Autotrophic carbon fixation pathways along the redox gradient in oxygen‐depleted oceanic waters

Abstract

Anoxic marine zones (AMZs), also known as 'oxygendeficient zones', contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the autotrophic carbon fixationa crucial component of the carbon cycle. Using metagenomic and metatranscriptomic data from major AMZs, we report an explicit partitioning of the marker genes associated with different autotrophic carbon fixation pathways along the redox gradient (from oxic to anoxic conditions) present in the water column of AMZs. Sequences related to the Calvin-Benson-Bassham cycle were found along the entire gradient, while those related to the reductive Acetyl-CoA pathway were restricted to suboxic and anoxic waters. Sequences putatively associated with the 3-hydroxypropionate/4-hydroxybutyrate cycle dominated in the upper and lower oxyclines. Genes related to the reductive tricarboxylic acid cycle were represented from dysoxic to anoxic waters. The taxonomic affiliation of the sequences is consistent with the presence of microorganisms involved in crucial steps of biogeochemical cycles in AMZs, such as the gamma-proteobacteria sulfur oxidisers, the anammox bacteria Candidatus Scalindua and the thaumarcheota ammonia oxidisers of the Marine Group I.

Unique bacterial communities and potential function along the vertical gradient in the deepest marine blue hole

“…By further investigation on pathway level 3, several functions were confirmed to be more abundant in water column below 90 m; for example, Pyruvate metabolism, Glyoxylate and dicarboxylate metabolism, amino sugar and nucleotide sugar metabolism and butanoate metabolism (affiliated to carbohydrate metabolism), carbon fixation pathways in prokaryotes (affiliated to energy metabolism), homologous recombination (affiliated to replication and repair), bacterial secretion system (affiliated to membrane transport), flagellar assembly and bacterial chemotaxis (affiliated to cell motility), and biofilm formation – Vibrio cholerae (affiliated to cellular community – prokaryotes). The results confirmed the vital processes of carbon and nutrient cycling in the anoxic environment in the deep blue hole (Ruiz‐Fernández et al ., 2020).…”

Metaomics unveils the contribution of Alteromonas bacteria to carbon cycling in marine oxygen minimum zones

“…In contrast to our current knowledge of the nitrogen, sulfur, and oxygen cycles in OMZs (Ganesh et al, 2014;Ganesh et al, 2015;Glass et al, 2015;Garcia-Robledo et al, 2016;Garcia-Robledo et al, 2017;Fuchsman et al, 2017;Saunders et al, 2019;Raven et al, 2021), the carbon cycle has been poorly characterized in these low-oxygen environments. Recently couplings between carbon, sulfur, and nitrogen metabolisms have been proposed (Plominsky et al, 2018), along with the partitioning of different carbon fixation pathways along the AMZ redox gradient (Ruiz-Fernańdez et al, 2020). Considering all the caveats regarding metatranscriptomic fragment recruitment, the data presented here suggests an in situ coupling of Alteromonas iron and carbon metabolisms and the potential importance of its glyoxylate cycle in the AMZs.…”

Metagenomics revealing molecular profiling of microbial community structure and metabolic capacity in Bamucuo, Tibet

“…The reductive acetyl-CoA pathway was found to be the most abundant carbon fixation pathway in deep biosphere (41, 42), however, our results suggested that this pathway does not work for the microorganisms in Bamucuo. The 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle pathways existed in thermophilic archaea, however, Ruiz-Fernandez et al concluded that the 3-hydroxypropionate/4-hydroxybutylate cycle is the dominant pathway in anoxic marine zones (43). Obviously, their conclusion is different from ours.…”

“…3b). The top three GO terms were as follows: cellular process (45,113), metabolic process (43,200) and response to stimulus (12,611) among the biological processes; catalytic activity (35,860), binding (24,853) and structural molecule activity (4,247) among the molecular functions; and cell (45,101), cell part (45,101) and membrane (19,524) among the cellular components.…”