variety of consumers and decomposers. These chemoorganoheterotrophic microorganisms, in their turn, form and sequester an equally wide variety of dissolved and particulate matter in marine waters and sediments. These biogeochemical transformations and recycling networks are central to the productivity, biodiversity, ecological balance, and resourcefulness of the oceanic waters and sediments. However, major microbe‐assisted functional metabolic processes identified so far in the water column of OMZ, include oxidative‐reductive cycling of sulfur compounds, methanogenesis, and N transformations.
1.7. NITROGEN METABOLISM IN THE MARINE MARINE OXYGEN MINIMUM ZONE WATER COLUMN
Bilogical nitrogen fixation (BNF) is the process by which N2 is converted to NH3 and subsequently into biomass by N2‐fixing bacteria and archaea (Sohm et al., 2011). The biomass produced during BNF and assimilation may then release N compounds into the ocean. The N loss through denitrification and anammox processes are dominant in the water column of the OMZs and the sediment underlying the OMZ (Capone and Knapp, 2007). For the last few decades, a substantial increase in oceanography and omics‐based data has dramatically improved our understanding of the marine N cycle, particularly in the OMZs. However, a contrasting influence of O2 concentrations on anammox and denitrification may be observed. On one hand, some experimental data shows 200 and 900 nM concentrations of DO cause a 50% drop in N2 production by the microbial community through denitrification and anammox metabolism, respectively (Dalsgaard et al., 2014). On the other hand, a separate study reports active denitrification and anammox metabolism in the presence of micromolar levels of DO in OMZ off Conceptión, Chile (Bristow et al., 2016).
Several literature reports show the selective prevalence of anammox group in the marine OMZ water column off northern Chile and ETSP ocean, compared with other types (Molina et al., 2005; Galán et al., 2009; Lam et al., 2009; Kalvelage et al., 2013), which may be attributed to release of NH4 + during decomposition of sinking organic matter in the water column and benthic NH4 + flux (Kalvelage et al., 2013).
Although some studies have revealed anammox (OMZs) off Namibia, Peru, and Chile (Thamdrup et al., 2006; Hamersley et al., 2007) as the predominant pathway of fixed N loss, data from the ASOMZ revealed dominance of denitrification metabolism over anammox activity in the water column (Ward et al., 2009; Bulow et al., 2010). Some recent studies have revealed the presence of Candidatus Scalindua clades 2 (predicted to have anammox activity) sequences from the ASOMZ (Woebken et al., 2008). The aerobic ammonia‐oxidizing archaea (AOA) and anaerobic ammonia‐oxidizing (anammox) bacteria show a unique depth distribution and niche segregation pattern (Pitcher et al., 2011) in the water column of ASOMZ, where the prevalence of AOA was found at a water depth of 170 m while anammox retained their highest abundance at a water depth of 450–750 m. However, archaeal and bacterial mediated ammonia oxidation also has been reported in OMZs of ETNP (Peng et al., 2015) (see Table 1.2 for detailed information). However, some recent reports also show nitrite oxidation in the OMZs of the ETNP and Namibian sea region (Füssel et al., 2012; Beman et al., 2013). The co‐existence of nitrite oxidation and anammox activity has been observed in the OMZ of the Namibian sea region,; indicating competition between the microbial population with each other for a common substrate, namely NO2 – (Füssel et al., 2012). Both Nitrococcus and Nitrospina were found to be the prevalent bacterial groups (9% of the total microbial community) in the OMZ of the Namibian sea region, whereas only the latter, was dominant for efficient nitrite oxidation in the OMZ of ETNP (Füssel et al., 2012; Beman et al., 2013). Moreover, functionally active microbial groups involved in OMZ water column nitrogen transformations identified to date through different omics‐based, culture‐based, and molecular approach includes Nitrosopumilus, Nitrosopelagicus, Nitrosospira, Nitrospina, Nitrococcus, Sagittula, Candidatus Scalindua, SAR11 group, SUP05/ARCTIC96BD‐19, Planctomycetes, among others (Molina et al., 2005; Beman et al., 2013; Bristow et al., 2016; Bertagnolli and Stewart, 2018). Furthermore, high‐throughput genetic and proteome‐level investigation (functional marker gene analysis, metatranscriptome, metaproteome) also highlighted the presence and functionality of microbes capable of nitrogen compound metabolism by the identification of respective enzymes from the OMZ waters such as ammonia monooxygenase enzyme active subunit (amoA), nitrous oxide reductase (nosZ), nitrite reductase (nirS), nitric oxide reductase (norB), nitrate reductase (narG), hydrazine oxidoreductase (hzo), nitrite reductase (nirK), nitrite oxidase (NXR) (Molina et al., 2005; Lam et al., 2009; Dalsgaard et al., 2014).
1.8. MICROBIOLOGICAL PERSPECTIVE OF SULFUR METABOLISM IN THE MARINE OXYGEN MINIMUM ZONE WATER COLUMN
Pioneering work by Canfield et al. (2010) first brought to the fore the role of sulfur species in the anaerobic sulfur cycling of Chilean OMZs. However, before this study, detection and isolation of several sulfur oxidizing–reducing, bacterial members from geographically distinct OMZ (off the coast of Peru and Chile) water also gave enough hints about their probable ecological relevance (Stevens and Ulloa, 2008; Finster and Kjeldsen, 2010). In general, sulfide produced in anoxic organic‐rich marine sediments via bacterial sulfate reduction is reoxidized within the sediment, resulting in minimal fluxes of the sulfide to the water column (Brüchert et al., 2003). Furthermore, retention sulfide in the water column also depends on biological or chemical oxidation: by precipitation as Fe sulfides and organic‐bound sulfur (OBS) formation (Brüchert, 1998). Nonetheless, some of the literature showed the presence of specific sulfide oxidizingand nitrate respiring or storing microbes (Thiomargarita sp.; Beggiatoa spp.) at the juncture of the sediment–water interface, although their ecological relevance in OMZ water column is not yet clearly understood (Schulz et al., 1999). However, for the last few years, advanced molecular‐omics and biogeochemical approaches have unravelled complex S‐cycling in the OMZ water column. For eample, a maximum abundance of metagenomic reads (individual DNA fragment sequenced) affiliated to sulfide oxidizing (6.3 to 16.2%) and sulfate reducing (2.1 to 2.4%) taxa have been detected in the Chilean OMZ water column (Canfield et al., 2010). Moreover, another bacterial group, Marinimicrobia clade SHBH1141, was also abundant in anoxic and anoxic–sulfidic OMZ waters, and can oxidize sulfide to polysulfide (polyS), that is ultimately stored and later regenerated to H2S. It also has the genetic potential for nitrous oxide reduction to N2 and is considered to have roles in both S and N cycles (Hawley et al., 2017; Bertagnolli and Stewart, 2018). However, as far as the sulfate‐reducing bacterial community in OMZ water is concerned, significant proportions of metagenomic reads ascribable to the genera Desulfatibacillum, Desulfobacterium, Desulfococcus, Syntrophobacter, and Desulfovibrio species have been found (Canfield et al., 2010; Bertagnolli and Stewart, 2018) (see Table 1.2 for detailed information). Furthermore, a survey of functional marker genes related to sulfur metabolism identified in the Chilean OMZ water column includes gene clusters for dissimilatory sulfite reductase enzyme (dsr), the sox gene complex, and the adenosine 5‐phosphosulfate (APS) reductase gene (apr) (Canfield et al., 2010). In the context of coupling between the S and N cycle, it is noteworthy that sulfate reduction may also contribute to the NH4 + requirements for anammox bacteria because there is ample evidence suggesting the inadequate liberation of NH4 + during the heterotrophic denitrification that is necessary to drive anammox activity in many OMZ waters (Thamdrup et al., 2006; Lam et al., 2009).
Table 1.2 Microbiological features of the well‐studied oxygen minimum zones (OMZs) water‐column of the global ocean.
| Sl. no | Name of the OMZ | O2 (μM) | In situ microbial processes detected so far (nitrogen metabolism) | Microbiology or molecular technique used for decrypting biogeochemical process |
Taxonomic
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