Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75‐m depth. The communities of microbial eukaryotes were clustered into shallow‐, middle‐, and deep‐water groups according to the depth from which they were collected, indicating a depth‐related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50‐m deep, being most abundant near the sea floor where they contributed ca. 64–97% and 40–74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area.     

Factors Controlling the Abundance and Size Distribution of the Phototrophic Ciliate Myrionecta rubra in Open Waters of the North Atlantic

ABSTRACT. Myrionecta rubra, a ubiquitous planktonic ciliate, has received much attention due to its wide distribution, occurrence as a red tide organism, and unusual cryptophyte endosymbiont. Although well studied in coastal waters, M. rubra is poorly examined in the open ocean. In the Irminger Basin, North Atlantic, the abundance of M. rubra was 0–5 cells/ml, which is low compared with that found in coastal areas. Distinct patchiness (100 km) was revealed by geostatistical analysis. Multiple regression indicated there was little relationship between M. rubra abundance and a number of environmental factors, with the exception of temperature and phytoplankton biomass, which influenced abundance in the spring. We also improve on studies that indicate distinct size classes of M. rubra; we statistically recognise four significantly distinct width classes (5–16, 12–23, 18–27, 21–33 μm), which decrease in abundance with increasing size. A multinomial logistic regression revealed the main variable correlated with this size distribution was ambient nitrate concentration. Finally, we propose a hypothesis for the distribution of sizes, involving nutrients, feeding, and dividing of the endosymbiont.     

A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province

Mosquitoes as one of the most common but important vectors have the potential to transmit or acquire a lot of viruses through biting, however viral flora in mosquitoes and its impact on mosquito-borne disease transmission has not been well investigated and evaluated. In this study, the metagenomic techniquehas been successfully employed in analyzing the abundance and diversity of viral community in three mosquito samples from Hubei, China. Among 92,304 reads produced through a run with 454 GS FLX system, 39% have high similarities with viral sequences belonging to identified bacterial, fungal, animal, plant and insect viruses, and 0.02% were classed into unidentified viral sequences, demonstrating high abundance and diversity of viruses in mosquitoes. Furthermore, two novel viruses in subfamily Densovirinae and family Dicistroviridae were identified, and six torque tenosus virus1 in family Anelloviridae, three porcine parvoviruses in subfamily Parvovirinae and a Culex tritaeniorhynchus rhabdovirus in Family Rhabdoviridae were preliminarily characterized. The viral metagenomic analysis offered us a deep insight into the viral population of mosquito which played an important role in viral initiative or passive transmission and evolution during the process.     

Viral Production, Decay Rates, and Life Strategies along a Trophic Gradient in the North Adriatic Sea

Although the relationships between trophic conditions and viral dynamics have been widely explored in different pelagic environments, there have been few attempts at independent estimates of both viral production and decay. In this study, we investigated factors controlling the balance between viral production and decay along a trophic gradient in the north Adriatic basin, providing independent estimates of these variables and determining the relative importance of nanoflagellate grazing and viral life strategies. Increasing trophic conditions induced an increase of bacterioplankton growth rates and of the burst sizes. As a result, eutrophic waters displayed highest rates of viral production, which considerably exceeded observed rates of viral decay (up to 2.9 × 10⁹ VLP liter⁻¹ h⁻¹). Viral decay was also higher in eutrophic waters, where it accounted for ca. 40% of viral production, and dropped significantly to 1.3 to 10.7% in oligotrophic waters. These results suggest that viral production and decay rates may not necessarily be balanced in the short term, resulting in a net increase of viruses in the system. In eutrophic waters nanoflagellate grazing, dissolved-colloidal substances, and lysogenic infection were responsible together for the removal of ca. 66% of viral production versus 17% in oligotrophic waters. Our results suggest that different causative agents are primarily responsible for the removal of viruses from the water column in different trophic conditions. Factors other than those considered in the past might shed light on processes responsible for the removal and/or decay of viral particles from the water column.     

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem.     

Diversity of Diazotrophic Unicellular Cyanobacteria in the Tropical North Atlantic Ocean

We present data on the genetic diversity and phylogenetic affinities of N₂-fixing unicellular cyanobacteria in the plankton of the tropical North Atlantic Ocean. Our dinitrogenase gene (nifH) sequences grouped together with a group of cyanobacteria from the subtropical North Pacific; another subtropical North Pacific group was only distantly related. Most of the 16S ribosomal DNA sequences from our tropical North Atlantic samples were closely allied with sequences from a symbiont of the diatom Climacodium frauenfeldianum. These findings suggest a complex pattern of evolutionary and ecological divergence among unicellular cyanobacteria within and between ocean basins.     

Diversity of diazotrophic unicellular cyanobacteria in the tropical North Atlantic Ocean

We present data on the genetic diversity and phylogenetic affinities of N2-fixing unicellular cyanobacteria in the plankton of the tropical North Atlantic Ocean. Our dinitrogenase gene (nifH) sequences grouped together with a group of cyanobacteria from the subtropical North Pacific; another subtropical North Pacific group was only distantly related. Most of the 16S ribosomal DNA sequences from our tropical North Atlantic samples were closely allied with sequences from a symbiont of the diatom Climacodium frauenfeldianum. These findings suggest a complex pattern of evolutionary and ecological divergence among unicellular cyanobacteria within and between ocean basins.     

Abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical North Atlantic Ocean

Microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. We examined the use of ³³P‐phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. Seawater from the sub‐tropical North Atlantic Ocean was incubated with ³³P‐phosphate and analysed by microautoradiography to determine the proportion and diversity of the bacterial community‐assimilating phosphate. Complementary incubations using ³H‐leucine and ³H‐thymidine were also conducted. We found that a higher proportion of total heterotrophic bacterial cells in surface water samples assimilated phosphate compared with leucine or thymidine. Bacteria from all of the phylogenetic groups we identified by CARD‐FISH were able to assimilate phosphate, although the abundances of cells within each group did not scale directly with the number found to assimilate phosphate. Furthermore, a significantly higher proportion of Alphaproteobacteria, Gammaproteobacteria and Cytophaga‐like cells assimilated phosphate compared with leucine or thymidine. Our results suggest that a greater proportion of bacterial cells in surface waters are actively participating in the biogeochemical cycling of phosphorus, and possibly other elements, than is currently estimated through the use of ³H‐leucine or ³H‐thymidine.     

Diversity and abundance of glycosyl hydrolase family 5 in the North Atlantic Ocean

The diversity and abundance of glycosyl hydrolase family 5 (GH5) were studied in the North Atlantic Ocean. This family was chosen because of the large number of available sequences from cultured bacteria, the variety of substrates it targets, and the high number of similar sequences in the Sargasso Sea environmental genome database. Three clone libraries of a GH5 subcluster were constructed from the Mid-Atlantic Bight and the eastern and western North Atlantic Ocean. The two North Atlantic Ocean libraries did not differ from each other but both were significantly less diverse than the Mid-Atlantic Bight library. The abundance of GH5 genes estimated by quantitative PCR was positively correlated with chlorophyll concentrations in the eastern part of a transect from Fort Pierce, Florida, to the Azores and in a depth profile, suggesting that the supply of labile organic material selects for GH5-bearing bacteria in these waters. However, the data suggest that only <1% of all bacteria harbor the GH5 subcluster. These and other data suggest that the hydrolysis of polysaccharides requires complicated multi-enzyme systems.     

Diversity and Dynamics of a North Atlantic Coastal Vibrio Community

Vibrios are ubiquitous marine bacteria that have long served as models for heterotrophic processes and have received renewed attention because of the discovery of increasing numbers of facultatively pathogenic strains. Because the occurrence of specific vibrios has frequently been linked to the temperature, salinity, and nutrient status of water, we hypothesized that seasonal changes in coastal water bodies lead to distinct vibrio communities and sought to characterize their level of differentiation. A novel technique was used to quantify shifts in 16S rRNA gene abundance in samples from Barnegat Bay, N.J., collected over a 15-month period. Quantitative PCR (QPCR) with primers specific for the genus Vibrio was combined with separation and quantification of amplicons by constant denaturant capillary electrophoresis (CDCE). Vibrio populations identified by QPCR-CDCE varied between summer and winter samples, suggesting distinct warm-water and year-round populations. Identification of the CDCE populations by cloning and sequencing of 16S rRNA genes from two summer and two winter samples confirmed this distinction. It further showed that CDCE populations corresponded in most cases to ~98% rRNA similarity groups and suggested that the abundance of these follows temperature trends. Phylogenetic comparison yielded closely related cultured and often pathogenic representatives for most sequences, and the temperature ranges of these isolates confirmed the trends seen in the environmental samples. Overall, this suggests that temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend.     

Virus Decay and Its Causes in Coastal Waters

Recent evidence suggests that viruses play an influential role within the marine microbial food web. To understand this role, it is important to determine rates and mechanisms of virus removal and degradation. We used plaque assays to examine the decay of infectivity in lab-grown viruses seeded into natural seawater. The rates of loss of infectivity of native viruses from Santa Monica Bay and of nonnative viruses from the North Sea in the coastal seawater of Santa Monica Bay were determined. Viruses were seeded into fresh seawater that had been pretreated in various ways: filtration with a 0.2-(mu)m-pore-size filter to remove organisms, heat to denature enzymes, and dissolved organic matter enrichment to reconstitute enzyme activity. Seawater samples were then incubated in full sunlight, in the dark, or under glass to allow partitioning of causative agents of virus decay. Solar radiation always resulted in increased rates of loss of virus infectivity. Virus isolates which are native to Santa Monica Bay consistently degraded more slowly in full sunlight in untreated seawater (decay ranged from 4.1 to 7.2% h(sup-1)) than nonnative marine bacteriophages which were isolated from the North Sea (decay ranged from 6.6 to 11.1% h(sup-1)). All phages demonstrated susceptibility to degradation by heat-labile substances, as heat treatment reduced the decay rates to about 0.5 to 2.0% h(sup-1) in the dark. Filtration reduced decay rates by various amounts, averaging 20%. Heat-labile, high-molecular-weight dissolved material (>30 kDa, probably enzymes) appeared responsible for about 1/5 of the maximal decay. Solar radiation was responsible for about 1/3 to 2/3 of the maximal decay of nonnative viruses and about 1/4 to 1/3 of that of the native viruses, suggesting evolutionary adaptation to local light levels. Our results suggest that sunlight is an important contributing factor to virus decay but also point to the significance of particles and dissolved substances in seawater.     

Ichthyoplankton of the Southern Waters of the North Atlantic: 2. Species Composition and Distribution Features

Journal of Ichthyology - The species composition of ichthyoplankton in the open waters of the North Atlantic at the cross-section from 30° N to the equator is considered. The study was...     

Diversity and density characteristics of Pliensbachian-Toarcian molluscan and brachiopod faunas of the North Atlantic margins

Pliensbachian and Toarcian molluscs and brachiopods of Morocco, Iberia, England, and Greenland are analysed in terms of diversity and density. With regard to local variations, Substrate and food supply are thought to be the major factors controlling the predominance of suspension-feeding bivalves in shallow water deposits while the greater physical stability of deeper water favoured the ammonites; high diversity of the gastropods relates to firm substrates. On a regional scale, both bivalve density and diversity tend to increase from the Tethyan to the Boreal redm, while there is a Variable tendency for a northward diversity reduction in other groups. The bivalve data are incompatible with either temperature or salinity control of faunal provinciality. To provide a better account of this, a model is developed which lays emphasis on the physical instability of a boreal inland sea as compared with the Tethys. Some broader implications for endemism in Jurassic faunas are briefly discussed.     

Links between the Environment,Abundance and Diversity of Andean Moths

Ideas on the spatial variation of biodiversity often imply a causal link between the abundance and species richness of organisms. We investigated this ‘more individuals hypothesis’ using light‐trapping data of three unrelated groups of moths (Arctiidae, Geometridae and Pyraloidea) from the Ecuadorian Andes. We analyzed environmental correlates of specimen densities found in different habitats, finding effects of temperature, moonlight, forest succession, elevation and season. We corrected abundance data for light‐trapping artefacts, and we measured species diversity with various metrics known to be unbiased by undersampling. We found significant positive correlations between abundance and species diversity for all three taxonomic groups. We discuss implications for a general evaluation of species‐energy theory as well as for a better understanding of ecological processes in montane habitats of the Andes.     

Meso- and bathypelagic distribution and abundance of chaetognaths in the Atlantic sector of the Southern Ocean

We conducted multinet sampling during winter and summer in the Southern Ocean (Atlantic sector) to investigate the effect of water mass, season and water depth on abundance and species composition of meso- and bathypelagic chaetognaths. Eukrohnia hamata (mean 115 ind. 1,000 m⁻³) and Sagitta marri (mean 51 ind. 1,000 m⁻³) were dominant, complemented by E. bathypelagica (mean 19 ind. 1,000 m⁻³) and E. bathyantarctica (mean 19 ind. 1,000 m⁻³) below 1,000 m. A further six species were identified, among them the rare bathypelagic species Heterokrohnia fragilis and the subtropical Eukrohnia macroneura that is new to the Antarctic. Water depth and season were the principal determinants of abundance and species composition patterns, indicating vertical seasonal migration and vertical segregation of species. The life cycles of E. hamata and S. marri were studied additionally. Their maturity stages were vertically segregated and prolonged reproductive periods are suggested for both species.     

Abundance and Diversity of Euglossine Bees in the Fragmented Landscape of the Brazilian Atlantic Forest1

Male euglossine bees were sampled with chemical baits every two months from September 1997 to July 1999 at nine sites in the Desengano mountain range, Rio de Janeiro State, Brazil. Four sites were located in Atlantic Forest mature second growth, two sites in disturbed forest, and three sites in forest fragments of 200, 156, and 14 ha, respectively. We collected 3653 male euglossine bees from at least 21 species. Analyses of variance indicated no differences among the three habitat types for total number of bees, and 5 of the 6 dominant species. Bootstrapping indicated significant variation in species richness and diversity for some sites, but there was no clear indication of differences among habitats. Similarity as measured with the Morisita–Horn index was inversely related to distance between sites, but relatively high for most site combinations. These results suggest that the euglossine bee community in the three habitats was essentially the same. Although some species were associated with each habitat type, most appeared to respond to temporal local conditions. Our results do not support the hypothesis that forest fragmentation or habitat alteration reduces abundance and diversity of euglossine bees.     

Abundance, distribution, reproduction and diet of notacanthid fishes from the north-east Atlantic

Notacanthid fishes were among the 10 most abundant species sampled in research surveys using fine meshed trawls fished to depths of 3000 m in the Rockall Trough and 4500 m in the Porcupine Seabight between 1975 and 1992. Two species, Noctacanthus bonapartei and Polyacanthonotus rissoanus , were dominant but their population structure and certain aspects of morphometric and reproductive biology differed between the two sampling areas. In general, sex ratios were skewed in favour of females, size increased with depth and male and immature individuals were restricted to shallower depth zones. Fecundity was highly correlated with total weight and showed a positive relationship with species' size. Ovaries contained two batches of eggs and the spawning season was protracted, occurring mostly over winter months. Dietary studies showed a dependence on benthic macro fauna though the two dominant species have different dentition and exploit different trophic niches. In the Rockall Trough, peak abundances for N. bonapartei and P. rissoanus occurred in the 750 m and 1250 m zones, respectively, lying within the depth range currently exploited by commercial deep-water trawls (600–1400 m). The probable impacts of commercial operations on notacanthid fishes are discussed.     

Ichthyoplankton of the Southern Waters of the North Atlantic: 1. Morphology in Poorly-Studied Larvae of Coastal Species

Journal of Ichthyology - The larvae and/or juveniles of coastal species were found in the composition of oceanic ichthyoplankton sampled during the 43rd expedition of R/V “Akademik...     

North winds and production in the eastern North Atlantic

A long-term increase in northerly wind componentl over the easternNorth Atlantic and European Seaboard between 1950 and 1980 isassociated both with a decline of phytoplankton and zooplanktonbiomass in sea-areas around the British Isles, and with an increasein upwelling intensity along the Iberian west coast. The implicationsfor certain pelagic fish stocks in the area are assessed.     

Swim Speed,Behavior, and Movement of North Atlantic Right Whales (Eubalaena glacialis) in Coastal Waters of Northeastern Florida,USA

In a portion of the coastal waters of northeastern Florida, North Atlantic right whales (Eubalaena glacialis) occur close to shore from December through March. These waters are included within the designated critical habitat for right whales. Data on swim speed, behavior, and direction of movement – with photo-identification of individual whales – were gathered by a volunteer sighting network working alongside experienced scientists and supplemented by aerial observations. In seven years (2001–2007), 109 tracking periods or “follows” were conducted on right whales during 600 hours of observation from shore-based observers. The whales were categorized as mother-calf pairs, singles and non-mother-calf pairs, and groups of 3 or more individuals. Sample size and amount of information obtained was largest for mother-calf pairs. Swim speeds varied within and across observation periods, individuals, and categories. One category, singles and non mother-calf pairs, was significantly different from the other two – and had the largest variability and the fastest swim speeds. Median swim speed for all categories was 1.3 km/h (0.7 kn), with examples that suggest swim speeds differ between within-habitat movement and migration-mode travel. Within-habitat right whales often travel back-and-forth in a north-south, along-coast, direction, which may cause an individual to pass by a given point on several occasions, potentially increasing anthropogenic risk exposure (e.g., vessel collision, fishing gear entanglement, harassment). At times, mothers and calves engaged in lengthy stationary periods (up to 7.5 h) that included rest, nursing, and play. These mother-calf interactions have implications for communication, learning, and survival. Overall, these behaviors are relevant to population status, distribution, calving success, correlation to environmental parameters, survey efficacy, and human-impacts mitigation. These observations contribute important parameters to conservation biology, predictive modeling, and management. However, while we often search for predictions, patterns, and means, the message here is also about variability and the behavioral characteristics of individual whales.