Abundance and Biomass from heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus in the Aegean Sea in April 2008 during SES_GR1

The HCMR_SES_LAGRANGIAN_GR1_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during April 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus abundance: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Heterotrophic Nanoflagellate abundance: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Ciliate abundance: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Heterotrophic bacteria, Synechococcus, Prochlorococcus biomass: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Abundance data were converted into C biomass using 250 fgC cell-1 (Kana & Glibert 1987) for Synechococcus, 50 fgC cell-1 (Campbell et al. 1994) for Prochlorococcus and 20fgC cell-1 (Lee & Fuhrman 1987) for heterotrophic bacteria. Heterotrophic Nanoflagellate biomass: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Abundance data were converted into C biomass using 183 fgC µm**3 (Caron et al. 1995). Ciliate biomass: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Ciliate cell sizes were measured and converted into cell volumes using appropriate geometric formulae using image analysis. For biomass estimation, the conversion factor 190 fgC µm**3 was used (Putt and Stoecker 1989).

Characterization of dead-zone eddies in the tropical Northeast Atlantic

Localized open-ocean low-oxygen dead-zones in the tropical Northeast Atlantic are recently discovered ocean features that can develop in dynamically isolated water masses within cyclonic eddies (CE) and anticyclonic modewater eddies (ACME). Analysis of a comprehensive oxygen dataset obtained from gliders, moorings, research vessels and Argo floats revealed that eddies with low oxygen concentrations at 50-150 m depths can be found in surprisingly high numbers and in a large area (from about 4°N to 22°N, from the shelf at the eastern boundary to 38°W). Minimum oxygen concentrations of about 9 µmol kg-1 in CEs and severely suboxic concentrations (< 1 µmol kg-1) in ACMEs were observed. In total, 173 profiles with oxygen concentrations below the minimum background concentration of 40 µmol kg-1 could be associated with 27 independent "dead-zone" eddies (10 CEs; 17 ACMEs) over a period of 10 years. The eddies' oxygen minimum is located in the eddy core beneath the mixed layer at a mean depth of 80 m. Compared to the surrounding waters, the mean oxygen anomaly between 50 and 150 m depth for CEs (ACMEs) is -38 (-79) µmol kg-1. The low oxygen concentration right beneath the mixed layer has been attributed to the combination of high productivity in the eddies' surface waters and the isolation of their cores with respect to lateral oxygen supply. Indeed, eddies of both types feature a cold sea surface temperature anomaly and enhanced chlorophyll concentrations in their center. The locally increased consumption within these eddies represents an essential part of the total consumption in the open tropical Northeast Atlantic Ocean and might be partly responsible for the formation of the shallow oxygen minimum zone. Eddies south of 12°N carry weak hydrographic anomalies in their cores and seem to be generated in the open ocean away from the boundary. North of 12°N, eddies of both types carry anomalously low salinity water of South Atlantic Central Water origin from the eastern boundary upwelling region into the open ocean. Water mass properties and satellite eddy tracking both point to an eddy generation near the eastern boundary.

Composition of bacterioplankton in the North Atlantic subtropical gyre

Subtropical oceanic gyres are the most extensive biomes on Earth where SAR11 and Prochlorococcus bacterioplankton numerically dominate the surface waters depleted in inorganic macronutrients as well as in dissolved organic matter. In such nutrient poor conditions bacterioplankton could become photoheterotrophic. We assessed the photoheterotrophy of the key microbial taxa in the North Atlantic oligotrophic gyre and adjacent regions. The experimental work was performed on board the Royal Research Ship James Cook (cruise no. JC53, October-November 2010) as part of the Atlantic Meridional Transect programme, and on board the Royal Research Ship Discovery (cruise no. D369, August-September 2011). At each station, samples were collected from 20m depth with a sampling rosette of 20-l Niskin bottles mounted on aconductivity-temperature-depth profiler. Samples were collected in 1 l thermos flasks (washed with10% v/v HCl) in the dark and processed immediately. Depth of 20m was chosen because it represents the mixed layer and it was the shallowest depth unaffected by the ship's movement, including thrusting, that could artificially affect microbial metabolism in nutrient-depleted stratified surfacewaters. Molecular identification of flow-sorted cells CARD-FISH was performed on flow-sorted cells to identify the groups for which uptake rates were measured. High nucleic acid-containing bacteria, based on SYBR Green DNA staining, that had virtually undetectable chlorophyll autofluorescence, were phylogenetically affiliated with Prochlorococcus,in agreement with our previously reported results (Zubkov et al., 2007; doi:10.1111/j.1462-2920.2007.01324.x).

Glycerol dialkyl glycerol tetraethers (GDGT) abundance in suspended particulate matter from the South-west and Equatorial Atlantic Ocean

The TEX86 paleotemperature proxy is based on archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids preserved in marine sediments, yet both the influence of different physiological factors on the structural distribution of GDGTs, and the mechanism(s) by which GDGTs are exported to marine sediments remain unclear. In particular, TEX86 temperatures derived directly from suspended particulate matter (SPM) in the water column can diverge strongly from corresponding in situ temperatures. Here we investigated the abundance and structural distribution of GDGTs in the South-west and Equatorial Atlantic Ocean by examining SPM collected from four surface 1000 m depth profiles spanning 48 degrees of latitude. The depth distribution of GDGTs was consistent with our current understanding of marine archaeal ecology, and specifically of ammonia-oxidizing Thaumarchaeota. Maximum GDGT concentrations occurred at the base of the primary NO2- maximum. Core GDGTs dominated the structural distribution in surface waters, while intact polar GDGTs - thought to potentially indicate live cells - were more abundant at all depths below the maximum NO2- concentration. When integrated through the upper 1000 m of the water column, > 98% of GDGTs were present in waters at and below the depth of the primary NO2- maximum. TEX86-calculated temperatures showed local minima at the depth of the NO2- maximum, while the ratio of GDGT 2:GDGT 3 [2/3] increased with depth throughout the upper water column. These results were used to model the depth of origin for GDGTs exported to sediments. By comparing our SPM data to published TEX86 values and [2/3] ratios from sediments near our study sites, we conclude that most GDGTs are exported from the depth of maximum GDGT concentrations, near the subsurface NO2- maximum (~80-250 m). This indicates that local ammonia oxidation dynamics are important regional controls on the GDGT ratios preserved in sediments. Predicting the extent to which subsurface variations in archaeal activity may influence the sedimentary TEX86 record will require a better understanding of how site-specific productivity and particle dynamics in the upper water column influence the depth of origin for exported organic matter.

NOR5/OM60 clade of the Yangtze River estuary

The phylogeny, abundance, and biogeography of the NOR5/OM60 clade was investigated. This clade includes "Congregibacter litoralis" strain KT71, the first cultured representative of marine aerobic anoxygenic phototrophic Gammaproteobacteria. Most of the NOR5/OM60 sequences were retrieved from marine coastal settings, whereas there were fewer from open-ocean surface waters, deep-sea sediment, freshwater, saline lakes and soil. The abundance of members of the NOR5/OM60 clade in various marine sites was determined by fluorescence in situ hybridization using a newly designed and optimized probe set. Relative abundances in coastal marine waters off the Yangtze estuary were up to 3% of the total 4',6-diamidino-2-phenylindole (DAPI) counts. A small cruise was undertaken from 2006-09-06 to 2006-09-08 in the Yangtze River estuary. Samples were taken from surface water, and immediately fixed with 1% paraformaldehyde (PFA) for 1 h, filtered onto polycarbonate filters (Millipore, 47 mm in diameter, 0.2 µm pore size) and stored frozen at -20 °C.

The response of Antarctic sea ice algae to changes in pH and CO2

Ocean acidification substantially alters ocean carbon chemistry and hence pH but the effects on sea ice formation and the CO2 concentration in the enclosed brine channels are unknown. Microbial communities inhabiting sea ice ecosystems currently contribute 10-50% of the annual primary production of polar seas, supporting overwintering zooplankton species, especially Antarctic krill, and seeding spring phytoplankton blooms. Ocean acidification is occurring in all surface waters but the strongest effects will be experienced in polar ecosystems with significant effects on all trophic levels. Brine algae collected from McMurdo Sound (Antarctica) sea ice was incubated in situ under various carbonate chemistry conditions. The carbon chemistry was manipulated with acid, bicarbonate and bases to produce a pCO2 and pH range from 238 to 6066 µatm and 7.19 to 8.66, respectively. Elevated pCO2 positively affected the growth rate of the brine algal community, dominated by the unique ice dinoflagellate, Polarella glacialis. Growth rates were significantly reduced when pH dropped below 7.6. However, when the pH was held constant and the pCO2 increased, growth rates of the brine algae increased by more than 20% and showed no decline at pCO2 values more than five times current ambient levels. We suggest that projected increases in seawater pCO2, associated with OA, will not adversely impact brine algal communities.