Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

Collectively, phagotrophic algae (mixotrophs) form a functional continuum of nutritional modes between autotrophy and heterotrophy, but the specific physiological benefits of mixotrophic nutrition differ among taxa. Ochromonas spp. are ubiquitous chrysophytes that exhibit high nutritional flexibility, although most species generally fall towards the heterotrophic end of the mixotrophy spectrum. We assessed the sources of carbon and nitrogen in Ochromonas sp. strain BG-1 growing mixotrophically via short-term stable isotope probing. An axenic culture was grown in the presence of either heat-killed bacteria enriched with ^(15)N and ^(13)C, or unlabeled heat-killed bacteria and labeled inorganic substrates (^(13)C-bicarbonate and ^(15)N-ammonium). The alga exhibited high growth rates (up to 2 divisions per day) only until heat-killed bacteria were depleted. NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84–99% of its carbon and 88–95% of its nitrogen from consumed bacteria. The chrysophyte assimilated inorganic ^(13)C-carbon and ^(15)N-nitrogen when bacterial abundances were very low, but autotrophic (photosynthetic) activity was insufficient to support net population growth of the alga. Our use of nanoSIMS represents its first application towards the study of a mixotrophic alga, enabling a better understanding and quantitative assessment of carbon and nutrient acquisition by this species

The limits of life and the biosphere in earth’s interior

Fifty years of scientific ocean drilling have shown that microorganisms are widespread deep inside the ocean floor. Microbial populations exist in both organic-matter-rich and nutrient-poor sediments (Kallmeyer et al., 2012; D’Hondt et al., 2015), in sediments that are millions of years old and are buried to over a kilometer depth (Roussel et al., 2008; Ciobanu et al., 2014; Inagaki et al., 2015), and deep inside the basaltic oceanic crust (Orcutt et al., 2011; Lever et al., 2013). In these varied environments, metabolic activity is extraordinarily low (D’Hondt et al., 2009; Hoehler and Jørgensen 2013; Lever et al. 2015a), but microbial cells remain physiologically active (Morono et al., 2011) or survive in their dormant phases (Lomstein et al., 2012). The total amount of sub-surface biomass is still being debated (Hinrichs and Inagaki, 2012; Kallmeyer et al., 2012; Parkes et al., 2014) and the factors posing ultimate limits to deep life and the habitability of Earth remain to be resolved

Modelling the Shimokita deep coalbed biosphere over deep geological time : Starvation, stimulation, material balance and population models

ACKNOWLEDGEMENTS The authors are grateful to all crews, drilling team members, lab technicians and scientists on the drilling vessel Chikyu for supporting core sampling and on board measurements during the Chikyu shakedown cruise CK06‐06 and the Integrated Ocean Drilling Program (IODP) Expedition 337. This work was supported in part by the Japan Society for the Promotion of Science (JSPS) Strategic Fund for Strengthening Leading‐Edge Research and Development (to F.I. and JAMSTEC), the JSPS Funding Program for Next Generation World‐Leading Researchers (NEXT Program, no. GR102 to F.I.). All shipboard and shore‐based data presented in this manuscript are archived and publicly available on‐line in either the IODP Expedition 337 Proceedings through the J‐CORES (http://sio7.jamstec.go.jp/j-cores.data/337/C0020A/), the PANGAEA database (www.pangaea.de, doi.org/10.1594/PANGAEA.845984), or Inagaki et al., 2015, respectively. Petromod Basin Modelling software was provided by Schlumberger to the University of Aberdeen. This is a contribution to the Deep Carbon Observatory (DCO). SAB wishes to thank HSB for support preparing the manuscript. DATA AVAILABILITY STATEMENT All shipboard and shore‐based data presented in this manuscript are archived and publicly available on‐line in either the IODP Expedition 337 Proceedings through the J‐CORES (http://sio7.jamstec.go.jp/j-cores.data/337/C0020A/), the PANGAEA database (www.pangaea.de, https://doi.org/10.1594/PANGAEA.845984), or Inagaki et al., 2015, respectively.Peer reviewedPostprin

Iron isotope signals: Use and limitations in natural marine sediments

Oral presentatio

Hot fluids, burial metamorphism and thermal histories in the underthrust sediments at IODP 370 site C0023, Nankai Accretionary Complex

This research used samples and data provided by the International Ocean Discovery Program (IODP). The authors are grateful to the IODP and the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). We thank crew, drilling team, geologists and lab technicians on D/V Chikyu and the staff of the Kochi Institute for Core Sample Research for supporting operations. This work was supported by the ECORD research grant [2017 to MYT]; and the NERC grant [NE/P015182/1 2017 to SAB]. ZW acknowledges technical support provided by Colin Taylor at the University of Aberdeen. Petromod 2017 was provided by Schlumberger. VBH and KUH acknowledge funding from the Deutsche Forschungsgemeinschaft through the Cluster of Excellence, The Ocean Floor – Earth’s Uncharted Interface“ and Project Grant HE8034/1-1 2019. This is a contribution to the Deep Carbon Observatory.Peer reviewedPublisher PD

Mineralization kinetics of biosiliceous sediments in hot subseafloors

Temperature affects the timing of the transformation of amorphous silica (opal-A) into crystalline (opal-CT) exponentially. Thus, in hot subseafloor environments opal-A is expected to convert into opal-CT at relatively shallow burial depths, where in situ temperatures do not exceed ∼56 °C, as it has been previously observed at various deep-sea sites and in onshore rock outcrops as well as assessed during lab experiments. The response of biosilica (biogenic opal-A) diagenesis to steep geothermal gradients (∼224–529 °C/km) at extremely high sedimentation rates (∼1 m/kyr) was examined in cores from off-axis boreholes drilled by the International Ocean Discovery Program (IODP) Expedition 385 in the actively spreading, intrusive sill-riddled Guaymas Basin at the Gulf of California (Mexico) rifted margin. At three sites drilled by IODP Expedition 385 (U1545, U1546, and U1547), the conversion from amorphous opal (−A) to crystalline opal (−CT) occurs in relatively deep (up to ∼330 mbsf) and unexpectedly hot (in situ temperatures of ∼74–79 °C) subseafloor conditions. This observation indicates a significantly slower reaction kinetics of biosilica transformation than previously reported. A compilation of empirical data that include biosiliceous basins with a similarly hot subseafloor (Sea of Japan and Bering Sea) yield new kinetic parameters that account for the slower rates of silica transformation. Thus, current kinetic models for the prediction of opal-A to −CT conversion face limitations when burial rates exceed those typical of biogenic sedimentation in open-ocean conditions. At Guaymas Basin Site U1545, where there is no evidence of sill-related metamorphic overprint, the d-spacing of the opal-CT (101) peak correlates linearly with in situ temperature between ∼75 and 110 °C throughout the opal-CT zone, thus, providing a local silica paleothermometry proxy that can be used to calculate the maximum temperature to which opal-CT sediment has been subjected

Nitrogen isotope homogenization of dissolved ammonium with depth and 15N enrichment of ammonium during incorporation into expandable layer silicates in organic-rich marine sediment from Guaymas Basin, Gulf of California

Sedimentary nitrogen isotopic ratios are used as a proxy for ancient biogeochemical cycles on Earth's surface. It is generally accepted that sediment hole tops record primary signatures because organic nitrogen (ON) is predominant in this part of the hole. In contrast to such early to middle diagenetic stages, it is well known that heavier nitrogen isotope 15N tends to enrich in sedimentary rocks during later diagenetic and metamorphic stages. However, there are some critical gaps in our understanding of nitrogen isotopic alteration associated with abiotic processes during early-middle diagenesis. In this study, we examined the isotope ratios of ammonium nitrogen in interstitial water (IW) and total nitrogen (TN), including exchangeable ammonium and mineral nitrogen, in the solid-phase of organic-rich-sediment recovered by International Ocean Discovery Program (IODP) Expedition 385 cores drilled in the Guaymas Basin, Gulf of California, that contained ammonium-rich IW. The isotopic ratios (δ15N value) of TN are the most variable with depth compared to any other type of nitrogen. This variation can be interpreted as reflecting changes in the water mass environment in the basin caused by glacial–interglacial climate changes, modifying the δ15N values of the marine primary producers. Thus, the δ15N value of TN is a proxy for environmental change in the basin, while each component of TN shows different trends. The δ15N values of IW and exchangeable ammonium did not exhibit significant changes with depth, but the latter values are about 3 ‰ enriched in 15N. This may be due to advective transport of solute into adjacent layers followed by the formation of an isotopic equilibrium between IW and exchangeable ammonium in the case of fast sediment accumulation rate. The δ15N value of exchangeable ammonium is the highest among the other types of nitrogen with one exception, where the δ15N value of TN is the highest. The calculated δ15N values of ON based on mass balance are almost the same as those of associated TN in the shallow sediment layers (< 150 m below seafloor), but the difference in the δ15N values of TN and ON are significant in the deeper layers, where proportions of ON contents are <50%. In particular, in the layer where the δ15N value of TN is the highest, that of ON shows an even higher value and the difference reaches 3.5 ‰. The δ15N values of mineral nitrogen are similar to that of IW ammonium except the surface layers. Under such conditions, when δ15N value of TN is intermediate between those of mineral nitrogen and exchangeable ammonium, calculated δ15N value of ON is close to that of TN. On the other hand, if δ15N value of TN is out of the range between mineral nitrogen and exchangeable ammonium, it causes further difference in δ15N value of ON. It means that the fluctuation of δ15N values of TN is reduced relative to those of ON through depth. It has been considered that δ15N value of TN in sediment is similar to that of ON, and changes in the δ15N value of TN due to diagenesis are limited, but in such environment ON fluctuations over depth may be slightly underestimated