Prokaryotic Activity Research Articles

Winter-spring transition in the subarctic Atlantic: microbial response to deep mixing and pre-bloom production

In temperate, subpolar and polar marine systems, the classical perception is that diatoms initiate the spring bloom and thereby mark the beginning of the productive season. Contrary to this view, we document an active microbial food web dominated by picoand nanoplankton prior to the diatom bloom, a period with excess nutrients and deep convection of the water column. During repeated visits to stations in the deep Iceland and Norwegian basins and the shallow Shetland Shelf (26 March to 29 April 2012), we investigated the succession and dynamics of photo synthetic and heterotrophic microorganisms. We observed that the early phytoplankton production was followed by a decrease in the carbon:nitrogen ratio of the dissolved organic matter in the deep mixed stations, an increase in heterotrophic prokaryote (bacteria) abundance and activity (indicated by the high nucleic acid:low nucleic acid bacteria ratio), and an increase in abundance and size of heterotrophic protists. The major chl a contribution in the early winter−spring transition was found in the fraction 50 μm) were stimulated by deep mixing later in the period, while picophytoplankton were unaffected by mixing; both physical and biological reasons for this development are discussed herein.

Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades.

To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO4 (2-) (≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO4 (2-)-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO4 (2-) concentrations; ≤4 μM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO4 (2-) (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ(13)CO2 + 1,000)/(amount of δ(13)CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO4 (2-). These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.

Patterns of Fungal and Bacterial Carbon Mineralization Across Northern European Peatlands

The fungal and bacterial activity was determined in 20 northern European peatlands ranging from ombrotrophic bogs to eutrophic fens with key differences in degree of humification, pH, dry bulk density, carbon (C) content and vegetation communities using the selective inhibition (SI) technique. These peatlands were partly disturbed and the respective water tables lowered below the surface layer. Basal respiration ranged from 24 to 128 µg CO2-C g−1 dry peat d−1. Bacterial contributions to CO2 production were high in most peatlands and showed the following pattern: eutrophic >> transitional ≥ mesotrophic >> ombrotrophic peatland types. The fungal-to-bacterial (F:B) ratios varied substantially within peatland type, and this was mainly attributed to differences in peat botanical compositions and chemistry. The computed mean Inhibitor Additivity Ratio (IAR) was quite close to 1 to suggest that the SI techniques can be used to partition eukaryotic and prokaryotic activity in wide range of peatlands. Overall, basal respiration, microbial biomass-C, fungal and bacterial activities varied across the studied peatland types, and such differences could have consequences for C- and nutrient-cycling as well as how bogs and fens will respond to environmental changes.

In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths.

The deep subseafloor, extending from a few centimeters below the sediment surface to several hundred meters into sedimentary deposits, constitutes the deep biosphere and harbors an unexpected microbial diversity. Several studies have described the occurrence, turnover, activity and function of subseafloor prokaryotes; however, subsurface eukaryotic communities still remain largely underexplored. Ribosomal RNA surveys of superficial and near-surface marine sediments have revealed an unexpected diversity of active eukaryotic communities, but knowledge of the diversity of deep subseafloor microeukaryotes is still scarce. Here, we investigated the vertical distribution of DNA and RNA fungal signatures within subseafloor sediments of the Canterbury basin (New Zealand) by 454 pyrotag sequencing of fungal genetic markers. Different shifts between the fungal classes of Tremellomycetes, Sordariomycetes, Eurotiomycetes, Saccharomycetes, Wallemiomycetes, Dothideomycetes, Exobasidiomycetes and Microbotryomycetes were observed. These data provide direct evidence that fungal communities occur at record depths in deep sediments of the Canterbury basin and extend the depth limit of fungal presence and activity, respectively 1740 and 346mbsf. As most of the fungal sequences retrieved have a cosmopolitan distribution, it indicates that fungi are able to adapt to the deep subseafloor conditions at record-depth and must play important ecological roles in biogeochemical cycles.

Prokaryotic expression and activity identification of gene recombinant protein of brain-derivedneurotrophic factor precursor

To generate the gene recombinant protein of brain-derived neurotrophic factor precursor (proBDNF) in prokaryotic cells and investigate its biological activity. Rat-derived cDNA of proBDNF with point mutation was amplified by polymerase chain reaction (PCR) and cloned into plasmid pET-28a for expression in E. coli BL21. Western blot was used to identify the product and DAPI performed to test its effect on apoptosis of PC12 cells. PCR product of recombinant gene was successfully expressed in E. coli. And the product agreed with the target protein in molecular weight and showed reactivity with its specific antibody. Apoptosis of PC12 cells was induced by a certain concentration of recombinant proBDNF. The prokaryotic expression vector has been successfully constructed for recombinant gene of proBDNF. And the product has biological toxicity and it may induce the apoptosis of PC12 cells.

Response of under-ice prokaryotes to experimental sea-ice DOM enrichment

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 73:17-28 (2014) - DOI: https://doi.org/10.3354/ame01706 Response of under-ice prokaryotes to experimental sea-ice DOM enrichment Andrea Niemi*, Guillaume Meisterhans, Christine Michel Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada *Corresponding author: andrea.niemi@dfo-mpo.gc.ca ABSTRACT: Marine dissolved organic matter (DOM) plays a key role in the global carbon cycle. In this study we show experimentally that Arctic sea-ice DOM can stimulate prokaryotic activity when added to surface waters. Time-series and dose-response enrichment microcosm experiments were conducted, in which first-year, sea-ice DOM was added to surface waters from Resolute Passage, Canadian Arctic Archipelago. Sea-ice DOM concentrations in this productive region averaged nearly 2000 µmol l-1 in May 2011 and 2012. The abundance, activity (high [HNA] versus low [LNA] nucleic acid cells) and apparent size of surface water prokaryotes were quantified along with dissolved organic carbon (DOC) and dissolved nitrogen (DN) concentrations during the experiments. Following a 4 d lag, prokaryotic abundance increased more than 30× in the time-series enrichment experiment and the proportion of HNA cells increased from 60 to >99% of total prokaryote abundance. DOM dose-response experiments conducted in 2011 and 2012 yielded prokaryotic growth rate estimates between 0.35 and 0.67 d-1 in response to the addition of sea-ice DOM. On average, 20% of the sea-ice DOC pool was utilized by the surface water prokaryotes and the observed increase in cell abundance and individual cell size indicated a release from carbon limitation of initial in situ conditions. Prokaryotic growth yields ranged from 0.02 to 0.07 cell µmol l-1 DOC and 0.01 to 0.06 cell µmol l-1 DN and experimental conditions shifted from net autotrophic to net heterotrophic. Heterotrophic activity at the ice-water boundary layer upon the release of labile first-year ice DOM is likely to impact current and future carbon flux estimates as seasonal ice becomes the predominant ice type in the Arctic. KEY WORDS: Dissolved organic carbon · Prokaryotes · Sea ice · Melt · Heterotrophy · Arctic Full text in pdf format PreviousNextCite this article as: Niemi A, Meisterhans G, Michel C (2014) Response of under-ice prokaryotes to experimental sea-ice DOM enrichment. Aquat Microb Ecol 73:17-28. https://doi.org/10.3354/ame01706 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 73, No. 1. Online publication date: August 15, 2014 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2014 Inter-Research.

Relationships between Meiofaunal Biodiversity and Prokaryotic Heterotrophic Production in Different Tropical Habitats and Oceanic Regions

Tropical marine ecosystems are among the most diverse of the world oceans, so that assessing the linkages between biodiversity and ecosystem functions (BEF) is a crucial step to predict consequences of biodiversity loss. Most BEF studies in marine ecosystems have been carried out on macrobenthic diversity, whereas the influence of the meiofauna on ecosystem functioning has received much less attention. We compared meiofaunal and nematode biodiversity and prokaryotic heterotrophic production across seagrass, mangrove and reef sediments in the Caribbean, Celebes and Red Seas. For all variables we report the presence of differences among habitats within the same region, and among regions within the same habitat. In all regions, the richness of meiofaunal taxa in reef and seagrass sediments is higher than in mangrove sediments. The sediments of the Celebes Sea show the highest meiofaunal biodiversity. The composition of meiofaunal assemblages varies significantly among habitats in the same region. The nematode beta diversity among habitats within the same region is higher than the beta diversity among regions. Although one site per habitat was considered in each region, these results suggest that the composition of meiofaunal assemblages varies primarily among biogeographic regions, whereas the composition of nematode assemblages varies more considerably among habitats. Meiofauna and nematode biodiversity and prokaryotic heterotrophic production, even after the removal of covariate effects linked with longitude and the quantity and nutritional quality of organic matter, are positively and linearly linked both across regions and within each habitat type. Our results confirm that meiofauna and nematode biodiversity may influence benthic prokaryotic activity, which, in turn, implies that diversity loss could have negative impacts on ecosystem functioning in these systems.

Impact of water mass mixing on the biogeochemistry and microbiology of the Northeast Atlantic Deep Water

The extent to which water mass mixing contributes to the biological activity of the dark ocean is essentially unknown. Using a multiparameter water mass analysis, we examined the impact of water mass mixing on the nutrient distribution and microbial activity of the Northeast Atlantic Deep Water (NEADW) along an 8000 km long transect extending from 62°N to 5°S. Mixing of four water types (WT) and basin scale mineralization from the site where the WT where defined to the study area explained up to 95% of the variability in the distribution of inorganic nutrients and apparent oxygen utilization. Mixing-corrected average O2:N:P mineralization ratios of 127(±11):13.0(±0.7):1 in the core of the NEADW suggested preferential utilization of phosphorus compounds while dissolved organic carbon mineralization contributed a maximum of 20% to the oxygen demand of the NEADW. In conjunction with the calculated average mineralization ratios, our results indicate a major contribution of particulate organic matter to the biological activity in the NEADW. The variability in prokaryotic abundance, high nucleic acid containing cells, and prokaryotic heterotrophic production in the NEADW was explained by large scale (64-79%) and local mineralization processes (21-36%), consistent with the idea that deep-water prokaryotic communities are controlled by substrate supply. Overall, our results suggest a major impact of mixing on the distribution of inorganic nutrients and a weaker influence on the dissolved organic matter pool supporting prokaryotic activity in the NEADW.

Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.

Seasonal Dynamics of Prokaryotic Abundance and Activities in Relation to Environmental Parameters in a Transitional Aquatic Ecosystem (Cape Peloro, Italy)

This study examines the effects of temporal changes on microbial parameters in a brackish aquatic ecosystem. To this aim, the abundances of prokaryotes and vibrios together with the rates of enzymatic hydrolysis of proteins by leucine aminopeptidase (LAP), polysaccharides by β-glucosidase (GLU) and organic phosphates by alkaline phosphatase (AP), heterotrophic prokaryotic production (HPP), respiration (R), were seasonally investigated, during a 2-year period in the coastal area of Cape Peloro (Messina, Italy), constituted by two brackish lakes (Faro and Ganzirri). In addition, physical and chemical parameters (temperature, salinity, nutrients) and particulate organic carbon and nitrogen (POC, PN) were measured. The influence of multiple factors on prokaryotic abundances and activities was analysed. The results showed that Cape Peloro area is characterised by high seasonal variability of the microbial parameters that is higher than the spatial one. Combined changes in particulate matter and temperature (T), could explain the variability in vibrios abundance, GLU and R activities in both lakes, indicating a direct stimulation of the warm season on the heterotrophic prokaryotic metabolism. Positive correlations between T (from 13.3 to 29.6°C) and HPP, LAP, AP, POC, PN are also observed in Ganzirri Lake. Moreover, the trophic status index and most of the microbial parameters show significant seasonal differences. This study demonstrates that vibrios abundance and microbial activities are responsive to the spatial and seasonal changes of examined area. The combined effects of temperature and trophic conditions on the microbial parameters lead us to suggest their use as potential indicators of the prokaryotic response to climate changes in temperate brackish areas.

Large-Scale Distribution and Activity of Prokaryotes in Deep-Sea Surface Sediments of the Mediterranean Sea and the Adjacent Atlantic Ocean

The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.

Functional genes (dsr) approach reveals similar sulphidogenic prokaryotes diversity but different structure in saline waters from corroding high temperature petroleum reservoirs

Oil reservoirs and production facilities are generally contaminated with H2S resulting from the activity of sulphidogenic prokaryotes (SRP). Sulphidogenesis plays a major role in reservoir souring and microbial influenced corrosion in oil production systems. In the present study, sulphidogenic microbial diversity and composition in saline production fluids retrieved from three blocks of corroding high temperature (79 ~ 95 °C) oil reservoirs with high sulfate concentrations were investigated by phylogenetic analyses of gene fragments of the dissimilatory sulfite reductase (dsr). Analysis of dsr gene fragments revealed the presence of several clusters of sulphidogenic prokaryotes that cover the orders Desulfovibrionales (Desulfovibrio, Desulfomicrobium thermophilum), Desulfobacterales (Desulfobacterium, Desulfosarcina, Desulfococcus, Desulfotignum, Desulfobotulus, Desulfobulbus), Syntrophobacterales (Desulfacinum, Thermodesulforhabdus, Desulforhabdus), Clostridiales (Desulfotomaculum) and Archaeoglobales (Archaeoglobus); among which sequences affiliated to members of Desulfomicrobium, Desulfotomaculum and Desulfovibrio appeared to be the most encountered genera within the three blocks. Collectively, phylogenetic and non-metric multidimensional scaling analyses indicated similar but structurally different sulphidogenic prokaryotes communities within the waters retrieved from the three Blocks. This study show the diversity and composition of sulphidogenic prokaryotes that may play a role in the souring mediated corrosion of the oilfield and also provides a fundamental basis for further investigation to control oil reservoir souring and corrosion of pipelines and topside installations.

Patterns of Prokaryotic Activities and Abundance among the Epi-Meso and Bathypelagic Zones of the Southern-Central Tyrrhenian Sea

The southern- central Tyrrhenian Sea is a poorly studied area of the Mediterranean Sea, although its importance for the biological fluxes among the western and eastern basins is recognised. This note aimed at evaluating in the waters of the Southern Tyrrhenian Sea the efficiency of some steps of the organic matter processing (enzymatic hydrolysis, prokaryotic production and oxidation) and the role played by the prokaryotic community in this context. During the MEDBIO multidisciplinary cruise performed in July 2005, the distribution of prokaryotic abundance and activities (exo enzymatic activity, heterotrophic production and respiratory activity) was studied. The results showed the presence of high exo enzymatic activity rates (mostly leucine amino peptidase) in the deep sea, while heterotrophic production and respiratory activity rates were high at surface. Some speculations on the different behaviors of the Carbon fluxes occurring among the different epi, meso and bathypelagic layers are reported. At the epipelagic layer both the decomposition and biomass production processes were high. At the mesopelagic layer the organic matter was quickly mobilised but not efficiently incorporated into biomass, therefore the dissolved monomers remained available in the water column for export to other trophic levels or utilization in other chemical processes (lateral advection, oxidation). The bathypelagic layer was characterised by high levels of hydrolytic activity coupled with relatively high prokaryotic production; in this layer, exo enzymatic activity levels fall in an order of magnitude similar to that observed at the epipelagic one. This finding highlights the importance of microbially mediated processes in sustaining life in the marine depths.

Impact of aquaculture on benthic virus–prokaryote interactions in the Mediterranean Sea

We investigated the effects of organic enrichment due to the biodeposition from fish farms on benthic prokaryotic and viral abundance and production, viral-induced prokaryotic mortality, enzymatic activities and bacterial diversity. We compared four areas across the Mediterranean Sea, from Cyprus to Spain, and two different habitats: sediments covered by the seagrass Posidonia oceanica and soft-bottom unvegetated sediments. In several cases, the sediments beneath the cages showed higher prokaryotic and viral abundance and production, and higher rates of organic matter decomposition. However, the differences between impact and control sediments were not consistent at all regions and habitats. Benthic bacterial diversity was always lower below the cages, where high viral-induced bacterial mortality rates were also observed. The δ- and γ-Proteobacteria dominated in both impacted and control sediments, but the relative importance of sulphate-reducing δ-Proteobacteria increased beneath the cages. We conclude that aquaculture can have a significant impact on benthic prokaryotes and viruses, by stimulating prokaryotic metabolism and viral infections, reducing bacterial diversity and altering assemblage composition. However, these impacts vary depending upon the sediment type and the habitat characteristics.

Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments

Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 10(4)-6.47 × 10(5) copies g(-1) sediment) was always greater than that of AOA amoA gene (7.98 × 10(3)-3.51 × 10(5) copies g(-1) sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03-5.39pmol N copy(-1) day(-1)) compared with winter (0.16-0.38pmol N copy(-1) day(-1)), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons.

Prokaryotic expression and activity analysis of 5′-methylthioadenosine nucleosidase in Mycobacterium tuberculosis

Objective To clone and express of Rv0091 encoding protein in Mycobacterium tuberculosis,identify and characterize of the enzyme activities.Methods Construct the Rv0091 prokaryotic expression plasmid,the vector was transformed into E.coli strain BL21trxB.After induced by IPTG,recombinant protein was purified by Ni2+-NTA chromatography and analyzed for purity by SDS-PAGE gels stained with Coomassie Blue.Immunological activity was identified by Western blot.The recombinant protein molecular weight was identified by Mass spectrometry.The enzyme-coupled assay detectes enzyme activity.Results The expression plasmid pET32a-Rv0091 was constructed and expressed in E.coli.BL21trxB,and the optimum expression system was conformed.The purity of the recombinant protein was more than 95％.Western blot analysis confirmed that recombinant protein was one of Mycobacterium tuberculosis proteins.Mass spectrometry identified the relative molecular weight and theoretical molecular weight was basically the same.Enzyme assay showed the recombinant protein able to catalyze the substrate MTA.Enzymatic properties showed that the optimal buffer for the phosphate and Hepes buffer,the poor thermal stability of the enzyme,the optimal temperature of 37℃,optimal pH10-12,when the pH ≤7,the protein denaturation and loss of some vitality.Conclusion The recombinant protein methylthioadenosine nucleosidase(MTAN) was obtained and enzyme activity was detected and plays a key role in the metabolism of Mycobacterium tuberculosis. Key words: Mycobacterium tuberculosis; MTAN; Rv0091; Recombinant protein; Enzyme activity analysis

Free-living and particle-associated prokaryote metabolism in giant kelp forests: Implications for carbon flux in a sub-Antarctic coastal area

Extensive beds of large subtidal kelps are characteristic of many temperate and subpolar coastlines. They provide habitats for a wide range of other species and are sites of high primary production that generate large quantities of water-borne particles and dissolved organic compounds that support distinctive communities of prokaryotes. We measured prokaryotic metabolism along transects from the shore to the outside of three giant kelp forests (Macrocystis pyrifera) located in the shelf waters of the Prince Edward Islands (Southern Ocean). Abundance, heterotrophic production (PHP), respiration rates (R-ETS) and growth efficiencies (PGE) were investigated within the particle-associated (PA) and the free-living (FL) communities. Temperature, salinity and inorganic nutrient concentrations indicated distinct hydrological differences among the kelp forests that were related to different levels of freshwater input through island run-off. In contrast, detritus and particulate organic matter concentrations showed a common pattern, decreasing from the near-shore to offshore at all sampling sites, suggesting the retention of organically enriched water masses inshore of the kelp forests. While FL and PA abundances did not differ significantly along transects, FL and PA-PHP and PGE all varied significantly across the kelp forests, following the same pattern across each forest. PA-PGE was significantly higher than FL-PGE in the near-shore waters and farther offshore, while FL-PGE was higher or equal to PA-PGE inside the kelp. This shift can be interpreted in terms of gradients in both the age and origins of organic material across the kelp forests. Higher PA-PGE implies that a larger fraction of organic carbon on colonized particles is converted into prokaryotic biomass and so becomes available to higher trophic levels inshore and offshore of M. pyrifera forests than inside the kelp bed. In contrast, low PA-PGE suggests that a large quantity of carbon passes through the PA-community and is mainly respired within the kelp forest. These results suggest the retention of particles within giant kelp forests. In controlling the metabolic activity of PA and FL prokaryotes, this retention will influence overall carbon flux around the archipelago. In particular, the observation of a common pattern across different M. pyrifera forests has important implications for the role of this species as an autogenic ecological engineer in coastal environments.

Microbial Functioning and Community Structure Variability in the Mesopelagic and Epipelagic Waters of the Subtropical Northeast Atlantic Ocean

We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0 to 200 m) and mesopelagic (200 to 1,000 m) subtropical Northeast Atlantic Ocean. We selectively sampled three contrasting regions covering a wide range of surface productivity and oceanographic properties within the same basin: (i) the eddy field south of the Canary Islands, (ii) the open-ocean NE Atlantic Subtropical Gyre, and (iii) the upwelling filament off Cape Blanc. In the epipelagic waters, a high regional variation in hydrographic parameters and bacterial community structure was detected, accompanied, however, by a low variability in microbial functioning. In contrast, mesopelagic microbial functioning was highly variable between the studied regions despite the homogeneous abiotic conditions found therein. More microbial functioning parameters indicated differences among the three regions within the mesopelagic (i.e., viability of cells, nucleic acid content, cell-specific heterotrophic activity, nanoflagellate abundance, prokaryote-to-nanoflagellate abundance ratio) than within the epipelagic (i.e., bulk activity, nucleic acid content, and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the Northeast Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations.

Abundance, Diversity and Activity of Sulfate-Reducing Prokaryotes in Heavy Metal-Contaminated Sediment from a Salt Marsh in the Medway Estuary (UK)

We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50cm of the sediment core making up 22.4% of the total bacterial community and were 13.6% at 250cm deep. Gene libraries for dsrA (dissimilatory sulfite reductase α-subunit) were constructed from the heavily contaminated (heavy metals) surface sediment (top 20cm) and from the less contaminated and sulfate-depleted, deeper zone (250cm). Certain cloned sequences were similar to dsrA found in members of the Syntrophobacteraceae, Desulfobacteraceae and Desulfovibrionaceae as well as a large fraction (60%) of novel sequences that formed a deep branching dsrA lineage. Phylogenetic analysis of metabolically active SRPs was performed by reverse transcription PCR and single strand conformational polymorphism analysis (RT-PCR-SSCP) of dsrA genes derived from extracted sediment RNA. Subsequent comparative sequence analysis of excised SSCP bands revealed a high transcriptional activity of dsrA belonging to Desulfovibrio species in the surface sediment. These results may suggest that members of the Desulfovibrionaceae are more active than other SRP groups in heavy metal-contaminated surface sediments.

Biogeochemical characterization of the laminated microbialites in the Lower Devonian Kess-Kess mounds (Hamar Laghdad, Morocco)

The Kess-Kess mounds of the Hamar Laghdad Ridge, SE Morocco, are spectacular carbonate buildups because the differential erosion, highlighted their original shapes and the relationships with associated beds. The origin of these buildups is still under debate and the most consistent hypothesis is related to submarine hydrocarbon seapage or less probably to hydrothermal vents in which bacteria and/or archaea played a prominent role in the carbonate biomineralization.To investigate the traces of prokaryotic metabolic activity, which possibly caused the laminated microbialite precipitation, the research was focused on micro-nanomorphology of the very fine dark and white wrinkled laminations and biogeochemical analyses of their organic remains. Epifluorescence observations put in evidence a high organic matter content mainly in the dark laminae. The geochemical characterization of extracted organic matter was performed through the functional group analyses by FT-IR Spectroscopy. FT-IR parameters indicate a marine origin and low thermal evolution for the organic compounds. The organic matter, correlated to the fine laminated micrite, is characterized by the presence of stretching νC=C vibrations attributable to alkene and/or unsatured carboxylic acids. These organic compounds are likely to be synthesized by bacteria and/or archaea communities. Gas Cromatography-Mass Spectrometry analyses on these low thermal maturity organic matter remains will reveal specifi c bacterial/archaeal biomarkers. These data will help to identify the metabolic pathways inducing the micrite precipitation in the Kess Kess mounds.