High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata

Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome--assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont

Contents and isotopic speciation of sedimentary carbon and nitrogen in sediment core MD01-2404, the Okinawa Trough

Total organic carbon to total nitrogen ratio (C/N) and their isotopic composition (d13CTOC vs. d15NTN) are oft-applied proxies to discern terrigenous from marine sourced organics and to unravel the ancient environmental information. In high depositional Asian marginal seas, matrixes, including N-bearing minerals, dilution leads to illusive and even contradictive interpretations. We use KOH-KOBr to separate operationally defined total organic matter into oxidizable (labile) and residual fractions for content and isotope measurements. In a sediment core in the Okinawa Trough, significant amounts of carbon and nitrogen existed in the residual phase, in which the C/N ratio was ~9 resembling most documented sedimentary bulk C/N ratios in the China marginal seas. Such similarity creates a pseudo-C/N interrupting the application of bulk C/N. The residual carbon, though composition unknown, it displayed a d13C range (-22.7 to -18.9 per mil, mean -20.7 per mil) similar to black carbon (-24.0 to -22.8 per mil) in East China Sea surface sediments. After removing residual fraction, we found the temporal pattern of d13CLOC in labile fraction (LOC) was more variable but broadly agreed with the atmospheric pCO2-induced changes in marine endmember d13C. Thus, we suggested adding pCO2-induced endmember modulation into two-endmember mixing model for paleo-environment reconstruction. Meanwhile, the residual nitrogen revealed an intimate association with illite content suggesting its terrestrial origin. Additionally, d15N in residual fraction likely carried the climate imprint from land. Further studies are required to explore the controlling factors for carbon and nitrogen isotopic speciation and to retrieve the information locked in the residual fraction

Isotopic composition and speciation of sedimentary nitrogen and carbon in the Okinawa Trough over the past 30 ka

Total organic carbon to total nitrogen ratios (C/N) and their isotopic compositions (δ13CTOC and δ15NTN) are oft-applied proxies to discern terrigenous from marine-sourced organics and to unravel ancient environmental information. In high depositional Asian marginal seas, the inclusion of N-bearing minerals in the bulk sediment dilutes or masks signals sought after in δ15N and δ13C analyses, thus leading to incorrect and even contradictory interpretations. We used KOH-KOBr to separate operationally defined total organic matter into oxidizable (labile) and residual fractions for content and isotope measurements. In a sediment core in the Okinawa Trough, significant amounts of carbon and nitrogen existed in the residual phase, in which the C/N ratio was ~9, resembling most documented sedimentary bulk C/N ratios in the China marginal seas. The residual carbon, which was included in operationally defined total organic carbon (TOC), displayed a δ13C range (−22.7 to −18.9‰, mean −20.7‰) similar to the oft-used marine end-member. After removing the interference from the residual fraction, we found that the temporal pattern of δ13CLOC (LOC denotes labile organic carbon) was more variable. The residual nitrogen content was associated with illite, suggesting a terrestrial origin. Additionally, δ15N in the residual fraction likely reflected the climatic controls (e.g., precipitation) on lithogenic source materials. Further studies are required to explore the controlling factors for carbon and nitrogen isotopic speciation and to retrieve the information locked in the residual fraction

Microstructural and Chemical Investigations of Presolar Silicates from Diverse Stellar Environments

We report the structural and chemical investigation of nine presolar silicate grains from the CH3/CB(b)3 chondrite Isheyevo and CR2 chondrite Northwest Africa (NWA) 801. Five of these grains belong to group 1, likely condensed in low- to intermediate-mass asymptotic giant branch (AGB) stars, super-AGB stars, or core-collapse supernovae, while the remaining four grains belong to group 4 and have a supernova origin. The advanced transmission electron microscopy and associated electron spectroscopy analyses show a diverse range of chemical and structural compositions for presolar silicates. Two GEMS (glass with embedded metal and sulfide)-like silicates, each from different groups, condensed under nonequilibrium conditions in stellar outflows. Two nonstoichiometric silicates from group 1 have dissimilar formation and alteration histories. An amorphous silicate from group 1 with olivine-like [(Mg,Fe)(2)SiO4] composition likely formed as a crystalline olivine that subsequently amorphized in the interstellar medium. An oldhamite (CaS) grain within a stoichiometric enstatite (MgSiO3) from group 1 probably formed by heterogeneous condensation in circumstellar outflows. Of the two crystalline grains from group 4, one is an antigorite [(Mg,Fe)(3)Si2O5(OH)(4)], while the other is a nontronite [Na,Fe-2(Si,Al)(4)O-10(OH)(2).nH(2)O], both formed as a crystalline forsterite and later altered to have hydrated silicate composition. A group-4 silicate has a chemical composition similar to a low Ca-pyroxene [(Ca,Mg)(Si,Al)(2)O-6]. Our data imply that presolar grains from different groups can have a similar range of grain-formation conditions.We thank Vikram Goyal at Physical Research Laboratory (PRL), India for his assistance on the NanoSIMS; Daniel Wielandt and Lalit Shukla for initial NanoSIMS measurements at PRL; Takeshi Kasama and Berit Wenzell at DTU-CEN, Copenhagen, Keulen Nynke and Alaei Mojagan at GEUS, Copenhagen, Deepak Panda at PRL, Yoshiyuki Iizuka at Academia Sinica, Taipei, and Zina Fihl at SNM, Copenhagen for help with the SEM. We also thank Larry Nittler at the Carnegie Institution for Science for help on the L'image software and interpretation of some of the grain data. Funding for this project was provided by the Carlsberg Foundation (CF18-1105), the Danish National Research Foundation (DNRF97), and the European Research Council (ERC Advanced grant Agreement, #833275-DEEPTIME) grants to M.B. The authors acknowledge the use of instrumentation provided by the National Facility ELECMI ICTS ("Division de Microscopia Electronica," Universidad de Cadiz, DME-UCA). L.L. acknowledges funding from the Andalusian regional government (FEDER-UCA-18-106613), the European Union's Horizon 2020 research and innovation program (grant agreement 823717-ESTEEM3), and the Spanish Ministerio de Economia y Competitividad (PID2019-107578GA-I00)

Sedimentary processes dominate nitrous oxide production and emission in the hypoxic zone off the Changjiang River estuary

Coastal oceans, known as the major nitrous oxide (N2O) source to the atmosphere, are increasingly subject to eutrophication and concurrent near-bottom hypoxia. The natural nitrogen cycle is likely to be altered markedly in hypoxic coastal oceans. However, the processes responsible for N2O production and emission remain elusive because of lacking field rate measurements simultaneously conducted in the water column and sediment. Here, we quantified N2O production rates using a N-15-labeled technique in the water-column and surface sediments off the Changjiang (Yangtze) River estuary, the largest hypoxic zone in the Pacific margins. Our results showed that the estuarine surface sediments were the major source for N2O production, accounting for approximately 90% of the total water-column accumulation and consequent efflux of N2O in the hypoxic zone, whereas the water-column nitrification and denitrification combined only contributed <10%. More importantly, the coupling of nitrification and denitrification at the presence of abundant supply and remineralization of labile organic matter was the main driver of the N2O release from the sediment-water interface in this region. This study highlights the dominant role of benthic processes occurring at the sediment-water interface controlling the coastal N2O budget, as the anthropogenic eutrophication and hypoxia are expanding in coastal oceans.11Nsciescopu

Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera

Abstract Background Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown. Results This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB’s abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP. Conclusion We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons