Halophila ovalis in the Tropical Atlantic Ocean

A species of seagrass in the genus Halophila was found growing in a shallow lagoon on the west shore of Antigua in the Caribbean West Indies. Genetic analysis showed the plants were Halophila ovalis. In addition, the samples had no genetic deviation (using nrDNA sequences) from Halophila johnsonii, considered to be an endemic and endangered species in Florida, USA. Morphological analysis demonstrated the Antiguan Halophila to be well within the range of plant characteristics previously described in the literature for H. ovalis, except for leaf width and number of seeds per fruit, and again, not different from H. johnsonii and very closely related to H. ovalis from the Indo-Pacific. Ours is the first report of H. ovalis in the Tropical Atlantic bioregion.     

Diazotrophic Diversity and Distribution in the Tropical and Subtropical Atlantic Ocean

To understand the structure of marine diazotrophic communities in the tropical and subtropical Atlantic Ocean, the molecular diversity of the nifH gene was studied by nested PCR amplification using degenerate primers, followed by cloning and sequencing. Sequences of nifH genes were amplified from environmental DNA samples collected during three cruises (November-December 2000, March 2002, and October-November 2002) covering an area between 0 to 28.3°N and 56.6 to 18.5°W. A total of 170 unique sequences were recovered from 18 stations and 23 depths. Samples from the November-December 2000 cruise contained both unicellular and filamentous cyanobacterial nifH phylotypes, as well as γ-proteobacterial and cluster III sequences, so far only reported in the Pacific Ocean. In contrast, samples from the March 2002 cruise contained only phylotypes related to the uncultured group A unicellular cyanobacteria. The October-November 2002 cruise contained both filamentous and unicellular cyanobacterial and γ-proteobacterial sequences. Several sequences were identical at the nucleotide level to previously described environmental sequences from the Pacific Ocean, including group A sequences. The data suggest a community shift from filamentous cyanobacteria in surface waters to unicellular cyanobacteria and/or heterotrophic bacteria in deeper waters. With one exception, filamentous cyanobacterial nifH sequences were present within temperatures ranging between 26.5 and 30°C and where nitrate was undetectable. In contrast, nonfilamentous nifH sequences were found throughout a broader temperature range, 15 to 30°C, more often in waters with temperature of <26°C, and were sometimes recovered from waters with detectable nitrate concentrations.     

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.     

Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.     

Aphotic N2 Fixation in the Eastern Tropical South Pacific Ocean

We examined rates of N₂ fixation from the surface to 2000 m depth in the Eastern Tropical South Pacific (ETSP) during El Niño (2010) and La Niña (2011). Replicated vertical profiles performed under oxygen-free conditions show that N₂ fixation takes place both in euphotic and aphotic waters, with rates reaching 155 to 509 µmol N m⁻² d⁻¹ in 2010 and 24±14 to 118±87 µmol N m⁻² d⁻¹ in 2011. In the aphotic layers, volumetric N₂ fixation rates were relatively low (<1.00 nmol N L⁻¹ d⁻¹), but when integrated over the whole aphotic layer, they accounted for 87–90% of total rates (euphotic+aphotic) for the two cruises. Phylogenetic studies performed in microcosms experiments confirm the presence of diazotrophs in the deep waters of the Oxygen Minimum Zone (OMZ), which were comprised of non-cyanobacterial diazotrophs affiliated with nifH clusters 1K (predominantly comprised of α-proteobacteria), 1G (predominantly comprised of γ-proteobacteria), and 3 (sulfate reducing genera of the δ-proteobacteria and Clostridium spp., Vibrio spp.). Organic and inorganic nutrient addition bioassays revealed that amino acids significantly stimulated N₂ fixation in the core of the OMZ at all stations tested and as did simple carbohydrates at stations located nearest the coast of Peru/Chile. The episodic supply of these substrates from upper layers are hypothesized to explain the observed variability of N₂ fixation in the ETSP.     

Structural and Functional Changes with Depth in Microbial Communities in a Tropical Malaysian Peat Swamp Forest

Tropical peat swamp forests are important and endangered ecosystems, although little is known of their microbial diversity and ecology. We used molecular and enzymatic techniques to examine patterns in prokaryotic community structure and overall microbial activity at 0-, 10-, 20-, and 50-cm depths in sediments in a peat swamp forest in Malaysia. Denaturing gradient gel electrophoresis profiles of amplified 16S ribosomal ribonucleic acid (rRNA) gene fragments showed that different depths harbored different bacterial assemblages and that Archaea appeared to be limited to the deeper samples. Cloning and sequencing of longer 16S rRNA gene fragments suggested reduced microbial diversity in the deeper samples compared to the surface. Bacterial clone libraries were largely dominated by ribotypes affiliated with the Acidobacteria, which accounted for at least 27–54% of the sequences obtained. All of the sequenced representatives from the archaeal clone libraries were Crenarchaeota. Activities of microbial extracellular enzymes involved in carbon, nitrogen, and phosphorus cycling declined appreciably with depth, the only exception being peroxidase. These results show that tropical peat swamp forests are unusual systems with microbial assemblages dominated by members of the Acidobacteria and Crenarchaeota. Microbial communities show clear changes with depth, and most microbial activity is likely confined to populations in the upper few centimeters, the site of new leaf litter fall, rather than the deeper, older, peat layers.     

Vertical distribution and phylogenetic composition of bacteria in the Eastern Tropical North Pacific Ocean

The vertical community structure of bacteria along a depth profile in the Eastern Tropical North Pacific Ocean (13 degrees N, 104 degrees W) was studied by flow cytometry measurement and 16S rRNA gene clone libraries analysis. Picoeukaryotes and Synechococcus peaked at 30 m and decreased sharply below 50 m, while Prochlorococcus peaked at both 30 and 100 m layers and disappeared below 200 m. Heterotrophic bacteria peaked above shallow thermocline and decreased along the depth profile. Sequences of total 322 clones from four clone libraries (10, 100, 1000, and 3000 m) clustered into nine major lineages. gamma-Proteobacteria dominated all the depths and occupied almost the whole bacterial community at the 3000 m. alpha-Proteobacteria was abundant throughout the water column except near the sea bottom, and delta-Proteobacteria peaked at the 1000 m depth. Cyanobacteria were primarily limited to the photic zone, and the genetic diversity of Prochlorococcus showed a good correlation with niche adaptation. The appearance of the Cytophaga-Flexibacter-Bacteroides (CFB) group did not show a clear relationship with depth. Actinobacteria were found both in the photic zone and in deep water. Planctomyetes, Acidobacteria, and Verrucomicrobia were present as minor groups and more dominant in the deeper layers of water.     

Abyssal Megafaunal Necrophages: Latitudinal Differences in the Eastern North Atlantic Ocean

A pop-up time-lapse camera system (BATHYSNACK) was used to study megafaunal organisms attracted to bait at three abyssal localities in the eastern North Atlantic Ocean, a northern site on the Porcupine Abyssal Plain and two sub-tropical sites on the Madeira Abyssal Plain. Fish and decapod crustaceans appeared on 47% of photographs taken during deployments of up to seven days duration. The fishes Coryphaenoides (Nematonurus) armatus and Pachycara bulbiceps and the decapod Munidopsis spp. dominated appearances at the northern locality whereas over 95% of records at the two subtropical localities were of the decapod Plesiopenaeus armatus. Cyclical variations in necrophage abundance did not correlate with tidal cycles of near-bottom currents, although high P. armatus numbers were inversely related to current speed. Most of the frequently recorded entities showed contagious intraspecific distributions. In contrast, many of the interspecies relationships were non-random, with co-occurrences lower than expected, probably as a result of physical disturbance or potential predation. Population densities based on times of first arrival were calculated. Assemblages dominated by fish at higher latitudes and crustaceans at lower latitudes are discussed in terms of organic carbon supply to the deep sea and pelagic community structures.     

The wild goats Capra aegagrus Erxleben, 1777 of the Mediterranean Sea and the Eastern Atlantic Ocean islands

• 1 Populations of wild goats that can be referred to as phenotypes of the pasang, or Bezoar goat, or wild goat Capra aegagrus Erxleben, 1777, still occur on several of the Mediterranean and Eastern Atlantic islands. Other populations became extinct not many decades ago.
• 2 Fossil evidence for the natural spread of the wild goat to any of these islands has not been found. Originating in the Near East, the region of its natural range and its earliest domestication, the species was introduced by humans onto the Mediterranean islands starting as early as the Pre‐Pottery Neolithic.
• 3 The islands of the Eastern Atlantic were colonized artificially by animals of ‘pre‐Hispanic’ origin. The principal phenotypes expressed by all these populations of goats can be matched with the characteristics of both C. a. aegagrus Erxleben, 1777 (aegagrus phenotype) and C. a. dorcas Reichenow, 1888 (dorcas phenotype).
• 4 Most of these animals currently survive on the islands without being fed by humans, and should be protected.

     

Drivers of reef fish assemblages in an upwelling region from the Eastern Tropical Pacific Ocean

Reef fish assemblages are exposed to a wide range of anthropogenic threats as well as chronic natural disturbances. In upwelling regions, for example, there is a seasonal influx of cool nutrient-rich waters that may shape the structure and composition of reef fish assemblages. Given that climate change may disrupt the natural oceanographic processes by altering the frequency and strength of natural disturbances, understanding how fish assemblages respond to upwelling events is essential to effectively manage reef ecosystems under changing ocean conditions. This study used the baited remote underwater video stations (BRUVS) and the traditional underwater visual census (UVC) to investigate the spatiotemporal patterns of reef fish assemblages in an upwelling region in the North Pacific of Costa Rica. A total of 183 reef fish species from 60 families were recorded, of which 166 species were detected using BRUVS and 122 using UVC. Only 66% of all species were detected using both methods. This study showed that the upwelling had an important role in shaping reef fish assemblages in this region, but there was also a significant interaction between upwelling and location. In addition, other drivers such as habitat complexity and habitat composition had an effect on reef fish abundances and species. To authors’ knowledge, this is the first study in the Eastern Tropical Pacific that combines BRUVS and UVC to monitor reef fish assemblages in an upwelling region, which provides more detailed information to assess the state of reef ecosystems in response to multiple threats and changing ocean conditions.     

Niche-Partitioning of Prochlorococcus Populations in a Stratified Water Column in the Eastern North Atlantic Ocean

The in situ community structure of Prochlorococcus populations in the eastern North Atlantic Ocean was examined by analysis of Prochlorococcus 16S rDNA sequences with three independent approaches: cloning and sequencing, hybridization to specific oligonucleotide probes, and denaturing gradient gel electrophoresis (DGGE). The hybridization of high-light (HL) and low-light (LL) Prochlorococcus genotype-specific probes to two depth profiles of PCR-amplified 16S rDNA sequences revealed that in these two stratified water columns, an obvious niche-partitioning of Prochlorococcus genotypes occurred. In each water column a shift from the HL to the LL genotype was observed, a transition correlating with the depth of the surface mixed layer (SML). Only the HL genotype was found in the SML in each water column, whereas the LL genotype was distributed below the SML. The range of in situ irradiance to which each genotype was subjected within these distinct niches was consistent with growth irradiance studies of cultured HL- and LL-adapted Prochlorococcus strains. DGGE analysis and the sequencing of Prochlorococcus 16S rDNA clones were in full agreement with the genotype-specific oligonucleotide probe hybridization data. These observations of a partitioning of Prochlorococcus genotypes in a stratified water column provide a genetic basis for the dim and bright Prochlorococcus populations observed in flow cytometric signatures in several oceanic provinces.     

Distribution and Ecophysiology of Calanoid Copepods in Relation to the Oxygen Minimum Zone in the Eastern Tropical Atlantic

Oxygen minimum zones (OMZs) affect distribution patterns, community structure and metabolic processes of marine organisms. Due to the prominent role of zooplankton, especially copepods, in the marine carbon cycle and the predicted intensification and expansion of OMZs, it is essential to understand the effects of hypoxia on zooplankton distribution and ecophysiology. For this study, calanoid copepods were sampled from different depths (0–1800 m) at eight stations in the eastern tropical Atlantic (3°47′N to 18°S) during three expeditions in 2010 and 2011. Their horizontal and vertical distribution was determined and related to the extent and intensity of the OMZ, which increased from north to south with minimum O₂ concentrations (12.7 µmol kg⁻¹) in the southern Angola Gyre. Calanoid copepod abundance was highest in the northeastern Angola Basin and decreased towards equatorial regions as well as with increasing depth. Maximum copepod biodiversity was observed in the deep waters of the central Angola Basin. Respiration rates and enzyme activities were measured to reveal species-specific physiological adaptations. Enzyme activities of the electron transport system (ETS) and lactate dehydrogenase (LDH) served as proxies for aerobic and anaerobic metabolic activity, respectively. Mass-specific respiration rates and ETS activities decreased with depth of occurrence, consistent with vertical changes in copepod body mass and ambient temperature. Copepods of the families Eucalanidae and Metridinidae dominated within the OMZ. Several of these species showed adaptive characteristics such as lower metabolic rates, additional anaerobic activity and diel vertical migration that enable them to successfully inhabit hypoxic zones.     

Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus)

Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater genetic differentiation within a species than neutral markers. We examined genetic diversity at the MHC-DQB locus and nine putatively neutral microsatellite markers in grey seals (Halichoerus grypus) from eight United Kingdom (UK) colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles were identified in grey seals, which varied in prevalence across the grey seal range. Among the seal colonies, significant differences in DQB allele and haplotype frequencies and in average DQB heterozygosity were observed. Additionally, the DQB gene exhibited greater differentiation among colonies compared with neutral markers, yet a weaker pattern of isolation by distance (IBD). After correcting for the underlying IBD pattern, subpopulations breeding in similar habitats were more similar to one another in DQB allele frequencies than populations breeding in different habitats, but the same did not hold true for microsatellites, suggesting that habitat-specific pathogen pressure influences MHC evolution. Overall, the data are consistent with selection at MHC-DQB loci in grey seals with both varying selective pressures and geographic population structure appearing to influence the DQB genetic composition of breeding colonies.     

Eastward and Westward Dispersal Across the Tropical Atlantic Ocean of Larvae Belonging to the Genus Bursa (Prosobranchia,Mesogastropoda, Bursidae)

Larvae of the genus Bursa are commonly found in the South Equatorial Current and the Equatorial Undercurrent of the tropical Atlantic Ocean. Identification of Bursa veliger larvae in the plankton of such tropical waters is made possible by a comparison of larval shells with protoconchs of juvenile and well-preserved adult specimens. The relationship between the average current velocity and the estimated minimum duration of larval development of Bursa thomae suggests that there is sufficient time to account for successful trans-Atlantic transport of its veligers in either direction between West Africa and South America. The dispersal of veliger larvae explains the wide geographical distribution attained by the genus Bursa.     

Potential Impacts of a Western Pacific Grapsid Crab on Intertidal Communities of the Northwestern Atlantic Ocean

Population density and size distribution, salinity tolerance, and feeding activity were examined in a western Pacific grapsid crab, Hemigrapsus sanguineus, that was recently introduced to the mid-Atlantic coast of North America. Seasonal abundance on a boulder/cobble shore (Crane Neck Pt.) in central Long Island Sound, New York, USA, during 1997–1998, ranged from 7 to 10 crabs m⁻² averaged over the entire intertidal zone. Crabs occurred throughout the intertidal during summer and fall, but appeared to move from high to low elevations during winter. In laboratory experiments, H. sanguineus tolerated salinity down to 10 ppt for 7 d, but showed significant preference for 20 or 27 ppt over 10 ppt. The crabs readily consumed juvenile snails (Littorina littorea) and mussels (Mytilus edulis), as well as other common species of macroalgae and invertebrates occurring at Crane Neck Pt. High feeding rates and the ability to consume littorine snails up to 13 mm in height and mussels up to 20 mm in length suggest that this nonindigenous species has the potential to significantly affect the structure of rocky intertidal communities in the northwestern Atlantic Ocean; however, rigorous field studies are needed to accurately determine the impact of this recent introduction. This revised version was published online in July 2006 with corrections to the Cover Date.     

Cobalamin and microbial plankton dynamics along a coastal to offshore transect in the Eastern North Atlantic Ocean

Cobalamin (B12) is an essential cofactor that is exclusively synthesized by some prokaryotes while many prokaryotes and eukaryotes require an external supply of B12. The spatial and temporal availability of B12 is poorly understood in marine ecosystems. Field measurements of B12 along with a large set of ancillary biotic and abiotic factors were obtained during three oceanographic cruises in the NW Iberian Peninsula, covering different spatial and temporal scales. B12 concentrations were remarkably low (<1.5 pM) in all samples, being significantly higher at the subsurface Eastern North Atlantic Central Water than at shallower depths, suggesting that B12 supply in this water mass is greater than demand. Multiple regression models excluded B12 concentration as predictive variable for phytoplankton biomass or production, regardless of the presence of B12-requiring algae. Prokaryote production was the best predictor for primary production, and eukaryote community composition was better correlated with prokaryote community composition than with nutritional resources, suggesting that biotic interactions play a significant role in regulating microbial communities. Interestingly, co-occurrence network analyses based on 16S and 18S rRNA sequences allowed the identification of significant associations between potential B12 producers and consumers (e.g. Thaumarchaeota and Dynophyceae, or Amylibacter and Ostreococcus respectively), which can now be investigated using model systems in the laboratory.