Functional gene diversity of oolitic sands from Great Bahama Bank

Abstract

Despite the importance of oolitic depositional systems as indicators of climate and reservoirs of inorganic C, little is known about the microbial functional diversity, structure, composition, and potential metabolic processes leading to precipitation of carbonates. To fill this gap, we assess the metabolic gene carriage and extracellular polymeric substance (EPS) development in microbial communities associated with oolitic carbonate sediments from the Bahamas Archipelago. Oolitic sediments ranging from high-energy 'active' to lower energy 'non-active' and 'microbially stabilized' environments were examined as they represent contrasting depositional settings, mostly influenced by tidal flows and wave-generated currents. Functional gene analysis, which employed a microarray-based gene technology, detected a total of 12,432 of 95,847 distinct gene probes, including a large number of metabolic processes previously linked to mineral precipitation. Among these, gene-encoding enzymes for denitrification, sulfate reduction, ammonification, and oxygenic/anoxygenic photosynthesis were abundant. In addition, a broad diversity of genes was related to organic carbon degradation, and N2 fixation implying these communities has metabolic plasticity that enables survival under oligotrophic conditions. Differences in functional genes were detected among the environments, with higher diversity associated with non-active and microbially stabilized environments in comparison with the active environment. EPS showed a gradient increase from active to microbially stabilized communities, and when combined with functional gene analysis, which revealed genes encoding EPS-degrading enzymes (chitinases, glucoamylase, amylases), supports a putative role of EPS-mediated microbial calcium carbonate precipitation. We propose that carbonate precipitation in marine oolitic biofilms is spatially and temporally controlled by a complex consortium of microbes with diverse physiologies, including photosynthesizers, heterotrophs, denitrifiers, sulfate reducers, and ammonifiers.

Geochemical evidence of microbial activity within ooids

“…Another plausible explanation, which is supported by the high levels in the leachate fluids, is that bacterial communities – many of which can have a regulatory mechanism to select for powerful oxidizing agents – are preferentially using over because is thermodynamically a more favourable electron acceptor. This latter hypothesis may also be consistent with Geochip4 studies on the apparent predominance of denitrification over sulphate reduction in ooid environments (Diaz et al ., ).…”

“…In contrast, the δ 13 C values of organic C in Butterfly Beach are within the levels reported for the carbonate sediments of GBB (−12·24‰; Oehlert et al ., ) and carbonate deposits colonized by EPS‐biofilm enriched with carbohydrates (−12‰; Klock et al ., ; Nitti et al ., ). Based on previous studies that include Bahamian ooids from high to low energy environments, a higher abundance of EPS is found in ooid environments that experience less shear and abrasion forces (Zhang et al ., ; Piggot et al ., ; Diaz et al ., , ). In view of the fact that Butterfly Beach is a protected leeward environment, sediments at this locality experience less hydrodynamic forces than those in the active shoals where velocities can exceed 100 cm sec −1 (Rankey et al ., ; Reeder & Rankey, ).…”

“…Based on this study, the δ 15 N fractionation patterns in the isolated organic fractions, which show a narrow range and vary between +0·5‰ and −1·7‰, are consistent with the δ 15 N fractionation pattern of nitrogen fixers with values ranging from −2 to +2‰ (Delwiche & Stein, ). Potential nitrogen fixers that contribute to the documented near zero fractionation values include cyanobacteria (for example, Lyngbya , Leptolynbya , Anabaena , Nostoc , Synechocystis , Synechococcus , etc) and members within the Proteobacteria , Firmicutes , Chlorobi and Euryarchaeota (Diaz et al ., , ). Although, nitrogen fixation is a complex and energy intensive metabolic process that requires abundant iron that is most likely to be supplied to the area by atmospheric sources (Swart et al ., ), based on these values, this process appears to be important in supporting new production in these otherwise oligotrophic waters (Carpenter & Romans, ; Karl et al ., ).…”

Comments on "Estimating the impact of early diagenesis on isotope records in shallow-marine carbonates: A case study from the Urgonian platform in western Swiss Jura" by A. Godet et al. [Palaeogeography Palaeoclimatology Palaeoecology 454 (2016) 125-138]

“…There is evidence that microbial processes are actively involved at various stages in their mineralization (BREHM et al, 2004;EDGCOMB et al, 2013;DIAZ et al, 2013DIAZ et al, , 2014DIAZ et al, , 2015O'REILLY et al, 2016). For instance, some microbes may promote mineralization of ooids that takes place in extracellular polymeric substances (EPS) whereas others may alter the original mineralization of ooid cortices (DUGUID et al, 2010).…”

Co‐existence of skeletal and ooid shoals as a result of antecedent topography—Cat cay shoal complex, Bahamas

“…Recently the change from skeletal to ooid formation has been considered an indicator of an environmental crisis caused by anoxic events based on the fact that microbial carbonates are indicators of environmental change (Whalen, Day, Eberli, & Homewood, ). The ooids in the Cat Cay ooid shoal harbour, like all ooids on Great Bahama Bank, a highly diverse microbial community with capabilities of carbonate precipitation (Diaz, Piggot, Eberli, & Klaus, ; Diaz et al, , ; Diaz, Eberli, Blackwelder, Phillips, & Swart, ; Edgcomb et al, ; O’Reilly et al, ). Microbial activities in tandem with the physicochemical conditions of the extracellular polymeric substances micro‐domains control the organomineralization processes in ooids through two distinct avenues: biologically induced and biologically influenced mechanisms (Diaz & Eberli, ; Harris et al, ).…”