Characterization of Fe(Ⅲ)-Reducing Enrichment Cultures and Isolation of Enterobacter sp. Nan-1 from the Deep-Sea Sediment, South China Sea

To characterize the Fe(III)-reducing bacteria,enrichment cultures were initiated by inoculating deep-sea sediment from the South China Sea(SCS)into the media with hydrous ferric oxide(HFO)as the sole electron acceptor.As indicated by Meta 16S rDNA Amplicon Sequencing,the microorganisms related to Fe(III)-reduction in the enrichment cultures were mainly Shewanella and Enterobacter.A new facultative Fe(III)-reducing bacterium was obtained and identified as Enterobacter sp.Nan-1 based on its 16S rRNA gene sequence and physiological characterizations.Enterobacter sp.Nan-1 was not only a mesophilic bacterium capable of reducing HFO with a wide range of salinity(4,34,40,50 and 60 g L−1)efficiently,but also a piezotolerant bacterium that can proceed Fe(III)-reduction sustainedly at hydrostatic pressures between 0.1 and 50 MPa using glucose and pyruvate as carbon source.Furthermore,the geochemical characteristics of deep-sea sediment indicated that the microbial metabolism and iron reduction both remain active in the well-developed Fe(III)-reducing zone where the strain Nan-1 was obtained.To our knowledge,Enterobacter sp.Nan-1 could serve as a new applicative Fe(III)-reducing bacterium for future investigation on the iron biogeochemical cycle and diagenetic process of organic matter in the deep-sea environment.

Development of the Miocene Guangle Carbonate Platform in the South China Sea:Architecture and Controlling Factors

This study investigates the evolution of the Miocene Guangle carbonate platform(or Triton Horst)of the northwestern South China Sea margin.The platform is located at a junction area surrounded by Yinggehai basin,Qiongdongnan basin and Zhongjiannan basin.Well and regional geophysical data allow the identification of the morphologic and stratigraphic patterns.The Guangle carbonate platform was initiated on a tectonic uplift during the Early Miocene.The early platform was limited at Mesozoic granitic basement,pre-Paleogene sediments localized tectonic uplift and was small extension at the beginning stage.While during the Middle Miocene,the carbonate buildup flourished,and grow a thrived and thick carbonate succession overlining the whole Guangle Uplift.The isolated platforms then united afterward and covered an extensive area of several tens of thousands of square kilometers.However,it terminated in the Late Miocene.What are the control factors on the initiation,growth and demise of the Guangle carbonate platform?The onset of widespread carbonate deposits largely reflected the Early Miocene transgression linked with early post-rift subsidence and the opening of the South China Sea.Stressed carbonate growth conditions on the Guangle carbonate platform probably resulted from increased inorganic nutrient input derived from the adjacent uplifted mainland,possibly enhanced by deteriorated climatic conditions promoting platform drowning.Therefore,tectonics and terrigenous input could be two main controlling factors on the development of the Guangle carbonate platforms and main evolution stages.

Resazurin as an indicator of reducing capacity for analyzing the physiologic status of deep-sea bacterium Photobacterium phosphoreum ANT-2200

Resazurin(RZ)is a weakly fl uorescent blue dye and can be reduced irreversibly to highly fl uorescent pink resorufi n(RF)that is reduced reversibly to colorless dihydroresorufi n(hRF)by photodeoxygenation,chemical reaction and reductive organic compounds produced through cell metabolism.Because of the reliable and sensitive fl uorescence-color change and noninvasive features,RZ has been used widely as a redox indicator in cell viability/proliferation assays for bacteria,yeast,and mammalian cells.However,RZ is used rarely for physiological characterization of marine microorganisms.Here,we developed a custom-made irradiation and absorption-analysis device to assess the reducing capacity and physiologic status of marine bacterial cultures.We measured the absorption spectra of RZ,RF,and hRF in the presence of the reducing compound Na 2 S and under visible-light irradiation.After establishing appropriate parameters,we monitored the color changes of RZ and its reduced derivatives to evaluate the coherence between reducing capacity,bioluminescence and growth of the deep-sea bacterium Photobacterium phosphoreum strain ANT-2200 under various conditions.Emission of bioluminescence is an oxidation process dependent upon cellular reducing capacity.Growth and bioluminescence of ANT-2200 cell cultures were impeded progressively with increasing concentrations of RZ,which suggested competition for reducing molecules between RZ at high concentration with reductive metabolism.Therefore,caution should be applied upon direct addition of RZ to growth media to monitor redox reactions in cell cultures.Analyses of the instantaneous reduction velocity of RZ in ANT-2200 cell cultures showed a detrimental eff ect of high hydrostatic pressure and high coherence between the reducing capacity and bioluminescence of cultures.These data clearly demonstrate the potential of using RZ to characterize the microbial metabolism and physiology of marine bacteria.

An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

The low biomass in environmental samples is a major challenge for microbial metagenomic studies. The amplification of a genomic DNA was frequently applied to meeting the minimum requirement of the DNA for a high-throughput next-generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles（MALBAC） kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms is examined. The DNA template of 10 pg in each reaction of the MALBAC amplification may generate enough DNA for Illumina sequencing. Using 10 pg and 100 pg templates for each reaction set, the MALBAC kit shows a stable and homogeneous amplification as indicated by the highly consistent coverage of the reads from the two amplified samples on the contigs assembled by the original unamplified sample. Although Genome Plex whole genome amplification kit allows one to generate enough DNA using 100 pg of template in each reaction, the minority of the mixed bacterial species is not linearly amplified. For both of the kits, the GC-rich regions of the genomic DNA are not efficiently amplified as suggested by the low coverage of the contigs with the high GC content. The high efficiency of the MALBAC kit is supported for the amplification of environmental microbial DNA samples, and the concerns on its application are also raised to bacterial species with the high GC content.

Analysis of deep-layer and bottom circulations in the South China Sea based on eight quasi-global ocean model outputs

This study is a preliminary analysis of the South China Sea(SCS)deep circulations using eight quasi-global high-resolution ocean model outputs.The goal is to assess models’ability to simulate these deep circulations.The analysis reveals that models’deep temperatures are colder than the observations in the World Ocean Atlas,while most models’deep salinity values are higher than the observations,indicating models’deep water is generally colder and saltier than the reality.Moreover,there are long-term trends in both temperature and salinity simulations.The Luzon Strait transport below 1500 m is 0.36 Sv when averaged for all models,smaller compared with the observation,which is about 2.5 Sv.Four assimilated models and one unassimilated(OCCAM)display that the Luzon deep-layer overflow reaches its minimum in spring and its maximum in winter.The vertically integrated streamfunctions below 2400 m from these models show a deep cyclonic circulation in the SCS on a large scale,but the pattern is different from the diagnostic streamfunction from the U.S Navy Generalized Digital Environment Model(GDEM-Version 3.0,GDEMv3).The meridional overturning structure above 1000 m is similar in all models,but the spatial distribution and intensity below 1500 m are quite different from model to model.Moreover,the meridional overturning below 2400 m in these models is weaker than that of the GDEMv3,which indicates a deep vertical mixing process in these models is biased weak.Based on the above evaluation,this paper discusses the impacts of T/S initial value,topography,and mixing scheme on the SCS deep circulations,which may provide a reference for future model improvement.

Biomediated Precipitation of Calcium Carbonate in a Slightly Acidic Hot Spring,Yunnan Province

A slightly acidic hot spring named ＂Female Tower＂（t=73.5°C, pH=6.64） is located in the Jifei Geothermal Field, Yunnan Province, southwestern China. The precipitates in the hot spring are composed of large amounts of calcite, aragonite and sulfur. Scanning electron microscopy（SEM） analyses reveal that the microbial mats were formed from various coccoid or rod-shaped filamentous microbes. Transmission electron microscopy（TEM） shows that the intracellular sulfur granules are commonly associated with these microbes. A culture-independent molecular phylogenetic analysis demonstrates that the majority of the bacteria in the spring are sulfur-oxidizing bacteria. In the spring water, H2S concentration is up to 60 ppm, while SO4-（2-） concentration is only about 10 ppm. We speculate that H2S might derive from sulfur-oxidizing bacteria in this hot spring water, leading to the intracellular formation of sulfur granules. Meanwhile, this reaction increased the p H in the micronscale microdomains, which fosters the precipitation of calcium carbonate in the microbial mats. The results of this study indicate that the sulfur-oxidizing bacteria might play an important role in calcium carbonate precipitation in slightly acidic hot spring environments.

Magnetic properties indicate the sources of hadal sediments in the Yap Trench,northwest Pacific Ocean

Magnetic minerals in marine sediments are often masked by the primary natural remanent magnetization and material source signals.In order to understand sedimentary environment and sources of sediments in the abyss,we studied 126 samples of five bottom surface cores collected by the Jiaolong Submersible at 4000-7000 m in depth during the third stage of the China's 38th Ocean Voyage.The magnetic properties of the sediments were analyzed using Thermosusceptibility(k-T)curves and Day plot.The results show that the magnetic minerals in the sediments of the Yap Trench are mainly maghemite,and the overall magnetic and soft magnetic properties were strong.The magnetic particles of sediments are dominated by pseudo single domains(PSD)grains.The main source of sediment is locally-derived basalt debris and volcanic debris,and the process of sedimentation is gravity-like flow deposition.

Opah(Lampris megalopsis)genome sheds light on the evolution of aquatic endothermy

Endothermy is the ability to generate and conserve metabolic heat to maintain body temperature above that of the surrounding environment.Endothermy enhances the physiological and ecological advantages of mammals,birds,and certain fish species.The opah,Lampris megalopsis(Lampridiformes),is the only known fish to exhibit whole-body endothermy.Currently,however,the underlying molecular mechanism for this remains unclear.Hence,the opah offers an excellent opportunity to study the evolutionary mechanism of whole-body endothermy in aquatic animals.In this study,we assembled a L.megalopsis genome(1.09 Gb in size)and performed comparative genomic analysis with ectothermic fish to reveal the genetic basis of endothermy.Based on analysis of positive selection,rapid evolution,and gene family expansion,we discovered several genes that likely contributed to thermogenesis and heat preservation.As the first reported L.megalopsis genome,our results not only clarify the possible molecular and genetic mechanisms involved in endothermic adaptation but also increase our understanding of endothermic fish biology.

Progress on deep circulation and meridional overturning circulation in the South China Sea

The deep overflow through the Luzon Strait drives the cyclonic deep circulation in the South China Sea(SCS). In the mean time, the intruding Pacific deep water transforms and upwells due to enhanced diapycnal mixing in the SCS. Both processes greatly contribute to the SCS meridional overturning circulation(SCSMOC). At the same time, both the deep circulation and meridional overturning circulation are modulated by rough topography in the SCS. Furthermore, the spatial structure of the SCSMOC infers a link between the upper-layer circulation and deep circulation in the SCS. This paper reviews recent advances in the SCS deep circulation and meridional overturning circulation, including the driving mechanism of the SCS deep circulation and its modulation by topography, as well as the spatial structure of the SCSMOC and its dynamical mechanism.

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

Aerophobetes(or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study,we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method.Analysis of 16 S r RNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1(at least 1.27 Mbp)contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-Co A and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved inthe sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-Co A via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens.Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps.

Exotic origin of the Chinese continental shelf: new insights into the tectonic evolution of the western Pacific and eastern China since the Mesozoic

The effect of paleo-Pacific subduction on the geological evolution of the western Pacific and continental China is likely complex. Nevertheless, our analysis of the distribution of Mesozoic granitoids in the eastern continental China in space and time has led us to an interesting conclusion: The basement of the continental shelf beneath East and South China Seas may actually be of exotic origin geologically unrelated to the continental lithosphere of eastern China. By accepting the notion that the Jurassic–Cretaceous granitoids in the region are genetically associated with western Pacific subduction and the concept that subduction may cease to continue only if the trench is being jammed, then the termination of the granitoidmagmatism throughout the vast region at *88 ± 2 Ma manifests the likelihood of ‘‘sudden'', or shortly beforehand(*100 Ma), trench jam of the Mesozoic western Pacific subduction. Trench jam happens if the incoming‘‘plate'' or portion of the plate contains a sizeable mass that is too buoyant to subduct. The best candidate for such a buoyant and unsubductable mass is either an oceanic plateau or a micro-continent. We hypothesize that the basement of the Chinese continental shelf represents such an exotic, buoyant and unsubductable mass, rather than seaward extension of the continental lithosphere of eastern China. The locus of the jammed trench(i.e., the suture) is predictably located on the shelf in the vicinity of, and parallel to, the arc-curved coastal line of the southeast continental China. It is not straightforward to locate the locus in the northern section of the East China Sea shelf because of the more recent(\20 Ma) tectonic re-organization associated with the opening of the Sea of Japan. We predict that the trench jam at *100 Ma led to the re-orientation of the Pacific plate motion in the course of NNW direction as inferred from the age-progressive Emperor Seamount Chain of Hawaiian hotspot origin(its oldest unsubdued Meiji and Detroit seamounts are *82 Ma),making the boundary between the Pacific plate and the newly accreted plate of eastern Asia a transform fault at the location east of the continental shelf of exotic origin. This explains the apparent *40 Myr magmatic gap from *88to *50 Ma prior to present-day western Pacific subduction initiation. We propose that basement penetration drilling on well-chosen sites is needed to test the hypothesis in order to reveal the true nature of the Chinese continental shelf basement. This testing becomes critical and cannot longer be neglected in order to genuinely understand the tectonic evolution of the western Pacific and its effect on the geology of eastern China since the Mesozoic, includingthe cratonic lithosphere thinning, related magmatism/mineralization, and the mechanism of the subsequent South China Sea opening, while also offering novel perspectives on aspects of the plate tectonics theory. We also suggest the importance of future plate tectonic reconstruction of the western Pacific to consider the nature and histories of the Chinese continental shelf of exotic origin as well as the probable transform plate boundary from *100 to*50 Ma. Effort is needed to reveal the true nature and origin of the *88 ± 2 Ma granitic gneisses in Taiwan and the 110–88 Ma granitoids on the Hainan Island.

Improved genome assembly of Chinese sucker(Myxocyprinus asiaticus)provides insights into the identification and characterization of pharyngeal teeth related maker genes in Cyprinoidei

The Chinese sucker,Myxocyprinus asiaticus(M.asiaticus,Catostomidae,Cypriniformes),is the only living species of Catostomidae in Asia.There are more than 75 species of this family in North America.The fossil record of this group dates back to the early Eocene.As the Chinese sucker is located at the base of the Cyprinoidei phylogeny,this species is also important in clarifying the evolutionary relationships within Cyprinoidei.Here,we assembled a high-quality genome of the Chinese sucker,contig N50(40.26 Mb),which is nearly ten times longer than the previous version(4.19 Mb).Phylogenetic analysis identified that Chinese sucker together with Cyprinidae groups are paraphyletic with respect to Cobitoidea.The specific whole genome duplication event of the Chinese sucker was estimated to have occurred~25.9 million years ago.Analysis of population historical changes indicated a trend of reduction for the Chinese sucker and T.tibetana.Since Dlx genes play a key role in Cypriniformes pharyngeal teeth development,we conducted a genome-wide identification of Dlx genes,and found that these genes were doubled in whole genome duplication events,followed by the loss of specific copies.Transcriptome results showed that the expression levels of these paralogous genes were similar.This genomic resource provides useful information for the protection of Chinese sucker and functional study of Dlx genes.

The use of single-cell sequencing to reveal stem/progenitor cells in animal organ regeneration

Advances in single-cell sequencing technologies have made it possible to reveal the cellular basis of complex organ regeneration processes.In this review,we briefly introduce commonly used high-throughput single-cell sequencing platforms and their characteristics.We discuss in depth how single-cell sequencing techniques can be used in the study of regeneration to reveal stem/progenitor cell types and their developmental trajectories.From the perspective of stem cells,we review animal models of regenerative biology and organ models involved in regenerative medicine,with a focus on limb/fin/digit-tip regeneration.Finally,we discuss previous prospective work on improving systematic approaches to explore the origin and evolution of cellular diversity,as well as future research directions.

Multi-scale variability of the tropical Indian Ocean circulation system revealed by recent observations

The tropical Indian Ocean circulation system includes the equatorial and near-equatorial circulations, the marginal sea circulation, and eddies. The dynamic processes of these circulation systems show significant multi-scale variability associated with the Indian Monsoon and the Indian Ocean dipole. This paper summarizes the research progress over recent years on the tropical Indian Ocean circulation system based on the large-scale hydrological observations and numerical simulations by the South China Sea Institute of Oceanology(SCSIO), Chinese Academy of Sciences. Results show that:(1) the wind-driven Kelvin and Rossby waves and eastern boundary-reflected Rossby waves regulate the formation and evolution of the Equatorial Undercurrent and the Equatorial Intermediate Current;(2) the equatorial wind-driven dynamics are the main factor controlling the inter-annual variability of the thermocline in the eastern Indian Ocean upwelling;(3) the equatorial waves transport large amounts of energy into the Bay of Bengal in forms of coastal Kelvin and reflected free Rossby waves. Several unresolved issues within the tropical Indian Ocean are discussed:(i) the potential effects of the momentum balance and the basin resonance on the variability of the equatorial circulation system, and(ii) the potential contribution of wind-driven dynamics to the life cycle of the eastern Indian Ocean upwelling. This paper also briefly introduces the international Indian Ocean investigation project of the SCSIO, which will advance the study of the multi-scale variability of the tropical Indian Ocean circulation system, and provide a theoretical and data basis to support marine environmental security for the countries around the Maritime Silk Road.

Metagenomic analysis reveals wide distribution of phototrophic bacteria in hydrothermal vents on the ultraslow-spreading Southwest Indian Ridge

Deep-sea hydrothermal vents are known as chemosynthetic ecosystems.However,high temperature vents emit light that hypothetically can drive photosynthesis in this habitat.Metagenomic studies have sporadically reported the occurrence of phototrophic populations such as cyanobacteria in hydrothermal vents.To determine how geographically and taxonomically widespread phototrophs are in deep-sea hydrothermal vents,we collected samples from three niches in a hydrothermal vent on the Southwest Indian Ridge and carried out an integrated metagenomic analysis.We determined the typical community structures of microorganisms found in active venting fields and identified populations of known potential chlorophototrophs and retinalophototrophs.Complete chlorophyll biosynthetic pathways were identified in all samples.By contrast,proteorhodopsins were only found in active beehive smoker diffusers.Taxonomic groups possessing potential phototrophy dependent on semiconductors present in hydrothermal vents were also found in these samples.This systematic comparative metagenomic study reveals the widespread distribution of phototrophic bacteria in hydrothermal vent fields.Our results support the hypothesis that the ocean is a seed bank of diverse microorganisms.Geothermal vent light may provide energy and confer a competitive advantage on phototrophs to proliferate in hydrothermal vent ecosystems.

Rare earth element geochemistry in soils along arid and semiarid grasslands in northern China

Background:Rare earth elements(REE)are a group of trace elements that behave geochemically coherently.REE fractionation patterns normalized to reference materials provide a powerful tool for documenting pedogenesis.Insoil processes are particularly difficult to illustrate with respect to contemporary and past climate conditions.In this study,we characterize the rare earth element(REE)contents in bulk soils and respective geochemical fractions(e.g.,exchangeable,carbonate‑bound,reducible,and oxidizable fractions)and to decipher the relationships between REE geochemistry components and climatic factors across a large‑scale northern China transect(NCT).Results:Across the NCT,bulk REE concentrations ranged from 55.2 to 241.1μg g^(−1)with a main portion in the residual fraction(49–79%),followed by oxidizable fraction(2–40%),reducible fraction(3–22%),carbonate‑bound fraction(0.1–16%),and negligible exchangeable fraction.The REE contents of geochemical components(carbonate‑bound,reducible,and oxidizable)in topsoils correlated to climate factors(mean annual precipitation,mean annual temperature,potential evaporation,and aridity index(AI)).The normalized abundances to the upper continental crust(UCC)composition show that the middle REE was generally enriched than the light REE and heavy REE in topsoils along the transect.The overall UCC‑normalized bulk REE patterns in topsoils and subsoils were similar,characterized by weak negative Ce anomalies and positive Eu anomalies.Conclusions:Our data in topsoils and depth profiles collectively suggest that cycling of REE was primarily regulated by abiotic processes in area with AI<0.2,while the biological effect on REE circulation in soil played a more effective role in area with AI>0.3.The similar UCC normalized patterns in topsoils suggest that the REE was originated from a common source with limited influences from other sources(e.g.,atmospheric dusts and anthropogenic contribu‑tions).Our results to some extent provide evidence for climatic influence REE distribution patterns both in topsoils and subsoils across the continental‑scale transect.Our investigation gives insights into future studies on vertical REE mobility and its associated biogeochemical pathways.