Prokaryotic Abundance Research Articles

Prokaryotic dynamics and heterotrophic metabolism in a deep convection site of Eastern Mediterranean Sea (the Southern Adriatic Pit)

We report on investigations of prokaryotic abundance, biomass, extracellular enzymatic activity, prokaryotic heterotrophic production and respiration in the full water column (∼1200m) of a deep convection site (the Southern Adriatic Pit), carried out on six cruises in 2006–2008. Prokaryotic abundance (PA) varied vertically and temporally and ranged from 1.2 to 20.4×105cellml−1. Cell volumes, generally increased with depth; the lowest mean cell volume was observed in a period with no active convective process (Feb-07) and the highest in a period of stratification (Jun-08) following the convection process occurred in Feb-08. Prokaryotic biomass decreased with the depth and was related with both seasonal cycles of organic matter and hydrological processes. The picophytoplankton ranged in the upper layer (UL) from 0.089 to 10.71×104cellml−1. Cells were also recorded till 500m depth in Feb-08 and this finding could be linked to water convection occurred in the Southern Adriatic Pit in that month. In UL the variations of enzymatic activities as well as leucine-aminopeptidase/ß-glucosidase ratio showed a seasonal trend probably linked to the productive processes of the photic layer. An inverse relation between alkaline phosphatase activity (APA) and phosphate concentrations was found (APA=0.0003PO4−1.7714, R2=0.333, P<0.05). Generally cell-specific enzymatic activities increased with depth as did cell-specific carbon dioxide production rates, while cell-specific prokaryotic heterotrophic production had an opposite trend. High values of prokaryotic growth efficiency registered in the deep layers in Nov-06 reflected a supply of preformed C transported within the deep water masses. Overall, in 2007 when no convective phenomenon was observed, the variability of prokaryotic metabolism was governed by the seasonal cycle of the organic matter, while in Nov-06 and Jun-08 the dynamics of deep water ventilation influenced the trend along the water column of many microbial parameters. The yearly trophic balance of the study site appeared to move towards autotrophy only in UL, whilst in the whole water column, the prokaryotic carbon demand exceeded POC availability rained down from euphotic zone. This mismatch was balanced by the DOC entrapped in the “younger waters” of new formation that alters the normal flux of the biological pump and fuels the deep marine biota in this area of deep water convection.

High Lytic Infection Rates but Low Abundances of Prokaryote Viruses in a Humic Lake (Vassivière, Massif Central, France)

We explored the abundance and infection rates of viruses on a time series scale in the euphotic zone of the humic mesotrophic Lake Vassivière (Massif Central, France) and compared them to nonhumic lakes of contrasting trophy (i.e., the oligomesotrophic Lake Pavin and the eutrophic Lake Aydat) located in the same geographical region and sampled during the same period. In Lake Vassivière, the abundances of virus-like particles (range, 1.7 × 10(10) to 2.6 × 10(10) liter(-1)) were significantly (P < 0.001) lower than in Lakes Pavin and Aydat. The percentage of virus-infected prokaryotic cells (mean, 18.0%) was significantly higher (P < 0.001) in Vassivière than in Pavin (mean, 11.5%) and Aydat (mean, 9.7%). In Vassivière, the abundance of prokaryotes was a good predictor (r = 0.78, P < 0.001) of the number of virus-like particles, while the potential grazing rate from heterotrophic nanoflagellates was positively correlated to the viral infection rate (r = 0.75, P < 0.001; n = 20), indicating the prevalence of cycling interactions among viruses, prokaryotes, and grazers, which is in agreement with past experiments. The absence of correlation between chlorophyll a concentrations (Chl) and viral parameters suggested that the resources for the lytic activity of viruses in Vassivière were mainly under allochthonous control, through host activity. Indeed, compilation of data obtained from several nonhumic lakes in the French Massif Central revealed that Chl was positively correlated to the abundance of virus-like particles at concentrations above 0.5 μg Chl liter(-1) and negatively at concentrations below 0.5 μg Chl liter(-1), suggesting that phytoplankton-derived resources could force prokaryotic growth to attain a certain threshold level when the host availability is sufficient to boost the proliferation of viruses. Therefore, based on the high level of lytic infection rates in Lake Vassivière, we conclude that viruses are key agents for prokaryotic mortality and could influence the food web dynamics in humic lakes, which may ultimately depend on the internal cycling of resources and, perhaps, mainly on the allochthonous inputs and the associated humic substances.

Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea

In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-011-9610-1) contains supplementary material, which is available to authorized users.

Changes in viral and bacterial communities during the ice‐melting season in the coastal Arctic (Kongsfjorden, Ny‐Ålesund)

Microbial communities in Arctic coastal waters experience dramatic changes in environmental conditions during the spring to summer transition period, potentially leading to major variations in the relationship between viral and prokaryotic communities. To document these variations, a number of physico-chemical and biological parameters were determined during the ice-melting season in the coastal Arctic (Kongsfjorden, Ny-Ålesund, Spitsbergen). The bacterial and viral abundance increased during the spring to summer transition period, probably associated to the increase in temperature and the development of a phytoplankton bloom. The increase in viral abundance was less pronounced than the increase in prokaryotic abundance; consequently, the viral to prokaryotic abundance ratio decreased. The bacterial and viral communities were stratified as determined by Automated Ribosomal Intergenic Spacer Analysis and Randomly Amplified Polymorphic DNA-PCR respectively. Both the bacterial and viral communities were characterized by a relatively low number of operational taxonomic units (OTUs). Despite the apparent low complexity of the bacterial and viral communities, the link between these two communities was weak over the melting season, as suggested by the different trends of prokaryotic and viral abundance during the sampling period. This weak relationship between the two communities might be explained by UV radiation and suspended particles differently affecting the viruses and prokaryotes in the coastal Arctic during this period. Based on our results, we conclude that the viral and bacterial communities in the Arctic were strongly affected by the variability of the environmental conditions during the transition period between spring and summer.

Contribution of Crenarchaeota and Bacteria to autotrophy in the North Atlantic interior

Marine Crenarchaeota are among the most abundant groups of prokaryotes in the ocean and recent reports suggest that they oxidize ammonia as an energy source and inorganic carbon as carbon source, while other studies indicate that Crenarchaeota use organic carbon and hence, live heterotrophically. We used catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) to determine the crenarchaeal and bacterial contribution to total prokaryotic abundance in the (sub)tropical Atlantic. Bacteria contributed ~ 50% to total prokaryotes throughout the water column. Marine Crenarchaeota Group I (MCGI) accounted for ~ 5% of the prokaryotes in subsurface waters (100 m depth) and between 10 and 20% in the oxygen minimum layer (250-500 m depth) and deep waters (North East Atlantic Deep Water). The fraction of both MCGI and Bacteria fixing inorganic carbon, determined by combining microautoradiography with CARD-FISH (MICRO-CARD-FISH), decreased with depth, ranging from ~ 30% in the oxygen minimum zone to < 10% in the intermediate waters (Mediterranean Sea Outflow Water, Antarctic Intermediate Water). In the deeper water masses, however, MCGI were not taking up inorganic carbon. Using quantitative MICRO-CARD-FISH to determine autotrophy activity on a single cell level revealed that MCGI are incorporating inorganic carbon (0.002-0.1 fmol C cell⁻¹ day⁻¹) at a significantly lower rate than Bacteria (0.01-0.6 fmol C cell⁻¹ day⁻¹). Hence, it appears that MCGI contribute substantially less to autotrophy than Bacteria. Taking the stoichiometry of nitrification together with our findings suggests that MCGI might not dominate the ammonia oxidation step in the mesopelagic waters of the ocean to that extent as the reported dominance of archaeal over bacterial amoA would suggest.

Viral abundance and activity in the deep sub-seafloor biosphere

Subsurface abundance and distribution of viruses and prokaryotes was determined along a depth profile, down to 96 m below seafloor (96 mbsf), at Challenger Mound from the Porcubine Seabight (IODP Expedition 307). Viral and prokary- otic abundance decreased exponentially with sedi- ment depth from 1.0 × 10 8 viruses cm -3 and 3.8 × 10 6 cells cm -3 at 4 mbsf to 4.9 × 10 6 viruses cm -3 and 9.8 × 10 5 cells cm -3 at 96 mbsf. The age of the sediment ranges from ca. 0.5 million yr before present (Ma) at 4 mbsf to ca. 2 Ma at 96 mbsf. Assuming that the decline in viral abundance with depth reflects a gradual decay of the viral assemblage over time, the estimated decay rate of the viral community is 1.2 × 10 -6 ± 0.3 × 10 -6 (SD) yr -1 , corresponding to a half-life of the viral community of 5.8 × 10 5 yr. Measurements of viral and prokaryotic change in abundance were performed in incubations of undi- luted, but homogenized, sediment samples (13.3 and 79.8 mbsf) in anaerobic bags. Viral abundance de- creased rapidly (decay rates of 0.010 ± 0.002 (SD) and 0.022 ± 0.018 (SD) h -1 , respectively) in the incu- bations, suggesting that homogenization exposed the viruses to degradation processes. We hypothe- size that most of the deep subsurface viral communi- ties inhabit a microenvironment where the viruses are protected against decay, and can therefore per- sist in undisturbed sediments for hundreds of thou- sands, perhaps even millions, of years.

Prokaryotic abundance and 16S rRNA gene sequences detected in marine aerosols on the East Sea (Korea)

Modern studies on marine airborne prokaryotes over open seas have been rare. Here, to understand their distribution and composition, aerosol as well as surface seawater samples were collected at three sites in the East Sea. The abundance of airborne prokaryotes was 0.7-1.2 × 10(5) cells m(-3) . Partial sequences of the 16S rRNA gene from the aerosols were dominated by Gammaproteobacteria and Bacteroidetes. Interestingly, the numbers of phylotypes of airborne bacteria were comparable to those of seawater bacteria in coastal and remote offshore sites. Over half of the bacterial operational taxonomic units (OTUs) detected in these aerosols (12 out of 20) were of marine origin. Eight of the 19 bacterial OTUs found in the surface waters occurred in the aerosols. Thus, surface seawater seems to be a main source of marine airborne bacteria. However, in the intermediate offshore site, airborne bacterial OTUs (n=4) were all terrestrial, indicating that variations of dominant airborne bacterial phylotypes occurred over the sites (each ∼160 km apart) sampled at 1-4-day intervals. Euryarchaeota sequences belonging to the MSP8 clade reported from geographically distant regions were detected in marine aerosols. Long-distance aerial transport of the marine prokaryotes seems to be quite possible.

Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient

Virus-prokaryote interactions were investigated in four natural sites in Senegal (West Africa) covering a salinity gradient ranging from brackish (10‰) to near salt saturation (360‰). Both the viral and the prokaryote communities exhibited remarkable differences in their physiological, ecological and morphological traits along the gradient. Above 240‰ salinity, viral and prokaryotic abundance increased considerably with the emergence of (1) highly active square haloarchaea and of (2) viral particles with pleiomorphic morphologies (predominantly spindle, spherical and linear shaped). Viral life strategies also showed some salinity-driven dependence, switching from a prevalence of lytic to lysogenic modes of infection at the highest salinities. Interestingly, the fraction of lysogenized cells was positively correlated with the proportion of square cells. Overall, the extraordinary abundance of viruses in hypersaline systems (up to 6.8 × 10(8) virus-like particles per milliliter) appears to be partly explained by their high stability and specific ability to persist and proliferate in these apparently restrictive habitats.

Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter

Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial amoA clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal amoA genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal amoA genes were more abundant than betaproteobacterial amoA genes in the first year, but betaproteobacterial amoA was more abundant than archaeal amoA the following year. The ratio of archaeal amoA gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in Crenarchaea at this location. Potential nitrification rates, as well as the total amoA gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing Betaproteobacteria and Crenarchaea.

Distribution of the prokaryotic biomass and community respiration in the main water masses of the Southern Tyrrhenian Sea (June and December 2005)

The distribution of the prokaryotic biomass (from both abundance and cell volume measurements) and microbial community respiration (by ETS activity) in the main water masses of the Southern Tyrrhenian Sea were studied. The data were collected from surface to the bottom depth (max 3600 m) in July and December 2005. Prokaryotic abundance and microbial respiration were higher in summer than late-autumn and decreased with depth in accordance with the water masses. The opposite was found for the prokaryotic cell volumes that increased with depth and were higher in December. The cell carbon content varied within the water masses and study periods (range 9–34 fg C cell−1) and overestimations and underestimations of biomass there would have been by using the routinely adopted conversion factor (20 fg C cell−1). The depth-integrated respiratory rates resulted comparable in the photic and aphotic layers. In July, 210 and 225 mg C m−2 day−1 in the euphotic and aphotic zones, respectively, were remineralized while in December, 112 and 134 mg C m−2 day−1, respectively, were. Speculations to quantify the carbon flow mediated by microbial community suggested the occurrence of different microbial behavior within the different water masses.

Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment

The oxidation of hydrogen sulfide is essential to sulfur cycling in marine habitats. However, the role of microbial sulfur oxidation in marine sediments and the microorganisms involved are largely unknown, except for the filamentous, mat-forming bacteria. In this study we explored the diversity, abundance and activity of sulfur-oxidizing prokaryotes (SOP) in sulfidic intertidal sediments using 16S rRNA and functional gene sequence analyses, fluorescence in situ hybridization (FISH) and microautoradiography. The 16S rRNA gene analysis revealed that distinct clades of uncultured Gammaproteobacteria are important SOP in the tidal sediments. This was supported by the dominance of gammaproteobacterial sequences in clone libraries of genes encoding the reverse dissimilatory sulfite reductase (rDSR) and the adenosine phosphosulfate reductase (APR). Numerous sequences of all three genes grouped with uncultured autotrophic SOP. Accordingly, Gammaproteobacteria accounted for 40-70% of all ¹⁴CO₂ -incorporating cells in surface sediments as shown by microautoradiography. Furthermore, phylogenetic analysis of all three genes consistently suggested a discrete population of SOP that was most closely related to the sulfur-oxidizing endosymbionts of the tubeworm Oligobrachia spp. FISH showed that members of this population (WS-Gam209 group) were abundant, reaching up to 1.3 × 10⁸ cells ml⁻¹ (4.6% of all cells). Approximately 25% of this population incorporated CO₂, consistent with a chemolithoautotrophic metabolism most likely based on sulfur oxidation. Thus, we hypothesize that novel, gammaproteobacterial SOP attached to sediment particles may play a more important role for sulfide removal and primary production in marine sediments than previously assumed.

Disentangling the effect of viruses and nanoflagellates on prokaryotes in bathypelagic waters of the Mediterranean Sea

Bathypelagic ecosystems depend on prokaryotic heterotrophic biomass fuelled by vertical particulate organic matter (POM) fluxes, but very little information is available on the interactions among viruses, prokaryotes and nanoflagellates in deep waters. We simultaneously investigated the relative importance of the viral and heterotrophic nanoflagellate (HNF) grazing-induced prokaryotic mortality in bathypelagic waters by means of dilution experiments performed on samples collected at 1500 m depth from the Atlantic Ocean to the Eastern Mediterranean Sea. Prokaryotic abundance (range: 1.4 to 8.9 × 104 cells ml–1), although different from one station to another, was on average not significantly different among biogeographic regions. The potential predators of prokaryotes (viruses, HNF and microzooplankton) followed a similar spatial pattern. Viruses were responsible for an important fraction of prokaryotic mortality (on average 13.4% d–1). Dilution experiments carried out to estimate the potential predation of HNF suggested a high effect on prokaryotic abundance. However, since the latter experiments also include the effect of viruses on prokaryotes, when this factor was disentangled from the overall mortality, the potential rates of HNF predation on prokaryotes (on average 49.5%) were ca. 4 times higher than the effect due to viral infections. Conversely to patterns of distribution, the relative importance of virus-mediated mortality vs. HNF predation changed significantly among different regions. Results should be treated with caution due to the intrinsic difficulty in reproducing experimentally natural deep-sea conditions, but they permit disentangling of the relative effect of viruses and HNF on prokaryotes and compare the potential predatory control in different biogeographic regions.

Community compositions of Bacteria and Archaea in the Sea of Okhotsk during summer

We investigated spatial variations of the bacterial and archaeal community composition in surface waters of the Sea of Okhotsk during summer of 2006, using denaturing gradient gel electrophoresis (DGGE). We determined phylogenetic assemblages, including Actinobacteria, Bacteroidetes, Cyanobacteria, Alpha- and Gammaproteobacteria, and Marine Group II Euryarchaea, and successfully revealed their spatial distribution patterns. At most stations, Bacteria had higher diversity than Archaea, indicated by the relatively higher Shannon-Weaver indexes and numbers of operational taxonomic units (OTUs). Canonical correspondence analysis (CCA) and redundancy analysis (RDA) demonstrated that the community compositions of bacterial populations in the Sea of Okhotsk were closely associated with total prokaryote abundance, while the spatial distributions of bacterial phylogenetic groups were more related to both the concentration of dissolved organic nitrogen (DON) and the ratio of DON versus dissolved organic carbon concentration (DOC:DON). On the other hand, the spatial variation of the community composition of Archaea had no significant association with environmental parameters.

Prokaryotic abundance and heterotrophic metabolism in the deep Mediterranean Sea

A synthesis of field data carried out in the Mediterranean Sea are presented, aimed at contributing to the knowledge of three prokaryotic-mediated processes and their implications on the Carbon cycle. The distribution of exoenzymatic activities, secondary production and respiration rates was studied together with the prokaryotic abundances. Particular attention was paid to the meso- and bathypelagic layers which play an important role in the Mediterranean carbon cycle. The study is noteworthy because of its large spatial scale spanning the entire Mediterranean Sea over 4 years. In addition, two Atlantic stations in front of the Gibraltar Strait were investigated. The longitudinal distribution of prokaryotic activities and abundance along the MED showed different trends along the depth-layers. In particular, higher exoenzymatic rates were detected in the Eastern basin compared to the Western one; carbon respiration rate showed patterns variable with the sampling periods in the epipelagic and bathypelagic layers, while a consistent Westwards decreasing trend at the mesopelagic layers occurred. Specific enzyme activities per cell showed high values in the deepest layers for leucine aminopeptidase. Comparison with Carbon respiration rate data collected before the 2000s showed changing patterns of microbial heterotrophic processes in the Mediterranean Sea.

Prokaryotic abundance and heterotrophic metabolism in the deep Mediterranean Sea

A synthesis of field data carried out in the Mediterranean Sea are presented, aimed at contributing to the knowledge of three prokaryotic-mediated processes and their implications on the Carbon cycle. The distribution of exoenzymatic activities, secondary production and respiration rates was studied together with the prokaryotic abundances. Particular attention was paid to the meso- and bathypelagic layers which play an important role in the Mediterranean carbon cycle. The study is noteworthy because of its large spatial scale spanning the entire Mediterranean Sea over 4 years. In addition, two Atlantic stations in front of the Gibraltar Strait were investigated. The longitudinal distribution of prokaryotic activities and abundance along the MED showed different trends along the depthlayers. In particular, higher exoenzymatic rates were detected in the Eastern basin compared to the Western one; carbon respiration rate showed patterns variable with the sampling periods in the epipelagic and bathypelagic layers, while a consistent Westwards decreasing trend at the mesopelagic layers occurred. Specific enzyme activities per cell showed high values in the deepest layers for leucine aminopeptidase. Comparison with Carbon respiration rate data collected before the 2000s showed changing patterns of microbial heterotrophic processes in the Mediterranean Sea.

Shallow hydrothermal vents in the southern Tyrrhenian Sea

Shallow hydrothermal systems represent particularly suitable fields for studying the interactions between fluids and microorganisms inhabiting extreme environments. Coastal zones of the southern Tyrrhenian Sea are home to shallow hydrothermal systems, related to both active and extinct volcanism, located in the Flegrean area, at Cape Palinuro and around the Eolian Islands. A great diversity of Archaea and Bacteria has been reported at shallow hydrothermal vents, where they are key elements in ecosystem functioning. When compared with deep-sea locations, photosynthetic microorganisms appear to be the main characteristic of shallow hydrothermal vents, where both light and hydrothermal energy support a complex microbial community displaying primary productivity (phototrophic and chemotrophic) of mixed origin. Viriobenthos abundances are low compared with other shallow marine systems, suggesting that viruses are less tolerant than prokaryotes of high temperatures and consequently are believed to have a low impact on prokaryotic abundance and biodiversity. Microorganisms from shallow hydrothermal vents represent an almost unexploited resource for thermostable enzymes and biomolecules potentially valuable in biotechnology.

Prokaryotic activities and abundance in pelagic areas of the Ionian Sea

The Ionian Sea represents a suitable basin for studying the biogeochemical processes mediated by microbial activities. Because of its characteristics as a crossing region between the western and eastern Mediterranean Sea, it is one of the sites most affected by changes in water mass composition and dynamics, caused by the Eastern Mediterranean Transient (EMT). To date, relatively few data exist on microbial activities in pelagic areas of the Ionian Sea. From 1998 to 2004, during different research cruises, prokaryotic parameters (abundance, extracellular enzyme activities leucine aminopeptidase, β-glucosidase, alkaline phosphatase, bacterial production and respiration) were measured together with culturable bacteria and the main physical, chemical and trophic parameters (temperature, salinity, nutrients, particulated organic matter). The aim of the study was to describe the spatial and temporal variability in microbial activities involved in the carbon and phosphorus cycles, in different layers. Results showed that organic matter transformation mediated by the microbial community displayed a significant increase in autumn, highlighting the occurrence of significant changes at meso- and bathypelagic depths. Unlike the dark ocean, bacterial growth efficiency in the Ionian Sea, which increased with depth, seemed to vary from being a source of carbon in the epipelagic layer to a sink in the meso- and bathypelagic layers. The mechanism of phosphatase regulation showed a weak inverse correlation between specific phosphatase and inorganic P in all seasons except autumn. It is worth mentioning that the reported results constitute, to the best of our knowledge, one of the available datasets giving information about microbial activities in the Ionian Sea.

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

Viral and prokaryotic abundance, production and diversity were determined throughout the water column of the subtropical Atlantic Ocean to assess potential variations in the relation between viruses and prokaryotes. Prokaryotic abundance and heterotrophic activity decreased by one and three orders of magnitude, respectively, from the epi- to the abyssopelagic layer. Although the lytic viral production (VP) decreased with depth, lysogenic VP was variable throughout the water column and did not show any trend with depth. The bacterial, archaeal and viral community composition were depth-stratified as determined by the automated ribosomal intergenic spacer analysis, terminal-restriction fragment length polymorphism and randomly amplified polymorphic DNA-PCR, respectively. Generally, the number of operational taxonomic units (OTUs) did not reveal consistent trends throughout the water column. Viral and prokaryotic abundance were strongly related to heterotrophic prokaryotic production, suggesting similar linkage strength between the viral and prokaryotic communities from the lower epi- to the abyssopelagic layer in the Atlantic Ocean. Strikingly, the prokaryotic and viral parameters exhibited a similar variability throughout the water column down to the abyssopelagic layers, suggesting that the dark ocean is as dynamic a system as is the lower epipelagic layer. It also indicates that viruses are apparently having a similar role for prokaryotic mortality in the dark oceanic realm as in surface waters. The more than twofold increase in bacterial OTUs from 2750 m depth to >5000 m depth and the concurrent decrease in viral OTUs, however, suggests that viruses might exhibit a wider host range in deep waters than in surface waters.

Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 59:185-195 (2010) - DOI: https://doi.org/10.3354/ame01393 Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea Taichi Yokokawa1,*, Daniele De Corte1,2, Eva Sintes3, Gerhard J. Herndl1,3 1Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO Box 59, 1790 AB, Den Burg, The Netherlands 2Center for Ecological and Evolutionary Studies, University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands 3University of Vienna, Department of Marine Biology, Faculty Center of Ecology, Althanstrasse 14, 1090 Vienna, Austria *Email: taichi.yokokawa@nioz.nl ABSTRACT: To determine the variation of bacterial activity and community composition between and within specific water masses, samples were collected throughout the water column at 5 stations in the eastern Mediterranean Sea corresponding to the regions of the northern Aegean, mid-Aegean, western Cretan, Ionian and southern Aegean Seas. Prokaryotic abundance below 100 m declined with depth at all the stations, while decreasing trends with depth in prokaryotic heterotrophic activity were present only at 2 out of the 5 stations. Bacterial community composition (BCC), determined using both automated rRNA intergenic spacer analysis and terminal-restriction-fragment length polymorphism, was also related to depth although the number of operational taxonomic units was remarkably constant throughout the water column. Overall, the maximums in similarity values of the BCC between water sample pairs decreased with increasing temperature–salinity (T–S) distance of the water samples probably due to distinct biogeochemical characteristics of water masses. However, considerable dissimilarity in the BCC between samples with identical T–S values, and hence within the same water mass, was also observed, possibly reflecting heterogeneity in the organic matter field or in biotic control within a given water body. Thus, we conclude that the richness of bacterial communities is remarkably constant with depth down to bathypelagic waters. The similarity of bacterial communities in water parcels with identical temperature and salinity can range from highly similar to very dissimilar, reflecting variability in substrate supply despite the physical uniformity of water parcels. KEY WORDS: Bacteria · Community composition · Patchiness · Spatial scale · Eastern Mediterranean Sea Full text in pdf format PreviousNextCite this article as: Yokokawa T, De Corte D, Sintes E, Herndl GJ (2010) Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea. Aquat Microb Ecol 59:185-195. https://doi.org/10.3354/ame01393 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 59, No. 2. Online publication date: April 08, 2010 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2010 Inter-Research.

Mesoscale eddies: hotspots of prokaryotic activity and differential community structure in the ocean

To investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic 'hotspots' of prokaryotic activity (in the epi- and mesopelagic realms).