Matter Degradation In Sediments Research Articles

Fish growth enhances microbial sulfur cycling in aquaculture pond sediments.

SummaryMicrobial sulfate reduction and sulfur oxidation are vital processes to enhance organic matter degradation in sediments. However, the diversity and composition of sulfate‐reducing bacteria (SRB) and sulfur‐oxidizing bacteria (SOB) and their environmental driving factors are still poorly understood in aquaculture ponds, which received mounting of organic matter. In this study, bacterial communities, SRB and SOB from sediments of aquaculture ponds with different sizes of grass carp (Ctenopharyngodon idellus) were analysed using high‐throughput sequencing and quantitative real‐time PCR (qPCR). The results indicated that microbial communities in aquaculture pond sediments of large juvenile fish showed the highest richness and abundance of SRB and SOB, potentially further enhancing microbial sulfur cycling. Specifically, SRB were dominated by Desulfobulbus and Desulfovibrio, whereas SOB were dominated by Dechloromonas and Leptothrix. Although large juvenile fish ponds had relatively lower concentrations of sulfur compounds (i.e. total sulfur, acid‐volatile sulfide and elemental sulfur) than those of larval fish ponds, more abundant SRB and SOB were found in the large juvenile fish ponds. Further redundancy analysis (RDA) and linear regression indicated that sulfur compounds and sediment suspension are the major environmental factors shaping the abundance and community structure of SRB and SOB in aquaculture pond sediments. Findings of this study expand our current understanding of microbial driving sulfur cycling in aquaculture ecosystems and also provide novel insights for ecological and green aquaculture managements.

Occurrence of benthic microbial nitrogen fixation coupled to sulfate reduction in the seasonally hypoxic Eckernförde Bay, Baltic Sea

Abstract. Despite the worldwide occurrence of marine hypoxic regions, benthic nitrogen (N) cycling within these areas is poorly understood and it is generally assumed that these areas represent zones of intense fixed N loss from the marine system. Sulfate reduction can be an important process for organic matter degradation in sediments beneath hypoxic waters and many sulfate-reducing bacteria (SRB) have the genetic potential to fix molecular N (N2). Therefore, SRB may supply fixed N to these systems, countering some of the N lost via microbial processes, such as denitrification and anaerobic ammonium oxidation. The objective of this study was to evaluate if N2 fixation, possibly by SRB, plays a role in N cycling within the seasonally hypoxic sediments from the Eckernförde Bay, Baltic Sea. Monthly samplings were performed over the course of one year to measure nitrogenase activity (NA) and sulfate reduction rates, to determine the seasonal variations in bioturbation (bioirrigation) activity and important benthic geochemical profiles, such as sulfur and N compounds, and to monitor changes in water column temperature and oxygen concentrations. Additionally, at several time points, the active N-fixing community was examined via molecular tools. Integrated rates of N2 fixation (approximated from NA) and sulfate reduction showed a similar seasonality pattern, with highest rates occurring in August (approx. 22 and 880 nmol cm−3 d−1 of N and SO42−, respectively) and October (approx. 22 and 1300 nmol cm−3 d−1 of N and SO42− respectively), and lowest rates occurring in February (approx. 8 and 32 nmol cm−3 d−1 of N and SO42−, respectively). These rate changes were positively correlated with bottom water temperatures and previous reported plankton bloom activities, and negatively correlated with bottom water oxygen concentrations. Other variables that also appeared to play a role in rate determination were bioturbation, bubble irrigation and winter storm events. Molecular analysis demonstrated the presence of nifH sequences related to two known N2 fixing SRB, namely Desulfovibrio vulgaris and Desulfonema limicola, supporting the hypothesis that some of the nitrogenase activity detected may be attributed to SRB. Overall, our data show that Eckernförde Bay represents a complex ecosystem where numerous environmental variables combine to influence benthic microbial activities involving N and sulfur cycling.

Organic matter degradation in sediments of the York River estuary: Effects of biological vs. physical mixing

We investigated the influence of biological and physical seabed disturbance on the degradation of bulk organic matter and source specific lipid biomarker compounds by measuring downcore changes in bulk elemental composition, bulk stable isotopic (δ 13C and δ 15N) signatures, and lipid biomarker compounds in sediment cores collected from two sites in the York River, a subestuary of the Chesapeake Bay, USA. One site (LY) is influenced by biological mixing (bioturbation), restricted to the upper 15–20 cm, while the other site (POD) experiences intense, episodic physical mixing events that penetrate 50–100 cm into the sediment. We utilized a suite of auxiliary measurements to constrain the sources of organic matter, depositional environments, and general ages of the cores. Diagenetic modeling of total organic carbon and total nitrogen in sediments yielded higher apparent rate constants for POD than LY suggesting that the physical mixing regime promotes enhanced degradation of bulk organic matter. Apparent rate constants for select lipids representing distinct sources of organic matter were also higher at POD than LY for all but the most labile (i.e., diatom-derived fatty acids) biomarkers. Differences in stanol/stenol ratios also supported enhanced diagenesis of stenols at POD. The source-specific biomarkers, while useful in qualitatively identifying the sources of sedimentary organic matter, likely do not represent the full spectrum of its reactivity. However, based on our results, we hypothesize that the intense sediment disturbance at POD promotes degradation of more recalcitrant organic material, due to prolonged exposure to oxygen and other electron acceptors (e.g., NO 3 −, Mn and Fe oxides). In contrast, the degradation of more labile constituents is equally facilitated by biological and physical disturbance.

A model of oxygen reduction, denitrification, and organic matter mineralization in marine sediments1

Porewater nutrient profiles are sensitive indicators of organic matter degradation in sediments. To interpret these data, we have derived a kinetic model of oxygen reduction, nitrification, and denitrification which quantitatively relates the rates of oxygen reduction and denitrification to the depth separating these processes and the carbon oxidation rate.We have compared model profiles with porewater profiles of the sum of NO2−, NO3−, and NH4+ (∑N) from both Atlantic and Pacific Ocean stations. Calculated rates of oxygen reduction and denitrification vary proportionally at these stations. Extrapolation along this relationship predicts a maximum in NO3− even where the nitrification zone is so thin that only a decrease from bottom water samples is measured with a 1–2‐cm sampling interval. The model also predicts that the maximum amount of organic matter that can be oxidized by denitrification is only 30% of that oxidized by oxygen respiration in the Pacific and only 13% in the Atlantic Ocean.