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Abstract Lacustrine carbonates are a powerful archive of paleoenvironmental information but are susceptible to post‐depositional alteration. Microbial metabolisms can drive such alteration by changing carbonate saturationin situ, thereby driving dissolution or precipitation. The net impact these microbial processes have on the primary δ¹⁸O, δ¹³C, and Δ₄₇values of lacustrine carbonate is not fully known. We studied the evolution of microbial community structure and the porewater and sediment geochemistry in the upper ~30 cm of sediment from two shoreline sites at Green Lake, Fayetteville, NY over 2 years of seasonal sampling. We linked seasonal and depth‐based changes of porewater carbonate chemistry to microbial community composition, in situ carbon cycling (using δ¹³C values of carbonate, dissolved inorganic carbon (DIC), and organic matter), and dominant allochems and facies. We interpret that microbial processes are a dominant control on carbon cycling within the sediment, affecting porewater DIC, aqueous carbon chemistry, and carbonate carbon and clumped isotope geochemistry. Across all seasons and sites, microbial organic matter remineralization lowers the δ¹³C of the porewater DIC. Elevated carbonate saturation states in the sediment porewaters (Ω > 3) were attributed to microbes from groups capable of sulfate reduction, which were abundant in the sediment below 5 cm depth. The nearshore carbonate sediments at Green Lake are mainly composed of microbialite intraclasts/oncoids, charophytes, larger calcite crystals, and authigenic micrite—each with a different origin. Authigenic micrite is interpreted to have precipitated in situ from the supersaturated porewaters from microbial metabolism. The stable carbon isotope values (δ¹³C_carb) and clumped isotope values (Δ₄₇) of bulk carbonate sediments from the same depth horizons and site varied depending on both the sampling season and the specific location within a site, indicating localized (μm to mm) controls on carbon and clumped isotope values. Our results suggest that biological processes are a dominant control on carbon chemistry within the sedimentary subsurface of the shorelines of Green Lake, from actively forming microbialites to pore space organic matter remineralization and micrite authigenesis. A combination of biological activity, hydrologic balance, and allochem composition of the sediments set the stable carbon, oxygen, and clumped isotope signals preserved by the Green Lake carbonate sediments. 

Abstract Organic and inorganic stable isotopes of lacustrine carbonate sediments are commonly used in reconstructions of ancient terrestrial ecosystems and environments. Microbial activity and local hydrological inputs can alter porewater chemistry (e.g., pH, alkalinity) and isotopic composition (e.g., δ¹⁸O_water, δ¹³C_DIC), which in turn has the potential to impact the stable isotopic compositions recorded and preserved in lithified carbonate. The fingerprint these syngenetic processes have on lacustrine carbonate facies is yet unknown, however, and thus, reconstructions based on stable isotopes may misinterpret diagenetic records as broader climate signals. Here, we characterize geochemical and stable isotopic variability of carbonate minerals, organic matter, and water within one modern lake that has known microbial influences (e.g., microbial mats and microbialite carbonate) and combine these data with the context provided by 16S rRNA amplicon sequencing community profiles. Specifically, we measure oxygen, carbon, and clumped isotopic compositions of carbonate sediments (δ¹⁸O_carb, δ¹³C_carb, ∆₄₇), as well as carbon isotopic compositions of bulk organic matter (δ¹³C_org) and dissolved inorganic carbon (DIC; δ¹³C_DIC) of lake and porewater in Great Salt Lake, Utah from five sites and three seasons. We find that facies equivalent to ooid grainstones provide time‐averaged records of lake chemistry that reflect minimal alteration by microbial activity, whereas microbialite, intraclasts, and carbonate mud show greater alteration by local microbial influence and hydrology. Further, we find at least one occurrence of ∆₄₇isotopic disequilibrium likely driven by local microbial metabolism during authigenic carbonate precipitation. The remainder of the carbonate materials (primarily ooids, grain coatings, mud, and intraclasts) yield clumped isotope temperatures (T(∆₄₇)), δ¹⁸O_carb, and calculated δ¹⁸O_waterin isotopic equilibrium with ambient water and temperature at the time and site of carbonate precipitation. Our findings suggest that it is possible and necessary to leverage diverse carbonate facies across one sedimentary horizon to reconstruct regional hydroclimate and evaporation–precipitation balance, as well as identify microbially mediated carbonate formation. 

Great Salt Lake hosts an ecosystem that is critical to migratory birds and international aquaculture, yet it is currently threatened by falling lake elevation and high lakewater salinity resulting from water diversions in the upstream watershed and the enduring megadrought in the western United States. Microbialite reefs underpin the ecosystem, hosting a surface microbial community that is estimated to contribute 30% of the lake’s primary productivity. We monitored exposure, desiccation, and bleaching over time in an area of microbialite reef. During this period, lake elevation fell by 1.8 m, and salinity increased from 11.0% to 19.5% in open-water portions of the outer reef, reaching halite saturation in hydrologically closed regions. When exposed, microbialite bleaching was rapid. Bleached microbialites are not necessarily dead, however, with communities and chlorophyll persisting beneath microbialite surfaces for several months of exposure and desiccation. However, superficial losses in the mat community resulted in enhanced microbialite weathering. In microbialite recovery experiments with bleached microbialite pieces, partial community recovery was rapid at salinities ≤ 17%. 16S and 18S rRNA gene sequencing indicated that recovery was driven by initial seeding from lakewater. At higher salinity levels, eventual accumulation of chlorophyll may reflect accumulation and preservation of lake material in halite crusts vs. true recovery. Our results indicate that increased water input should be prioritized in order to return the lake to an elevation that submerges microbialite reefs and lowers salinity levels. Without quick action to reverse diversions in the watershed, loss of pelagic microbial community members due to sustained high salinity could prevent the recovery of the ecosystem-critical microbialite surface communities in Great Salt Lake.