Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

Abstract

Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor.

Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia

“…At the SWI, Gammaproteobacteria prevailed in the taxonomic assemblage (Fig. 2), evidencing a benthic-pelagic transition where denitrification and DNRA can be coupled with sulfur oxidation (Callbeck et al, 2018) as sulfate reduction is the prevailing process in the underlying sediment (Vuillemin et al, 2022). Because nitrate is used as an oxidant by sulfur-oxidizing bacteria (Zhu et al, 2018) to drive DNRA, we suspect that anammox processes may be inhibited in the surface sediment (Jensen et al, 2008; Jin et al, 2013; Schunck et al, 2013).…”

“…As stratification decreases along the shelf, NH 4 + can be locally released from the seafloor into the benthic boundary layer (Füssel et al, 2012; Neumann et al, 2016). Seasonal variations in Namibian coastal waters may thereby promote chemolithoautotrophy with sulfur and NH 4 + as successive electron donors (Farías et al, 2009; Lam and Kuypers, 2011) to drive sulfur-dependent denitrification by Gammaproteobacteria (Lipsewers et al, 2017; Vuillemin et al, 2022) pursued by nitrifier denitrification by Nitrososphaeria and Nitrospinota in the water column (Wrage-Mönnig et al, 2018; Ruiz-Fernández et al, 2020).…”

“…In spite of members of the Gammaproteobacteria, e.g. Beggiatoa, Thiothrix, Thioploca (Vuillemin et al, 2022), being capable of coupling DNRA with sulfide oxidation (Schunck et al, 2013; Crowe et al, 2018; Zhu et al, 2018), the abundance of ORFs expressing ammonia-forming nrf genes (i.e. DNRA) was minor (Figs.…”

“…1C) results from amino acid remineralization (i.e. algal necromass) via expression of proteases by heterotrophic bacteria (Neumann et al, 2016) rather than DNRA (Pantoja and Lee, 2003; Vuillemin et al, 2022). In the bottom part of the core (28 cmbsf), ORFs assigned to nar and nir genes were mainly expressed by Proteobacteria, whereas nor and nos genes were also expressed by taxa among Methylomirabilota (former candidate NC10) (Padilla et al, 2016) and Desulfobacterota, but gene expression of these final steps of denitrification was minor in the sediment (Figs.…”

“…For size-fractionated filters, DNA was extracted by adding 850 mL of a sucrose ethylenediaminetetraacetic acid (EDTA) lysis buffer (0.75 M sucrose, 0.05 M Tris-Base, 0.02 M EDTA, 0.4 M NaCl, pH 9.0) and 100 mL of 10% sodium dodecyl sulfate to 2 mL bead-beating tubes containing the filters and 0.1 mm sterile glass beads, following a published protocol (Orsi et al, 2015; Vuillemin et al, 2022). After bead beating for 1 min and heating at 99 °C for 2 min, we added 25 mL of 20 mg × mL −1 proteinase K to the samples and incubated them at 55 °C overnight.…”