Mollisol Erosion-Driven Efflux of Energetic Organic Carbon and Microflora Increases Greenhouse Gas Emissions from Cold-Region Rivers.

Massive soil erosion occurs in the world's Mollisol regions due to land use change and climate warming. The migration of Mollisol organic matter to river systems and subsequent changes in carbon biogeochemical flow and greenhouse gas fluxes are of global importance but little understood. By employing comparative mesocosm experiments simulating varying erosion intensity in Mollisol regions of northeastern China, this research highlights that erosion-driven export and biomineralization of terrestrial organic matter facilitates CO2 and CH4 emission from receiving rivers. Stronger Mollisol erosion, as represented by a higher soil-to-water ratio in suspensions, increased CO2 efflux, particularly for the paddy Mollisols. This is mechanistically attributable to increased bioavailability of soluble organic carbon in river water that is sourced back to destabilized organic matter, especially from the cultivated Mollisols. Concurrent changes in microbial community structure have enhanced both aerobic and anaerobic processes as reflected by the coemission of CO2 and CH4. Higher greenhouse gas effluxes from paddy Mollisol suspensions suggest that agricultural land use by supplying more nitrogen-containing, higher-free-energy organic components may have enhanced microbial respiration. These new findings highlight that Mollisol erosion is a hidden significant contributor to greenhouse gas emissions from river water, given that the world's four major Mollisol belts are all experiencing intensive cultivation.

Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea.

Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ13CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.

Metal-Driven Anaerobic Oxidation of Methane as an Important Methane Sink in Methanic Cold Seep Sediments.

Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Here, we combined geochemistry, muti-omics, and numerical modeling to study metal-dependent AOM in methanic cold seep sediments in the northern continental slope of the South China Sea. Geochemical data based on methane concentrations, carbon stable isotope, solid-phase sediment analysis, and pore water measurements indicate the occurrence of anaerobic methane oxidation coupled to metal oxides reduction in the methanic zone. The 16S rRNA gene and transcript amplicons, along with metagenomic and metatranscriptomic data suggest that diverse anaerobic methanotrophic archaea (ANME) groups actively mediated methane oxidation in the methanic zone either independently or in syntrophy with, e.g., ETH-SRB1, as potential metal reducers. Modeling results suggest that the estimated rates of methane consumption via Fe-AOM and Mn-AOM were both 0.3 µmol cm-2 year-1, which account for ~3% of total CH4 removal in sediments. Overall, our results highlight metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments. IMPORTANCE Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Our findings provide a comprehensive view of metal-dependent AOM in the methanic cold seep sediments and uncovered the potential mechanisms for involved microorganisms. High amounts of buried reactive Fe(III)/Mn(IV) minerals could be an important available electron acceptors for AOM. It is estimated that metal-AOM at least contributes 3% of total methane consumption from methanic sediments to the seep. Therefore, this research paper advances our understanding of the role of metal reduction to the global carbon cycle, especially the methane sink.

A new eyeless species of Nereis (Annelida, Nereididae) from deep-sea sediments of the northern South China Sea.

A variety of nereidid species have been reported from the South China Sea, although little is known about the deep-sea species in this area. Recently, two specimens belonging to a novel nereidid polychaete were collected from a sedimentary habitat during an environmental survey to a deep-sea basin where cold seeps occur. This new species, Nereistricirrata sp. nov., is described herein, based on morphological and molecular analyses. The most noteworthy feature is the absence of eyes on the prostomium; it can be distinguished from other eyeless Nereis species by the arrangement of conical paragnaths on the pharynx, the nature of homogomph falcigers and the shape of notopodial lobes in posterior chaetigers. The reconstructed phylogenetic tree, using concatenated sequences of mtCOI, 16S, and 18S rRNA, showed that all Nereis species included in this study form a monophyletic clade with full support. The mtCOI-based interspecific comparisons revealed a high genetic divergence (23.1%-37.3% K2P) from four-eyed Nereis species with the available sequences. This is the first record of an eyeless Nereis species in the South China Sea.

Corrigendum: Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea.

[This corrects the article DOI: 10.3389/fmicb.2020.612135.].

Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea.

Methane is a potent greenhouse gas; methane production and consumption within seafloor sediments has generated intense interest. Anaerobic oxidation of methane (AOM) and methanogenesis (MOG) primarily occur at the depth of the sulfate-methane transition zone or underlying sediment respectively. Methanogenesis can also occur in the sulfate-reducing sediments through the utilization of non-competitive methylated compounds; however, the occurrence and importance of this process are not fully understood. Here, we combined a variety of data, including geochemical measurements, rate measurements and molecular analyses to demonstrate the presence of a cryptic methane cycle in sulfate-reducing sediments from the continental shelf of the northern South China Sea. The abundance of methanogenic substrates as well as the high MOG rates from methylated compounds indicated that methylotrophic methanogenesis was the dominant methanogenic pathway; this conclusion was further supported by the presence of the methylotrophic genus Methanococcoides. High potential rates of AOM were observed in the sediments, indicating that methane produced in situ could be oxidized simultaneously by AOM, presumably by ANME-2a/b as indicated by 16S rRNA gene analysis. A significant correlation between the relative abundance of methanogens and methanotrophs was observed over sediment depth, indicating that methylotrophic methanogenesis could potentially fuel AOM in this environment. In addition, higher potential rates of AOM than sulfate reduction rates at in situ methane conditions were observed, making alternative electron acceptors important to support AOM in sulfate-reducing sediment. AOM rates were stimulated by the addition of Fe/Mn oxides, suggesting AOM could be partially coupled to metal oxide reduction. These results suggest that methyl-compounds driven methane production drives a cryptic methane cycling and fuels AOM coupled to the reduction of sulfate and other electron acceptors.

Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea.

Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.

Characteristics of phytoplankton communities and their biomass variation in a gas hydrate drilling area in the northern South China Sea.

We analyzed the data obtained from field observations on a gas hydrate drilling area in Dongsha of northern South China Sea (SCS) in middle May (before drilling) and early October (after drilling) in 2013. The variation in the phytoplankton communities and biomass as well as the impacts of environmental factors including dissolved methane was studied. Results indicated that the gas hydrate drilling area in Dongsha, SCS exhibited a typical low-nutrients low-chlorophyll a (LNLC) environment accompanied with low phytoplankton abundance. A total of 103 taxa belonging to 52 genera of 5 classes were identified, with diatoms and dinoflagellates dominating the community. Both phytoplankton abundance and chlorophyll a (Chl a) were highest at the subsurface maximum layer. The subsurface chlorophyll maximum (SCM) before and after drilling were stabilized at 75 m (0.30 ±â€¯0.06 mg/m3 and 0.51 ±â€¯0.29 mg/m3, respectively), while the subsurface maximum of abundance after drilling went deeper to 75 m (604.17 ±â€¯313.22 cells/L) from the surface (707.14 ±â€¯243.98 cells/L) before drilling. After drilling, phosphate and Chl a increased significantly, but no significant differences were observed on abundance. Dominant species of diatoms were basically constant with dinoflagellates becoming more apparent in higher occurrence and abundance, while Cyanophyta was diverse after drilling. Redundancy analysis (RDA) and Spearman's correlation analysis both indicated that temperature, pH and phosphates were major factors causing fluctuation in phytoplankton community structure, while dissolved methane had non-significant impact directly. We clearly found both abundance and Chl a increased in particular water layers (between 50 and 75 m) and at stations (DS06, DS08 and DS15) where dissolved methane concentrations were also abnormally high. This study appeared to partly coincide with the findings of natural oil seeps in the Gulf of Mexico, which assumed that the turbulence from the natural oil and gas leaking zone could raise the bottom water through the rising bubbles and bring cold nutrient rich waters to the thermocline from the deep seeps. This plume-generated upwelling could then fuel a bottom-up effect on the photosynthetic species in the upper pelagic waters within the euphotic zone.

The mitochondrial genome of the deep-sea tubeworm Paraescarpia echinospica (Siboglinidae, Annelida) and its phylogenetic implications.

Paraescarpia echinospica is a conspicuous annelid living in the cold seeps and hydrothermal vents of the Western Pacific region and relying on their endosymbiont bacteria as a source of energy and organic carbon. We report the complete mitochondrial genome of P. echinospica, which is 15,280 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes and a putative control region. The overall base composition is AT-biased. The control region contains repeated nucleotide motifs. Phylogenetic analyses of the concatenated mitochondrial genes strongly support a sister relationship of P. echinospica with a clade containing Escarpia and Seepiophila.

Methane-metabolizing microbial communities in sediments of the Haima cold seep area, northwest slope of the South China Sea.

Cold seeps are widespread chemosynthetic ecosystems in the deep-sea environment, and cold seep microbial communities of the South China Sea are poorly constrained. Here we report on the archaeal communities, particularly those involved in methane metabolization, in sediments of a newly discovered cold seep (named 'Haima') on the northwest slope of the South China Sea. Archaeal diversity, abundance and distribution were investigated in two piston cores collected from a seep area (QDN-14B) and a non-seep control site (QDN-31B). Geochemical investigation of the QDN-14B core identified an estimated sulfate-methane transition zone (Estimated SMTZ) at 300-400 cm below sea floor (cmbsf), where a high abundance of anaerobic methane-oxidizing archaea (ANME) occurred, as revealed by analysis of the 16S rRNA gene and the gene (mcrA) encoding the α-subunit of the key enzyme methyl-coenzyme M reductase. ANME-2a/b was predominant in the upper and middle layers of the estimated SMTZ, whereas ANME-1b outcompeted ANME-2 in the sulfate-depleted bottom layers of the estimated SMTZ and the methanogenic zone. Fine-scale phylogenetic analysis further divided the ANME-1b group into three subgroups with different distribution patterns: ANME-1bI, ANME-1bII and ANME-1bIII. Multivariate analyses indicated that dissolved inorganic carbon and sulfate may be important factors controlling the composition of the methane-metabolizing community. Our study on ANME niche separation and interactions with other archaeal groups improves our understanding of the metabolic diversity and flexibility of ANME, and the findings further suggest that ANME subgroups may have evolved diversified/specified metabolic capabilities other than syntrophic anaerobic oxidation of methane coupled with sulfate reduction in marine sediments.

High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers.

The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep-sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy-2, Bathy-8 and Bathy-10 were dominant bathyarchaeotal members of the deep-sea sediments in the SCS. Bathy-8 was found predominantly within the reducing and deeper sediment layers, while Bathy-10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well-understood sedimentary archaeal group.

A new species of Hemichela Stock, 1954 from the South China Sea (Arthropoda, Pycnogonida, Ammotheidae).

A new species of pycnogonid collected by the Chinese research vessel, R/V HY IV, during deep sea cruises to the South China Sea in 2013, is described. The new species, Hemichela nanhaiensis, obtained from more than 1300 m depth, is distinguished from the other two species in the genus by the characters of the chela dactylus with 12 denticulations on the inner margin and by the presence of taller tubercles on the lateral processes.

Application of headspace single-drop microextraction coupled with gas chromatography for the determination of short-chain fatty acids in RuO4 oxidation products of asphaltenes.

In this study, headspace single-drop microextraction (HS-SDME) coupled with gas chromatography-flame ionization detection (GC-FID), was employed to determine short-chain fatty acids (SCFAs) in ruthenium tetroxide (RuO(4)) oxidation products of asphaltenes. Several significant parameters, such as drop solvent type, drop volume, sample solution ionic strength, agitation speed, extraction time, and ratio of headspace volume to sample volume were optimized. Under optimum extraction conditions (i.e., a 3-microL drop of 1-butanol, 20 min exposure to the headspace of a 6 mL aqueous sample placed in a 10 mL vial, stirring at 1000 rpm at room temperature, and 30% (w/v) NaCl content), the reproducibility and accuracy of the method have been tested and found to be satisfactory. The analysis of a real asphaltene sample using this method proved that HS-SDME can be a promising tool for the determination of volatile SCFAs in complex matrices.

Application of hollow fiber liquid-phase microextraction in identification of oil spill sources.

In this study, hollow fiber based liquid-phase microextraction (HF-LPME), coupled with GC, GC-MS and GC-IRMS detections, was employed to determine petroleum hydrocarbons in spilled oils. According to the results, the HF-LPME method collected more low-molecular weight components, such as C(7)-C(11)n-alkanes, naphthalene, and phenanthrene, than those collected in conventional liquid-liquid extraction (LLE). The results also showed that this method had no remarkable effect on the distributions of high-molecular weight compounds such as >C(18)n-alkanes, C(1)-C(3) phenanthrene, and hopanes. Also, the carbon isotopic compositions of individual n-alkanes in the two preparation processes were identical. Accordingly, HF-LPME, as a simple, fast, and inexpensive sample preparation technique, could become a promising method for the identification of oil spill sources.