Chloroflexi persisting for millions of years in oxic and anoxic deep-sea clay

Chloroflexi are widespread in energy-limited subseafloor sediments, but how Chloroflexi respond to subseafloor energy limitation under oxic and anoxic conditions is poorly understood. Here, we characterize the diversity, abundance, activity, and metabolic potential of Chloroflexi in oxic and anoxic abyssal clay from three deep-sea cores covering up to 15 million years of sediment deposition, where Chloroflexi are a major component of the community throughout the entire cored sequence at all sites. In oxic red clay at two different sites, Chloroflexi communities exhibit net death over both 10-15 million year cored sequences, and gene expression was below detection despite the availability of oxygen as a high energy electron acceptor, indicating a reduced level of activity. In contrast at the anoxic site, Chloroflexi abundance and gene expression increase below the seafloor and peak in 2 to 3 million year old sediment. The anaerobic subseafloor Chloroflexi exhibited a homoacetogenic metabolism and potential for energetically efficient intracellular H2 recycling that have been proposed to confer a fitness advantage in energy-limited subseafloor habitats. Our findings indicate that the expression of this energy efficient metabolism in Chloroflexi coincides with net growth over million year timescales in deep-sea anoxic clay. Significance statementChloroflexi are widespread in energy-limited subseafloor sediments, both in oxic subseafloor sediments that are energetically limited by the availability of electron donors (organic matter) and in anoxic sediments that are energetically limited by the availability of high energy terminal electron acceptors. How Chloroflexi respond to these different forms of energy limitation over long time scales is poorly understood. We present new data that demonstrates how key differences in metabolism are manifested in different communities of aerobic and anaerobic Chloroflexi subsisting over millions of years in oxic and anoxic deep-sea clay. These data provide new insights into how certain Chloroflexi respond to different types of long-term energy limitation.