Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain

Sulfur bacteria such as Beggiatoa or Thiomargarita have a particularly high capacity for storage because of their large size. In addition to sulfur and nitrate, these bacteria also store phosphorus in the form of polyphosphate. Thiomargarita namibiensis has been shown to release phosphate from internally stored polyphosphate in pulses creating steep peaks of phosphate in the sediment and thereby inducing the precipitation of phosphorus-rich minerals. Large sulfur bacteria populate sediments at the sites of recent phosphorite formation and are found as fossils in ancient phosphorite deposits. Therefore, it can be assumed that this physiology contributes to the removal of bioavailable phosphorus from the marine system and thus is important for the global phosphorus cycle. We investigated under defined laboratory conditions which parameters stimulate the decomposition of polyphosphate and the release of phosphate in a marine Beggiatoa strain. Initially, we tested phosphate release in response to anoxia and high concentrations of acetate, because acetate is described as the relevant stimulus for phosphate release in activated sludge. To our surprise, the Beggiatoa strain did not release phosphate in response to this treatment. Instead, we could clearly show that increasing sulfide concentrations and anoxia resulted in a decomposition of polyphosphate. This physiological reaction is a yet unknown mode of bacterial polyphosphate usage and provides a new explanation for high phosphate concentrations in sulfidic marine sediments.     

Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments

Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi, and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.     

Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis

Marine phosphate‐rich sedimentary deposits (phosphorites) are important geological reservoirs for the biologically essential nutrient phosphorous. Phosphorites first appear in abundance approximately 600 million years ago, but their proliferation at that time is poorly understood. Recent marine phosphorites spatially correlate with the habitats of vacuolated sulfide‐oxidizing bacteria that store polyphosphates under oxic conditions to be utilized under sulfidic conditions. Hydrolysis of the stored polyphosphate results in the rapid precipitation of the phosphate‐rich mineral apatite—providing a mechanism to explain the association between modern phosphorites and these bacteria. Whether sulfur bacteria were important to the formation of ancient phosphorites has been unresolved. Here, we present the remains of modern sulfide‐oxidizing bacteria that are partially encrusted in apatite, providing evidence that bacterially mediated phosphogenesis can rapidly permineralize sulfide‐oxidizing bacteria and perhaps other types of organic remains. We also describe filamentous microfossils that resemble modern sulfide‐oxidizing bacteria from two major phosphogenic episodes in the geologic record. These microfossils contain sulfur‐rich inclusions that may represent relict sulfur globules, a diagnostic feature of modern sulfide‐oxidizing bacteria. These findings suggest that sulfur bacteria, which are known to mediate the precipitation of apatite in modern sediments, were also present in certain phosphogenic settings for at least the last 600 million years. If polyphosphate‐utilizing sulfide‐oxidizing bacteria also played a role in the formation of ancient phosphorites, their requirements for oxygen, or oxygen‐requiring metabolites such as nitrate, might explain the temporal correlation between the first appearance of globally distributed marine phosphorites and increasing oxygenation of Neoproterozoic oceans.     

Lithotrophic and Heterotrophic Bacteria in Deep Subsurface Sediments and Their Relation to Sediment Properties

Subsurface sediments obtained from three cores drilled to depths of 260 m below the surface in South Carolina were analyzed for heterotrophic bacteria; N₂‐fixing microaerophiles; and nitrifying, sulfur‐oxidizing, and H₂‐oxidizing lithotrophic bacteria. In addition, pore waters were extracted for chemical analysis of inorganic nitrogen species, sulfate, dissolved organic carbon, pH, and Eh. Autotroph populations were generally less than 10³ most probable number (MPN) g^‐1 dry sediment with sulfur‐oxidizing bacteria, detected in 60% of the sediment samples, being the most frequently encountered group. Nitrifying bacteria were detected mainly in sediments from one borehole (P28), and their populations in those sediments were correlated with pore‐water ammonium concentrations. Populations of heterotrophic bacteria in 60% of the sediments were greater than 10⁶ colony forming units (CFU) g^‐1 dry sediment and were typically lower in sediments of high clay content and low pH. Microaerophilic N₂‐fixing bacteria were cultured from >50% and bacteria capable of growth on H₂ were cultured from 35% of the subsurface sediments examined. Sediment texture, which controls porosity, water potential, and hydraulic conductivity, appears to be a major factor influencing microbial populations in coastal plain subsurface sediments.     

Site-specific microbial communities in three PCB-impacted sediments are associated with different in situ dechlorinating activities

Competitive PCR and denaturing HPLC analyses together with an assay detecting potential polychlorinated biphenyl (PCB) dechlorinating activities were combined with physical-chemical site characterizations to identify factors affecting the reductive dechlorination of PCBs in the three historically impacted sediments: Grasse and Buffalo Rivers, NY and Anacostia River, DC. In Grasse River sediment an in situ enriched population of Dehalococcoides phylotypes was abundant in high numbers together with a relatively high dechlorination activity and a high concentration of congeners containing unflanked chlorine substitutions. In contrast microbial communities in Anacostia and Buffalo Rivers sediments consisted of similar total numbers of putative dechlorinating bacteria, but the populations consisted of more diverse putative dechlorinating phylotypes and were associated with lower dechlorination activities and higher concentrations of flanked congeners. Differences observed in the PCB dechlorination activity were not influenced by the chemical PCB availability in spiked sediment or physical sediment characteristics, but were consistent with the concentration of PCBs and total organic carbon in the native sediment. Application of molecular methods for selective detection of indigenous microbial dechlorinating communities combined with assessment of the dechlorinating activity and analysis of the in situ congener profiles provided a comprehensive approach for characterization and identification of sites that are amenable to bioremediation, which is essential for the development of in situ treatment strategies.     

Species inventory and the local uses of the plants and fishes of the Lower Sondu Miriu wetland of Lake Victoria,Kenya

The release of phosphate from anoxic sediments is still not precisely understood. The proposal by Einsele (1936), later adapted by Mortimer (1941, 1942), that this release is caused by the reduction of a FeOOH-phosphate complex, is generally accepted as the reaction mechanism, although there is no experimental evidence for it. Golterman (1995a) and De Groot (1991) have shown that this P-release may indeed be brought about by H₂S, but only if a large excess of H₂S is available. In lakes, however, the reducing capacity is relatively small as most of the organic carbon produced by primary production is used for other reduction processes. The solubilization of apatite is a likely alternative, as anoxic conditions are automatically concomitant with a pH decrease, and in hard waters the formation of apatite is well demonstrated. This mechanism is not active in soft waters, such as those studied by Mortimer. Another proposed process is the release of polyphosphate by sediment bacteria. Experimental evidence for this mechanism is, however, weak. The fourth possibility is the need for bacteria to mineralize a larger part of the sediment organic matter under anoxic conditions in order to obtain the same amount of energy, as some energy will be retained in the fermentation products. There is circumstantial evidence for this hypothesis, but laboratory experiments are needed before real evidence will be available.     

Phosphogenesis in the 2460 and 2728 million‐year‐old banded iron formations as evidence for biological cycling of phosphate in the early biosphere

The banded iron formation deposited during the first 2 billion years of Earth's history holds the key to understanding the interplay between the geosphere and the early biosphere at large geological timescales. The earliest ore‐scale phosphorite depositions formed almost at ~2.0–2.2 billion years ago bear evidence for the earliest bloom of aerobic life. The cycling of nutrient phosphorus and how it constrained primary productivity in the anaerobic world of Archean–Palaeoproterozoic eons are still open questions. The controversy centers about whether the precipitation of ultrafine ferric oxyhydroxide due to the microbial Fe(II) oxidation in oceans earlier than 1.9 billion years substantially sequestrated phosphate, and whether this process significantly limited the primary productivity of the early biosphere. In this study, we report apatite radial flowers of a few micrometers in the 2728 million‐year‐old Abitibi banded iron formation and the 2460 million‐year‐old Kuruman banded iron formation and their similarities to those in the 535 million‐year‐old Lower Cambrian phosphorite. The lithology of the 535 Million‐year‐old phosphorite as a biosignature bears abundant biomarkers that reveal the possible similar biogeochemical cycling of phosphorus in the Later Archean and Palaeoproterozoic oceans. These apatite radial flowers represent the primary precipitation of phosphate derived from the phytoplankton blooms in the euphotic zones of Neoarchean and Palaoeproterozoic oceans. The unbiased distributions of the apatite radial flowers within sub‐millimeter bands do not support the idea of an Archean Crisis of Phosphate. This is the first report of the microbial mediated mineralization of phosphorus before the Great Oxidation Event when the whole biosphere was still dominated by anaerobic microorganisms.     

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by pyrosequencing 16S rRNA V4‐region gene fragments obtained by PCR amplification of community genomic DNA with bacterial‐ or archaeal‐specific primers. Duplicate LCS sediment cores collected during hypoxia had higher concentrations of Fe(II), and dissolved inorganic carbon, phosphate, and ammonium than cores collected when overlying water oxygen concentrations were normal. Pyrosequencing yielded 158 686 bacterial and 225 591 archaeal sequences from 20 sediment samples, representing five 2‐cm depth intervals in the duplicate cores. Bacterial communities grouped by sampling date and sediment depth in a neighbor‐joining analysis using Chao–Jaccard shared species values. Redundancy analysis indicated that variance in bacterial communities was mainly associated with differences in sediment chemistry between oxic and hypoxic water column conditions. Gammaproteobacteria (26.5%) were most prominent among bacterial sequences, followed by Firmicutes (9.6%), and Alphaproteobacteria (5.6%). Crenarchaeotal, thaumarchaeotal, and euryarchaeotal lineages accounted for 57%, 27%, and 16% of archaeal sequences, respectively. In Thaumarchaeota Marine Group I, sequences were 96–99% identical to the Nitrosopumilus maritimus SCM1 sequence, were highest in surficial sediments, and accounted for 31% of archaeal sequences when waters were normoxic vs. 13% of archaeal sequences when waters were hypoxic. Redundancy analysis showed Nitrosopumilus‐related sequence abundance was correlated with high solid‐phase Fe(III) concentrations, whereas most of the remaining archaeal clusters were not. In contrast, crenarchaeotal sequences were from phylogenetically diverse lineages, differed little in relative abundance between sampling times, and increased to high relative abundance with sediment depth. These results provide further evidence that marine sediment microbial community composition can be structured according to sediment chemistry and suggest the expansion of hypoxia in coastal waters may alter sediment microbial communities involved in carbon and nitrogen cycling.     

Microbial communities of the discharge zone of oil- and gas-bearing fluids in low-mineral Lake Baikal

At the site of natural ingress of oil, microbial diversity in the Central Baikal bottom sediments differing in the chemical composition of pore waters was studied by molecular biological techniques. The sediments saturated with oil and methane were found to contain members of 10 bacterial and 2 archaeal phyla. The oxidized sediment layer contained methanotrophic bacteria belonging to the Alphaproteobacteria, which had a specific structure of the pmoA gene and clustered together with uncultured methanotrophs from cold ecosystems. The upper sediment layer also contained oil-oxidizing bacteria and the alkB genes most closely related to those of Rhodococcus. The microbial community of reduced sediments exhibited lower diversity and was represented mostly by the organisms involved in hydrocarbon biodegradation.     

Entrapment of pollutants in Mediterranean sediments and biogeochemical indicators of their impact

The transit and fate of certain pollutants (Cd, Pb, Zn and P) transported to the western Mediterranean sea-floor and a method to assess their impact are described. The spatial distribution of pollutant concentrations in the Rhône prodelta shows that their decline with distance from their source is due both to mixing with unpolluted sediments, release from contaminated particles during transit and release from sediments after deposition. Beyond the continental shelf, metals of anthropogenic origin, mainly incorporated in faecal pellets, sink and become entrapped in deep sea sediments. Because subsaturating concentrations of trace metals are often found in surface pore waters and storage, therefore, still occurs, co-precipitation with other metal ions existing in slightly supersaturated states has also to be considered. Although phosphate tends to precipitate as apatite after entering sea water, its `definitive' storage in sediments is hindered by certain forms of pollution. Low pH and reducing conditions in sediments enhance phosphate release to the overlying water . Eutrophication may then occur in localised areas. The effects of urban waste water contamination on biogeochemical processes in sediments are examined, in particular processes responsible for the transformation of organic nitrogen. Sediment quality appears to be better defined by the effectiveness of diagenetic processes than by pollutant concentration per se. In general, polluted sediments possess weak capacities to transform organic nitrogen relative to the quantities of organic matter that are available. Such sediment characteristics are indicated by the preferential growth of Caulerpa taxifolia over that of Posidonia oceanica.     

The influence of the Benguela upwelling system on Namibia's marine biodiversity

Namibia's marine environment falls within the Benguela system, an eastern boundary current upwelling system in the south eastern Atlantic Ocean. Conditions within much of this environment change continuously as a consequence of the upwelling of nutrient-rich water into the surface zone. In addition, irregular anomalies in temperature, oxygen concentration and salinity occur, particularly in shelf waters. These fluctuations, which are inherent in the functioning of the Benguela system, tend to favour the persistence of few, generalist species, while at the same time high productivity supports large abundances. This trend is evident in all the major marine habitats off Namibia, where diversity is often lower than in comparable habitats in the southern Benguela system off the west coast of South Africa. Namibia's marine environment is considered 'relatively pristine', although threats to biodiversity are posed by both natural and anthropogenic phenomena.     

Bacterial diversity in organically-enriched fish farm sediments

The bacterial diversity and community structure within both organically enriched and adjacent, unimpacted, near-shore marine sediments at two fish farms in southern Tasmania, Australia, was examined using 16S rRNA gene clone library construction and analysis. Sediments at both caged and reference sites at both farms showed a very high level of microbial diversity. Over 900 clones were analysed and grouped into 631 unique phylotypes. Reference sites were dominated by Delta- and Gammaproteobacteria and the Cytophaga-Flavobacteria-Bacteroides group. Cage site sediments were also dominated by these phylotypes, as well as members of the Alpha- and Epsilonproteobacteria. Diversity and coverage indices indicated that the actual diversity of the sediments was much greater than that detected, despite a large sampling effort. All libraries were shown to be statistically different from one another (P < 0.05). Many phylotypes did not group with cultured bacteria, but grouped with other environmental clones from a wide array of marine benthic environments. Diversity and evenness indices suggested that although both parameters changed after farming, diverse communities were present in all sediments. The response of the microbial community to organic load suggested that random, rather than predictable, succession events determine community composition and diversity, and that sediment type may influence bacterial community and sediment response to organic perturbation.     

Speciation and bioavailability of zinc in amended sediments

Abstract

The speciation and bioavailability of zinc (Zn) in smelter-contaminated sediments were investigated as a function of phosphate (apatite) and organic amendment loading rate. Zinc species identified in preamendment sediment were zinc hydroxide-like phases, sphalerite, and zinc sorbed to an iron oxide via X-ray adsorption near edge structure (XANES) spectroscopy. Four months after adding the amendments to the contaminated sediment, hopeite, a Zn phosphate mineral, was identified indicating phosphate was binding and sequestering available Zn and Zn pore water concentrations were decreased at levels of 90% or more. Laboratory experiments indicate organic amendments exhibit a limited effect and may hinder sequestration of pore water Zn when mixed with apatite. The acute toxicity of the sediment Zn was evaluated with Hyalella azteca, and bioaccumulation of Zn with Lumbriculus variegates. The survivability of H. azteca increased as a function of phosphate (apatite) loading rate. In contaminated sediment without apatite, no specimens of H. azteca survived. The bioaccumulation of Zn in L. variegates also followed a trend of decreased bioaccumulation with increased phosphate loading in the contaminated sediment. The research supports an association between Zn speciation and bioavailability.     

The microbial composition of three limnologically disparate hypersaline Antarctic lakes

16S rRNA clone library analysis was used to examine the biodiversity and community structure within the sediments of three hypersaline Antarctic lakes. Compared to sediment of low to moderate salinity Antarctic lakes the species richness of the hypersaline lake sediments was 2-20 times lower. The community of Deep Lake (32% salinity, average sediment temperature -15 degrees C) was made up almost entirely of halophilic Archaea. The sediment communities of two meromictic hypersaline lakes, Organic Lake (20% salinity, -7 degrees C) and Ekho Lake (15% salinity, 15 degrees C) were more complex, containing phylotypes clustering within the Proteobacteria and Cytophagales divisions and with algal chloroplasts. Many phylotypes of these lakes were related to taxa more adapted to marine-like salinity and perhaps derive from bacteria exported into the sediment from the lower salinity surface waters. The Ekho Lake clone library contained several major phylotypes related to the Haloanaerobiales, the growth of which appears to be promoted by the comparatively high in situ temperature of this lake.     

Dinoflagellate cyst distribution along a shelf to slope transect of an oligotrophic tropical sea (Sunda Shelf, South China Sea)

From 51 surface samples collected along a shelf to slope transect of the Sunda Shelf, South China Sea, 36 taxa of organic‐walled dinoflagellate cysts are identified. Oligotrophic tropical shelf assemblages on the Sunda Shelf are dominated by gonyaulacoids such as Spiniferites species, Operculodinium centmcarpum and Operculodinium israelianum. Concentrations of dinoflagellate cysts in the shelf sediments are generally low and correlate well with the content of fine‐grained (clay and silt fraction) sediments. Detailed comparisons of sediment grain‐size distributions to concentrations of dominant dinoflagellate taxa (Spiniferites species, 0. centmcarpum and 0. israelianum) in the shelf sediments indicate that these taxa behave in water like sediment particles with size range φ 5.75–6.25 (13–18 μm). In contrast, slope assemblages in fine‐grained sediments are dominated by protoperidinioids. This may reflect higher nutrient availability as a result of weak winter upwelling. The concentrations of dinoflagellate cysts in the shelf sediments are mainly controlled by transport and winnowing processes and are probably not representative of surface water conditions.     

Metabolically active microbial communities in uranium-contaminated subsurface sediments

In order to develop effective bioremediation strategies for radionuclide contaminants, the composition and metabolic potential of microbial communities need to be better understood, especially in highly contaminated subsurface sediments for which little cultivation-independent information is available. In this study, we characterized metabolically active and total microbial communities associated with uranium-contaminated subsurface sediments along geochemical gradients. DNA and RNA were extracted and amplified from four sediment-depth intervals representing moderately acidic (pH 3.7) to near-neutral (pH 6.7) conditions. Phylotypes related to Proteobacteria (Alpha-, Beta-, Delta- and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Firmicutes and Planctomycetes were detected in DNA- and RNA-derived clone libraries. Diversity and numerical dominance of phylotypes were observed to correspond to changes in sediment geochemistry and rates of microbial activity, suggesting that geochemical conditions have selected for well-adapted taxa. Sequences closely related to nitrate-reducing bacteria represented 28% and 43% of clones from the total and metabolically active fractions of the microbial community, respectively. This study provides the first detailed analysis of total and metabolically active microbial communities in radionuclide-contaminated subsurface sediments. Our microbial community analysis, in conjunction with rates of microbial activity, points to several groups of nitrate-reducers that appear to be well adapted to environmental conditions common to radionuclide-contaminated sites.     

Biodiversity, Community Structural Shifts, and Biogeography of Prokaryotes within Antarctic Continental Shelf Sediment

16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r-strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically divergent phylotypes and a decline in the predominance of Proteobacteria. Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity (>95%) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment.     

Organic geochemical changes in Pliocene sediments of ODP Site 1083 (Benguela Upwelling System)

The intensification of the Northern Hemisphere Glaciation (INHG) was a major event in the development of the current climate state, and as one of the most productive regions in the world's oceans, the behaviour of the Benguela Upwelling System (BUS) following the INHG is of wide interest. To investigate post-INHG changes in productivity and organic matter accumulation, total organic carbon and biomarker accumulation rates were determined for sediments from ODP Site 1083 and compared to alkenone-derived sea surface temperatures and nitrogen isotopic compositions. These data indicate that the interval between 2.6 and 2.4 Ma was characterized by dramatic changes in upwelling intensity and organic carbon export on the northern edge of the modern BUS. The upwelling is reflected by significant changes in alkenone-derived SST estimates between glacial and interglacial intervals, with a total variability of 16 °C. The studied interval is also characterized by large changes in organic matter export as reflected by changes in TOC and biomarker accumulation rates, which show maxima during OIS 98 and during the transition from OIS 97 to 96. Intervals of elevated TOC are also characterized by elevated concentrations of sedimentary microbial biomarkers and lower %CaCO₃, suggesting that enhanced delivery of labile organic matter to the seafloor resulted in enhanced remineralisation with released CO₂ being consumed by CaCO₃ dissolution. However, in apparent contrast to recent Pleistocene sediments at the same site, organic matter export after the INHG was not solely driven by upwelling intensity. Of the three Pliocene glacial–interglacial cycles examined (OIS 101 to 96), each is unique with respect to the timing and magnitude of changes in organic matter accumulation. Each is also characterized by different algal assemblages as inferred from biomarker distributions, with OIS 97 and 96 particularly dominated by diatoms. We suggest that these differences reflect the important but evolving role of Southern Ocean waters in the Pliocene BUS: nutrient depletion of SO waters occurred during parts of Pliocene glacial intervals such that even intense upwelling did not persistently result in enhanced organic matter accumulation rates.     

Biodiversity,community structural shifts,and biogeography of prokaryotes within Antarctic continental shelf sediment

16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r-strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically divergent phylotypes and a decline in the predominance of Proteobacteria. Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity (>95%) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment.     

Spatial variability of sulfate reduction in a shallow aquifer

The distribution and metabolic activity of sulfate-reducing bacteria (SRB) in a shallow, suboxic aquifer were studied. A radioimaging technique was used to visualize and quantify the activity of sulfate reducers in sediments at a centimetre-level scale. The distribution of SRB metabolic activity was heterogeneous with areas showing little activity far outnumbering areas with high activity. Variation in sulfate-reducing activity was not statistically correlated with variation in depth, bacterial numbers, or the following sediment properties: sediment type (sand, peat or silt), grain size, permeability and hydraulic conductivity. Sulfate-reducing bacteria activity did vary significantly with sediment porosity (multivariate analysis, r = 0.48). We hypothesized that the small pore sizes associated with sediments with low porosity restricted the ability of SRB to grow to high numbers as well as their access to nutrients. To further explore the relationship between pore size and microbial metabolic activity, columns with varying pore diameters were constructed. Sulfate-reducing bacteria in the columns with the smallest pore diameters had the lowest rates of metabolism and SRB metabolic rates increased as the pore diameter increased. For the aquifer studied, sediment porosities and pore sizes were the main factor controlling SRB activity.