynthetic microbes to the N cycle. © 2011 Elsevier Ltd. Source

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