Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
The complex interplay of climate shifts over Eurasia and global sea level changes modulates freshwater and saltwater inputs to the Black Sea. The dynamics of the hydrologic changes from the Late Glacial into the Holocene remain a matter of debate, and information on how these changes affected the ecology of the Black Sea is sparse. Here we used Roche 454 next-generation pyrosequencing of sedimentary 18S rRNA genes to reconstruct the plankton community structure in the Black Sea over the last ca. 11,400 y. We found that 150 of 2,710 species showed a statistically significant response to four environmental stages. Freshwater chlorophytes were the best indicator species for lacustrine conditions (>9.0 ka B.P.), although the copresence of previously unidentified marine taxa indicated that the Black Sea might have been influenced to some extent by the Marmara Sea since at least 9.6 ka calendar (cal) B.P. Dinoflagellates, cercozoa, eustigmatophytes, and haptophytes responded most dramatically to the gradual increase in salinity after the latest marine reconnection and during the warm and moist mid-Holocene climatic optimum. According to paired analysis of deuterium/hydrogen (D/H) isotope ratios in fossil alkenones, salinity increased rapidly with the onset of the dry Subboreal after ∼5.2 ka B.P., leading to an increase in marine fungi and the first occurrence of marine copepods. A gradual succession of dinoflagellates, diatoms, and chrysophytes occurred during the refreshening after ∼2.5 ka cal B.P. with the onset of the cool and wet Subatlantic climate and recent anthropogenic perturbations.