Oxic Surface Layer Research Articles

Differential assemblage of functional units in paddy soil microbiomes.

Flooded rice fields are not only a global food source but also a major biogenic source of atmospheric methane. Using metatranscriptomics, we comparatively explored structural and functional succession of paddy soil microbiomes in the oxic surface layer and anoxic bulk soil. Cyanobacteria, Fungi, Xanthomonadales, Myxococcales, and Methylococcales were the most abundant and metabolically active groups in the oxic zone, while Clostridia, Actinobacteria, Geobacter, Anaeromyxobacter, Anaerolineae, and methanogenic archaea dominated the anoxic zone. The protein synthesis potential of these groups was about 75% and 50% of the entire community capacity, respectively. Their structure-function relationships in microbiome succession were revealed by classifying the protein-coding transcripts into core, non-core, and taxon-specific transcripts based on homologous gene distribution. The differential expression of core transcripts between the two microbiomes indicated that structural succession is primarily governed by the cellular ability to adapt to the given oxygen condition, involving oxidative stress, nitrogen/phosphorus metabolism, and fermentation. By contrast, the non-core transcripts were expressed from genes involved in the metabolism of various carbon sources. Among those, taxon-specific transcripts revealed highly specialized roles of the dominant groups in community-wide functioning. For instance, taxon-specific transcripts involved in photosynthesis and methane oxidation were a characteristic of the oxic zone, while those related to methane production and aromatic compound degradation were specific to the anoxic zone. Degradation of organic matters, antibiotics resistance, and secondary metabolite production were detected to be expressed in both the oxic and anoxic zones, but by different taxonomic groups. Cross-feeding of methanol between members of the Methylococcales and Xanthomonadales was suggested by the observation that in the oxic zone, they both exclusively expressed homologous genes encoding methanol dehydrogenase. Our metatranscriptomic analysis suggests that paddy soil microbiomes act as complex, functionally coordinated assemblages whose taxonomic composition is governed by the prevailing habitat factors and their hierarchical importance for community succession.

Trace metal behavior along fluvio-marine gradients in the Samborombón Bay, outer Río de la Plata estuary, Argentina

Water and sediment samples were collected in the Samborombón Bay, outer Río de la Plata estuary to evaluate the dynamics of trace metals along the fluvial–marine transition. This estuarine environment presented strong salinity (0.11–31.4) and turbidity (21 to >999mgL−1) gradients with a consistent turbidity maximum zone (TMZ:>1g suspended solids L−1) in the low salinity region. Suspended particulate metals showed different spatial patterns: homogeneous distributions (Fe, Zn) and progressive enrichment from the TMZ to the maritime area (Cu, Ni). The influence of the TMZ is clearly reflected by the enrichment of flocculated clays which in turns control the distribution of sedimentary TOC and trace metals resulting in a prevailing decreasing land–sea gradient. Mn has a particular behavior along the salinity gradient denoting intense dissolved-particulated phase changes both in the water column and bottom sediments. An average 36% drop of particulate Mn observed in parallel with a strong dissolved peak suggests a rapid Mn desorption/dissolution in the water column whereas bottom sediments display an average 72% Mn enrichment in the TMZ relative to the riverine sector reflecting the diffusive escape from anoxic sediments and reprecipitation in oxic surface layers.

No Nitrification in Lakes Below pH 3

Lakes affected by acid mine drainage (AMD) or acid rain often contain elevated concentrations of ammonium, which threatens water quality. It is commonly assumed that this is due to the inhibition of microbial nitrification in acidic water, but nitrification was never directly measured in mine pit lakes. For the first time, we measured nitrification by (15)NH4Cl isotope tracer addition in acidic as well as neutral mine pit lakes in Spain and Germany. Nitrification activity was only detected in neutral lakes. In acidic lakes no conversion of (15)NH4(+) to (15)NO3(-) was observed. This was true both for the water column as well as for biofilms on the surface of macrophytes or dead wood and the oxic surface layer of the sediment. Stable isotope analysis of nitrate showed (18)O values typical for nitrification only in neutral lakes. In a comparison of NH4(+) concentrations in 297 surface waters with different pH, ammonium concentrations higher 10 mg NH4-N L(-1) were only observed in lakes below pH 3. On the basis of the results from stable isotope investigations and the examination of a metadata set we conclude that the lower limit for nitrification in lakes is around pH 3.

Source identification of nitrous oxide on autotrophic partial nitrification in a granular sludge reactor

Emission of nitrous oxide (N2O) during biological wastewater treatment is of growing concern since N2O is a major stratospheric ozone-depleting substance and an important greenhouse gas. The emission of N2O from a lab-scale granular sequencing batch reactor (SBR) for partial nitrification (PN) treating synthetic wastewater without organic carbon was therefore determined in this study, because PN process is known to produce more N2O than conventional nitrification processes. The average N2O emission rate from the SBR was 0.32 ± 0.17 mg-N L−1 h−1, corresponding to the average emission of N2O of 0.8 ± 0.4% of the incoming nitrogen load (1.5 ± 0.8% of the converted NH4+). Analysis of dynamic concentration profiles during one cycle of the SBR operation demonstrated that N2O concentration in off-gas was the highest just after starting aeration whereas N2O concentration in effluent was gradually increased in the initial 40 min of the aeration period and was decreased thereafter. Isotopomer analysis was conducted to identify the main N2O production pathway in the reactor during one cycle. The hydroxylamine (NH2OH) oxidation pathway accounted for 65% of the total N2O production in the initial phase during one cycle, whereas contribution of the NO2− reduction pathway to N2O production was comparable with that of the NH2OH oxidation pathway in the latter phase. In addition, spatial distributions of bacteria and their activities in single microbial granules taken from the reactor were determined with microsensors and by in situ hybridization. Partial nitrification occurred mainly in the oxic surface layer of the granules and ammonia-oxidizing bacteria were abundant in this layer. N2O production was also found mainly in the oxic surface layer. Based on these results, although N2O was produced mainly via NH2OH oxidation pathway in the autotrophic partial nitrification reactor, N2O production mechanisms were complex and could involve multiple N2O production pathways.

Iron traps terrestrially derived dissolved organic matter at redox interfaces

Reactive iron and organic carbon are intimately associated in soils and sediments. However, to date, the organic compounds involved are uncharacterized on the molecular level. At redox interfaces in peatlands, where the biogeochemical cycles of iron and dissolved organic matter (DOM) are coupled, this issue can readily be studied. We found that precipitation of iron hydroxides at the oxic surface layer of two rewetted fens removed a large fraction of DOM via coagulation. On aeration of anoxic fen pore waters, >90% of dissolved iron and 27 ± 7% (mean ± SD) of dissolved organic carbon were rapidly (within 24 h) removed. Using ultra-high-resolution MS, we show that vascular plant-derived aromatic and pyrogenic compounds were preferentially retained, whereas the majority of carboxyl-rich aliphatic acids remained in solution. We propose that redox interfaces, which are ubiquitous in marine and terrestrial settings, are selective yet intermediate barriers that limit the flux of land-derived DOM to oceanic waters.

Sulphur compounds, methane, and phytoplankton: interactions along a north–south transit in the western Pacific Ocean

Abstract. Here we present results of the first comprehensive study of sulphur compounds and methane in the oligotrophic tropical western Pacific Ocean. The concentrations of dimethylsuphide (DMS), dimethylsulphoniopropionate (DMSP), dimethylsulphoxide (DMSO), and methane (CH4), as well as various phytoplankton marker pigments in the surface ocean were measured along a north–south transit from Japan to Australia in October 2009. DMS (0.9 nmol L−1), dissolved DMSP (DMSPd, 1.6 nmol L−1) and particulate DMSP (DMSPp, 2 nmol L−1) concentrations were generally low, while dissolved DMSO (DMSOd, 4.4 nmol L−1) and particulate DMSO (DMSOp, 11.5 nmol L−1) concentrations were comparably enhanced. Positive correlations were found between DMSO and DMSP as well as DMSP and DMSO with chlorophyll a, which suggests a similar source for both compounds. Similar phytoplankton groups were identified as being important for the DMSO and DMSP pool, thus, the same algae taxa might produce both DMSP and DMSO. In contrast, phytoplankton seemed to play only a minor role for the DMS distribution in the western Pacific Ocean. The observed DMSPp : DMSOp ratios were very low and seem to be characteristic of oligotrophic tropical waters representing the extreme endpoint of the global DMSPp : DMSOp ratio vs SST relationship. It is most likely that nutrient limitation and oxidative stress in the tropical western Pacific Ocean triggered enhanced DMSO production leading to an accumulation of DMSO in the sea surface. Positive correlations between DMSPd and CH4, as well as between DMSO (particulate and total) and CH4, were found along the transit. We conclude that DMSP and DMSO and/or their degradation products might serve as potential substrates for CH4 production in the oxic surface layer of the western Pacific Ocean.

Pyrite morphology and redox fluctuations recorded in the Ediacaran Doushantuo Formation

Recent geochemical studies of the Doushantuo Formation (ca. 635–551Ma) in South China suggested that the Ediacaran ocean was strongly stratified, with an oxic surface layer above a euxinic wedge that was sandwiched within ferruginous deep waters. This ocean redox model, however, was derived largely from the data obtained from stratigraphic sections in the Yangtze Gorges area that, according to recent paleogeographic reconstruction, were deposited in a restricted intrashelf lagoon. In order to test the redox conditions in open-ocean, deep-water environments, we have conducted a detailed morphological analysis of authigenic pyrites from the upper to lower slope sections of the Doushantuo Formation. In analogy to modern euxinic basins such as the Black Sea, framboidal pyrites with smaller and less variable size distribution are taken as evidence for sulfide precipitation in euxinic water column, while larger and more variable framboidal and euhedral pyrites are formed or diagenetically altered in sediments with an overlying oxic/dysoxic water column. Except for a few brief intervals, pyrites from the Doushantuo Formation in upper slope sections (Siduping and Taoying sections) are mainly of early diagenetic origin and do not record water column euxinia during deposition. In contrast, pyrites from the Doushantuo Formation in the lower slope section (Wuhe section) are dominated by fine-grained framboids indicative of pervasive water column euxinia below chemocline. In both upper and lower slope sections, temporal changes in genetic pyrite types occur at centimeter to decameter scales, suggesting frequent chemocline fluctuations. The overall decrease in abundance of framboidal pyrites toward the upper Doushantuo Formation in upper slope sections suggests increasing water column oxygenation and deepening of the chemocline. Macroalgae and metazoan fossils are found mainly from shale intervals without syngenetic pyrites in upper slope sections, indicating the sensitivity of macroscopic eukaryotes to the ocean chemocline. The redox fluctuations recorded by the Doushantuo pyrites compels for comprehensive geochemical data in deep-water successions to further test the existing paleoceanographic models of the Ediacaran ocean.

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.

Nickel Phase Partitioning and Toxicity in Field-Deployed Sediments

The pool of bioavailable metal in sediments can be much smaller than total metal concentration due to complexation and precipitation with ligands. Metal bioavailability and toxicity in sediment is often predicted from models of simultaneous extracted metal and acid volatile sulfide (SEM-AVS); however, studies of the applicability of these models for Ni-contaminated sediments have been conducted primarily in laboratory settings. We investigated the utility of the SEM-AVS models under field conditions: Five lotic sediments with a range of sulfide and organic carbon contents were amended with four concentrations of Ni, deployed in streams for eight weeks, and examined for colonizing macroinvertebrates. After four weeks, colonizing macroinvertebrates showed a strong negative response to the Ni-treated sediments and SEM-AVS models of bioavailability differentiated between toxic and nontoxic conditions. By Week 8, relationships deteriorated between colonizing macroinvertebrates and SEM-AVS model predictions. Total Ni in the sediment did not change through time; however, Ni partitioning shifted from being dominated by organic cabon at deployment to associations with Fe and Mn. Combined geochemical and toxicity results suggest that Fe and Mn oxides in surface sediments resulted in Ni being less available to biota. This implies that current SEM-AVS models may overestimate bioavailable Ni in sediments with oxic surface layers and sufficient Fe and Mn.

Trace metal composition of suspended particulate matter in the water column of the Black Sea

We analyzed the chemical composition of suspended matter from the Black Sea for a complete suite of elements used as tracers for various sources and processes. Samples of suspended matter were collected at four stations from the Bosporus to the center of the western gyre during a R/V Bilim cruise in September 2000. Sample depths were from the oxic surface layer, the suboxic zone and the upper part of the anoxic (sulfidic) layer. All samples were analyzed for Al, Ti, V, Cr, Mn, Fe, Co, Cu, Zn, Mo, Ag, Cd, Ba, Pb, U and P using ICP-MS, AAS, and spectrophotometer. The main objective of this study was to determine the processes that influence the distributions of particulate trace metals in the water column under various redox environments. The composition of the particulate matter was influenced by lithogenic input from surrounding rivers, biological production in the surface layer, biogeochemical (e.g. redox) processes and anthropogenic inputs. Almost all elemental concentrations decreased from the coastal to the offshore stations to the center of the western gyre. Metal/Al ratios were compared with the ratios of average crust and Danube and Turkish rivers. Deviations from these lithogenic sources were used to examine the anomalies due to geochemical, biological and anthropogenic processes. In general, the largest metal enrichments relative to crust were observed inthe surface samples away from coastal sources. Metal/P ratios were used to compare data for some of the elements with previous data from the open ocean. The Me/P ratios for Cu, Zn, Mo and Ni were much higher than open ocean studies, while the ratios for Cd and Co were comparable. The high Me/P (and Me/Al) for several elements suggest anthropogenic input may contribute to these high surface concentrations. The composition of particulate matter from the suboxic zone showed that some elements were strongly enriched. Enrichments of Mn and Fe in the suboxic zone were observed, as expected. Mn and Fe oxides play an important role in scavenging processes. The redox dependent processes in the suboxic - anoxic interface influence the vertical distribution of U, V, Ni, Co, Cu, Zn, Ba and possibly Mo, Cr. Elements influenced by sulfide formation in the anoxic layer were Fe, Cr, Ni, Co, Mo, and Ag.

The active methanotrophic community in a wetland from the High Arctic

The dominant terminal process of carbon mineralization in most freshwater wetlands is methanogenesis. With methane being an important greenhouse gas, the predicted warming of the Arctic may provide a positive feedback. However, the amount of methane released to the atmosphere may be controlled by the activity of methane-oxidizing bacteria (methanotrophs) living in the oxic surface layer of wetlands. Previously, methanotrophs have been isolated and identified by genetic profiling in High Arctic wetlands showing the presence of only a few genotypes. Two isolates from Solvatnet (Ny-Ålesund, Spitsbergen; 79°N) are available: Methylobacter tundripaludum (type I) and Methylocystis rosea (type II), raising the question whether the low diversity is a cultivation effect. We have revisited Solvatnet applying stable isotope probing (SIP) with (13) C-labelled methane. 16S rRNA profiling revealed active type I methanotrophs including M. tundripaludum, while no active type II methanotrophs were identified. These results indicate that the extant M. tundripaludum is an active methane oxidizer at its locus typicus; furthermore, Methylobacter seems to be the dominant active genus. Diversity of methanotrophs was low as compared, e.g. to wetland rice fields in the Mediterranean. This low diversity suggests a high vulnerability of Arctic methanotroph communities, which deserves more attention.

Structural and functional responses of microbial mats to reductions in nutrient and salinity stressors in a Bahamian hypersaline lagoon

Microbial mats in Bahamian hypersaline lagoons are affected by the combination of salinity fluctuations and external nutrient inputs, both of which are seasonally variable. The purpose of this study was to examine the singular and combined effects of salinity and nutrient (N+P) stress on primary production, extracellular enzyme activity, and the composition of the photoautotroph community in this episodically varying extreme environment. Anoxygenic phototrophic bacteria were able to increase their relative abundance when nutrients were supplied under hypersaline con- ditions (300 g l -1 ). When salinities were lowered (38 g l -1 ) and nutrients added, extracellular enzyme activity (aminopeptidase, α-glucosidase, and β-glucosidase), rates of oxygenic photosynthesis, and phototroph biomass increased in the oxic surface layers of the mat. Once salinity stress had been low- ered, oxygenic photosynthesis allowed the proliferation of Cyanobacteria, heterotrophic activity, and a corresponding reduction in the abundance of anoxygenic phototrophic bacteria. On reduction of nutrient stress, mat phototrophs responded by increasing biomass (using either anoxygenic or oxy- genic photosynthesis, or both). In this hypersaline system, seasonal as well as short-term (days) vari- ations in environmental conditions may promote structural changes in the mat community which alter the rates of major processes such as oxygenic photosynthesis and heterotrophy, and illustrate the cyclic behavior of microbial dormancy and proliferation in this extreme environment. Cycles in nutrient input and salinity are primary forcing factors for the maintenance of a dynamic and diverse (both structurally and functionally) benthic microbial community in a small hypersaline lagoon, Salt Pond, on San Salvador Island, Bahamas.

Biogeochemical controls on microbial diversity in seafloor sulphidic sediments

The ultimate fate of hydrothermal sulphides on the seafloor depends on the nature and rate of abiotic and microbially catalysed reactions where sulphide minerals are exposed to oxic seawater. This study combines organic and inorganic geochemical with microbiological measurements across a suboxic transition zone of highly altered sulphidic sediments from the Trans-Atlantic Geotransverse hydrothermal field to characterize the reaction products and microbial communities present. There is distinct biogeochemical zonation apparent within the sediment sequence from oxic surface layers through a suboxic transition zone into the sulphide material. The microbial communities in the sediment differ significantly between the biogeochemical horizons sampled, with the identified microbes inferred to be associated with Fe and S redox cycling. In particular, Marinobacter species, organisms associated with circumneutral Fe oxidation, are dominant in a sulphide lens present in the lower core. The dominance of Marinobacter-related sequences within the relict sulphide lens implies that these organisms play an important role in the alteration of sulphides at the seafloor once active venting has ceased.

Biosensor for laboratory and lander‐based analysis of benthic nitrate plus nitrite distribution in marine environments

We present a psychotropic bacteria—based biosensor that can be used in low—temperature seawater for the analysis of nitrate + nitrite (NOx−). The sensor can be used to resolve concentrations below 1 µmol L−1 at low temperature (<2.5°C) and high salinity (35‰), and in situ use in the deep sea was demonstrated by measuring NOx− profiles in sediment at 1500 m depth, where the temperature was 2.5°C. Analysis of marine sediment at 70 m depth showed very heterogeneous NOx− profiles, most of which exhibited pronounced maxima due to nitrification in the oxic surface layer. At this shallow water site, the in situ profiles were similar to profiles measured in the laboratory, but generally laboratory profiles appeared more uniform, presumably as a result of reduced fauna activity and disturbance of the microstructure of the sediment surface during core recovery.

A multilayered water column in the Ediacaran Yangtze platform? Insights from carbonate and organic matter paired δ13C

Large carbon isotope fluctuations have been systematically reported for Ediacaran carbonate rocks, the meaning of which remains controversial. In order to better understand the mechanisms behind such variations, we present new paired δ 13C data on carbonates ( δ 13C carb) and their associated organic matter ( δ 13C org) from a shelf-margin section (Yangjiaping) of the Doushantuo Formation. In this section, the Doushantuo Formation starts with cap dolostones presenting δ 13C carb values around − 5‰ and δ 13C org values between − 30.3 and − 27.6‰. Up-section, phased variations in δ 13C carb and δ 13C org describe positive and negative excursions, while their difference (Δ 13C dol–org = δ 13C carb − δ 13C org) remains around + 29.2‰. These new data allow the first reconstruction of lateral variations of δ 13C carb, δ 13C org and Δ 13C carb–org for a shelf-to-basin cross-section of the Yangtze platform (South China) after integration with results reported previously for two other sections. Across the Yangtze platform, the isotope signals reveal strong lateral heterogeneities, with complex variations of δ 13C carb and Δ 13C dol–org in the inner-shelf section, phased variations in the shelf-margin section with positive δ 13C carb and Δ 13C dol–org close to 29‰, and dominantly negative δ 13C carb with δ 13C org as low as − 35‰ in the basin. These variations are incompatible with the idea that the δ 13C carb can systematically be used as a proxy of ocean surface waters. Assuming that δ 13C carb are acquired in bottom waters and/or upper sediments, we show that the heterogeneous δ 13C carb and Δ 13C dol–org are compatible with a stratified water column composed of up to three layers: (i) an oxic surface layer, where dissolved inorganic carbon (DIC) is probably in isotope equilibrium with the atmosphere; (ii) an intermediate euxinic layer with a lower δ 13C DIC due to organic matter oxidation by ongoing sulphate reduction; (iii) a bottom euxinic layer that seems to be restricted to the inner-shelf lagoonal facies, lacking sulphate, containing methane and with a higher δ 13C DIC due to DIC production by methanogenesis. If our model holds true, it suggests that not only negative but also positive Ediacaran carbon isotope excursions may reflect ocean stratification, the positive excursion possibly recording a sulphate-free methanogenic layer at the bottom of restricted basins.

Porewater geochemistry in a Galician Ria (NW Iberian Peninsula): Implications for benthic fluxes of dissolved trace elements (Co, Cu, Ni, Pb, V, Zn)

The geochemical behaviour of dissolved trace elements in sediment interstitial waters from the Vigo Ria (Galicia, Spain) has been determined. Dissolved concentrations in the pore waters ranged between 1.7–23.2 nM for Co, 1.5–131 nM for Cu, 19.5–159 nM for Ni, 0.02–19.3 nM for Pb, 5.4–260 nM for V and 0.2–241 nM for Zn. Values for Cu, Pb and Zn were highest along the axis of the ria, whereas Co, Ni, V and Zn were more abundant in the area of the industrialised shipyards. The metal profiles were affected by sedimentary redox processes, which were monitored by means of Mn and Fe concentrations and pore water pH. Dissolved Cu and V had relatively high concentrations in the oxic surface layer and their concentrations decreased with depth, although in deeper layers concentrations of V increased in association with the presence of dissolved organic ligands. Cobalt and Ni followed the behaviour of Mn, although they were depleted in surface oxic layers their concentrations increased in the Mn reduction zone. Lead and Zn had highly irregular profiles because of their lower redox-sensitivity and their complexation with organic material is not as pronounced as that for Cu. Dissolved metal concentrations in overlying waters oscillated between 0.7–2.1 nM for Co, 5.5–50.5 nM for Cu, 4.6–10.0 nM for Ni, 1.4–9.1 for Pb, 5.7–28.5 nM for V and 14.6–66.5 nM for Zn. Using Fick's first law of diffusion, the benthic fluxes of the elements varied between 0.03–0.24 nmol cm − 2 y − 1 for Co, (− 0.02)–1.11 nmol cm − 2 y − 1 for Cu, 0.16–1.70 nmol cm − 2 y − 1 for Ni, (−0.14)–0.03 nmol cm − 2 y − 1 for Pb, 1.52–4.35 nmol cm − 2 y − 1 for V and (− 0.37)–0.90 nmol cm − 2 y − 1 for Zn. Fluxes were higher in the ria axis for Cu, Ni, V and Zn and in the shipyard area for Co, while Pb fluxes were negligible at all the stations. This work has demonstrated that the redox geochemistry and diagenetic processes of the sediments and pore waters control the benthic fluxes in the Vigo Ria. When the upper layer of the sediment is oxic a high exportation of Cu and V to the overlying waters occurs and during less oxidizing conditions of this layer, Ni and Co exportation from the pore water increases. Dissolved trace metal benthic fluxes to the Vigo Ria were significant for most of the metals (Cu, Ni and V) and were of the same order of magnitude to the riverine inputs.

Nitrate, nitrite, and nitrous oxide transformations in sediments along a salinity gradient in the Weser Estuary

The dynamics of the nitrogen intermediates N 2 O and NO 2 - in estuarine sediments were studied along a salinity gradient in the eutrophied Weser Estuary (Germany) using microsensors for N 2 O, NO 2 - , NO x - , and O 2 . During dark incubations in the laboratory of sediment samples from a freshwater site, a brackish water site with fluctuating salinity, and a marine site, the effects of environmental changes in nitrogen availability and salinity on microscale sediment dynamics were examined. Generally, sediment levels of intermediates were low: 1 to 25 μM NO 2 - and 0 to 8 μM N 2 O. However, significant variation was found in accumulation patterns and in the potential of the residing microbial community to control sediment releases of the intermediates. At fresh- and brackish water sites, NO 2 - production was found in the anoxic denitrification zone, and release from the sediments was effectively prevented by activity of nitrite oxidisers in oxic surface layers. In contrast, high rates of NO 2 - release occurred in marine sediment, where NO 2 - production was predominantly associated with incomplete nitrification in oxic layers. Similarly, stimulated partial nitrification due to NH 4 + addition led to NO 2 - liberation from brackish water sediment. Production of N 2 O was never observed in sediment from the brackish water site, which is naturally exposed to a daily regime of water column variations, but transient N 2 O accumulation was observed in the other sediments. The production of N 2 O could be induced by an abrupt change in either NO 3 - or salinity, and was found in anoxic or micro-oxic sediment layers. Because oxic sediment layers showed little or no potential for N 2 O consumption (in contrast to NO 2 - ) the accumulation of N 2 O always resulted in release from the sediment surface. Results demonstrate that changes in environmental parameters such as salinity and NO 3 - can trigger sediment production and release of NO 2 - and N 2 O, but further suggest that microbial sediment communities are highly adaptive and can become resistant towards intermediate release when regularly exposed to fluctuating conditions.

Vertical diversity of bacteria in an oxygen-stratified humic lake, evaluated using DNA and phospholipid analyses

Microbes play a particularly important role in the food web in lakes with high dissolved organic carbon content. The bacterial community of a polyhumic lake, Mekkojarvi, was studied using DNA techniques and phospholipid fatty acid (PLFA) analysis during the mid-summer period of water column strati- fication. According to the 16S rRNA gene clone libraries and length heterogeneity analysis (LH-PCR), heterotrophic bacteria dominated only in the oxic epilimnion, in which various Actinobacteria (mostly cluster acI-B) and Betaproteobacteria (especially Poly- nucleobacter subcluster PnecC) were common. Se- quences assigned to heterotrophic, methylotrophic, photoautotrophic, and chemoautotrophic genera were all abundant in the oxic-anoxic boundary layer. Methylobacter and Methylophilus were dominant genera among methylotrophic bacteria. Sequences assigned to the photoautotrophic green sulfur bac- terium Chlorobium sp. dominated in the anoxic water column, in which the microbial PLFA biomass was 6 times higher than in the oxic surface layer. All PLFA- profiles were dominated by 16 monounsaturated fatty acids typical of Gram-negative bacteria, whereas iso- and anteiso-branched PLFAs typical of Actinobacteria were present only in minor proportions. The high bio- mass of the potentially autotrophic meta- and hypolim- netic bacteria may form an important carbon source for the whole lake after spring and autumn overturns; thus, the role of these bacteria in the seasonal energy mobilization deserves more study in oxygen-stratified humic lakes and ponds.

Highly metalliferous carbonaceous shale and Early Cambrian seawater

We report evidence for the seawater origin of an extremely metal-enriched sulfide- and organic carbon–rich marker bed in a transgressive Early Cambrian black shale sequence along the passive margin of the Yangtze platform. The element concentration pattern in this marker bed suggests that it formed in a sediment-starved, stratified basin with a euxinic water column below an oxic surface layer. Biological activity was high in the surface layer, which was resupplied by communication with oxic oceans. The extremely low terrigenous input and the sulfate-reducing environment in the deeper part of the basin led to exceptionally high metal enrichments by factors of ∼107 with respect to modern seawater. The composition of the sulfidic rocks reflects the composition of the Early Cambrian oceans. The molybdenum isotope ratio suggests that during this time <35% of marine Mo was deposited in oxic sediments, and that suboxicanoxic marine environments were more widespread during the Early Cambrian than today.

Impact of protists on the activity and structure of the bacterial community in a rice field soil.

Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a gamma-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G + C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH4+ was lower and the level of extractable SO4(2-) was higher without protists, indicating that nitrogen mineralization and SO4(2-) reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O2 was a major control, and O2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.