Search

Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data’s utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems., Simons Foundation (Award 337262), Simons Foundation (Award 329108), Gordon and Betty Moore Foundation (Grant GBMF495), Gordon and Betty Moore Foundation (Grant GBMF4511), National Science Foundation (Grant OCE-1153588), National Science Foundation (Grant OCE-1356460), National Science Foundation (Grant DBI-0424599)

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography., Simons Foundation (Award 337262), Simons Foundation (Award 329108), Gordon and Betty Moore Foundation (Grant GBMF495), Gordon and Betty Moore Foundation (Grant GBMF4511), National Science Foundation (Grant OCE-1153588), National Science Foundation (Grant OCE-1356460), National Science Foundation (Grant DBI-0424599)

Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data's utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems.

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e49474, doi:10.1371/journal.pone.0049474., Patterns of genetic connectivity are increasingly considered in the design of marine protected areas (MPAs) in both shallow and deep water. In the New Zealand Exclusive Economic Zone (EEZ), deep-sea communities at upper bathyal depths (<2000 m) are vulnerable to anthropogenic disturbance from fishing and potential mining operations. Currently, patterns of genetic connectivity among deep-sea populations throughout New Zealand’s EEZ are not well understood. Using the mitochondrial Cytochrome Oxidase I and 16S rRNA genes as genetic markers, this study aimed to elucidate patterns of genetic connectivity among populations of two common benthic invertebrates with contrasting life history strategies. Populations of the squat lobster Munida gracilis and the polychaete Hyalinoecia longibranchiata were sampled from continental slope, seamount, and offshore rise habitats on the Chatham Rise, Hikurangi Margin, and Challenger Plateau. For the polychaete, significant population structure was detected among distinct populations on the Chatham Rise, the Hikurangi Margin, and the Challenger Plateau. Significant genetic differences existed between slope and seamount populations on the Hikurangi Margin, as did evidence of population differentiation between the northeast and southwest parts of the Chatham Rise. In contrast, no significant population structure was detected across the study area for the squat lobster. Patterns of genetic connectivity in Hyalinoecia longibranchiata are likely influenced by a number of factors including current regimes that operate on varying spatial and temporal scales to produce potential barriers to dispersal. The striking difference in population structure between species can be attributed to differences in life history strategies. The results of this study are discussed in the context of existing conservation areas that are intended to manage anthropogenic threats to deep-sea benthic communities in the New Zealand region., This work was funded in part by a Fulbright Fellowship administered by Fulbright New Zealand and the U.S. Department of State, awarded in 2011 to EKB. Funding and support for research expedition was provided by Land Information New Zealand, New Zealand Ministry of Fisheries, NIWA, Census of Marine Life on Seamounts (CenSeam), and the Foundation for Research, Science and Technology. Other research funding was provided by the New Zealand Ministry of Science and Innovation project “Impacts of resource use on vulnerable deep-sea communities” (FRST contract CO1X0906), the National Science Foundation (OCE-0647612), and the Deep Ocean Exploration Institute (Fellowship support to TMS).

The Antarctic and Arctic regions offer a unique opportunity to test factors shaping the biogeography of marine microbial communities as they represent extremes in geographic separation yet share similar selection pressures. Here we report the most comprehensive comparison of bacterioplankton diversity between the polar oceans conducted to date, using standardized methods for pyrosequencing the V6 region of 16S rRNA gene. This effort included lower latitude ocean microbiomes to provide a global perspective for a global comparison of 837 844 sequence tags. Unexpectedly, we found a clear difference between Southern and Arctic Ocean microbiomes: 78.0% of the OTUs were unique to the Southern Ocean and 70.4% were unique to the Arctic Ocean. Even though polar ocean bacteria were more similar to each other than to lower latitude pelagic communities, analyses comparing depths, seasons and coastal versus open ocean demonstrated that Southern and Arctic Ocean bacterioplankton communities always clustered separately. Coastal surface Southern and Arctic Ocean communities were more dissimilar than open ocean communities. In contrast, deep ocean microbiomes were less different between poles and to lower latitude deep ocean waters, and they contained different patterns of diversity accumulation compared to surface, suggesting different mechanisms controlling surface and deep ocean community structures. We propose that surface bacterioplankton are more influenced by contemporary environmental conditions such as light, resource variability and climate, whereas deep communities are structured by a history of longer isolation and connectivity through ocean circulation. This work has identified major players in polar coastal and open ocean surface and deep communities, and provides a framework for understanding bacterioplankton biogeography

The amphipod genus Epimeria is species rich in the Southern Ocean and at present eight of its 19 species are reported with circum-Antarctic distributions. For the first time, specimens of epimeriid species from the Antarctic Peninsula, the Weddell Sea and the Ross Sea were analysed using partial COI genes sequences and morphological characters. In total 37 specimens of 14 species of Epimeria and two species of Epimeriella were analysed and the resulting molecular topology checked by critically reviewing taxonomic characters. The genus Epimeriella, genetically grouping within Epimeria is synonymised with the genus Epimeria. Sequences distances between populations of the nominal species Epimeria robusta from the Weddell and Ross Sea led to detailed morphological investigations, resulting in the description of Epimeria robustoides sp. n. from the Weddell Sea. Epimeria robusta Barnard, 1930 from the Ross Sea is redescribed. Sequences of a damaged Epimeria specimen of a species new to science from the lower continental shelf of the eastern Weddell Sea were included. Based on the current study, the hypothesis of circum-Antarctic species' distributions in brooding amphipods proved to be unlikely.

Epimeria schiaparelli sp. nov. from the Ross Sea, Antarctica, is described in detail. The new species occurs on the shelf in 130–350 m depth. Epimeria schiaparelli can be distinguished from the most similar species, E. similis Chevreux, 1912 and E. macrodonta Walker, 1906 by a relatively short rostrum and a short second pereonite amongst other characters. Two distinct colour patterns are reported. Partial gene sequences of the mitochondrial cytochrome oxidase subunit I (COI) from 11 specimens of E. schiaparelli confirm that this species is new to science and closely related to E. similis, E. macrodonta and E. reoproi. The recent and historical separation of this Antarctic species is discussed. The syntypes of E. macrodonta consist of two species, so a lectotype is here designated.