redox species of S cannot be ruled out in the S cycle of the OMZ water column.
1.9. MICROBIOLOGY OF METHANE CYCLING IN THE OXYGEN MINIMUM ZONE WATER COLUMN
High‐resolution water‐column studies revealed the existence of a 300 m thick layer with elevated methane concentrations (20–105 nM) in the anoxic core of ETNP (Chronopoulou et al., 2017). Another geochemical investigation also revealed presence of CH4 in the eastern ETNP water column (Pack et al., 2015) (for concentrations and its oxidation rates see Table 1.2). Several omics‐based investigations revealed the presence of genes (particulate methane monooxygenase: pMMO) and transcripts (16S rRNA and other relevant functional genes) belonging to a unique group of denitrifying methanotrophs in the candidate bacterial division NC10 from Eastern Pacific OMZs (Padilla et al., 2016). This bacterial group has the genetic potential to perform nitric oxide dismutation along with oxygen production, thus holding significant importance in coupling the NO2 – and CH4 cycle. However, successive high‐throughput genome binning experiments from the aforementioned ecosystem recovered near‐complete (95%) draft genome representing another methanotroph clade OPU3 (having genomic potential for partial denitrification) that forms a maximum abundance of (4%) of the total microbial community sequenced (Padilla et al., 2017). Although metagenomic studies on the ASOMZ water column showed the existence of CH4 cycling, the active functionality of this cycle needs further biogeochemical and microbiological substantiation (Lüke et al., 2016).
1.10. MICROBIAL METABOLISM IN MARINE OXYGEN MINIMUM ZONE SEDIMENTS
In general, OMZ sediments are characterized by two predominant microbial processes: sulfate reduction and methanogenesis. However, most of the well‐characterized OMZ sediments exhibited distinct zonation patterns depending on these two metabolic processes. It has generally been observed that sulfate reducing bacteria and methanogenic archaea compete for the common substrates such as hydrogen and acetate. Owing to higher substrate affinity, sulfate reducing bacteria have the ability to outcompete methanogenic archaea as long as SO4 2– ions are present in the sediment porewaters to act as electon acceptor (Treude et al., 2014; Maltby et al., 2016). As seawater is the main source of SO4 2– in the marine sediment, a downward replenishing of the SO4 2– concentration in the sediment‐pore‐water influences the sulfate reduction rate. However, microbial methanogenesis only starts when the SO4 2– in the sediment is nearly or entirely exhausted. The overlapping zone between these two is generally known as a sulfate methane transition zone (SMTZ), where both the SO4 2‐ and CH4 coexist (Treude et al., 2014; Maltby et al., 2016). Irrespective of the depth at which they occur, SMTZs are commonly found in all anoxic sediments where SO4 2– is transported from above and CH4 is transported from the bottom. Thus, SMTZ is considered a hot spot for anaerobic oxidation of methane via the syntrophic relationship between sulfate reducers and methanotrophs (Knittel and Boetius, 2009).
Sulfate reduction is generally carried out by both bacteria and archaeal groups. They typically couple the oxidation of organic compounds or molecular hydrogen to the reduction of SO4 2– to H2S to obtain their energy. Sulfate reducing bacteria are also able to utilize a variety of low molecular mass organic compounds such as monocarboxylic and dicarboxylic aliphatic acids, alcohols, polar aromatic compounds, and hydrocarbons as electron donors (Rabus et al., 2006). In contrast, methanogenesis, is restricted only to archaea. They are obligate CH4 producers: i.e. they obtain all of their required energy by producing CH4 only. Methanogenic archaea can use a restricted number of substrates for CH4 production, such as CO2 and H2 (for the hydrogenotrophic group) along with acetate (acetoclastic group) and methanol, methylamine, etc. (methylotrophic group) (Hedderich and Whitman, 2006). Substrates for both sulfate reduction and methanogenesis are formed as the end products of biodegradation and fermentation of organic macromolecules. While hydrogenotrophic and acetoclastic methanogenesis depends on common substrates with sulfate reduction, methylotrophic methanogenesis uses distinct substrates. Having a higher affinity towards their substrates, sulfate reducers always outcompete hydrogenotrophic and acetoclastic methanogens.
However, methylotrophic methanogens can escape this competition with sulfate reducers and operate methanogenesis metabolism simultaneously with sulfate reduction in the SO4 2– containing sediment zone. However, the co‐occurrence of sulfate reduction and methanogenesis is also possible and mostly observed in organic‐rich sediments. Anaerobic methanotrophic archaea (with AOM potential) are also found in syntrophic association with sulfate reducing bacteria. So far as their taxonomic affiliations are concerned, methanotrophic archaea are formed three distinct clusters related to orders Methanosarcinales and Methanomicrobiales under the phylum Euryarchaeota (Knittel and Boetius 2009). Moreover, AOM enriches the sediment with HCO3 – and HS– and selectively increases the 12C in the in situ DIC.
Notably, an abundance of sulfate reducing bacteria along with high aerial sulfate reduction rate, high pore‐water sulfide concentration, and shallowing of the SMTZ depth has been detected in the ASOMZ sediments located in the center of the vertical expanse of the OMZ (Fernandes et al., 2018). The AOM was also identified in the same sediment cores from the signature of significant 13C depletion in the DIC content (Fernandes et al., 2018). However, another recent study based on seasonal oxygen minimum zones (sOMZ) and pOMZ across the western Indian shelf; revealed the abundance of methanogens/anaerobic‐methane‐oxidizers/sulfate‐reducers/acetogens that heightened in the topmost sediment layer and then declined via synchronized fluctuations until the SMTZ was reached (Bhattacharya et al., 2021). Furthermore, another recent study based on the same ASOMZ sediment system also revealed the functionally active aerobic bacterial community that belongs to a diverse bacterial group (sulfur chemolithotrophs; methylotrophs etc.) (Bhattacharya et al., 2020) (see Table 1.3 for detailed information). The functional genomics and transcriptomics approach detected several genes responsible for aerobic respiration and oxidation of methane, ammonia, alcohol, thiosulfate,sulfite, and organosulfur compounds, thereby indicating the existence of diverse metabolic groups distinct from prototypical sulfate reducers or methanogens. Notably, in this context, another work by Mandal et al. (2020) also revealed the dynamics of functionally active tetrathionate metabolizing bacterial community along with decrypting the role of tetrathionate in the sedimentary S cycle of ASOMZ sediments. Conversely, although some other geochemical exploration based on OMZs of the Pakistan margin of the AS revealed sedimentary Mn, P, Fe, and S cycling, microbial involvement for those metabolism has still to be addressed (Law et al., 2009; Kraal et al., 2012).
Another study revealed the co‐occurrence of methanogenesis and sulfate reduction in the sediment surface of the upwelling region off the Peruvian coast, which is considered to be one of the most intense OMZs (Maltby et al., 2016). This study indirectly indicated the use of non‐competitive substrates for methanogenesis in the sulfate reducing zone and a higher availability of organic carbon in the sediments as the potential cause of this unusual phenomenon. Furthermore, active benthic N cycling in the Peruvian OMZ was also reported by Dale et al. (2016), who also elucidated the role of Thioploca community dynamics as a NO3 – reservoir and an effective barrier to H2S emissions to the water column. Nevertheless, taxon‐specific meta‐omics exploration from physiographically distinct marine OMZ identified a diverse bacterial group that thus far includes Deltaproteobacteria (Syntrophobacterales and Desulfovibrionales), Chloroflexi, Planctomycetes, Spirochetes, Firmicutes, Acidobacteria, and Verrucomicrobia, etc.(Divya et al., 2010; Podlaska et al., 2012; Fernandes et al., 2018).
Table 1.3 Microbiological features of the well‐studied oxygen minimum zones (OMZs) sediment of the global ocean.
