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A new component of the benthic Thioploca mat microbial ecosystem on the Chilean continental shelf was detected by epifluorescence microscopy: filamentous, bacterial endobionts of 4–5-μm filament diameter and length sometimes exceeding 1 mm. These filaments were identified as growing within Thioploca sheaths located between the sediment surface and c. 5 cm depth. Their location coincided with maximal biomass and biovolume of Thioploca filaments in surficial sediments, and with maximal abundance and activity of sulfate-reducing bacterial populations near the sediment/water interface. FISH and environmental characteristics support the working hypothesis that these endobiont populations are members of the filamentous, sulfate-reducing bacterial genus Desulfonema. Found at several sampling stations over a decade-long interval (1994–2006), these populations appear to be a stable component of the Chilean Thioploca mat ecosystem. [ABSTRACT FROM AUTHOR]

Abstract: The spatial distribution of total hydrolysable amino acids (THAA) and amino acid enantiomers (d- and l-forms) was investigated in sediments underlying two contrasting Chilean upwelling regions: at ∼23°S off Antofagasta and at ∼36°S off Concepción. The contribution of amino acids to total organic carbon (%TAAC: 7–14%) and total nitrogen (%TAAN: 23–38%) in surface sediments decreased with increasing water depth (from 126 to 1350m) indicating that organic matter becomes increasingly decomposed in surface sediments at greater water depth. Changes in the ratio between the protein amino acid aspartate and its non-protein degradation product β-alanine confirmed this observation. Furthermore, estimates of THAA mineralization showed that sedimentary amino acid reactivity decreased with both increasing water depth as well as progressive degradation status of the organic matter that was incorporated into the sediment. Reactivity of organic matter in the sediment was also assessed using the Degradation Index (DI) developed by [Dauwe, B., Middelburg, J.J., 1998. Amino acids and hexosamines as indicators of organic matter degradation state in North Sea sediments. Limnol. Oceanogr. 43, pp. 782–798.]. Off Concepción, DI was successfully applied to examine the degradation status of sedimentary organic matter at different water depths. However, unexpected results were obtained at the Antofagasta stations as DI increased with sediment depth, suggesting more degraded organic matter at the surface than deeper in the cores. The contribution of peptidoglycan amino acids to THAA was estimated from the concentrations of d-aspartate, d-glutamic acid, d-serine, and d-alanine. Peptidoglycan amino acids accounted for >18% of THAA in all investigated samples. In surface sediments peptidoglycan amino acids accounted for a progressively larger fraction of THAA at increasing water depths (up to >26%). Further, the contribution of peptidoglycan amino acids to THAA increased with increased sediment depth and age (up to 288-year-old) reaching up to 59%. Independent estimates based on d-amino acid concentrations in selected laboratory strains, bacterial counts and the sedimentary concentrations of d-amino acids indicate that a large fraction of the measured d-amino acids (>47 to >97%) originated from cell wall residues rather than from enumerated cells. [Copyright &y& Elsevier]

Pyritization in late Pleistocene sediments of the Black Sea is driven by sulfide formed during anaerobic methane oxidation. A sulfidization front is formed by the opposing gradients of sulfide and dissolved iron. The sulfidization processes are controlled by the diffusion flux of sulfide from above and by the solid reactive iron content. Two processes of diffusion-limited pyrite formation were identified. The first process includes pyrite precipitation with the accumulation of iron sulfide precursors with the average chemical composition of FeSn (n = 1.10–1.29), including greigite. Elemental sulfur and polysulfides, formed from H2S by a reductive dissolution of Fe(III)-containing minerals, serve as intermediates to convert iron sulfides into pyrite. In the second process, a “direct” pyrite precipitation occurs through prolonged exposure of iron-containing minerals to dissolved sulfide. Methane-driven sulfate reduction at depth causes a progressive formation of pyrite with a δ34S of up to +15.0‰. The S-isotopic composition of FeS2 evolves due to contributions of different sulfur pools formed at different times. Steady-state model calculations for the advancement of the sulfidization front showed that the process started at the Pleistocene/Holocene transition between 6360 and 11 600 yr BP. Our study highlights the importance of anaerobic methane oxidation in generating and maintaining S-enriched layers in marine sediments and has paleoenvironmental implications. [Copyright &y& Elsevier]

In the past, enumeration of sulphate-reducing bacteria (SRB) by cultivation-based methods generally contradicted measurements of sulphate reduction, suggesting unrealistically high respiration rates per cell. Here, we report evidence that quantification of SRB rRNA by slot-blot hybridization is a valuable tool for a more realistic assessment of SRB abundance in the natural environment. The distribution of SRB was investigated in a coastal marine sediment by hybridization of membrane-immobilized rRNA with oligonucleotide probes. As represented by general probe–target groups, SRB rRNA contributed between 18% and 25% to the prokaryotic rRNA pool. The dominant SRB were related to complete oxidizing genera (Desulphococcus , Desulphosarcina and Desulphobacterium ), while Desulphobacter could not be detected. The vertical profile and quantity of rRNA from SRB was compared with sulphate reduction rates (SRR) measured with 35 SO4 2- tracer in whole-core incubations. While SRB abundance was highest near the surface, peaking at around 1.5 cm, measured sulphate reduction rates were lowest in this region. A second peak of SRB rRNA was observed at the transition zone from oxidized to reduced sediment, directly above the sulphate reduction maximum. Cell numbers calculated by converting the relative contribution of SRB rRNA to the percentage of DAPI-stained cells indicated a population size for SRB of 2.4–6.1 × 108 cells cm-3 wet sediment. Cellular sulphate reduction rates calculated on the basis of these estimated cell numbers were between 0.01 and 0.09 fmol SO4 2- cell-1 day-1 , which is below the rates that have been determined for pure cultures (0.2–50 fmol SO4 2- cell-1 day-1 ) growing exponentially at near- optimal temperature with a surplus of substrates. [ABSTRACT FROM AUTHOR]

Dissimilatory iron reduction and sulfate reduction are the most important processes for anaerobic mineralization of organic carbon in marine sediments. The thermodynamics and kinetics of microbial Fe(III) reduction depend on the characteristics of the Fe(III) minerals, which influence the potential of Fe(III)-reducers to compete with sulfate-reducers for common organic substrates. In the present study, we tested different methods to quantify and characterize microbially reducible Fe(III) in sediments from a transect in Kongsfjorden, Svalbard, using different standard sequential endpoint extractions and time-course extractions with either ascorbate or a Fe(III)-reducing microbial culture. Similar trends of increasing 'reactive Fe' content of the sediment along the fjord transect were found using the different extraction methods. However, the total amount of 'reactive Fe' extracted differed between the methods, due to different Fe dissolution mechanisms and different targeted Fe fractions. Time-course extractions additionally provided information on the reactivity and heterogeneity of the extracted Fe(III) minerals, which also impact the favorability for microbial reduction. Our results show which fractions of the existing Fe extraction protocols should be considered 'reactive' in the sense of being favorable for microbial Fe(III) reduction, which is important in studies on early diagenesis in marine sediments. [ABSTRACT FROM AUTHOR]

Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, therewas no detectable change inmutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation. [ABSTRACT FROM AUTHOR]

The modern Baltic Sea is the world's largest anthropogenically forced anoxic basin. Using integrated geochemical records collected during Integrated Ocean Drilling Program (IODP) Expedition 347 from the deepest and one of the most reducing sub-basins in the Baltic Sea, Landsort Deep, we explore the degree and frequency of natural anoxia through the Baltic Holocene. A marked decrease in carbon-to-sulfur ratios (C/S) from the cores indicate the transition from the Baltic Ice Lake to the current brackish sea, which occurred about 8.5 kyrs B.P. Following this, laminations throughout sediments recording brackish deposition suggest sustained anoxia or extreme low oxygen, while high molybdenum (Mo) concentrations of >100 ppm and iron (Fe) geochemistry suggest water column sulfide accumulation, or euxinia, that persisted beyond seasonal timescales during deposition of two distinct sapropel units. Sedimentary Moisotope values range from +1.11 to +0.50 permil, which are distinctly fractionated from modern Baltic seawater (+2.26 to +2.67‰) and thus indicate that each of the sapropels experienced only weak and/or oscillatory euxinia--in contrast to the more stable euxinic conditions of more restricted basins. A shift in δ98Mo starting above the lower sapropel to a distinctly more negative range suggests particularly weak and oscillatory euxinia, with an enhanced contribution of manganese (Mn) redox cycling to Mo deposition relative to the lower portion of the profile. This conclusion is supported by extreme sedimentary Mn enrichments of up to 15 weight percent. We interpret the combined data to indicate episodic but major Baltic inflow events of saline and oxygenated North Sea water into the anoxic Landsort Deep that limited the concentrations and residence time of water column sulfide and caused episodic oxide deposition. Considering the temporal overlap between the most reducing conditions and periods of redox instability, we hypothesize that major Baltic inflows, as is observed today, lead to short-term instability while simultaneously supporting longer-term Baltic anoxia by strengthening the halocline. Ultimately, our results indicate that periods more reducing than the modern Baltic Sea have occurred naturally over the Holocene, but the characteristic dynamic saline inputs have historically prevented the relatively more widespread and stable anoxia observed in other classic restricted basins and will likely continue to do so. [ABSTRACT FROM AUTHOR]

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23–28 fg cell −1 and 2.3 fg cell −1 , respectively, with an estimated carbon content of 19–24 fg cell −1 . In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass. [ABSTRACT FROM AUTHOR]

Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities ( AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes ( amoA). The relative abundance of archaeal and bacterial amoA (g−1 DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to N itrososphaera and N itrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the N itrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle. [ABSTRACT FROM AUTHOR]

Abstract: In order to study bacterial activity, and turnover times of bacterial necromass and biomass in marine sediment, two stations from the Aarhus Bay, Denmark were analyzed. Sediment cores were up to 11m deep and covered a timescale from the present to ∼11,000years ago. Sediment was analyzed for total hydrolysable amino acids (THAA), total hydrolysable amino sugars, the bacterial endospore marker dipicolinic acid (DPA), and amino acid enantiomers (l- and d-form) of aspartic acid. Turnover times of bacterial necromass and vegetative cells, as well as carbon oxidation rates were estimated by use of the d:l-amino acid racemization model. Diagenetic indicators were applied to evaluate the diagenetic state of the sedimentary organic matter. The contribution of amino acids to total organic carbon, and the ratio between the amino acids aspartic acid and glutamic acid, and their respective non protein degradation products, β-alanine and γ-amino butyric acid, all indicated increasing degradation state of the organic matter with sediment depth and age. Quantification of DPA showed that endospores were abundant, and increased with depth relative to vegetative cells. Most of the amino acids (97%) could be ascribed to microbial necromass, i.e. the remains of dead bacterial cells. Model estimates showed that the turnover times of microbial necromass were in the range of 0.5–1×105 years, while turnover times of vegetative cells were in the range of tens to hundreds of years. The turnover time of the TOC pool increased with depth in the sediment, indicating that the TOC pool became progressively more refractory and unavailable to microorganisms with depth and age of the organic matter. [Copyright &y& Elsevier]

Bacterial biomarkers (D-amino acids and muramic acid) were investigated in surface sediments (0-1 cm) at 22 stations in the Peru margin. Concentrations were used to quantitatively estimate the relative importance of peptidoglycan in the preservation of prokaryotic remains during diagenesis. The bacterial imprint in organic matter was also evident from low molar ratios (average of 1.6) of glucosamine and galactosamine. Estimates of the fraction of biomarkers associated with intact peptidoglycan showed that peptidoglycan became a progressively less important component of prokaryotic remains with ongoing diagenesis, whereas other prokaryotic biomolecules increased in importance. The exact nature of these biomolecules remains unknown, but constant ratios between individual D-amino acids and amino sugars observed in this study provide novel information on their molecular composition. Examination of total hydrolyzable amino acids revealed systematic compositional changes with increasing water depth and age of the sediment, reflecting increased diagenetic alteration of the organic matter. The time scale integrated in the upper 1 cm of the sediment was ca. 2 yr at the shallow sites and up to 20 yr at the deeper stations. The alteration stages of organic matter ranged from coastal and ocean margin sediments at shallow water depth to organic matter as degraded as hemipelagic surface sediments at greater water depths. [ABSTRACT FROM AUTHOR]

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach-the d:l-amino-acid model-to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years. [ABSTRACT FROM AUTHOR]

Abstract: Carbon oxidation rates and pathways were determined in two sediments at latitude 75° and 77°N southeast of Svalbard in the northern Barents Sea. Seasonal ice cover restricts primary production to few months a year, which determines the sedimentation rate of organic material to the seafloor. At one station, with seasonally extended ice cover, low organic carbon content and sedimentation rate combined with relatively high concentrations of Mn and Fe(III) oxides favored dissimilatory Fe and Mn reduction (98% of anaerobic carbon oxidation) over sulfate reduction in the top 12cm of the sediment. In contrast, in a sediment that had not been ice covered for at least 12 months and with more organic carbon and a higher sedimentation rate, sulfate reduction was the most important anaerobic electron-accepting process (>80% of anaerobic carbon oxidation). In the upper 3cm, microbial Fe and sulfate reduction occurred simultaneously, and sulfate reduction dominated at 3–12cm. Oxygen consumption rates (1.9 and 3.7mmolm−2 d−1) and anaerobic CO2 production rates (1.3 and 6.4mmolm−2 d−1) of both stations were similar to rates from open-ocean sediments farther north in the Barents Sea but lower compared to those in fjords of Svalbard. [Copyright &y& Elsevier]

Abstract: The free energy yield of microbial respiration reactions in anaerobic marine sediments must be sufficient to be conserved as biologically usable energy in the form of ATP. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SRR) has a very low standard free energy yield of ΔG ∘ =−33kJmol−1, but the in situ energy yield strongly depends on the concentrations of substrates and products in the pore water of the sediment. In this work ΔG for the AOM–SRR process was calculated from the pore water concentrations of methane, sulfate, sulfide, and dissolved inorganic carbon (DIC) in sediment cores from different sites of the European continental margin in order to determine the influence of thermodynamic regulation on the activity and distribution of microorganisms mediating AOM–SRR. In the zone of methane and sulfate coexistence, the methane-sulfate transition zone (SMTZ), the energy yield was rarely less than −20kJmol−1 and was mostly rather constant throughout this zone. The kinetic drive was highest at the lower part of the SMTZ, matching the occurrence of maximum AOM rates. The results show that the location of maximum AOM rates is determined by a combination of thermodynamic and kinetic drive, whereas the rate activity mainly depends on kinetic regulation. [Copyright &y& Elsevier]

Abstract: The organic rich sediments of the Skagerrak contain high quantities of shallow gas of mostly biogenic origin that is transported to the sediment surface by diffusion. The sulfate methane transition zone (SMTZ), where anaerobic oxidation of methane (AOM) and sulfate reduction occur, functions as a methane barrier for this upward diffusing methane. To investigate the regulation of AOM and sulfate reduction rates (SRR) and the controls on the efficiency of methane consumption, pore water concentrations, and microbial rates of AOM, sulfate reduction and methanogenesis were determined in three gravity cores collected along the slope of the Norwegian Trench in the Skagerrak. SRR occurred in two distinct peaks, at the sediment surface and the SMTZ, the latter often exceeding the peak AOM rates that occurred at the bottom of the SMTZ. Highest rates of both AOM and SRR were observed in a core from a pockmark, where advective methane transport occurred, generating high methane and sulfate fluxes. But even at this site with a shallow SMTZ, the entire flux of methane was oxidized below the sediment surface. AOM, SRR and methanogenesis seem to be closely associated and strongly regulated by sulfate concentrations, which were, in turn, regulated by the methane flux. Rate measurements of SRR, AOM and methanogenesis revealed a tight coupling of these processes. Bicarbonate-based methanogenesis occurred at moderate sulfate concentrations (>5mM) above the AOM zone but seemed to be inhibited in the depth where AOM occurred. The unbalanced stoichiometry of AOM and SRR in the SMTZ was more pronounced in rate measurements than in methane and sulfate fluxes, and seemed more likely be related to enhanced SRR in this zone than an underestimation of methane fluxes. [Copyright &y& Elsevier]

Examining the genome of single filaments of Beggiatoa deepens our understanding of their contribution to sulfur and nitrogen cycling in marine sediments. [ABSTRACT FROM AUTHOR]

This biogeochemical, molecular genetic and lipid biomarker study of sediments (∼4 m cores) from the Skagerrak (Denmark) investigated methane cycling in a sediment with a clear sulfate-methane-transition zone (SMTZ) and where CH4 supply was by diffusion, rather than by advection, as in more commonly studied seep sites. Sulfate reduction removed sulfate by 0.7 m and CH4 accumulated below. 14C-radiotracer measurements demonstrated active H2/CO2 and acetate methanogenesis and anaerobic oxidation of CH4 (AOM). Maximum AOM rates occurred near the SMTZ (∼3 nmol cm−3 day−1 at 0.75 m) but also continued deeper, overall, at much lower rates. Maximum rates of H2/CO2 and acetate methanogenesis occurred below the SMTZ but H2/CO2 methanogenesis rates were × 10 those of acetate methanogenesis, and this was consistent with initial values of 13C-depleted CH4 (δ13C c.−80‰). Areal AOM and methanogenic rates were similar (∼1.7 mmol m−2 day−1), hence, CH4 flux is finely balanced. A 16S rRNA gene library from 1.39 m combined with methanogen (T-RFLP), bacterial (16S rRNA DGGE) and lipid biomarker depth profiles showed the presence of populations similar to some seep sites: ANME-2a (dominant), ANME-3, Methanomicrobiales, Methanosaeta Archaea, with abundance changes with depth corresponding to changes in activities and sulfate-reducing bacteria (SRB). Below the SMTZ to ∼1.7 m CH4 became progressively more 13C depleted (δ13C −82‰) indicating a zone of CH4 recycling which was consistent with the presence of 13C-depleted archaeol (δ13C −55‰). Pore water acetate concentrations decreased in this zone (to ∼5 μM), suggesting that H2, not acetate, was an important CH4 cycling intermediate. The potential biomarkers for AOM-associated SRB, non-isoprenoidal ether lipids, increased below the SMTZ but this distribution reflected 16S rRNA gene sequences for JS1 and OP8 bacteria rather than those of SRB. At this site peak rates of methane production and consumption are spatially separated and seem to be conducted by different archaeal groups. Also AOM is predominantly coupled to sulfate reduction, unlike recent reports from some seep and gassy sediment sites. [ABSTRACT FROM AUTHOR]

Increasing levels of CO2 in the atmosphere are expected to cause climatic change with negative effects on the earth's ecosystems and human society. Consequently, a variety of CO2 disposal options are discussed, including injection into the deep ocean. Because the dissolution of CO2 in seawater will decrease ambient pH considerably, negative consequences for deep-water ecosystems have been predicted. Hence, ecosystems associated with natural CO2 reservoirs in the deep sea, and the dynamics of gaseous, liquid, and solid CO2 in such environments, are of great interest to science and society. We report here a biogeochemical and microbiological characterization of a microbial community inhabiting deep-sea sediments overlying a natural CO2 lake at the Yonaguni Knoll IV hydrothermal field, southern Okinawa Trough. We found high abundances (>109 cm-3) of microbial cells in sediment pavements above the CO2 lake, decreasing to strikingly low cell numbers (107 cm-3) at the liquid CO2/CO2-hydrate interface. The key groups in these sediments were as follows: (i) the anaerobic methanotrophic archaea ANME-2c and the Eel-2 group of Deltaproteobacteria and (ii) sulfur-metabolizing chemolithotrophs within the Gamma- and Epsilonproteobacteria. The detection of functional genes related to one-carbon assimilation and the presence of highly 13C-depleted archaeal and bacterial lipid biomarkers suggest that microorganisms assimilating CO2 and/or CH4 dominate the liquid CO2 and CO2-hydrate-bearing sediments. Clearly, the Yonaguni Knoll is an exceptional natural laboratory for the study of consequences of CO2 disposal as well as of natural CO2 reservoirs as potential microbial habitats on early Earth and other celestial bodies. [ABSTRACT FROM AUTHOR]

The sub-seafloor biosphere is the largest prokaryotic habitat on Earth but also a habitat with the lowest metabolic rates. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales. [ABSTRACT FROM AUTHOR]

Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. Here, using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), we provide direct quantification of live cells as defined by the presence of ribosomes. We show that a large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (>400?m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25-22?yr, comparable to surface sediments. [ABSTRACT FROM AUTHOR]

Zooxanthellae, endosymbiotic algae of reef-building corals, substantially contribute to the high gross primary production of coral reefs, but corals exude up to half of the carbon assimilated by their zooxanthellae as mucus. Here we show that released coral mucus efficiently traps organic matter from the water column and rapidly carries energy and nutrients to the reef lagoon sediment, which acts as a biocatalytic mineralizing filter. In the Great Barrier Reef, the dominant genus of hard corals, Acropora, exudes up to 4.8 litres of mucus per square metre of reef area per day. Between 56% and 80% of this mucus dissolves in the reef water, which is filtered through the lagoon sands. Here, coral mucus is degraded at a turnover rate of at least 7% per hour. Detached undissolved mucus traps suspended particles, increasing its initial organic carbon and nitrogen content by three orders of magnitude within 2?h. Tidal currents concentrate these mucus aggregates into the lagoon, where they rapidly settle. Coral mucus provides light energy harvested by the zooxanthellae and trapped particles to the heterotrophic reef community, thereby establishing a recycling loop that supports benthic life, while reducing loss of energy and nutrients from the reef ecosystem. [ABSTRACT FROM AUTHOR]

Scalar irradiance, oxygen concentration, and oxygenic photosynthesis were measured at 0.I mm spatial resolution within the tissue of the siphonous green macroalga Codium fragile subsp. Tomentosoides (van Goor) Silva by fiber-optic scalar irradiance microsnsors and oxygen microeletrodes. The scalar irradiance of visible light was strongly attenuated in the outer 0.2 mm of the tissue but was nearly constant for the subsequent 1.0 mm of photosynthetic tissue. Far-red scalar irradiance at 750 nm in creased below the tissue surface to a maximum of 200% of incident irradiance at 1.2 mm depth due to multiple scattering in the medullary tissue. The constant intensity of visible light below 0.2 mm was thus a result of the combined effects of absorption and backscattering from the medulla. The oxygen exchanger between the alga and the surrounding water was diffusion-limited with a steep O[SUB2] gradient inside and around the alga. In darkness, the tissue below 0.6 mm became anoxic, and endophytic extracellular space provided on environment where anoxygenic microbial processes may occur. When illuminated at 160 μmol photons·m[SUP-2], O[SUB2] concentrations exceeded ambient levels throughout the thallus, with a maximum of 250% of air saturation just below the surface. The amplitude of oxygen variation was buffered by gas bubbles formed in the medullary tissue. [ABSTRACT FROM AUTHOR]