Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis

Subsurface sediments are among the largest, but also among the least understood ecosystems on Earth. However, novel analytical methods are contributing to constrain uncertainties regarding this unique environment. Here, the microbial community in subsurface sediments was investigated along a transect through the Benguela upwelling system from the organic-rich shelf to the organic-lean bottom of the slope. For this, we combined examination of intact polar lipids (IPLs), purified using a selective clean-up protocol, with analysis of non-soluble DNA (nsDNA) using a quantitative polymerase chain reaction. Both methods aimed at overcoming potential bias introduced by a fossil fraction of either lipids or DNA. Our data revealed an abundant microbial community, which decreased with sediment depth and distance from the shore. Interestingly, both methods revealed similar trends in microbial abundance for three of the four sample locations and the ratio of Archaea to Bacteria showed consistency for the two techniques in samples from the deeper sediment column (> 50 cm). Both techniques suggested that Bacteria dominated the surface samples. The deeper subsurface sediment exhibited an increasing relative abundance of Archaea, yet only in the organic-rich inner shelf, while Bacteria remained dominant in sediments on the slope. With increasing subsurface depth, glycerol diether lipids became the dominant bacterial lipid type, suggesting changes in the bacterial community structure. This may implicate a membrane lipid adaptation to cope with severe energy limitation and thereby allow Bacteria to outcompete Archaea.