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.

Identification of phytodetritus‐degrading microbial communities in sublittoral Gulf of Mexico sands

“…This area is adjacent to an uninhabited region of the island and is considered relatively unaffected by anthropogenic effects. Sediments at the site consist of well-sorted quartz sand (grain median 209 to 220 mm) with a low organic matter content (,0.1%), a permeability of 1.6 to 2.9 3 10 211 m 2 , and a porosity of 31% to 37% (Mills et al 2008). Sediment cores of 10-cm depth were collected by hand at 1.5-2.0-m water depth using 9-cm-diameter, 20-cm-long acrylic core tubes.…”

Structure of denitrifying communities reducing N2O at suboxic waters off northern Chile and Perú

“…A selection of environmental nosZ clones from marine sediment (Scala & Kerkof 1999, Mills et al 2008, soils (Stres et al 2004, Horn et al 2006, wastewater (Sakano et al 2002) and coastal seawater (unpublished, Accession #AB089825, AB089829 and AB089832) were chosen to cover the greatest possible sequence variation. The tree was reconstructed using sequences of partial gene fragments (1137-bp) with Neighbor Joining and Maximum Likelihood method integrated in the Bosque program.…”

“…There are only a few reports carried out in marine environments such as coastal sediments (Scala & Kerkof 1999, Mills et al 2008, estuarine wetlands (Chon et al 2011) and seawater (Stewart et al 2012, Ganesh et al 2013.…”

Start-up and performance of UASB reactors using zeolite for improvement of nitrate removal process

“…Gammaproteobacteria include Pseudomonas, some of which use nitrate as an electron acceptor, and, therefore, play a key role in denitrification systems. Recent studies related to marine sediments (Mills et al, 2008) show a high abundance of Gammaproteobacteria in processes of nitrification and denitrification, attributable to a high level of metabolism of these microorganisms, which leads to rapid changes in oxygen and substrates as occurs in the sands of the sea. Figure 1 shows the images of FISH obtained for the reactors with zeolite diameters of 1.0 and 0.5 mm.…”