Publisher Correction: Marine microbial metagenomes sampled across space and time.

Due to a typesetting error, 25 rows were omitted from Table 3 in the original version of this Data Descriptor. These missing rows correspond to the following sample names.

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.

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.

12-Year Use of a Digital Reference Library (VitalBook) at a U.S. Dental School: Students' and Alumni Perceptions.

Digital textbooks are being used to reduce production and storage costs of printed copies, enhance usage, and include search capabilities, but the use of digital texts is not universally accepted. In 2001, the New York University College of Dentistry introduced a digital reference library, the VitalBook. Beginning in 2005, the college annually surveyed senior students and, from 2012, also surveyed alumni on their opinions and extent of use of the VitalBook. The aim of this study was to evaluate 12 years of students' perspectives and three years of alumni perspectives on the value of the VitalBook to their dental educational experience. Students were asked how frequently they used the VitalBook, if it was a good investment, if they would use it after graduation, and if they would recommend it to others. Alumni were asked the last three questions. This study reports the results from 4,105 students over 12 years (average response rate 95.3%) and 184 alumni over three years (average response rate 17.4%). The results indicated that students used the VitalBook on average 24% of their study time, but they were split regarding the other questions. The majority opinion in 2005 was negative on all questions. These opinions shifted to become more favorable to a peak in 2010, but declined since then to a more negative overall view of the VitalBook. A split opinion among students continued through 2016, with fewer recommending it although more considered it a good investment with plans to use it after graduation. Alumni mirrored their responses as students. These results suggest that, as more flexible and dynamic digitized reference systems emerge, the use of student-paid traditional digitized textbooks may become an even less favored choice.

In situ light responses of the proteorhodopsin-bearing Antarctic sea-ice bacterium, Psychroflexus torques.

Proteorhodopsin (PR) is a wide-spread protein found in many marine prokaryotes. PR allows for the potential conversion of solar energy to ATP, possibly assisting in cellular growth and survival during periods of high environmental stress. PR utilises either blue or green light through a single amino acid substitution. We incubated the PR-bearing bacterium Psychroflexus torquis 50 cm deep within Antarctic sea ice for 13 days, exposing cultures to diurnal fluctuations in light and temperature. Enhanced growth occurred most prominently in cultures incubated under irradiance levels of ∼50 µmol photons m-2 s-1, suggesting PR provides a strong selective advantage. In addition, cultures grown under blue light yielded over 5.5 times more live cells per photon compared to green-light incubations. Because P. torquis expresses an apparently 'green-shifted' PR gene variant, this finding infers that the spectral tuning of PR is more complex than previously thought. This study supports the theory that PR provides additional energy to bacteria under sub-optimal conditions, and raises several points of interest to be addressed by future research.

Bacterial abundance, processes and diversity responses to acidification at a coastal CO2 vent.

Shallow CO2 vents are used as natural laboratories to study biological responses to ocean acidification, and so it is important to determine whether pH is the primary driver of bacterial processes and community composition, or whether other variables associated with vent water have a significant influence. Water from a CO2 vent (46 m, Bay of Plenty, New Zealand) was compared to reference water from an upstream control site, and also to control water acidified to the same pH as the vent water. After 84 h, both vent and acidified water exhibited higher potential bulk water and cell-specific glucosidase activity relative to control water, whereas cell-specific protease activities were similar. However, bulk vent water glucosidase activity was double that of the acidified water, as was bacterial secondary production in one experiment, suggesting that pH was not the only factor affecting carbohydrate hydrolysis. In addition, there were significant differences in bacterial community composition in the vent water relative to the control and acidified water after 84 h, including the presence of extremophiles which may influence carbohydrate degradation. This highlights the importance of characterizing microbial processes and community composition in CO2 vent emissions, to confirm that they represent robust analogues for the future acidified ocean.

Effect of Beetroot Juice on Moderate-Intensity Exercise at a Constant Rating of Perceived Exertion.

Dietary nitrate supplementation has been shown to reduce oxygen consumption at a fixed work rate. We questioned whether a similar effect would be observed during variable work rate exercise at a specific rating of perceived exertion (RPE), as is commonly prescribed for aerobic training sessions. Using a double-blind, placebo controlled, crossover design, ten females (25 ± 3 years; VO2peak 37.1 ± 5.3 ml/kg/min) performed two 20-min cycle ergometer trials at a constant RPE of 13 (somewhat hard) 2.5 hours following ingestion of 140 ml of concentrated beetroot juice (12.9 mmol nitrate), or nitrate-depleted placebo. Performance was measured in terms of total VO2 (L) consumed and total mechanical work (kJ) accomplished across each trial. Following each experimental trial, subjects rode at 75W for an additional 5 min to determine the effect of beetroot juice on fixed work rate exercise. Coefficients of variation in total VO2 (L) and work performed (kJ) during the RPE 13 clamp trials were 8.2 and 9.5%, respectively. Consumption of beetroot juice did not affect total VO2 or work performed during RPE 13 exercise, but lowered resting systolic blood pressure by ~5 mmHg (P=0.041) and oxygen consumption at 75W by ~4% (P=0.048), relative to placebo. Since the effect of beetroot juice on oxygen consumption is small and may be masked by daily variability during self-regulated exercise, it is unlikely to have a notable effect on daily training.

Temporal changes in particle-associated microbial communities after interception by nonlethal sediment traps.

Using marine sediment traps (named RESPIRE for REspiration of Sinking Particles In the subsuRface ocEan) designed to collect sinking particles and associated microbial communities in situ, we collected and incubated marine aggregates/particles in the southern Pacific Ocean from separate phytoplankton bloom events in situ. We determined the phylogenetic affiliation for the microorganisms growing on aggregates by pyrosequencing partial 16S rRNA gene amplicons. Water column samples were also collected and sequenced for comparison between sinking-particle-associated and planktonic bacterial communities. Statistically significant differences were found between the water column and sediment trap bacteria. Relative abundances of Pelagibacter sp. and multiple members of the Flavobacteria, Actinobacteria, and α-Proteobacteria were elevated in water column samples, while trap samples contained members of the Roseobacter clade of α-Proteobacteria in high relative abundances. Our findings indicated that rapid changes - within 24 h of collection - occurred to the microbial community associated with aggregates from either bloom type. There was a little change in the bacterial assemblage after the initial 24-h incubation period. The most abundant early colonizer was a Sulfitobacter sp. This study provides further evidence that Roseobacters are rapid colonizers of marine aggregates and that colonization can occur on short timescales. This study further demonstrates that particle origin may be insignificant regarding the heterotrophic bacterial population that degrades them.

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

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.

Pole-to-pole biogeography of surface and deep marine bacterial communities.

The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

Marine bacterial succession as a potential indicator of postmortem submersion interval.

The process of decomposition of bodies in the marine environment is poorly understood and almost nothing is currently known about the microorganisms involved. This study aimed to investigate the microbes involved in decomposition in the sea and to evaluate the potential use of marine bacterial succession for postmortem submersion interval (PMSI) estimation, for which there is currently no reliable method. Partial pig remains were completely submerged during autumn and winter and were regularly sampled to document marine bacterial colonisation and the changes in community composition over time. Five stages of decomposition were recognised, some of which exhibited characters specific for partial carrion. Marine bacteria rapidly colonised the submerged remains in a successional manner. Seasonal differences were observed for the rate of decomposition and also for several groups of colonising bacteria. Marine bacteria specific for particular PMSIs were identified. This study provides an insight into the involvement of saprophytic marine bacteria in the decomposition of mammalian remains in the sea and is the first to explore the use of marine bacterial colonisation and succession as a novel tool for PMSI estimation. We propose that with further study, marine bacterial succession will prove useful for determination of the length of time a body may have been immersed in a marine environment.

Proteorhodopsin-bearing bacteria in Antarctic sea ice.

Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the protein's ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.

Cryopreservation of marine thraustochytrids (Labyrinthulomycetes).

In this research, the viability of three marine thraustochytrid isolates (fungoid protists) (WSG05, W15 and WH3) were investigated after freezing in liquid nitrogen. Five cryopreservative combinations containing horse serum, glycerol and dimethylsulfide (Me(2)SO) were used. The thraustochytrids were assessed directly after removal from liquid nitrogen and cell concentration measured for 10 days post-thawing. Results indicated that a combination of horse serum and Me(2)SO were the most effective cryoprotectants for each of the strains tested. Glycerol was only successful in producing growth in one of the strains once thawed. The protocols developed and tested in this study may have further application for cryopreserving other isolates in this class.

Placental characteristics and birthweight.

Standard gross placental measures capture dimensions relevant to specific placental functions. Our objective was to determine their accountability independent of placental weight for variance in birthweight, an important proxy for intrauterine 'adequacy' in fetal origins studies. The sample consisted of 24 152 singleton liveborn children of the Collaborative Perinatal Project delivered from 34 to 42 completed weeks gestation, with complete data for six placental measures (placental disc shape, umbilical cord length, distance from cord insertion to nearest margin, large diameter, small diameter, placental thickness) and placental weight. Associations between birthweight and placental measures were examined using multiple linear regression. Placental weight alone accounted for 36.6% of birthweight variation; the six other placental measures accounted for 28.1%. Combined, all placental measures accounted for 39.1% of birthweight variation. Seven maternal characteristics (age, height, weight, parity, socio-economic status, cigarette use, and race) were investigated to determine whether their known associations with birthweight were mediated by placental markers. Analysis suggested that the impact of all maternal characteristics except smoking was consistent with mediation by placental characteristics.

Anti-inflammatory thiazine alkaloids isolated from the New Zealand ascidian Aplidium sp.: inhibitors of the neutrophil respiratory burst in a model of gouty arthritis.

Ascidiathiazones A (3) and B (4), two new tricyclic thiazine-containing quinolinequinone alkaloids, were isolated from the New Zealand ascidian Aplidium species. Both compounds inhibited the in vitro production of superoxide by PMA-stimulated human neutrophils in a dose-dependent manner with IC50 1.55 +/- 0.32 and 0.44 +/- 0.09 microM, respectively. In vivo inhibition of superoxide production by peritoneal neutrophils in a murine model of gout was observed for both compounds with oral doses of 25.6 micromol/kg. Ascidiathiazone A (3) was synthesized in four steps from 8-hydroxyquinoline-2-carboxylic acid.

Description of Pseudochrobactrum kiredjianiae sp. nov.

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain CCUG 49584(T)), isolated from a seafood processing plant sample in New Zealand, was subjected to a polyphasic taxonomic study. On the basis of 16S rRNA and recA gene sequence similarities, the isolate was allocated to the genus Pseudochrobactrum. This was confirmed by fatty acid data (major fatty acids: C(18 : 1)omega7c and C(19 : 0) cyclo omega8c), a polar lipid profile exhibiting major characteristics of Pseudochrobactrum (phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine), quinone system Q-10 and a polyamine pattern with the predominant compounds spermidine and putrescine. DNA-DNA hybridization with the type strains of the two established species of Pseudochrobactrum and physiological and biochemical data clearly differentiated the isolate from established Pseudochrobactrum species. As a consequence, this organism represents a novel species, for which the name Pseudochrobactrum kiredjianiae sp. nov. is proposed, with the type strain CCUG 49584(T) (=CIP 109227(T)).

E/Z-rubrolide O, an anti-inflammatory halogenated furanone from the New Zealand ascidian Synoicum n. sp.

Bioassay-directed fractionation of extracts of a Synoicum n. sp. ascidian from New Zealand led to the isolation of the principal anti-inflammatory component, which was identified by spectroscopic methods as a new member of the rubrolide family, rubrolide O (1), existing as a mixture of E/Z isomers.

Placenta and fetal growth restriction.

The placenta, as the vector for all maternal-fetal oxygen and nutrient exchange, is a principal influence on birthweight. Placental weight summarizes laterally expanding growth of the chorionic disc, and villous arborization yielding the nutrient exchange surface. These different growth dimensions alter fetoplacental weight ratio and ponderal index, and thus may modify placental functional efficiency. The placenta may show a range of histopathologies, some of which are also associated with fetal growth restriction. Different fetal intrinsic abilities to compensate for gross and histo-pathology may clarify the imperfect relationships between fetal growth and both intrauterine pathology, and the long-term health risks associated with poor fetal growth.

Measures of placental growth in relation to birth weight and gestational age.

Fetal growth depends in part on placental growth. The authors tested placental measures derived from digital images for reliability and to evaluate their association with birth weight and gestational age. A total of 628 women recruited into the Pregnancy, Infection, and Nutrition Study, a prospective cohort study of preterm birth in central North Carolina between 2002 and 2004, delivered singleton liveborn infants after 24 completed weeks' gestation. Novel chorionic plate morphometric parameters captured off digital images of the gross placenta were analyzed as estimators of gestational age and birth weight. Without acknowledgment to placental weight, digitally obtained lateral chorionic plate growth measures accounted for 17 percent of gestational age variance and 35 percent of birth weight variance, overall. Chorionic plate measures accounted for 10 percent of birth weight variance beyond that accounted for by placental weight alone. Among preterm births, 34 percent of gestational age variance and 63 percent of birth weight variance were accounted for by lateral chorionic plate growth measures. Intraclass correlation coefficients for the novel digital measures ranged from 0.96 to 0.98. Reliable digital measures of lateral chorionic plate growth estimate birth weight variance more strongly than gestational age, project variance that is not accounted for by placental weight, and project these outcomes to a greater degree in preterm births than at term.

Morphometry of the basal plate superficial uteroplacental vasculature in normal midtrimester and at term.

Uteroplacental (UP) vascular arterial pathology has been associated with pregnancy complications. UP arterial structure has been characterized in placental bed biopsies, at the decidual-myometrial junction. Basal plate UP arteries, which are delivered with the placenta and thus routinely available, are not well characterized. We compared basal plate UP arterial segment morphometry in cases of elective termination of a clinically normal pregnancy at 11 to 24 weeks and of term birth. This study was done in a community-based obstetric service in New York City. UP arteries were identified in placentas of 20 midtrimester (MT) cases and 17 term (TERM) cases. We measured 336 UP artery cross-sections from 46 TERM and 290 MT cases. The basal plate UP artery path length was calculated as the distance between (x,y) coordinates of estimated centers of lumen cross-sections. Basal plate thickness near UP arteries, UP artery cross-sectional areas, vascular luminal eccentricity, and radial standard deviation were directly measured off digital images. Nonparametric and parametric methods compared groups, with P < 0.05 considered statistically significant. In TERM cases, the basal plate thickness near UP arteries was 1.8-fold thinner (P = 0.002) and mean basal plate path lengths were 2.13-fold shorter (P < 0.0001) than in MT cases. Mean TERM UP artery cross-sectional area was 3.15-fold larger, the major axis was 1.95-fold larger, and the minor axis was 1.75-fold larger than in MT arteries (P = 0.001 to 0.008). Our data demonstrate that basal plate UP arteries (delivered with the placenta) are less tortuous, with shorter path lengths and larger areas as gestation advances. Normative morphometric data may allow improved diagnostics of placentas from complicated pregnancies.