Denitrification of Permeable Sand Sediment in a Headwater River Is Mainly Influenced by Water Chemistry, Rather Than Sediment Particle Size and Heterogeneity

Sediment particle size and heterogeneity play an important role in sediment denitrification through direct and indirect effects on, for example, the material exchange rate, environmental gradients, microbial biomass, and grazing pressure. However, these effects have mostly been observed in impermeable sediments. On the other hand, the material exchange of permeable sediments is dominated by advection instead of diffusion, with the exchange or transport rates exceeding those of diffusion by two orders of magnitude relative to impermeable sediments. The impact of permeable sediment particle size and heterogeneity on denitrification remains poorly understood, especially at the millimeter scale. Here, we conducted an in situ control experiment in which we sorted sand sediment into four homogeneous-particle-sizes treatments and four heterogeneous treatments. Each treatment was deployed, in replicate, within the riffle in three different river reaches with contrasting physicochemical characteristics. After incubating for three months, sediment denitrifier communities (nirS, nirK, nosZ), denitrification gene abundances (nirS, nirK, nosZ), and denitrification rates in all treatments were measured. We found that most of the denitrifying microbes in permeable sediments were unclassified denitrifying microbes, and particle size and heterogeneity were not significantly correlated with the functional gene abundances or denitrification rates. Water chemistry was the key controlling factor for the denitrification of permeable sediments. Water NO3−-N directly regulated the denitrification rate of permeable sediments, instead of indirectly regulating the denitrification rate of sediments by affecting the chemical characteristics of the sediments. Our study fills a knowledge gap of denitrification in permeable sediment in a headwater river and highlights that particle size and heterogeneity are less important for permeable sediment denitrification.

Benthic Oxygen dynamics: Influence of pore water advection and microphytobenthos in a permeable sediment

<p>The benthic oxygen consumption rate (OCR) has been widely used to measure the total benthic organic carbon degradation rate, while the oxygen distribution provides the general biogeochemistry state of marine sediments. In shallow coastal environments the light driven photosynthesis by benthic microalgae, resulting in large diurnal oscillations of oxygen concentration, further affects the oxygenation of the sediment. Yet, for permeable sediments, studies incorporating pore water advection driven by physical forces into oxygen consumption and distribution measurements are  still limited. Here we examine the combined effect of benthic oxygen production and advective oxygen transport on oxygen dynamics and consumption rate in a microphytobenthos-dominated sediment (permeability <em>k </em>=2 x 10<sup>-11</sup> to 5 x 10<sup>-11</sup> m<sup>2</sup>) in a laboratory simulation with stirred benthic chambers at 40 rpm. Under alternating light (50 μE m<sup>−2</sup> s<sup>-1</sup>) and flow regimes, oxygen concentration, penetration depth and consumption rates were monitored by means of micro-profiling and planar optode measurements. In all cases, we found that oxygen penetration depth increased up to a factor of 2 with pore water flow simulation. On the other hand, advective transport was found to reduce maximum oxygen concentration in the sediment by up to 30 %.  The OCR were up to 2-times higher with only light (28 ± 3.5 µM/min) compared to combined light and flow simulation, however the total oxygen uptake was generally uniform in all chambers (41.83 ± 5.9 mmol/m<sup>2 </sup>d<sup>-1</sup>), suggesting the local redistribution of oxygen with flow without marked overall changes in O<sub>2</sub> consumption. Our result emphasized the importance of advective transport controlling benthic oxygenation in photic permeable sediment.</p>

Characterization of Nitrifying, Denitrifying, and Overall Bacterial Communities in Permeable Marine Sediments of the Northeastern Gulf of Mexico

ABSTRACT Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.