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PubMed | University of California at Santa Barbara, ETH Zurich, Santa Fe Institute, Hellenic Center for Marine Research and 20 more.
Type: | Journal: GigaScience | Year: 2016

Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.

Feehery G.R.,New England Biolabs | Yigit E.,New England Biolabs | Oyola S.O.,Wellcome Trust Sanger Institute | Langhorst B.W.,New England Biolabs | And 9 more authors.
PLoS ONE | Year: 2013

DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8-11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types. © 2013 Feehery et al.

Field D.,UK Center for Ecology and Hydrology | Amaral-Zettler L.,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution | Cochrane G.,European Bioinformatics Institute | Cole J.R.,Michigan State University | And 21 more authors.
PLoS Biology | Year: 2011

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences. © 2011 Field et al.

Toney J.L.,Brown University | Theroux S.,Brown University | Theroux S.,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution | Andersen R.A.,West Marine | And 4 more authors.
Geochimica et Cosmochimica Acta | Year: 2012

Long chain alkenones (LCAs) are potential biomarkers for quantitative paleotemperature reconstructions from lacustrine environments. However, progress in this area has been hindered, because the conditions necessary for the growth of haptophytes responsible for alkenone distributions in lake sediments: the predominance of C 37:4 LCA are not known. Here we report the first enrichment culturing of a novel haptophyte phylotype (Hap-A) from Lake George, ND that produces predominantly C 37:4-LCA. Hap-A was enriched from its resting phase collected from deep sediments rather than from water column samples. In contrast, enrichments from near surface water yielded a different haptophyte phylotype (Hap-B), closely related to Chrysotila lamellosa and Pseudoisochrysis paradoxa, which does not display C 37:4-LCA predominance (similar enrichments have been reported previously). The LCA profile in sediments resembles that of enrichments containing Hap-A, suggesting that Hap-A is the dominant alkenone producer of the sedimentary LCAs. In enrichments, increased lighting appeared to be crucial for triggering alkenone production. Both U37K and U38K indices show a promising, positive relationship with temperature for Hap-A in enrichments, but the offset from the environmental calibration suggests that other factors (e.g., the growth stage or nutrients) may influence the absolute U37K value. Based on 18S rRNA gene analyses, several lakes from the Northern Great Plains, as well as Pyramid Lake, NV and Tso Ur, Tibetan Plateau, China contain the same two haptophyte phylotypes. Analysis of surface sediment from the Great Plains lakes show the Hap-A-type LCA distribution, whereas Pyramid and Tso Ur show the Hap-B type distribution. Waters of the Great Plain lakes are dominated by sulfate ions, whereas those Pyramid and Tso Ur are dominated by carbonate ions, suggesting that the sulfate to carbonate ratio may be a determining factor for the dominance of the Hap-A and Hap-B phylotypes in natural settings. © 2011 Elsevier Ltd.

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.

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.

Zheng Y.,Brown University | Zheng Y.,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution | Huang Y.,Brown University | Andersen R.A.,University of Washington | And 2 more authors.
Geochimica et Cosmochimica Acta | Year: 2016

Alkenone unsaturation indices, represented by either UK 37 or UK' 37, are important tools for paleoclimate studies. The UK 37 index is a reflection of the average number of double bonds from di-, tri-, tetra-unsaturated alkenones, but UK' 37 excludes the C37:4 in the calculation. Extensive studies indicate UK' 37 provides better regressions against in situ Sea Surface Temperatures (SST) than UK 37 and is the most widely used SST proxy. However, recent studies have shown that including C37:4 alkenones for lacustrine or brackish water haptophytes such as Ruttnera (Chrysotila) lamellosa and Isochrysis galbana improves temperature correlations although there are still significant deviations at the extreme high and low temperatures. In this study, we use new culture-based calibration experiments alongside published culture data and in situ water column or surface sediment data, to demonstrate that a further improved temperature calibration for alkenones is, in fact, achieved when the di-unsaturated alkenone is excluded from the computation of the unsaturation index. We propose new indices, termed UK" [UK" 37 = C37:3/(C37:3 + C37:4) or UK" 38 = C38:3/(C38:3 + C38:4)], for lacustrine, brackish and estuarine waters. Our observation suggests that di-unsaturated alkenones play a less important role than tri- and tetra-unsaturated alkenones in regulating cell functions to temperature variations in lacustrine and brackish waters. We suggest using UK" indices for paleotemperature reconstructions in the lacustrine and estuarine settings. © 2015 Elsevier Ltd.

Smith K.F.,Brown University | Schmidt V.,Brown University | Schmidt V.,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution | Rosen G.E.,Brown University | And 3 more authors.
PLoS ONE | Year: 2012

Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing >80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species. © 2012 Smith et al.

Post A.F.,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution | Post A.F.,Interuniversity Institute for Marine science | Penno S.,Interuniversity Institute for Marine science | Zandbank K.,Interuniversity Institute for Marine science | And 3 more authors.
Frontiers in Microbiology | Year: 2011

Spatial patterns of marine Synechococcus diversity across ocean domains have been reported on extensively. However, much less is known of seasonal and multiannual patterns of change in Synechococcus community composition. Here we report on the genotypic diversity of Synechococcus populations in the Gulf of Aqaba, Northern Red Sea, over seven annual cycles of deep mixing and stabile stratification, using ntcA as a phylogenetic marker. Synechococcus clone libraries were dominated by clade II and XII genotypes and a total of eight different clades were identified. Inclusion of ntcA sequences from the Global Ocean Sampling database in our analyses identified members of clade XII from beyond the Gulf of Aqaba, extending its known distribution. Most of the Synechococcus diversity was attributed to members of clade II during the spring bloom, while clade III contributed significantly to diversity during summer stratification. Clade XII diversity was most prevalent in fall and winter. Clade abundances were estimated from pyrosequencing of the V6 hypervariable region of 16S rRNA. Members of clade II dominated Synechococcus communities throughout the year, whereas the less frequent genotypes showed a pattern of seasonal succession. Based on the prevailing nutritional conditions we observed that clade I members thrive at higher nutrient concentrations during winter mixing. Clades V, VI and X became apparent during the transition periods between mixing and stratification. Clade III became prominent during sumeer stratification. We propose that members of clades V, VI, and X, and clade III are Synechococcus ecotypes that are adapted to intermediate and low nutrient levels respectively. This is the first time that molecular analyses have correlated population dynamics of Synechococcus genotypes with temporal fluctuations in nutrient regimes. Since these Synechococcus genotypes are routinely observed in the Gulf of Aqaba we suggest that seasonal fluctuations in nutrient levels create temporal niches that sustain their coexistence. © 2011 Post Penno Zand bank Paytan Huse and Welch.

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.

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