Using Molecular Tools to Understand Microbial Carbonates

Abstract

Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized the overall community composition of mats, pinpointed microbes involved in key metabolisms, and revealed patterns in the distributions of microbial groups and functional genes. Molecular tools have become widely accessible, and we can now aim to establish firmer links between microbes and mineralization. Two promising future directions include “zooming in” to assess the roles of specific organisms, microbial groups, and surfaces in carbonate biomineralization and “zooming out” to consider broader spans of space and time. A middle ground between the two can include model systems that contain representatives of important microbial groups, processes, and metabolisms in mats and simplify hypothesis testing. These directions will benefit from expanding reference datasets of marine microbes and enzymes and enrichments of representative microbes from mats. Such applications of molecular tools should improve our ability to interpret ancient and modern microbialites and increase the utility of these rocks as long-term recorders of microbial processes and environmental chemistry.

A review of microbial‐environmental interactions recorded in Proterozoic carbonate‐hosted chert

“…The precipitation of calcium carbonate in modern microbial mats has well‐documented connections to microbial activity and organic compounds (Cutts et al, 2022; Dupraz et al, 2009 and references therein). Experimental studies have highlighted the contribution of metabolic activity to the alkalinity engine and carbonate precipitation (Cutts et al, 2022; Dupraz et al, 2009 and references therein). Both oxygenic photosynthesis (reaction 1; Arp et al, 2001; Dupraz & Visscher, 2005; Kranz et al, 2010; Schneider & Campion‐Alsumard, 1999; Zaitseva et al, 2006) and sulfate reduction (reaction 2; Arp et al, 2003; Dupraz & Visscher, 2005; Kempe & Kazmierczak, 1994; Lith et al, 2003; Lyons et al, 1984; Visscher et al, 1998, 2000; Visscher & Stolz, 2005; Walter et al, 1993; Zavarzin, 2002) have been linked to carbonate precipitation through their influence on local alkalinity. …”

“…incorporation into incipient carbonate minerals following the initial degradation of EPS (Cutts et al, 2022;Skoog et al, 2022).…”

“…The nucleation of silica may require metabolically-driven pH changes and fresh cyanobacterial EPS (Moore et al, 2020(Moore et al, , 2021, whereas anoxic conditions, degradation of EPS, and anaerobic microbial communities may favor the precipitation of dolomite and calcite. If so, the distributions of early diagenetic dolomite, calcite, and chert in time and space may reflect the compositional variations of microbial communities, surfaces, and redox conditions within a mat (Cutts et al, 2022), as well as the temporal trends in seawater Ca:Mg ratios and silica concentrations. In the following section, we review the distributions and spatial correlations of microbially laminated dolomite with fossiliferous chert in light of the potential microbial contributions to the precipitation of both minerals.…”

“…The precipitation of calcium carbonate in modern microbial mats has well‐documented connections to microbial activity and organic compounds (Cutts et al, 2022 ; Dupraz et al, 2009 and references therein). Experimental studies have highlighted the contribution of metabolic activity to the alkalinity engine and carbonate precipitation (Cutts et al, 2022 ; Dupraz et al, 2009 and references therein).…”

“…Recent experimental work additionally revealed that the presence and activity of anoxygenic photosynthetic bacteria and the presence of reduced cations such as Mn 2+ (Daye et al, 2019 ; DiLoreto et al, 2019 ) can lead to the precipitation of dolomite, which in some cases can be fine‐crystalline and fabric retentive (Daye et al, 2019 ) (Figure 9b ). More recent analyses also noted the large Mg‐binding capacity of the EPS produced by pustule‐forming cyanobacteria (Moore et al, 2020 , 2021 ), inviting questions about the release of this cation and its incorporation into incipient carbonate minerals following the initial degradation of EPS (Cutts et al, 2022 ; Skoog et al, 2022 ).…”