Do circum-Antarctic species exist in peracarid Amphipoda? A case study in the genus Epimeria Costa, 1851 (Crustacea, Peracarida, Epimeriidae)

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

Marine microbial metagenomes sampled across space and time

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

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

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

Patterns of deep-sea genetic connectivity in the New Zealand region : implications for management of benthic ecosystems

© 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)

Neighborhood deprivation and biomarkers of health in Britain: The mediating role of the physical environment

Background: Neighborhood deprivation has been consistently linked to poor individual health outcomes; however, studies exploring the mechanisms involved in this association are scarce. The objective of this study was to investigate whether objective measures of the physical environment mediate the association between neighborhood socioeconomic deprivation and biomarkers of health in Britain. Methods: We linked individual-level biomarker data from Understanding Society: The UK Household Longitudinal Survey (2010-2012) to neighborhood-level data from different governmental sources. Our outcome variables were forced expiratory volume in 1 s (FEV1%; n=16,347), systolic blood pressure (SBP; n=16,846), body mass index (BMI; n=19,417), and levels of C-reactive protein (CRP; n=11,825). Our measure of neighborhood socioeconomic deprivation was the Carstairs index, and the neighborhood-level mediators were levels of air pollutants (sulphur dioxide [SO2], particulate matter [PM10], nitrogen dioxide [NO2], and carbon monoxide [CO]), green space, and proximity to waste and industrial facilities. We fitted a multilevel mediation model following a multilevel structural equation framework in MPlus v7.4, adjusting for age, gender, and income. Results: Residents of poor neighborhoods and those exposed to higher pollution and less green space had worse health outcomes. However, only SO2exposure significantly and partially mediated the association between neighborhood socioeconomic deprivation and SBP, BMI, and CRP. Conclusion: Reducing air pollution exposure and increasing access to green space may improve population health but may not decrease health inequalities in Britain

Consistent patterns of common species across tropical tree communities

Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1,2,3,4,5,6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.Publisher PDFPeer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Epimeria schiaparelli sp. nov., an amphipod crustacean (family Epimeriidae) from the Ross Sea, Antarctica, with molecular characterisation of the species complex

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

Ferrioxamine siderophores detected amongst iron binding ligands produced during the remineralization of marine particles

The microbial degradation of marine particles is an important process in the remineralization of nutrients including iron. As part of the GEOTRACES process study (FeCycle II), we conducted incubation experiments with marine particles obtained from 30 and 100 m depth at two stations during austral spring in the subtropical waters east of the North Island of New Zealand. The particles were collected using in-situ pumps, and comprised mainly of suspended and slow sinking populations along with associated attached heterotrophic bacteria. In treatments with live bacteria, increasing concentrations of Fe binding ligands were observed with an average stability constant of logKFeL,Fe3+ = 21.11±0.37 for station 1 and 20.89±0.25 for station 2. The ligand release rates varied between 2.54 and 11.8 pmol L-1 d-1 (calculated for ambient seawater particle concentration) and were similar to those found in two Southern Ocean subsurface studies from ~110 m depths in subpolar and polar waters. Dissolved iron (DFe) was released at a rate between 0.33 and 2.09 pmol Fe L-1 d-1 with a column integrated (30 -100 m) flux of 107 and 58 nmol Fe m-2 day-1 at station 1 and 2, respectively. Given a mixed layer DFe inventory of ~48 µmol m-2 and ~4 µmol m-2 at the time of sampling for station 1 and 2, this will therefore result in a DFe residence time of 1.2 and 0.18 years, assuming particle remineralization was the only source of iron in the mixed layer. The DFe release rates calculated were comparable to those found in the previously mentioned study of Southern Ocean water masses. Fe-binding ligand producing bacteria (CAS positive) abundance was found to increase throughout the duration of the experiment of 7 to 8 days. For the first time ferrioxamine type siderophores, including the well-known ferrioxamine B and G, have been quantified using chemical assays and LC-ESI-MS. Our subtropical study corroborates prior reports from the Southern Ocean of particle remineralization being an important source of DFe and ligands, and adds unprecedented detail by revealing that siderophores are probably an important component of the ligands released into subsurface waters during particle remineralisation