Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.

Florida Bay, a shallow, seagrass-dominated bay in southern Florida, USA, receives significant nutrient inputs and has experienced seagrass losses and microalgal blooms within the last several decades. Inorganic nutrient inputs have been well characterized, but the role of organic nutrients, specifically of dissolved organic nitrogen (DON) and organic phosphorus (DOP), in supporting microbial processes in the bay is unknown. In this study various techniques were used to assess the importance of these nutrients along a transect in Florida Bay when a cyanobacterial bloom occurred in the central region in November 2002. These techniques included measurements of ambient particulate and dissolved nutrients, enzyme (urease and alkaline phosphatase) activities, and experiments to determine rates of 15 N uptake (nitrate, ammonium, urea, and amino acids over a period of 0.5 h) and long-term (48 h) changes in microbial biomass and 15 N natural abundance in enrichment bioassays. The cyanobacterial bloom in central Florida Bay was associated with the highest concentrations of DON and DOP, whereas the microflagellate-and diatom-dominated eastern bay region was associated with the highest concentrations of inorganic nutrients. The zeaxanthin:chlorophyll a ratio (an indicator of the relative contribution of cyanobacteria to phytoplankton biomass) was positively correlated with the rate of uptake of urea, and negatively correlated with the rate of uptake of inorganic nitrogen. The opposite pattern was observed for the fucoxanthin:chlorophyll a ratio (indicative of relative diatom biomass) and the peridinin:chlorophyll a ratio (indicative of relative photosynthetic dinoflagellate biomass), suggesting that different algal groups were using different N substrates. Biomass responses in the bioassay experiments showed that phytoplankton (as chlorophyll a) responded to DON additions in the western region and to DOP additions in the eastern region, but heterotrophic bacteria, in contrast, responded to DOP additions in the west and DON additions in the east. These findings thus demonstrate the potential for different sources of N, including DON, to stimulate different components of the algal community, and for the phytoplankton and bacteria to respond differently to N and P.KEY WORDS: Florida Bay · Cyanobacteria · Organic N · Organic P · Nutrient limitation · Urease · Alkaline phosphatase · Bioassay · Nutrient uptake rates Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 280: [73][74][75][76][77][78][79][80][81][82][83] 2004 changes. Since the onset of industrialization in the 1880s, the health of the Florida Bay ecosystem has been negatively impacted on both decadal (e.g. increasing eutrophication) and centurial (e.g. changes in land use and water management practices within southern Florida) time-scales (Fourqurean & Robblee 1999). These anthropogenic changes have led to a significant alteration in freshwater flow patterns within the Everglades, causing declines in seagrass d...

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