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1.  The ocean sampling day consortium 
Kopf, Anna | Bicak, Mesude | Kottmann, Renzo | Schnetzer, Julia | Kostadinov, Ivaylo | Lehmann, Katja | Fernandez-Guerra, Antonio | Jeanthon, Christian | Rahav, Eyal | Ullrich, Matthias | Wichels, Antje | Gerdts, Gunnar | Polymenakou, Paraskevi | Kotoulas, Giorgos | Siam, Rania | Abdallah, Rehab Z | Sonnenschein, Eva C | Cariou, Thierry | O’Gara, Fergal | Jackson, Stephen | Orlic, Sandi | Steinke, Michael | Busch, Julia | Duarte, Bernardo | Caçador, Isabel | Canning-Clode, João | Bobrova, Oleksandra | Marteinsson, Viggo | Reynisson, Eyjolfur | Loureiro, Clara Magalhães | Luna, Gian Marco | Quero, Grazia Marina | Löscher, Carolin R | Kremp, Anke | DeLorenzo, Marie E | Øvreås, Lise | Tolman, Jennifer | LaRoche, Julie | Penna, Antonella | Frischer, Marc | Davis, Timothy | Katherine, Barker | Meyer, Christopher P | Ramos, Sandra | Magalhães, Catarina | Jude-Lemeilleur, Florence | Aguirre-Macedo, Ma Leopoldina | Wang, Shiao | Poulton, Nicole | Jones, Scott | Collin, Rachel | Fuhrman, Jed A | Conan, Pascal | Alonso, Cecilia | Stambler, Noga | Goodwin, Kelly | Yakimov, Michael M | Baltar, Federico | Bodrossy, Levente | Van De Kamp, Jodie | Frampton, Dion MF | Ostrowski, Martin | Van Ruth, Paul | Malthouse, Paul | Claus, Simon | Deneudt, Klaas | Mortelmans, Jonas | Pitois, Sophie | Wallom, David | Salter, Ian | Costa, Rodrigo | Schroeder, Declan C | Kandil, Mahrous M | Amaral, Valentina | Biancalana, Florencia | Santana, Rafael | Pedrotti, Maria Luiza | Yoshida, Takashi | Ogata, Hiroyuki | Ingleton, Tim | Munnik, Kate | Rodriguez-Ezpeleta, Naiara | Berteaux-Lecellier, Veronique | Wecker, Patricia | Cancio, Ibon | Vaulot, Daniel | Bienhold, Christina | Ghazal, Hassan | Chaouni, Bouchra | Essayeh, Soumya | Ettamimi, Sara | Zaid, El Houcine | Boukhatem, Noureddine | Bouali, Abderrahim | Chahboune, Rajaa | Barrijal, Said | Timinouni, Mohammed | El Otmani, Fatima | Bennani, Mohamed | Mea, Marianna | Todorova, Nadezhda | Karamfilov, Ventzislav | ten Hoopen, Petra | Cochrane, Guy | L’Haridon, Stephane | Bizsel, Kemal Can | Vezzi, Alessandro | Lauro, Federico M | Martin, Patrick | Jensen, Rachelle M | Hinks, Jamie | Gebbels, Susan | Rosselli, Riccardo | De Pascale, Fabio | Schiavon, Riccardo | dos Santos, Antonina | Villar, Emilie | Pesant, Stéphane | Cataletto, Bruno | Malfatti, Francesca | Edirisinghe, Ranjith | Silveira, Jorge A Herrera | Barbier, Michele | Turk, Valentina | Tinta, Tinkara | Fuller, Wayne J | Salihoglu, Ilkay | Serakinci, Nedime | Ergoren, Mahmut Cerkez | Bresnan, Eileen | Iriberri, Juan | Nyhus, Paul Anders Fronth | Bente, Edvardsen | Karlsen, Hans Erik | Golyshin, Peter N | Gasol, Josep M | Moncheva, Snejana | Dzhembekova, Nina | Johnson, Zackary | Sinigalliano, Christopher David | Gidley, Maribeth Louise | Zingone, Adriana | Danovaro, Roberto | Tsiamis, George | Clark, Melody S | Costa, Ana Cristina | El Bour, Monia | Martins, Ana M | Collins, R Eric | Ducluzeau, Anne-Lise | Martinez, Jonathan | Costello, Mark J | Amaral-Zettler, Linda A | Gilbert, Jack A | Davies, Neil | Field, Dawn | Glöckner, Frank Oliver
GigaScience  2015;4:27.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
PMCID: PMC4473829  PMID: 26097697
Ocean sampling day; OSD; Biodiversity; Genomics; Health Index; Bacteria; Microorganism; Metagenomics; Marine; Micro B3; Standards
2.  Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes 
The ISME Journal  2013;8(4):778-789.
High-latitude environments, such as the Antarctic McMurdo Dry Valley lakes, are subject to seasonally segregated light–dark cycles, which have important consequences for microbial diversity and function on an annual basis. Owing largely to the logistical difficulties of sampling polar environments during the darkness of winter, little is known about planktonic microbial community responses to the cessation of photosynthetic primary production during the austral sunset, which lingers from approximately February to April. Here, we hypothesized that changes in bacterial, archaeal and eukaryotic community structure, particularly shifts in favor of chemolithotrophs and mixotrophs, would manifest during the transition to polar night. Our work represents the first concurrent molecular characterization, using 454 pyrosequencing of hypervariable regions of the small-subunit ribosomal RNA gene, of bacterial, archaeal and eukaryotic communities in permanently ice-covered lakes Fryxell and Bonney, before and during the polar night transition. We found vertically stratified populations that varied at the community and/or operational taxonomic unit-level between lakes and seasons. Network analysis based on operational taxonomic unit level interactions revealed nonrandomly structured microbial communities organized into modules (groups of taxa) containing key metabolic potential capacities, including photoheterotrophy, mixotrophy and chemolithotrophy, which are likely to be differentially favored during the transition to polar night.
PMCID: PMC3960534  PMID: 24152712
ice-covered lake; McMurdo Dry Valleys; microbial diversity; MIRADA-LTERS; network analysis; polar night
3.  Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes 
Applied and Environmental Microbiology  2014;80(14):4363-4373.
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.
PMCID: PMC4068655  PMID: 24814788
4.  Oligotyping reveals community level habitat selection within the genus Vibrio 
The genus Vibrio is a metabolically diverse group of facultative anaerobic bacteria, common in aquatic environments and marine hosts. The genus contains several species of importance to human health and aquaculture, including the causative agents of human cholera and fish vibriosis. Vibrios display a wide variety of known life histories, from opportunistic pathogens to long-standing symbionts with individual host species. Studying Vibrio ecology has been challenging as individual species often display a wide range of habitat preferences, and groups of vibrios can act as socially cohesive groups. Although strong associations with salinity, temperature and other environmental variables have been established, the degree of habitat or host specificity at both the individual and community levels is unknown. Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats. Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments. Our analyses show that Vibrio communities share considerable overlap between two distinct hosts (i.e., sponge and fish), yet are distinct from the abiotic plastic substrates. Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others. In addition to providing insights into Vibrio ecology across a broad range of habitats, our study shows the utility of oligotyping as a facile, high-throughput and unbiased method for large-scale analyses of publically available sequence data repositories and suggests its wide application could greatly extend the range of possibilities to explore microbial ecology.
PMCID: PMC4230168  PMID: 25431569
oligotyping; Vibrio ecology; host-microbe interactions; illumina sequencing; 16S rRNA analysis; plastisphere; aquaculture pathogens; meta-analysis
5.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing 
Keeling, Patrick J. | Burki, Fabien | Wilcox, Heather M. | Allam, Bassem | Allen, Eric E. | Amaral-Zettler, Linda A. | Armbrust, E. Virginia | Archibald, John M. | Bharti, Arvind K. | Bell, Callum J. | Beszteri, Bank | Bidle, Kay D. | Cameron, Connor T. | Campbell, Lisa | Caron, David A. | Cattolico, Rose Ann | Collier, Jackie L. | Coyne, Kathryn | Davy, Simon K. | Deschamps, Phillipe | Dyhrman, Sonya T. | Edvardsen, Bente | Gates, Ruth D. | Gobler, Christopher J. | Greenwood, Spencer J. | Guida, Stephanie M. | Jacobi, Jennifer L. | Jakobsen, Kjetill S. | James, Erick R. | Jenkins, Bethany | John, Uwe | Johnson, Matthew D. | Juhl, Andrew R. | Kamp, Anja | Katz, Laura A. | Kiene, Ronald | Kudryavtsev, Alexander | Leander, Brian S. | Lin, Senjie | Lovejoy, Connie | Lynn, Denis | Marchetti, Adrian | McManus, George | Nedelcu, Aurora M. | Menden-Deuer, Susanne | Miceli, Cristina | Mock, Thomas | Montresor, Marina | Moran, Mary Ann | Murray, Shauna | Nadathur, Govind | Nagai, Satoshi | Ngam, Peter B. | Palenik, Brian | Pawlowski, Jan | Petroni, Giulio | Piganeau, Gwenael | Posewitz, Matthew C. | Rengefors, Karin | Romano, Giovanna | Rumpho, Mary E. | Rynearson, Tatiana | Schilling, Kelly B. | Schroeder, Declan C. | Simpson, Alastair G. B. | Slamovits, Claudio H. | Smith, David R. | Smith, G. Jason | Smith, Sarah R. | Sosik, Heidi M. | Stief, Peter | Theriot, Edward | Twary, Scott N. | Umale, Pooja E. | Vaulot, Daniel | Wawrik, Boris | Wheeler, Glen L. | Wilson, William H. | Xu, Yan | Zingone, Adriana | Worden, Alexandra Z.
PLoS Biology  2014;12(6):e1001889.
Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
PMCID: PMC4068987  PMID: 24959919
6.  Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. 
Standards in Genomic Sciences  2014;9(3):1236-1250.
This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.
PMCID: PMC4148987
7.  The founding charter of the Genomic Observatories Network 
GigaScience  2014;3:2.
The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.
An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.
PMCID: PMC3995929  PMID: 24606731
Biodiversity; Genomics; Biocode; Earth observations
8.  Comparison of Bacterial Communities in Sands and Water at Beaches with Bacterial Water Quality Violations 
PLoS ONE  2014;9(3):e90815.
Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.
PMCID: PMC3944938  PMID: 24599478
9.  Genomic Standards Consortium Projects 
Standards in Genomic Sciences  2014;9(3):599-601.
The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently has 18 ongoing projects, with additional projects regularly proposed from within and outside the GSC. Here we describe our recently enacted policy for proposing new activities that are intended to be taken on by the GSC, along with the template for proposing such new activities.
PMCID: PMC4148985  PMID: 25197446
10.  A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA 
PLoS ONE  2013;8(10):e76096.
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.
PMCID: PMC3810253  PMID: 24204593
11.  Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils 
The ISME Journal  2012;6(9):1629-1639.
Microbes are transported in hydrological networks through many environments, but the nature and dynamics of underlying microbial metacommunities and the impact of downslope inoculation on patterns of microbial diversity across landscapes are unknown. Pyrosequencing of small subunit ribosomal RNA gene hypervariable regions to characterize microbial communities along a hydrological continuum in arctic tundra showed a pattern of decreasing diversity downslope, with highest species richness in soil waters and headwater streams, and lowest richness in lake water. In a downstream lake, 58% and 43% of the bacterial and archaeal taxa, respectively, were also detected in diverse upslope communities, including most of the numerically dominant lake taxa. In contrast, only 18% of microbial eukaryotic taxa in the lake were detected upslope. We suggest that patterns of diversity in surface waters are structured by initial inoculation from microbial reservoirs in soils followed by a species-sorting process during downslope dispersal of both common and rare microbial taxa. Our results suggest that, unlike for metazoans, a substantial portion of bacterial and archaeal diversity in surface freshwaters may originate in complex soil environments.
PMCID: PMC3498914  PMID: 22378536
Bacteria; Archaea; Eukarya; metacommunity; landscape; MIRADA-LTERS
12.  An all-taxon microbial inventory of the Moorea coral reef ecosystem 
The ISME Journal  2011;6(2):309-319.
The Moorea Coral Reef Long Term Ecological Research (LTER) Site (17.50°S, 149.83°W) comprises the fringe of coral reefs and lagoons surrounding the volcanic island of Moorea in the Society Islands of French Polynesia. As part of our Microbial Inventory Research Across Diverse Aquatic LTERS biodiversity inventory project, we characterized microbial community composition across all three domains of life using amplicon pyrosequencing of the V6 (bacterial and archaeal) and V9 (eukaryotic) hypervariable regions of small-subunit ribosomal RNA genes. Our survey spanned eight locations along a 130-km transect from the reef lagoon to the open ocean to examine changes in communities along inshore to offshore gradients. Our results illustrate consistent community differentiation between inshore and offshore ecosystems across all three domains, with greater richness in all domains in the reef-associated habitats. Bacterial communities were more homogenous among open ocean sites spanning >100 km than among inshore sites separated by <1 km, whereas eukaryotic communities varied more offshore than inshore, and archaea showed more equal levels of dissimilarity among subhabitats. We identified signature communities representative of specific geographic and geochemical milieu, and characterized co-occurrence patterns of specific microbial taxa within the inshore ecosystem including several bacterial groups that persist in geographical niches across time. Bacterial and archaeal communities were dominated by few abundant taxa but spatial patterning was consistent through time and space in both rare and abundant communities. This is the first in-depth inventory analysis of biogeographic variation of all three microbial domains within a coral reef ecosystem.
PMCID: PMC3260501  PMID: 21900967
coral reef; MIRADA-LTERS; pyrosequencing; V6; V9
13.  Eukaryotic diversity at pH extremes 
Extremely acidic (pH < 3) and extremely alkaline (pH > 9) environments support a diversity of single-cell and to a lesser extent, multicellular eukaryotic life. This study compared alpha and beta diversity in eukaryotic communities from seven diverse aquatic environments with pH values ranging from 2 to 11 using massively-parallel pyrotag sequencing targeting the V9 hypervariable region of the 18S ribosomal RNA (rRNA) gene. A total of 946 operational taxonomic units (OTUs) were recovered at a 6% cut-off level (94% similarity) across the sampled environments. Hierarchical clustering of the samples segregated the communities into acidic and alkaline groups. Similarity percentage (SIMPER) analysis followed by indicator OTU analysis (IOA) and non-metric multidimensional scaling (NMDS) were used to determine which characteristic groups of eukaryotic taxa typify acidic or alkaline extremes and the extent to which pH explains eukaryotic community structure in these environments. Spain's Rio Tinto yielded the fewest observed OTUs while Nebraska Sandhills alkaline lakes yielded the most. Distinct OTUs, including metazoan OTUs, numerically dominated pH extreme sites. Indicator OTUs included the diatom Pinnularia and unidentified opisthokonts (Fungi and Filasterea) in the extremely acidic environments, and the ciliate Frontonia across the extremely alkaline sites. Inferred from NMDS, pH explained only a modest fraction of the variation across the datasets, indicating that other factors influence the underlying community structure in these environments. The findings from this study suggest that the ability for eukaryotes to adapt to pH extremes over a broad range of values may be rare, but further study of taxa that can broadly adapt across diverse acidic and alkaline environments, respectively present good models for understanding adaptation and should be targeted for future investigations.
PMCID: PMC3547282  PMID: 23335919
acidophiles; alkaliphiles; pyrosequencing; protists; V9; indicator OTU analysis
14.  Comparative Molecular Microbial Ecology of the Spring Haptophyte Bloom in a Greenland Arctic Oligosaline Lake 
The Arctic is highly sensitive to increasing global temperatures and is projected to experience dramatic ecological shifts in the next few decades. Oligosaline lakes are common in arctic regions where evaporation surpasses precipitation, however these extreme microbial communities are poorly characterized. Many oligosaline lakes, in contrast to freshwater ones, experience annual blooms of haptophyte algae that generate valuable alkenone biomarker records that can be used for paleoclimate reconstruction. These haptophyte algae are globally important, and globally distributed, aquatic phototrophs yet their presence in microbial molecular surveys is scarce. To target haptophytes in a molecular survey, we compared microbial community structure during two haptophyte bloom events in an arctic oligosaline lake, Lake BrayaSø in southwestern Greenland, using high-throughput pyrotag sequencing. Our comparison of two annual bloom events yielded surprisingly low taxon overlap, only 13% for bacterial and 26% for eukaryotic communities, which indicates significant annual variation in the underlying microbial populations. Both the bacterial and eukaryotic communities strongly resembled high-altitude and high latitude freshwater environments. In spite of high alkenone concentrations in the water column, and corresponding high haptophyte rRNA gene copy numbers, haptophyte pyrotag sequences were not the most abundant eukaryotic tag, suggesting that sequencing biases obscured relative abundance data. With over 170 haptophyte tag sequences, we observed only one haptophyte algal Operational Taxonomic Unit, a prerequisite for accurate paleoclimate reconstruction from the lake sediments. Our study is the first to examine microbial diversity in a Greenland lake using next generation sequencing and the first to target an extreme haptophyte bloom event. Our results provide a context for future explorations of aquatic ecology in the warming arctic.
PMCID: PMC3523315  PMID: 23251134
haptophytes; pyrosequencing; alkenones; lake bloom; arctic
15.  Microbial Diversity and Potential Pathogens in Ornamental Fish Aquarium Water 
PLoS ONE  2012;7(9):e39971.
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.
PMCID: PMC3435374  PMID: 22970112
16.  Toward interoperable bioscience data 
Nature genetics  2012;44(2):121-126.
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared ‘Investigation-Study-Assay’ framework to support that vision.
PMCID: PMC3428019  PMID: 22281772
17.  Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem 
The ISME Journal  2011;5(8):1374-1387.
Coral reefs are highly productive ecosystems bathed in unproductive, low-nutrient oceanic waters, where microbially dominated food webs are supported largely by bacterioplankton recycling of dissolved compounds. Despite evidence that benthic reef organisms efficiently scavenge particulate organic matter and inorganic nutrients from advected oceanic waters, our understanding of the role of bacterioplankton and dissolved organic matter (DOM) in the interaction between reefs and the surrounding ocean remains limited. In this study, we present the results of a 4-year study conducted in a well-characterized coral reef ecosystem (Paopao Bay, Moorea, French Polynesia) where changes in bacterioplankton abundance and dissolved organic carbon (DOC) concentrations were quantified and bacterial community structure variation was examined along spatial gradients of the reef:ocean interface. Our results illustrate that the reef is consistently depleted in concentrations of both DOC and bacterioplankton relative to offshore waters (averaging 79 μmol l−1 DOC and 5.5 × 108 cells l−1 offshore and 68 μmol l−1 DOC and 3.1 × 108 cells l−1 over the reef, respectively) across a 4-year time period. In addition, using a suite of culture-independent measures of bacterial community structure, we found consistent differentiation of reef bacterioplankton communities from those offshore or in a nearby embayment across all taxonomic levels. Reef habitats were enriched in Gamma-, Delta-, and Betaproteobacteria, Bacteriodetes, Actinobacteria and Firmicutes. Specific bacterial phylotypes, including members of the SAR11, SAR116, Flavobacteria, and Synechococcus clades, exhibited clear gradients in relative abundance among nearshore habitats. Our observations indicate that this reef system removes oceanic DOC and exerts selective pressures on bacterioplankton community structure on timescales approximating reef water residence times, observations which are notable both because fringing reefs do not exhibit long residence times (unlike those characteristic of atoll lagoons) and because oceanic DOC is generally recalcitrant to degradation by ambient microbial assemblages. Our findings thus have interesting implications for the role of oceanic DOM and bacterioplankton in the ecology and metabolism of reef ecosystems.
PMCID: PMC3146267  PMID: 21390080
pyrosequencing; dissolved organic carbon; bacterioplankton; MIRADA; flow cytometry; coral reef
18.  RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011 
Standards in Genomic Sciences  2012;7(1):159-165.
Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.
PMCID: PMC3570804  PMID: 23451294
19.  A call for an international network of genomic observatories (GOs) 
GigaScience  2012;1:5.
We are entering a new era in genomics–that of large-scale, place-based, highly contextualized genomic research. Here we review this emerging paradigm shift and suggest that sites of utmost scientific importance be expanded into ‘Genomic Observatories’ (GOs). Investment in GOs should focus on the digital characterization of whole ecosystems, from all-taxa biotic inventories to time-series ’omics studies. The foundational layer of biodiversity–genetic variation–would thus be mainstreamed into Earth Observation systems enabling predictive modelling of biodiversity dynamics and resultant impacts on ecosystem services.
PMCID: PMC3617453  PMID: 23587188
Ecogenomics; Earth observation; Biodiversity; Ecosystems; Biocode; Genomic observatory; DNA
20.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 
Yilmaz, Pelin | Kottmann, Renzo | Field, Dawn | Knight, Rob | Cole, James R | Amaral-Zettler, Linda | Gilbert, Jack A | Karsch-Mizrachi, Ilene | Johnston, Anjanette | Cochrane, Guy | Vaughan, Robert | Hunter, Christopher | Park, Joonhong | Morrison, Norman | Rocca-Serra, Philippe | Sterk, Peter | Arumugam, Manimozhiyan | Bailey, Mark | Baumgartner, Laura | Birren, Bruce W | Blaser, Martin J | Bonazzi, Vivien | Booth, Tim | Bork, Peer | Bushman, Frederic D | Buttigieg, Pier Luigi | Chain, Patrick S G | Charlson, Emily | Costello, Elizabeth K | Huot-Creasy, Heather | Dawyndt, Peter | DeSantis, Todd | Fierer, Noah | Fuhrman, Jed A | Gallery, Rachel E | Gevers, Dirk | Gibbs, Richard A | Gil, Inigo San | Gonzalez, Antonio | Gordon, Jeffrey I | Guralnick, Robert | Hankeln, Wolfgang | Highlander, Sarah | Hugenholtz, Philip | Jansson, Janet | Kau, Andrew L | Kelley, Scott T | Kennedy, Jerry | Knights, Dan | Koren, Omry | Kuczynski, Justin | Kyrpides, Nikos | Larsen, Robert | Lauber, Christian L | Legg, Teresa | Ley, Ruth E | Lozupone, Catherine A | Ludwig, Wolfgang | Lyons, Donna | Maguire, Eamonn | Methé, Barbara A | Meyer, Folker | Muegge, Brian | Nakielny, Sara | Nelson, Karen E | Nemergut, Diana | Neufeld, Josh D | Newbold, Lindsay K | Oliver, Anna E | Pace, Norman R | Palanisamy, Giriprakash | Peplies, Jörg | Petrosino, Joseph | Proctor, Lita | Pruesse, Elmar | Quast, Christian | Raes, Jeroen | Ratnasingham, Sujeevan | Ravel, Jacques | Relman, David A | Assunta-Sansone, Susanna | Schloss, Patrick D | Schriml, Lynn | Sinha, Rohini | Smith, Michelle I | Sodergren, Erica | Spor, Aymé | Stombaugh, Jesse | Tiedje, James M | Ward, Doyle V | Weinstock, George M | Wendel, Doug | White, Owen | Whiteley, Andrew | Wilke, Andreas | Wortman, Jennifer R | Yatsunenko, Tanya | Glöckner, Frank Oliver
Nature Biotechnology  2011;29(5):415-420.
Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
PMCID: PMC3367316  PMID: 21552244
21.  Amoebae and Legionella pneumophila in saline environments 
Journal of water and health  2011;9(1):37-52.
Amoeboid protists that harbor bacterial pathogens are of significant interest as potential reservoirs of disease-causing organisms in the environment, but little is known about them in marine and other saline environments. We enriched amoeba cultures from sediments from four sites in the New England estuarine system of Mt. Hope Bay, Massachusetts and from sediments from six sites in the Great Salt Lake, Utah. Cultures of amoebae were enriched using both minimal- and non-nutrient agar plates, made with fresh water, brackish water or saltwater. Recovered amoeba cultures were assayed for the presence of Legionella species using nested polymerase chain reactions (PCR) and primers specific for the genus. Positive samples were then screened with nested amplification using primers specific for the macrophage infectivity potentiator surface protein (mip) gene from L. pneumophila. Forty-eight percent (185 out of 388) of isolated amoeba cultures were positive for the presence of Legionella species. Legionella pneumophila was detected by PCR in 4% of the amoeba cultures (17 out of 388), and most of these amoebae were growing on marine media. Our results show that amoebae capable of growing in saline environments may harbor not only a diverse collection of Legionella species, but also species potentially pathogenic to humans.
PMCID: PMC3109871  PMID: 21301113
Amoeba; diversity; Legionella; marine; salt
22.  Microbial community structure across the tree of life in the extreme Río Tinto 
The ISME journal  2010;5(1):42-50.
Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.
PMCID: PMC3105667  PMID: 20631808
community phylogenetics, astrobiology, CCA
24.  Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems 
PLoS ONE  2011;6(9):e24570.
Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems.
Methodology/Principal Findings
The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities.
This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.
PMCID: PMC3169623  PMID: 21931760
25.  The Genomic Standards Consortium 
PLoS Biology  2011;9(6):e1001088.
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.
PMCID: PMC3119656  PMID: 21713030

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