Distribution Of Prokaryotes Research Articles

Glacier inputs influence organic matter composition and prokaryotic distribution in a high Arctic fjord (Kongsfjorden, Svalbard)

With climate change, the strong seasonality and tight pelagic-benthic coupling in the Arctic is expected to change in the next few decades. It is currently unclear how the benthos will be affected by changes of environmental conditions such as supplies of organic matter (OM) from the water column. In the last decade, Kongsfjorden (79°N), a high Arctic fjord in Svalbard influenced by several glaciers and Atlantic water inflow, has been a site of great interest owing to its high sensitivity to climate change, evidenced by a reduction in ice cover and an increase in melting freshwater. To investigate how spatial and seasonal changes in vertical fluxes can impact the benthic compartment of Kongsfjorden, we studied the organic matter characteristics (in terms of quantity and quality) and prokaryotic distribution in sediments from 3 stations along a transect extending from the glacier into the outer fjord in 4 different seasons (spring, summer, autumn and winter) in 2012–2013. The biochemical parameters used to describe the sedimentary organic matter were organic carbon (OC), total nitrogen, bulk stable isotope ratios, pigments (chorophyll-a and phaeopigments) and biopolymeric carbon (BPC), which is the sum of the main macromolecules, i.e. lipids, proteins and carbohydrates. Prokaryotic abundance and distribution were estimated by 4′,6-diamidino-2-phenylindole (DAPI) staining. This study identifies a well-marked quantitative gradient of biogenic compounds throughout all seasons and also highlights a discrepancy between the quantity and quality of sedimentary organic matter within the fjord. The sediments near the glacier were organic-poor (<0.3%OC), however the high primary productivity in the water column displayed during spring was reflected in summer sediments, and exhibited higher freshness of material at the inner station compared to the outer basin (means C-chlorophyll-a/OC ~5 and 1.5%, respectively). However, sediments at the glacier front were depleted in BPC (~0.2–0.3mgCg−1DW) by 4.5 and 9 times compared to sediments from the inner and outer stations. δ13C values in sedimentary organic matter of Kongsfjorden varied between −23.8 and −19.3‰ and reflected distinct sources of organic matter between basins. Bacterial total cell numbers in sediments of Kongsfjorden were <2×108cellsml−1 and the prokaryotic community structure was strongly influenced by the marked environmental biogenic gradients. Overall, the spatial variability prevailed over the seasonal variability in sediments of Kongsfjorden suggesting that glacier inputs prominently control the functioning of this benthic ecosystem and its communities.Regional index terms: Norway, Svalbard, Kongsfjorden.

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field.

Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.

Ultra- and microplankton assemblages as indicators of trophic status in a Mediterranean lagoon

The seasonal abundance distribution of heterotrophic prokaryotes, pico- and nanophytoplankton, was investigated in connection with environmental variables and microplankton abundance at five stations in Ghar El Melh Lagoon (northeastern Tunisia). Flow cytometry analysis of ultraplankton resolved (i) five heterotrophic prokaryote groups labelled LNA1, LNA2 (low nucleic acid content), HNA1, HNA2 and HNA3 (high nucleic acid content) and (ii) at least 14 ultraphytoplankton groups assigned to picoeukaryotes, picoprokaryotes, nanoeukaryotes, cryptophyte-like cells and some unknown communities. Redundancy analysis (RDA) revealed (i) autumn-summer outbreaks of heterotrophic prokaryotes dominated by HNA groups and (ii) winter-summer proliferation of ultraphytoplankton dominated by nanophytoplankton groups. Generalized additive models (GAM) highlighted the role of (i) water temperature and orthophosphate concentrations in heterotrophic prokaryote distribution and (ii) water temperature and salinity in ultraphytoplankton abundance variation. Based on Spearman's rank correlation, significant negative correlations were established between ultra- and microplankton communities suggesting that, through grazing pressure, microplankton may be behind the drastic decrease in ultraplankton abundances in spring.

Heterotrophic prokaryote distribution along a 2300 km transect in the North Pacific subtropical gyre during a strong La Niña conditions: relationship between distribution and hydrological conditions

Abstract. The spatial distribution of heterotrophic prokaryotes was investigated during the Tokyo–Palau cruise in the western part of the North Pacific subtropical gyre (NPSG) along a north–south transect between 33.60 and 13.25° N. The cruise was conducted in three different hydrological areas identified as the Kuroshio region, the subtropical gyre area and the transition zone. Two eddies were crossed along the transect: one cold-core cyclonic eddy and one warm-core anticyclonic eddy and distributions of the heterotrophic prokaryotes were recorded. By using analytical flow cytometry and a nucleic acid staining protocol, heterotrophic prokaryotes were discriminated into three subgroups depending on their nucleic acid content (low, high and very high nucleic acid contents labelled LNA, HNA and VHNA, respectively). Statistical analyses performed on the data set showed that LNA, mainly associated with low temperature and low salinity, were dominant in all the hydrological regions. In contrast, HNA distribution seemed to be associated with temperature, salinity, Chl a and silicic acid. A latitudinal increase in the HNA / LNA ratio was observed along the north–south transect and was related to higher phosphate and nitrate concentrations. However, the opposite relationship observed for the VHNA / HNA ratio suggested that the link between nucleic acid content and oligotrophic conditions is not linear, underlying the complexity of the biodiversity in the VHNA, HNA and LNA subgroups. In the Kuroshio Current, it is suggested that the high concentration of heterotrophic prokaryotes observed at station 4 was linked to the path of the cold cyclonic eddy core. In contrast, it is thought that low concentrations of heterotrophic prokaryotes in the warm core of the anticyclonic gyre (Sta. 9) are related to the low nutrient concentrations measured in the seawater column. Our results showed that the high variability between the various heterotrophic prokaryote cluster abundances depend both on the mesoscale structures and the oligotrophic gradient.

Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes

Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.

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.

Heterogeneous distribution of prokaryotes and viruses at the microscale in a tidal sediment

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 69:183-192 (2013) - DOI: https://doi.org/10.3354/ame01639 FEATURE ARTICLEHeterogeneous distribution of prokaryotes and viruses at the microscale in a tidal sediment Cátia Carreira1,2, Morten Larsen3,4,5, Ronnie N. Glud3,4,5,6, Corina P. D. Brussaard2, Mathias Middelboe1,* 1Section for Marine Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark 2Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO Box 50, NL 1790, AB Den Burg, The Netherlands 3Scottish Marine Institute, Scottish Association for Marine Science, Oban PA37 1QA, UK 4Institute of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, 5320 Odense M, Denmark 5Greenland Climate Research Centre (CO Greenland Institute of National resources), Kivioq 2, Box 570, 3900 Nuuk, Greenland 6Arctic Research Center, University of Aarhus, 8000 Aarhus C, Denmark *Corresponding author. Email: mmiddelboe@bio.ku.dk ABSTRACT: In this study we show for the first time the microscale (mm) 2- and 3-dimensional spatial distribution and abundance of prokaryotes, viruses, and oxygen in a tidal sediment. Prokaryotes and viruses were highly heterogeneously distributed with patches of elevated abundances surrounded by areas of ca. 3-fold lower abundance within distances of <2 mm. Abundances of prokaryotes and viruses ranged from 1.3 × 109 to 4.2 × 109 cells cm-3 and 4.1 × 109 to 13.1 × 109 viruses cm-3, respectively. The results showed oxygen concentration and uptake rates to be heterogeneously distributed at the same spatial scale, with the oxygen penetration depth varying from 1.5 to 5.8 mm and with an average (±SD) diffusive oxygen uptake of 18.9 ± 6.4 mmol m-2 d-1. Locally, prokaryotes, viruses, and oxygen were found to be positively, negatively, or not correlated, but overall no significant relationship was detected. The lack of consistent spatial correlation between viruses and prokaryotes was explained by a temporal experiment using organic carbon-enriched homogenized sediment samples. Enhancement in metabolic activity and the proliferation of prokaryotes and viruses were not completely phased. These results suggest that local nourishment is likely to be an important driver of a high small-scale heterogeneity in abundance and dynamics of benthic viruses and prokaryotes. This is expected to influence the rates and regulation of benthic virus-host interactions and thus microbial biogeochemical cycling. KEY WORDS: Spatial heterogeneity · Temporal dynamic · Hot spots · Virus–host interactions Full text in pdf format Information about this Feature Article NextCite this article as: Carreira C, Larsen M, Glud RN, Brussaard CPD, Middelboe M (2013) Heterogeneous distribution of prokaryotes and viruses at the microscale in a tidal sediment. Aquat Microb Ecol 69:183-192. https://doi.org/10.3354/ame01639Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 69, No. 3. Online publication date: June 14, 2013 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2013 Inter-Research.

Low virus to prokaryote ratios in the cold: benthic viruses and prokaryotes in a subpolar marine ecosystem (Hornsund, Svalbard).

The density and spatial distribution of benthic viruses and prokaryotes in relation to biotic and abiotic factors were investigated in sediment cores collected in Hornsund, a permanently cold fjord on the West coast of Svalbard, Norway. The cores were obtained from the mouth of the fjord to the central basin, along a longitudinal transect. The results of our analyses showed lower densities of viruses (0.2 x 10(8) to 5.4 x 10(8) virus-like particles/g) and lower virus-to-prokaryote ratios (0.2-0.6, with the exception of the uppermost layer in the central basin, where the ratio was about 1.2) at the study site than generally found in the temperate areas, despite the relatively high organic matter content in subpolar sediments. Variations in benthic viral and prokaryote abundances along gradients of particle sedimentation rates, phytopigment concentrations, and macrobenthic species composition together suggested the influence of particle sedimentation and macrobenthic bioturbation on the abundance and spatial distribution ofprokaryotes and viruses in cold habitats.

Regional Variation in Lytic and Lysogenic Viral Infection in the Southern Ocean and Its Contribution to Biogeochemical Cycling

Lytic and lysogenic viral infection was investigated throughout the Southern Ocean at sites spanning the sub-Antarctic zone, the Antarctic Circumpolar Current, and an Antarctic continental sea. Higher lytic virus activity was recorded in the more productive sub-Antarctic zone than in the iron-limited waters of the Antarctic Circumpolar Current during two transects. Reduced lytic viral activity in the Antarctic Circumpolar Current was combined with a shift toward lysogenic infection, probably resulting from the lower concentration of potential prokaryotic hosts. Superimposed on this variation, lytic viral production was lower in a transect completed in the Drake Passage in autumn (1.8 × 10(8) to 1.5 × 10(9) liter(-1) day(-1)) than over the Greenwich Meridian during summer (5.1 × 10(8) to 2.0 × 10(10) cells liter(-1) day(-1)), indicating that viral activity is linked to the overall seasonal fluctuations in biotic activity. Interestingly, while prokaryotic abundance was lowest in the coastal Weddell Sea, levels of bacterial and lytic viral production (4.3 × 10(8) to 1.7 × 10(10) cells liter(-1) day(-1)) in this area were similar to those of the other zones. This may explain the weak relationship between the distribution of prokaryotes and chlorophyll in the Weddell Sea, as a high turnover of prokaryotic biomass may have been stimulated by the availability of substrates in the form of viral lysate. With estimated carbon and iron releases of 0.02 to 7.5 μg liter(-1) day(-1) and 1.5 to 175.7 pg liter(-1) day(-1), respectively, viral activity in the Southern Ocean is shown to be a major contributor to satisfying the elemental requirements of microbes, notably prokaryotes in the Weddell Sea and phytoplankton in the sub-Antarctic zone.

Factors influencing prokaryotic community structure composition in sub-surface coastal sediments

Despite the major influence of the marine sub-surface area in carbon cycling and global biogeochemistry, there is little known of prokaryotic distribution and community structure information of the marine sub-surface and the factors that influence sub-surface prokaryotic assemblages. We provide quantitative estimations of active Bacteria and Archaea down vertical profiles of sub-surface coastal sediments from the southern Adriatic Sea (Manfredonia Gulf). Prokaryotic biomass, carbon incorporation and the metabolically active fraction were compared with environmental, trophic, and predatory variables down 100-cm sediment cores sectioned into 21 layers. Multiple regression analysis was used to identify variables that can explain the variance of community compositions down vertical profiles. CARD-FISH analysis showed Bacteria dominance for the first 11 cm below sediment surface. The community then changed significantly at increasing depth, towards Archaea dominance. The models tested show that prokaryotic abundance in superficial marine sediments is controlled by organic trophic resources, while in sub-surface sediments, active prokaryotic abundance is driven by environmental factors and predatory pressure, suggesting that the shift in prokaryotic community structure could be coupled to a change in life-style of microbial assemblages.

Large-scale distribution and production of bacterioplankton in the Adriatic Sea

Two oceanographic cruises encompassing the whole Adriatic Sea were carried out during February and October 2008. Selected stations were sampled at several depths to determine total prokaryotes and picocyanobacteria abundance using epifluorescence microscopy, and to estimate prokaryotic carbon production by 3H-leucine incorporation. Biological data were related to physical parameters including temperature, salinity and fluorescence, and an attempt to associate bacterial dynamics to water mass characteristics was performed. In both seasons prokaryotic distribution and production showed a decreasing latitudinal gradient likely dependent on riverine inputs highlighted by a strong negative correlation with salinity ( P < 0.001). A vertical gradient with higher cell numbers at the surface and lower values at the bottom layer was also always detected. In the southern basin in February, however, picocyanobacteria were retrieved also in deep waters, probably linked to higher nutrient loads carried by the Levantine Intermediate Waters and/or the deep water ventilation known to occur in this area. From an oceanographic point of view, we sampled within four different water types, but no relationship between these water types and bacterioplankton abundances was found. The present work contributes to the acquisition of a more holistic overview of prokaryotic distribution and production in the Adriatic Sea, both on a spatial and temporal scale.

DNA phosphorothioation is widespread and quantized in bacterial genomes

Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.

Paracrine and autocrine functions of the placenta: a key to the success of viviparity?

The evolution of specific nuclear transcriptional regulators has endowed tissues of the reproductive system with responsiveness to small hydrophobic compounds such as steroids. Steroids are widely distributed in Nature and their distribution in prokaryotes and eukaryotes has given rise to the concept that their hormonal role came about by target organ specialization and not by the evolution of steroids themselves. Specific nuclear receptors for progesterone in the uterus are prominent during the establishment and maintenance of pregnancy. Anti-progesterone antagonists which interfere with receptor-mediated DNA activation abrogate pregnancy and thus emphasize the functional importance of the pathways by which the effects of progesterone as an extracellular signal are transduced. Comparative studies show that progesterone itself can be ovarian or placental in origin. This seems to reflect the evolution of different mechanisms of endocrine function rather than any obvious selective advantage being associated with the source of hormone secretion. For this reason, the question of whether the endocrine function of the placenta is obligatory for the adoption of viviparity in mammals is far from certain, and should be considered as an evolutionary option rather than a sine qua non. Of growing importance is the idea that the interaction between trophoblast and endometrial cells controls the degree of invasiveness at implantation and immunoreactivity.(ABSTRACT TRUNCATED AT 250 WORDS)

Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (∼13°N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) approximately 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.

Microbial community structure along 18°W (39°N–44.5°N) in the NE Atlantic in late summer 2001 (POMME programme)

The spatial and vertical distribution of heterotrophic prokaryotes and ultraphytoplankton (< 10 μm) was investigated by flow cytometry in the NE Atlantic Ocean (Programme Océan Multidisciplinaire Méso Echelle, POMME 3 cruise, 39°N–45°N) with the aim to document the relationships between these distributions and the hydrodynamic features prevailing in the NE Atlantic. A particular interest was given to the north–south transect 18°W (12 stations) because it crossed an anticyclonic cold-core SWODDY-type eddy (slope water oceanic anticyclonic eddy) and was sampled within less than 3 days. Four ultraphytoplankton (< 10 μm) groups ( Prochlorococcus, Synechococcus, pico- and nanoeukaryotes) were distinguished by flow cytometry on the basis of their optical properties (scatter, natural fluorescence). Three heterotrophic prokaryotes groups were resolved (two High Nucleic Acid: HNA1 and HNA2 and one Low Nucleic Acid: LNA) after nucleic acid staining. Results showed significant latitudinal variations in biogeochemical parameters as well as in ultraphytoplankton and heterotrophic prokaryote distribution. The inner domain of the eddy also showed variations in heterotrophic prokaryote abundances with respect to the spring situation [Thyssen, M., Lefèvre, D., Caniaux, G., Ras, J., Dugrais, L., Fernández I.C., Denis, M., 2005. Spatial distribution of heterotrophic bacteria in the North East Atlantic (POMME study area) during spring 2001. J. Geophys. Res., 110, C07S16, doi:10.1029/2004JC002670], with higher values of HNA2 during late summer. The same trend was observed on the abundance of cyanobacteria ( Prochlorococcus, Synechococcus) and small size ultraphytoplankton. Despite the observed differences in microbial distributions inside and outside the eddy, the biological features appeared insufficient to independently characterize this anticyclonic eddy and provide information on its microbial dynamics.

Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin

The deep subseafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass therein plays an important role for potential long-term controls on global biogeochemical cycles. We report here the vertical and geographical distribution of microbes and their phylogenetic diversities in deeply buried marine sediments of the Pacific Ocean Margins. During the Ocean Drilling Program Legs 201 and 204, we obtained sediment cores from the Peru and Cascadia Margins that varied with respect to the presence of dissolved methane and methane hydrate. To examine differences in prokaryotic distribution patterns in sediments with or without methane hydrates, we studied >2,800 clones possessing partial sequences (400-500 bp) of the 16S rRNA gene and 348 representative clone sequences (approximately 1 kbp) from the two geographically separated subseafloor environments. Archaea of the uncultivated Deep-Sea Archaeal Group were consistently the dominant phylotype in sediments associated with methane hydrate. Sediment cores lacking methane hydrates displayed few or no Deep-Sea Archaeal Group phylotypes. Bacterial communities in the methane hydrate-bearing sediments were dominated by members of the JS1 group, Planctomycetes, and Chloroflexi. Results from cluster and principal component analyses, which include previously reported data from the West and East Pacific Margins, suggest that, for these locations in the Pacific Ocean, prokaryotic communities from methane hydrate-bearing sediment cores are distinct from those in hydrate-free cores. The recognition of which microbial groups prevail under distinctive subseafloor environments is a significant step toward determining the role these communities play in Earth's essential biogeochemical processes.

Laccases: structure, reactions, distribution

Laccases (EC 1.10.3.2, p-diphenol: dioxygen oxidoreductases) are multi-copper proteins that use molecular oxygen to oxidize various aromatic and non-aromatic compounds by a radical-catalyzed reaction mechanism. The enzymes are involved in the pathogenicity, immunity and morphogenesis of organisms and in the metabolic turnover of complex organic substances such as lignin or humic matter. Owing to their high non-specific oxidation capacity, laccases are useful biocatalysts for diverse biotechnological applications. Until recently, laccases were only found in eukaryotes (fungi, higher plants, insects), but now there is strong evidence for their widespread distribution in prokaryotes and the first crystal structure of a bacterial laccase is already available. Phylogenetically, laccases are members of the multi-copper protein family including ascorbate oxidase, ceruloplasmin and bilirubin oxidase.

Laccases and their occurrence in prokaryotes.

Laccases are copper-containing proteins that require O(2) to oxidize phenols, polyphenols, aromatic amines, and different non-phenolic substrates by one-electron transfer, resulting in the formation of reactive radicals. Although their specific physiological functions are not completely understood, there are several indications that laccases are involved in the morphogenesis of microorganisms (e.g., fungal spore development, melanization) and in the formation and/or degradation of complex organic substances such as lignin or humic matter. Owing to their high relative non-specific oxidation capacity, laccases are useful biocatalysts for diverse biotechnological applications. To date, laccases have been found only in eukaryotes (fungi, plants); however, databank searches and experimental data now provide evidence for their distribution in prokaryotes. This survey shows that laccase-like enzymes occur in many gram-negative and gram-positive bacteria. Corresponding genes have been found in prokaryotes that are thought to have branched off early during evolution, e.g., the extremely thermophilic Aquifex aeolicus and the archaeon Pyrobaculum aerophilum. Phylogenetically, the enzymes are members of the multi-copper protein family that have developed from small-sized prokaryotic azurins to eukaryotic plasma proteins.

Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters

After our analysis of the distribution of predicted intrinsic curvature along all available complete prokaryotic genomes, the genomes were divided into two groups. Curvature distribution in all prokaryotes of the first group indicated a substantial fraction of promoters characterized by intrinsic DNA curvature located within or upstream of the promoter region. We did not find this peculiar DNA curvature distribution in prokaryotes in the second group. Remarkably, all bacteria of the first group were mesophilic, whereas many prokaryotes of the second group were hyperthermophilic. We hypothesize that DNA curvature plays a biologic role in gene regulation in mesophilic as opposed to hyperthermophilic prokaryotes, i.e., DNA curvature presumably has a functional adaptive significance determined by temperature selection.

Specific phytoplankton signatures and their relationship to hydrographic conditions in the coastal northwestern Mediterranean Sea

Between March 1992 and April 1993, an intensive sampling program was carried out al a coastal station in the Northwestern Mediterranean Sea to study the relationship between phytoplankton distributions, as evaluated by taxonomic pigments, and the hydrographic structures of the water column. The study period covered the range of hydrographic conditions which prevail in the Mediterranean Sea. The 0 to 75 m integrated chlorophyll a concentration averaged 23.3 mg m(-2), with the highest values (above 45 mg m(-2)) restricted to semi-mixed periods. The major phytoplankton signature and water column structure relationships were: (1) phytoplanktonic prokaryotes (cyanobacteria and prochlorophytes) appear sensitive to water column mixing with prochlorophytes being the most sensitive group as strong stratification is associated with the highest biomass found mainly in deeper waters; (2) prymnesiophytes and chrysophytes (19'-BF and 19'-HF) appear the most abundant under a variety of conditions and therefore seem able to adapt to various water column structures; (3) diatoms bloom in semi-mixed conditions, but while these conditions are necessary, they are not sufficient for bloom formation; and (4) green chlorophyll b-containing flagellates appear to require strong mixing. During the stratification period, 2 noticeable wind-induced mixing events occurred, and while the first did not have any marked influence on the phytoplankton community, the second was followed by a subsurface development of green flagellates and diatoms. This second wind-mixing event also altered the vertical prokaryote distribution, but 1 wk alter this perturbation vertical segregation of prochlorophytes and cyanobacteria was reestablished. The results suggest that, while different phytoplankton taxa are generally adapted to specific water column structures, this is not always the case, especially at small scales where specific light/nutrient requirements may have to be met.