CPI, d13C, Corg and diploptene from ODP Hole 169-1034B varved sediments

Saanich Inlet has been a highly productive fjord since the last glaciation. During ODP Leg 169S, nearly 70 m of Holocene sediments were recovered from Hole 1034 at the center of the inlet. The younger sediments are laminated, anaerobic, and rich in organic material (1-2.5 wt.% Corg), whereas the older sediments below 70 mbsf are non-laminated, aerobic, with glacio-marine characteristics and have a significantly lower organic matter content. This difference is also reflected in the changes of interstitial fluids, and in biomarker compositions and their carbon isotope signals. The bacterially-derived hopanoid 17alpha(H),21beta(H)-hop-22(29)-ene (diploptene) occurs in Saanich Inlet sediments throughout the Holocene but is not present in Pleistocene glacio-marine sediments. Its concentration increases after ~6000 years BP up to present time to about 70 µg/g Corg, whereas terrigenous biomarkers such as the n-alkane C31 are low throughout the Holocene (<51 µg/g Corg) and even slightly decrease to 36 µg/g Corg at the most recent time. The increasing concentrations of diploptene in sediments younger than ~6000 years BP separate a recent period of higher primary productivity, stronger anoxic bottom waters, and higher bacterial activity from an older period with lesser activity, heretofore undifferentiated. Carbon isotopic compositions of diploptene in the Holocene are between ~31.5 and ~39.6 per mil PDB after ~6000 years BP. These differences in the carbon isotopic record of diploptene probably reflect changes in microbial community structure of bacteria living at the oxic-anoxic interface of the overlying water column. The heavier isotope values are consistent with the activity of nitrifying bacteria and the lighter isotope values with that of aerobic methanotrophic bacteria. Therefore, intermediate delta13C values probably represent mixtures between the populations. In contrast, carbon isotopic compositions of n-C31 are roughly constant at ~31.4 ± 1.1 per mil PDB throughout the Holocene, indicating a uniform input from cuticular waxes of higher plants. Prior to ~6000 years BP, diploptene enriched in 13C of up to -26.3 per mil PDB is indicative of cyanobacteria living in the photic zone and suggests a period of lower primary productivity, more oxygenated bottom waters, and hence lower bacterial activity during the earliest Holocene.

Seagrass biofilm communities at a naturally CO2-rich vent at Papua New Guinea

Seagrass meadows are a crucial component of tropical marine reef ecosystems. The seagrass plants are colonized by a multitude of epiphytic organisms that contribute to determining the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of Enhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next generation sequencing of 16S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2-impacted site compared to the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased abundance of bacterial types associated with coral diseases at the CO2-impacted site (Fusobacteria, Thalassomonas) whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E. acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios.

Geochemistry of pockmark sediments from the inner Oslofjord

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslo Fjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmark and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial surface sediment communities are affect by the water column, while the 40 cm communities are affect by local conditions within the sediment.

(Table) Bacterial counts and Fe, Mn and SO4 content in sediments and pore waters of two cores from Lake Baikal

Sediments at the bottom of Lake Baikal are mostly oxidized at their surface, and the oxidized sedimentary deposits are enriched in Fe and Mn hydroxides. The thickness of the oxidized zone of the pelagic sediments averages at 5 cm and locally reaches 10-15, occasionally exceeding 20 cm. Both the thickness of the oxidized layer and the degree of its enrichment in iron and manganese hydroxides are controlled by the depth to which oxygen can penetrate into the sedimentary deposits, which is, in turn, closely related to the sedimentation conditions in the lake (which broadly vary). The sedimentation rate far off the shores of Lake Baikal ranges from <0.02 mm/year to 1.5 mm/year, and the content of organic matter buried in the sediments varies from 0.1 to >4%. The variability of the sedimentation process makes Lake Baikal very convenient to study its diagenetic processes related to redox reactions in sediments, first of all, processes responsible for the redistribution of Fe and Mn compounds. Although the diagenetic enrichment of Fe and Ni in bottom sediments is known to be of biogenic character, very scarce information is available so far on the microorganisms involved in the redistribution of these elements in sediments in Lake Baikal, which lately led us to explore this issue in detail. Our research was centered on the role played by the microbial community in the diagenetic transformations of Fe and Mn with reference to sedimentation conditions in Lake Baikal.

Relative abundance of prokaryotic picoplankton populations in the Atlantic Ocean

Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9°S) to the UK (46.4°N) during boreal spring. Depth profiles down to 500 m at 65 stations were analysed by catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and automated epifluorescence microscopy. There was no obvious overall difference in microbial community composition between the surface water layer and the deep chlorophyll maximum (DCM) layer. There were, however, significant differences between the two photic water layers and the mesopelagic zone. SAR11 (35 ± 9%) and Prochlorococcus (12 ± 8%) together dominated the surface waters, whereas SAR11 and Crenarchaeota of the marine group I formed equal proportions of the picoplankton community below the DCM (both ~15%). However, due to their small cell sizes Crenarchaeota contributed distinctly less to total microbial biomass than SAR11 in this mesopelagic water layer. Bacteria from the uncultured Chloroflexi-related clade SAR202 occurred preferentially below the DCM (4-6%). Distinct latitudinal distribution patterns were found both in the photic zone and in the mesopelagic waters: in the photic zone, SAR11 was more abundant in the Northern Atlantic Ocean (up to 45%) than in the Southern Atlantic gyre (~25%), the biomass of Prochlorococcus peaked in the tropical Atlantic Ocean, and Bacteroidetes and Gammaproteobacteria bloomed in the nutrient-rich northern temperate waters and in the Benguela upwelling. In mesopelagic waters, higher proportions of SAR202 were present in both central gyre regions, whereas Crenarchaeota were clearly more abundant in the upwelling regions and in higher latitudes. Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance.

Geochemistry, microbiology and phospholipid fatty acid content of ODP Site 169-1036 sediments

Phospholipid fatty acids were measured in samples of 60°-130°C sediment taken from three holes at Site 1036 (Ocean Drilling Program Leg 169) to determine microbial community structure and possible community replacement at high temperatures. Five of six samples had similar concentrations of phospholipid fatty acids (2-6 pmol/g dry weight of sediment), and biomass estimates from these measurements compare favorably with direct microscopic counts, lending support to previous microscopic measures of deep sedimentary biomass. Very long-chain phospholipid fatty acids (21 to 30 carbons) were detected in the sediment and were up to half the total phospholipid fatty acid measured; they appear to increase in abundance with temperature, but their significance is not known. Community composition from lipid analysis showed that samples contained standard eubacterial membrane lipids but no detectable archaeal lipids, though archaea would be expected to dominate the samples at high temperatures. Cluster analysis of Middle Valley phospholipid fatty acid compositions shows that lipids in Middle Valley sediment samples are similar to each other at all temperatures, with the exception of very long-chain fatty acids. The data neither support nor deny a shift to a high-temperature microbial community in hot cores, so at the present time we cannot draw conclusions about whether the microbes observed in these hot sediments are active.

Environmental characteristics and gas composition of Lost Hammer, Canadian Arctic

We report the first microbiological characterization of a terrestrial methane seep in a cryo-environment in the form of an Arctic hypersaline (~24% salinity), subzero (-5 C), perennial spring, arising through thick permafrost in an area with an average annual air temperature of -15 C. Bacterial and archaeal 16S rRNA gene clone libraries indicated a relatively low diversity of phylotypes within the spring sediment (Shannon index values of 1.65 and 1.39, respectively). Bacterial phylotypes were related to microorganisms such as Loktanella, Gillisia, Halomonas and Marinobacter spp. previously recovered from cold, saline habitats. A proportion of the bacterial phylotypes were cultured, including Marinobacter and Halomonas, with all isolates capable of growth at the in situ temperature (-5 C). Archaeal phylotypes were related to signatures from hypersaline deep-sea methane-seep sediments and were dominated by the anaerobic methane group 1a (ANME-1a) clade of anaerobic methane oxidizing archaea. CARD-FISH analyses indicated that cells within the spring sediment consisted of ~84.0% bacterial and 3.8% archaeal cells with ANME-1 cells accounting for most of the archaeal cells. The major gas discharging from the spring was methane (~50%) with the low CH4/C2 + ratio and hydrogen and carbon isotope signatures consistent with a thermogenic origin of the methane. Overall, this hypersaline, subzero environment supports a viable microbial community capable of activity at in situ temperature and where methane may behave as an energy and carbon source for sustaining anaerobic oxidation of methane-based microbial metabolism. This site also provides a model of how a methane seep can form in a cryo-environment as well as a mechanism for the hypothesized Martian methane plumes.

Geochemical data from pore water and solids from cores GS08-153-91GC12 and GS08-153-53-GC6, Arctic Mid-Ocean Ridge

Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki's Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria- and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments.

PEECE II mesocosm experiment: Dynamics of extracellular enzyme activities in seawater under changed atmospheric pCO2, 2011

As part of the PeECE II mesocosm project, we investigated the effects of pCO2 levels on the initial step of heterotrophic carbon cycling in the surface ocean. The activities of microbial extracellular enzymes hydrolyzing 4 polysaccharides were measured during the development of a natural phytoplankton bloom under pCO2 conditions representing glacial (190 µatm) and future (750 µatm) atmospheric pCO2. We observed that (1) chondroitin hydrolysis was variable throughout the pre-, early- and late-bloom phases, (2) fucoidanase activity was measurable only in the glacial mesocosm as the bloom developed, (3) laminarinase activity was low and constant, and (4) xylanase activity declined as the bloom progressed. Concurrent measurements of microbial community composition, using denaturing-gradient gel electrophoresis (DGGE), showed that the 2 mesocosms diverged temporally, and from one another, especially in the late-bloom phase. Enzyme activities correlated with bloom phase and pCO2, suggesting functional as well as compositional changes in microbial communities in the different pCO2 environments. These changes, however, may be a response to temporal changes in the development of phytoplankton communities that differed with the pCO2 environment. We hypothesize that the phytoplankton communities produced dissolved organic carbon (DOC) differing in composition, a hypothesis supported by changing amino acid composition of the DOC, and that enzyme activities responded to changes in substrates. Enzyme activities observed under different pCO2 conditions likely reflect both genetic and population-level responses to changes occurring among multiple components of the microbial loop.

Empirical Evidence Reveals Seasonally Dependent Reduction in Nitrification in Coastal Sediments Subjected to Near Future Ocean Acidification

Research so far has provided little evidence that benthic biogeochemical cycling is affected by ocean acidification under realistic climate change scenarios. We measured nutrient exchange and sediment community oxygen consumption (SCOC) rates to estimate nitrification in natural coastal permeable and fine sandy sediments under pre-phytoplankton bloom and bloom conditions. Ocean acidification, as mimicked in the laboratory by a realistic pH decrease of 0.3, significantly reduced SCOC on average by 60% and benthic nitrification rates on average by 94% in both sediment types in February (pre-bloom period), but not in April (bloom period). No changes in macrofauna functional community (density, structural and functional diversity) were observed between ambient and acidified conditions, suggesting that changes in benthic biogeochemical cycling were predominantly mediated by changes in the activity of the microbial community during the short-term incubations (14 days), rather than by changes in engineering effects of bioturbating and bio-irrigating macrofauna. As benthic nitrification makes up the gross of ocean nitrification, a slowdown of this nitrogen cycling pathway in both permeable and fine sediments in winter, could therefore have global impacts on coupled nitrification-denitrification and hence eventually on pelagic nutrient availability.

Chemical and isotopic compositions of samples from the Haakon Mosby mud volcano and nearby

Authigenic carbonates in the caldera of an Arctic (72°N) submarine mud volcano with active methane-bearing fluid discharge are formed at the bottom surface during anaerobic microbial methane oxidation. The microbial community consists of specific methane-producing bacteria, which act as methanotrophic ones in conditions of excess methane, and sulfate reducers developing on hydrogen, which is an intermediate product of microbial CH4 oxidation. Isotopically light carbon (aver. d13C = -28.9 per mil) of CO2 produced during CH4 oxidation is the main carbonate carbon source. Heavy oxygen isotope ratio (aver. d18O = 5 per mil) in carbonates is inherited from seawater sulfate. Rapid sulfate reduction (up to 12 mg S/dm**3/day) results in total exhausting of sulfate ion in the upper sediment layer (10 cm). Because of this carbonates can only be formed in surface sediments near the water-bottom interface. Salinity as well as CO3/Ca and Mg/Ca ratios correspond to the field of non-magnesian calcium carbonate precipitation. Calcite is the dominant carbonate mineral in the methane seep caldera, where it occurs in the paragenetic association with barite. Radiocarbon age of carbonates is about 10 Ka.

Bacterioplankton and bacteriobenthos in surface layer waters and sediments between the Sakhalin Island and the Eastern Asia in June 2006

This work presents results of a study of plankton and benthic microbiocenoses of the Amur River estuary. It is shown that distribution of total abundance and indicator groups of bacteriobenthos are characterized by stronger heterogeneity compared with bacterioplankton and that it depends on the Amur River runoff and bottom type. The river runoff helps by increasing overall bacterioplankton abundance in the near-mouth part of the estuary. Microorganisms utilizing low concentrations of organic matter (OM) play major role in processes of OM utilization in water and bottom sediments. Saprophytic bacteria play a significant role in OM utilization only in water at certain sampling sites in the Tatarsky Strait and Sakhalin Bay and in bottom sediments sampled in the mouth part of the estuary. Some parts of the estuary subjected to organic contamination are found according to microbiological characteristics. It is shown that fluctuation of salinity leads to change of the role of bacteria with different food demands in the microbial community.

Dissolved organic matter composition derived from FT-ICR-MS analyses during HEINCKE cruise HE361

Dissolved organic matter (DOM) is the main substrate and energy source for heterotrophic bacterioplankton. To understand the interactions between DOM and the bacterial community (BC), it is important to identify the key factors on both sides in detail, chemically distinct moieties in DOM and the various bacterial taxa. Next-generation sequencing facilitates the classification of millions of reads of environmental DNA and RNA amplicons and ultrahigh-resolution mass spectrometry yields up to 10,000 DOM molecular formulae in a marine water sample. Linking this detailed biological and chemical information is a crucial first step toward a mechanistic understanding of the role of microorganisms in the marine carbon cycle. In this study, we interpreted the complex microbiological and molecular information via a novel combination of multivariate statistics. We were able to reveal distinct relationships between the key factors of organic matter cycling along a latitudinal transect across the North Sea. Total BC and DOM composition were mainly driven by mixing of distinct water masses and presumably retain their respective terrigenous imprint on similar timescales on their way through the North Sea. The active microbial community, however, was rather influenced by local events and correlated with specific DOM molecular formulae indicative of compounds that are easily degradable. These trends were most pronounced on the highest resolved level, that is, operationally defined 'species', reflecting the functional diversity of microorganisms at high taxonomic resolution.