The effect of seafloor cold seeps on the biogeochemical cycling of mercury (Hg) remains enigmatic. Here we demonstrate substantial enrichments of mercury and methylmercury, along with the presence of microbes capable of metabolizing mercury in sediments of the Haima cold seep, South China Sea, by analyzing mercury and methylmercury concentrations, mercury isotopic composition analyses and metagenomic analyses of sediment cores. Compared to the reference area, the sediments in the upper sediment column of the active-seep area were 2.4 times enriched in Hg and 10.5 times in methylmercury. The slope of the capital delta ratio of mercury 199 to mercury 201 (Δ¹⁹⁹Hg/Δ²⁰¹Hg) with 1.23 ± 0.10 in the active-seep area indicate the occurrence of dark redox reactions. Genes related to mercury methylation (hgcA), demethylation (merB) and reduction (merA) were phylogenetically associated with several bacterial and archaeal linages. We roughly estimated an additional 2,835 Mg mercury and 9 Mg methylmercury are stored in cold seep globally. In summary, we propose that cold seeps globally function as a previously unrecognized sink for mercury and source for methylmercury in the deep ocean.

Phosphorus (P) is an important nutrient for biological communities in cold seeps. However, our knowledge on the source, species, and cycling of P in cold seep environments is limited. In this study, the concentration, species, and micro to nanometer scale distribution of P in seep carbonates were examined at three deep-sea cold seeps in the South China Sea and East China Sea. The Ca-P accounts for the largest proportion of P—followed by detrital-P, Fe-P, organic-P, and exchangeable-P. The distribution patterns of Ca-P, detrital-P, and organic-P in the seep carbonates differ from one another, as shown by elemental mapping with NanoSIMS and scanning electron microscopy. The covariation of P with Ca and C reveals that Ca-P co-precipitates with Ca-carbonate, which is linked to the process of sulfate-driven anaerobic oxidation of methane. Organic-P is also observed within biofilm-like organic carbon aggregates, revealing the microbial enrichment of P by fluids in the process of anaerobic oxidation of methane. P with a granulated morphology was identified as detrital-P derived from deep sediments. Most importantly, it is evident that Ca-P is positively correlated to the Fe content in all the seep carbonates. This indicates the likelihood that the dissolved P in cold-seep fluids is released primarily from Fe oxides through Fe-driven anaerobic oxidation of methane in deep sediments. These processes associated with different species of P may have significant implications for P geochemical cycling and anaerobic oxidation of methane impelled by Fe and sulfate reduction in cold seep environments.

The occurrence of deep-sea ferromanganese nodules and crusts on the seafloor is widespread, providing an important resource for numerous metals such as Ni, Co, and Cu. Although they have been intensively studied in the past, the formation of micro-manganese nodules within carbonate rocks has received less attention, despite the considerable amounts of manganese released from the dissolution of the calcareous framework. The micro-petrographic and geochemical characteristics of reef carbonate rocks recovered from the Zhaoshu plateau in the Xisha uplift, north of the South China Sea, were studied using optical microscopy, scanning electron microscopy, confocal Raman spectrometry, and an electron probe micro-analyzer. The carbonate rocks are composed of biogenic debris, including frameworks of coralline algae and chambers of foraminifer, both of which are suffering strong micritization. Within the calcite micrite, numerous micro-manganese nodules were identified with laminated patterns. Mineral and elemental evidence showed that the Mn oxides in the carbonates are mixed with 10 Å vernadite, 7 Å vernadite and todorokite, both of which are closely associated with the carbonate matrix. The micro-nodules were found to have high Mn/Fe ratios, enriched in Ni and Cu and depleted in Co. We infer that theses nodules are mixed type with early diagenetic growth under oxic–suboxic conditions. The re-distribution of manganite within the rocks is likely influenced by micritization of the calcareous framework. We deduce that microbial-associated reduction of manganite induces the formation of diagenetic todorokite similar to nodules buried in marine sediments.

Volcanic ash is a major component of marine sediment, but its effect on the deep-sea carbon cycle remains enigmatic. Here, we analyzed mineralogical compositions and glycerol dialkyl glycerol tetraether (GDGT) membrane lipids in submarine tuffs from the Mariana Trough, demonstrating a fraction of organic carbon associated with volcanic ash is produced in situ. This likely derives from chemolithotrophic communities supported by alteration of volcanic material. Tuff GDGTs are characterized by enrichment of branched GDGTs, as in chemolithotrophic communities. Scanning electron microscope, Raman spectrum and nano secondary ion mass spectrometry analysis demonstrates organic carbon exists around secondary heamatite veins in the altered mafic minerals, linking mineral alteration to chemolithotrophic biosynthesis. We estimate organic carbon production of between 0.7 − 3.7 × 10¹¹g if all the chemical energy produced by ash alteration was fully utilized by microorganisms. Therefore, the chemolithotrophic ecosystem maintained by ash alteration likely contributes considerably to organic carbon production in the seafloor.

Whale falls are biodiversity oases at seabeds^1,2,3,4,5,6, yet their record from the oceans has remained sparse and fragmentary^6,7. Here we report the discovery of a vast whale necropolis in the Diamantina Zone (4,616- to 7,001-m depth), extending about 1,200 km along the sea floor of the southeastern Indian Ocean. This area has a deep and extensive accumulation comprising five modern natural whale-fall communities and 476 fossil cetaceans recorded. We show that carcasses host specialized communities dominated by brittle stars, bone-boring worms and chemosynthesis-based bivalves and that the fossil record in this area comprises both extant and extinct deep-diving beaked whales. Isotopic dating shows that whale falls in this region have occurred since at least 5.3 million years ago. These findings reshape the understanding of the limits and biogeography of whale-fall ecosystems and establish some deep sea floors as a fossil archive for tracing cetacean evolution over geological time.