EPOCA Svalbard 2009 benthic experiment: Serripes study, 2009

Ocean acidification influences sediment/water nitrogen fluxes, possibly by impacting on the microbial process of ammonia oxidation. To investigate this further, undisturbed sediment cores collected from Ny Alesund harbour (Svalbard) were incubated with seawater adjusted to CO2 concentrations of 380, 540, 760, 1,120 and 3,000 µatm. DNA and RNA were extracted from the sediment surface after 14 days' exposure and the abundance of bacterial and archaeal ammonia oxidising (amoA) genes and transcripts quantified using quantitative polymerase chain reaction. While there was no change to the abundance of bacterial amoA genes, an increase to 760 µatm pCO2 reduced the abundance of bacterial amoA transcripts by 65 %, and this was accompanied by a shift in the composition of the active community. In contrast, archaeal amoA gene and transcript abundance both doubled at 3,000 µatm, with an increase in species richness also apparent. This suggests that ammonia oxidising bacteria and archaea in marine sediments have different pH optima, and the impact of elevated CO2 on N cycling may be dependent on the relative abundances of these two major microbial groups. Further evidence of a shift in the balance of key N cycling groups was also evident: the abundance of nirS-type denitrifier transcripts decreased alongside bacterial amoA transcripts, indicating that NO3 ? produced by bacterial nitrification fuelled denitrification. An increase in the abundance of Planctomycete-specific 16S rRNA, the vast majority of which grouped with known anammox bacteria, was also apparent at 3,000 µatm pCO2. This could indicate a possible shift from coupled nitrification-denitrification to anammox activity at elevated CO2.

Environmental data from coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea

Natural CO2 venting systems can mimic conditions that resemble intermediate to high pCO2 levels as predicted for our future oceans. They represent ideal sites to investigate potential long-term effects of ocean acidification on marine life. To test whether microbes are affected by prolonged exposure to pCO2 levels, we examined the composition and diversity of microbial communities in oxic sandy sediments along a natural CO2 gradient. Increasing pCO2 was accompanied by higher bacterial richness and by a strong increase in rare members in both bacterial and archaeal communities. Microbial communities from sites with CO2 concentrations close to today's conditions had different structures than those of sites with elevated CO2 levels. We also observed increasing sequence abundance of several organic matter degrading types of Flavobacteriaceae and Rhodobacteraceae, which paralleled concurrent shifts in benthic cover and enhanced primary productivity. With increasing pCO2, sequences related to bacterial nitrifying organisms such as Nitrosococcus and Nitrospirales decreased, and sequences affiliated to the archaeal ammonia-oxidizing Thaumarchaeota Nitrosopumilus maritimus increased. Our study suggests that microbial community structure and diversity, and likely key ecosystem functions, may be altered in coastal sediments by long-term CO2 exposure to levels predicted for the end of the century.

Particle fluxes of the bathypelagic sediment trap CVOO-3 in the eastern tropical North Atlantic for the period December 2009 until May 2011

Particle fluxes at the Cape Verde Ocean Observatory (CVOO) in the eastern tropical North Atlantic for the period December 2009 until May 2011 are discussed based on bathypelagic sediment trap time-series data collected at 1290 and 3439 m water depth. The typically oligotrophic particle flux pattern with weak seasonality is modified by the appearance of a highly productive and low oxygen (minimum concentration below 2 µmol kg**-1 at 40 m depth) anticyclonic modewater eddy (ACME) in winter 2010. The eddy passage was accompanied by unusually high mass fluxes of up to 151 mg m**-2 d**-1, lasting from December 2009 to May 2010. Distinct biogenic silica (BSi) and organic carbon flux peaks of ~15 and 13.3 mg m**-2 d**-1, respectively, were observed in February-March 2010 when the eddy approached the CVOO. The flux of the lithogenic component, mostly mineral dust, was well correlated with that of organic carbon, in particular in the deep trap samples, suggesting a tight coupling. The lithogenic ballasting obviously resulted in high particle settling rates and, thus, a fast transfer of epi-/meso-pelagic signatures to the bathypelagic traps. We suspect that the two- to three-fold increase in particle fluxes with depth as well as the tight coupling of mineral dust and organic carbon in the deep trap samples might be explained by particle focusing processes within the deeper part of the eddy. Molar C : N ratios of organic matter during the ACME passage were around 18 and 25 for the upper and lower trap samples, respectively. This suggests that some productivity under nutrient (nitrate) limitation occurred in the euphotic zone of the eddy in the beginning of 2010 or that a local nitrogen recycling took place. The d15N record showed a decrease from 5.21 to 3.11 per mil from January to March 2010, while the organic carbon and nitrogen fluxes increased. The causes of enhanced sedimentation from the eddy in February/March 2010 remain elusive, but nutrient depletion and/or an increased availability of dust as a ballast mineral for organic-rich aggregates might have contributed. Rapid remineralisation of sinking organic-rich particles could have contributed to oxygen depletion at shallow depth. Although the eddy formed in the West African coastal area in summer 2009, no indications of coastal flux signatures (e.g. from diatoms) were found in the sediment trap samples, confirming the assumption that the suboxia developed within the eddy en route. However, we could not detect biomarkers indicative of the presence of anammox (anaerobic ammonia oxidation) bacteria or green sulfur bacteria thriving in photic zone suboxia/hypoxia, i.e. ladderane fatty acids and isorenieratene derivatives, respectively. This could indicate that suboxic conditions in the eddy had recently developed and/or the respective bacterial stocks had not yet reached detection thresholds. Another explanation is that the fast-sinking organic-rich particles produced in the surface layer did not interact with bacteria from the suboxic zone below. Carbonate fluxes dropped from -52 to 21.4 mg m**-2 d**-1 from January to February 2010, respectively, mainly due to reduced contribution of shallow-dwelling planktonic foraminifera and pteropods. The deep-dwelling foraminifera Globorotalia menardii, however, showed a major flux peak in February 2010, most probably due to the suboxia/hypoxia. The low oxygen conditions forced at least some zooplankton to reduce diel vertical migration. Reduced "flux feeding" by zooplankton in the epipelagic could have contributed to the enhanced fluxes of organic materials to the bathypelagic traps during the eddy passage. Further studies are required on eddy-induced particle production and preservation processes and particle focusing.

FISH analysis of biofilm samples from five CANON reactors in Beijing

Completely autotrophic nitrogen removal over nitrite (CANON) has been regarded as an efficient and economical process for nitrogen removal from wastewater. The distribution and genetic diversity of the functional microorganisms in five lab-scale CANON reactors have been investigated by using some molecular biology methods. Nitrosomonas-like aerobic ammonium oxidizing bacteria (AerAOB) and Candidatus Brocadia-related anaerobic ammonium oxidizing bacteria (AnAOB) were detected as predominant functional microbes in the five reactors while Nitrobacter-like nitrite oxidizing bacteria (NOB) existed only in the systems operated at ambient temperature. Communities of AerAOB and AnAOB were almost similar among the five reactors while the distribution of the functional microbes was either scattered or densely packed. Meanwhile, this study has demonstrated the feasibility of starting up CANON by inoculating conventional activated sludge in low ammonium content at ambient temperature.

Lipid biomarkers of shelf sediments from upwelling regions off Namibia, Peru, and Chile

Sediments of upwelling regions off Namibia, Peru, and Chile contain dense populations of large nitrate-storing sulfide-oxidizing bacteria, Thiomargarita, Beggiatoa, and Thioploca. Increased contents of monounsaturated C16 and C18 fatty acids have been found at all stations studied, especially when a high density of sulfide oxidizers in the sediments was observed. The distribution of lipid biomarkers attributed to sulfate reducers (10MeC16:0 fatty acid, ai-C15:0 fatty acid, and mono-O-alkyl glycerol ethers) compared to the distribution of sulfide oxidizers indicate a close association between these bacteria. As a consequence, the distributions of sulfate reducers in sediments of Namibia, Peru, and Chile are closely related to differences in the motility of the various sulfide oxidizers at the three study sites. Depth profiles of mono-O-alkyl glycerol ethers have been found to correlate best with the occurrence of large sulfide-oxidizing bacteria. This suggests a particularly close link between mono-O-alkyl glycerol ether-synthesizing sulfate reducers and sulfide oxidizers. The interaction between sulfide-oxidizing bacteria and sulfate-reducing bacteria reveals intense sulfur cycling and degradation of organic matter in different sediment depths.

Glycerol dialkyl glycerol tetraethers (GDGT) abundance in suspended particulate matter from the South-west and Equatorial Atlantic Ocean

The TEX86 paleotemperature proxy is based on archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids preserved in marine sediments, yet both the influence of different physiological factors on the structural distribution of GDGTs, and the mechanism(s) by which GDGTs are exported to marine sediments remain unclear. In particular, TEX86 temperatures derived directly from suspended particulate matter (SPM) in the water column can diverge strongly from corresponding in situ temperatures. Here we investigated the abundance and structural distribution of GDGTs in the South-west and Equatorial Atlantic Ocean by examining SPM collected from four surface 1000 m depth profiles spanning 48 degrees of latitude. The depth distribution of GDGTs was consistent with our current understanding of marine archaeal ecology, and specifically of ammonia-oxidizing Thaumarchaeota. Maximum GDGT concentrations occurred at the base of the primary NO2- maximum. Core GDGTs dominated the structural distribution in surface waters, while intact polar GDGTs - thought to potentially indicate live cells - were more abundant at all depths below the maximum NO2- concentration. When integrated through the upper 1000 m of the water column, > 98% of GDGTs were present in waters at and below the depth of the primary NO2- maximum. TEX86-calculated temperatures showed local minima at the depth of the NO2- maximum, while the ratio of GDGT 2:GDGT 3 [2/3] increased with depth throughout the upper water column. These results were used to model the depth of origin for GDGTs exported to sediments. By comparing our SPM data to published TEX86 values and [2/3] ratios from sediments near our study sites, we conclude that most GDGTs are exported from the depth of maximum GDGT concentrations, near the subsurface NO2- maximum (~80-250 m). This indicates that local ammonia oxidation dynamics are important regional controls on the GDGT ratios preserved in sediments. Predicting the extent to which subsurface variations in archaeal activity may influence the sedimentary TEX86 record will require a better understanding of how site-specific productivity and particle dynamics in the upper water column influence the depth of origin for exported organic matter.

Dynamics of halocarbons in coastal surface waters during short term mesocosm experiments

The aim of the present study was to evaluate the influence of different light quality, especially ultraviolet radiation (UVR), on the dynamics of volatile halogenated organic compounds (VHOCs) at the sea surface. Short term experiments were conducted with floating gas-tight mesocosms of different optical qualities. Six halocarbons (CH3I, CHCl3, CH2Br2, CH2ClI, CHBr3 and CH2I2), known to be produced by phytoplankton, together with a variety of biological and environmental variables were measured in the coastal southern Baltic Sea and in the Raunefjord (North Sea). These experiments showed that ambient levels of UVR have no significant influence on VHOC dynamics in the natural systems. We attribute it to the low radiation doses that phytoplankton cells receive in a normal turbulent surface mixed layer. The VHOC concentrations were influenced by their production and removal processes, but they were not correlated with biological or environmental parameters investigated. Diatoms were most likely the dominant biogenic source of VHOCs in the Baltic Sea experiment, whereas in the Raunefjord experiment macroalgae probably contributed strongly to the production of VHOCs. The variable stable carbon isotope signatures (d13C values) of bromoform (CHBr3) also indicate that different autotrophic organisms were responsible for CHBr3 production in the two coastal environments. In the Raunefjord, despite strong daily variations in CHBr3 concentration, the carbon isotopic ratio was fairly stable with a mean value of -26 per mil. During the declining spring phytoplankton bloom in the Baltic Sea, the d13C values of CHBr3 were enriched in 13C and showed noticeable diurnal changes (-12 per mil ± 4). These results show that isotope signature analysis is a useful tool to study both the origin and dynamics of VHOCs in natural systems.

PeECE II - Pelagic Ecosystem CO2 Enrichment Study, Raunefjord, Bergen, Norway

The effects of CO2-induced seawater acidification on plankton communities were also addressed in a series of 3 mesocosm experiments, called the Pelagic Ecosystem CO2 Enrichment (PeECE I-III) studies, which were conducted in the Large-Scale Mesocosm Facilities of the University of Bergen, Norway in 2001, 2003 and 2005, respectively. Each experiment consisted of 9 mesocosms, in which CO2 was manipulated to initial concentrations of 190, 350 and 750 µatm in 2001 and 2003, and 350, 700 and 1050 µatm in 2005. The present dataset concerns PeECE II.

PeECE III - Pelagic Ecosystem CO2 Enrichment Study, Raunefjord, Bergen, Norway, 2005

The effects of CO2-induced seawater acidification on plankton communities were also addressed in a series of 3 mesocosm experiments, called the Pelagic Ecosystem CO2 Enrichment (PeECE I-III) studies, which were conducted in the Large-Scale Mesocosm Facilities of the University of Bergen, Norway in 2001, 2003 and 2005, respectively. Each experiment consisted of 9 mesocosms, in which CO2 was manipulated to initial concentrations of 190, 350 and 750 µatm in 2001 and 2003, and 350, 700 and 1050 µatm in 2005. The present dataset concerns PeECE III.

Organic geochemistry of ODP Hole 162-985A sediments

Dark, organic-rich sediments were recovered from the lower Miocene section (~16.6 Ma) in Hole 985A in the Norway Basin during Ocean Drilling Program Leg 162. Organic carbon and total sulfur contents of the dark sediments showed a maximum concentration of 5.6 and 26.1 wt%, respectively. Sulfur enrichment in the sediments indicates that these dark layers were formed under anoxic conditions in bottom water. Four dark and eight greenish gray sediment samples, ranging in age from early Miocene to Pleistocene, were analyzed for lipid-class compounds (aliphatic hydrocarbons, fatty alcohols, and sterols) using gas chromatography (GC) and GC/mass spectrometry to better understand the formation processes of the organic-rich dark layers and to reconstruct the paleoenvironmental changes. The molecular distributions of n-alkanes and fatty alcohols indicate that terrigenous organic matter largely contributed to both types of sediments. Significant amounts of hopanoid hydrocarbons, such as diploptene and hop-17(21)-ene, however, were detected characteristically in the dark sediments, which suggests that prokaryotes such as methane-oxidizing bacteria or cyanobacteria may have significantly contributed to the formation of these organic-rich, dark sediments. These results indicate that the bottom waters of the Norway Basin had been subjected to anoxic conditions during the early Miocene.

(Table 1) Methane concentrations, MOX rates and MOB abundance in arctic aquatic ecosystems of the Lena Delta, Northeast Siberia

Large amounts of organic carbon are stored in Arctic permafrost environments, and microbial activity can potentially mineralize this carbon into methane, a potent greenhouse gas. In this study, we assessed the methane budget, the bacterial methane oxidation (MOX) and the underlying environmental controls of arctic lake systems, which represent substantial sources of methane. Five lake systems located on Samoylov Island (Lena Delta, Siberia) and the connected river sites were analyzed using radiotracers to estimate the MOX rates, and molecular biology methods to characterize the abundance and the community composition of methane-oxidizing bacteria (MOB). In contrast to the river, the lake systems had high variation in the methane concentrations, the abundance and composition of the MOB communities, and consequently, the MOX rates. The highest methane concentrations and the highest MOX rates were detected in the lake outlets and in a lake complex in a floodplain area. Though, in all aquatic systems we detected both, Type I and II MOB, in lake systems we observed a higher diversity including MOB, typical of the soil environments. The inoculation of soil MOB into the aquatic systems, resulting from permafrost thawing, might be an additional factor controlling the MOB community composition and potentially methanotrophic capacity.

Collection of data on particulate and dissolved soil phosphorus in the Jena Experiment (Main Experiment, time series since 2002)

This data set contains two time series of measurements of dissolved phosphorus (organic, inorganic and total with a biweekly resolution) and dissolved inorganic phosphorus with a seasonal resolution. In addition, data on phosphorus from soil samples measured in 2007 and fractionated by different acid-extrations (Hedley fractions) are provided. All data measured at the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. 1. Dissolved phosphorus in soil solution: Suction plates installed on the field site in 10, 20, 30 and 60 cm depth were used to sample soil pore water. Cumulatively extracted soil solution was collected every two weeks from October 2002 to May 2006. The biweekly samples from 2002, 2003 and 2004 were analyzed for dissolved organic phosphorus (DOP), dissolved inorganic phosphorus (PO4P) and dissolved total phosphorus (TDP) by Continuous Flow Analyzer (CFA SAN ++, SKALAR [Breda, The Netherlands]). 2. Seasonal values of dissolved inorganic phosphorus in soil solution were calculated as volume-weighted mean values of the biweekly measurements (spring = March to May, summer = June to August, fall = September to November, winter = December to February). 3. Phosphorus fractions in soil: Five independent soil samples per plot were taken in a depth of 0-15 cm using a soil corer with an inner diameter of 1 cm. The five samples per plot were combined to one composite sample per plot. A four-step sequential P fractionation (Hedley fractions) was applied and concentrations of P fractions in soil were measured photometrically (molybdenum blue-reactive P) with a Continuous Flow Analyzer (Bran&Luebbe, Germany).

The influence of ocean acidification on nitrogen regeneration and nitrous oxide production in the northwest European shelf sea

The assimilation and regeneration of dissolved inorganic nitrogen, and the concentration of N2O, was investigated at stations located in the NW European shelf sea during June/July 2011. These observational measurements within the photic zone demonstrated the simultaneous regeneration and assimilation of NH4+, NO2- and NO3-. NH4+ was assimilated at 1.82-49.12 nmol N/L/h and regenerated at 3.46-14.60 nmol N/L/h; NO2- was assimilated at 0-2.08 nmol N/L/h and regenerated at 0.01-1.85 nmol N/L/h; NO3-was assimilated at 0.67-18.75 nmol N/L/h and regenerated at 0.05-28.97 nmol N/L/h. Observations implied that these processes were closely coupled at the regional scale and that nitrogen recycling played an important role in sustaining phytoplankton growth during the summer. The [N2O], measured in water column profiles, was 10.13 ± 1.11 nmol/L and did not strongly diverge from atmospheric equilibrium indicating that sampled marine regions were neither a strong source nor sink of N2O to the atmosphere. Multivariate analysis of data describing water column biogeochemistry and its links to N-cycling activity failed to explain the observed variance in rates of N-regeneration and N-assimilation, possibly due to the limited number of process rate observations. In the surface waters of five further stations, ocean acidification (OA) bioassay experiments were conducted to investigate the response of NH4+ oxidising and regenerating organisms to simulated OA conditions, including the implications for [N2O]. Multivariate analysis was undertaken which considered the complete bioassay data set of measured variables describing changes in N-regeneration rate, [N2O] and the biogeochemical composition of seawater. While anticipating biogeochemical differences between locations, we aimed to test the hypothesis that the underlying mechanism through which pelagic N-regeneration responded to simulated OA conditions was independent of location. Our objective was to develop a mechanistic understanding of how NH4+ regeneration, NH4+ oxidation and N2O production responded to OA. Results indicated that N-regeneration process responses to OA treatments were location specific; no mechanistic understanding of how N-regeneration processes respond to OA in the surface ocean of the NW European shelf sea could be developed.