Molecular characterization of organic matter transformation mediated by microorganisms under anoxic/hypoxic conditions

Dissolved organic matter(DOM) in the ocean is one of the largest carbon pools on Earth. Microbial metabolism is an important process that shapes the marine DOM pool. Current studies on the interactions between microorganisms and DOM focus mainly on oxic environments. Few studies have addressed the molecular characteristics of DOM in microbial-mediated transformation under anoxic/hypoxic conditions. As a result of deteriorating water quality due to eutrophication and global warming, anoxia occurs...     

The effect of iron on the preservation of organic carbon in marine sediments and its implications for carbon sequestration

Marine sediments are the most significant reservoir of organic carbon(OC) in Earth′s surface system. Iron, a crucial component of the marine biogeochemical cycle, has a considerable impact on marine ecology and carbon cycling. Understanding the effect of iron on the preservation of OC in marine sediments is essential for comprehending biogeochemical processes of carbon and climate change. This review summarizes the methods for characterizing the content and structure of iron-bound OC and explore...     

The research of typical microbial functional group reveals a new oceanic carbon sequestration mechanism——A case of innovative method promoting scientific discovery

Marine microbes are major drivers of marine biogeochemical cycles and play critical roles in the ecosystems. Aerobic anoxygenic phototrophic bacteria(AAPB) are an important bacterial functional group with capability of harvesting light energy and wide distribution, and appear to have a particular role in the ocean's carbon cycling. Yet the global pattern of AAPB distribution was controversial at the beginning of the 21 st century due to the defects of the AAPB enumeration methods. An advanced time-series observation-based infrared epifluorescence microscopy(TIREM) approach was established to amend the existing AAPB quantitative deviation and led to the accurate enumeration of AAPB in marine environments. The abundance of AAPB and AAPB% were higher in coastal and continental shelf waters than in oceanic waters, which does not support the idea that AAPB are specifically adapted to oligotrophic conditions due to photosynthesis in AAPB acting a supplement to their organic carbon respiration. Further investigation revealed that dependence of AAPB on dissolved organic carbon produced by phytoplankton(PDOC) may limit their competition and control AAPB distribution. So, the selection of carbon sources by AAPB indicated that they can effectively fractionate the carbon flow in the sea. Enlightened by these findings, the following studies on the interactions between marine microbes and DOC led to the discovery of a new mechanism of marine carbon sequestration—the Microbial Carbon Pump(MCP). The conceptual framework of MCP addresses the sources and mechanism of the vast DOC reservoir in the ocean and represents a breakthrough in the theory of ocean carbon sequestration.     

Inspirations from the scientific discovery of the anammox bacteria: A classic example of how scientific principles can guide discovery and development

Anaerobic ammonium oxidation(anammox) is a relatively new pathway within the N cycle discovered in the late 1990 s. This eminent discovery not only modified the classical theory of biological metabolism and matter cycling, but also profoundly influenced our understanding of the energy sources for life. A new member of chemolithoautotrophic microorganisms capable of carbon fixation was found in the vast deep dark ocean. If the discovery of the chemosynthetic ecosystems in the deep-sea hydrothermal vent environments once challenged the old dogma "all living things depend on the sun for growth," the discovery of anammox bacteria that are widespread in anoxic environments fortifies the victory over this dogma. Anammox bacteria catalyze the oxidization of NH_4~+ by using NO_2~- as the terminal electron acceptor to produce N_2. Similar to the denitrifying microorganisms, anammox bacteria play a biogeochemical role of inorganic N removal from the environment. However, unlike heterotrophic denitrifying bacteria, anammox bacteria are chemolithoautotrophs that can generate transmembrane proton motive force, synthesize ATP molecules and further carry out CO_2 fixation through metabolic energy harvested from the anammox process. Although anammox bacteria and the subsequently found ammonia-oxidizing archaea(AOA), another very important group of N cycling microorganisms are both chemolithoautotrophs, AOA use ammonia rather than ammonium as the electron donor and O_2 as the terminal electron acceptor in their energy metabolism. Therefore, the ecological process of AOA mainly takes place in oxic seawater and sediments, while anammox bacteria are widely distributed in anoxic water and sediments, and even in some typical extreme marine environments such as the deep-sea hydrothermal vents and methane seeps. Studies have shown that the anammox process may be responsible for 30%–70% N_2 production in the ocean. In environmental engineering related to nitrogenous wastewater treatment, anammox provides a new technology with low energy consumption, low cost, and high efficiency that can achieve energy saving and emission reduction. However, the discovery of anammox bacteria is actually a hard-won achievement. Early in the 1960 s, the possibility of the anammox biogeochemical process was predicted to exist according to some marine geochemical data. Then in the 1970 s, the existence of anammox bacteria was further predicted via chemical reaction thermodynamic calculations. However, these microorganisms were not found in subsequent decades. What hindered the discovery of anammox bacteria, an important N cycling microbial group widespread in hypoxic and anoxic environments? What are the factors that finally led to their discovery? What are the inspirations that the analyses of these questions can bring to scientific research? This review article will analyze and elucidate the above questions by presenting the fundamental physiological and ecological characteristics of the marine anammox bacteria and the principles of scientific research.     

Quantitative model evaluation of organic carbon oxidation hypotheses for the Ediacaran Shuram carbon isotopic excursion

The largest global carbon-cycle perturbation in Earth history was recorded in the Ediacaran—a persistent negative shift in the global marine dissolved inorganic carbon(DIC) reservoir that lasted for ~25–50 million years, with a nadir of –12‰(i.e.,the Shuram Excursion, or SE). This event is considered to have been a result of full or partial oxidation of a large dissolved organic carbon(DOC) reservoir, which, if correct, provides evidence for massive DOC storage in the Ediacaran ocean owing to an intensive microbial carbon pump(MCP). However, this scenario was recently challenged by new hypotheses that relate the SE to oxidization of recycled continentally derived organic carbon or hydrocarbons from marine seeps. In order to test these competing hypotheses,this paper numerically simulates changes in global carbon cycle fluxes and isotopic compositions during the SE, revealing that:(1) given oxygen levels in the Ediacaran atmosphere-ocean of ≤40% PAL, the recycled continental organic carbon hypothesis and the full oxidation of oceanic DOC reservoir hypothesis are challenged by the atmospheric oxygen availability which would have been depleted in 4 and 6 million years, respectively;(2) the marine-seep hydrocarbon oxidation hypothesis is challenged by the exceedingly large hydrocarbon fluxes required to sustain the SE for 25 Myr; and(3) the heterogeneous(partial) DOC oxidation hypothesis is quantitatively able to account for the SE because the total amount of oxidants needed for partial oxidation(50%)of the global DOC reservoir could have been met.     

Some aspects of excellent marine source rock formation:implications on enrichment regularity of organic matter in continental margin basins

Through the analysis of ocean organisms, the distribution characteristics and enrichment of organic matters in modern marine sediments and ancient marine strata, this paper shows that the main factors influencing the formation of excellent marine source rocks are the paleoclimate, biologic productivity, terrestrial organic matter, oxidation–reduction environment, sedimentation rate, and the type of the basin. In addition to those factors,high biologic productivity or high content of terrestrial organic matter input is a requirement for the enrichment of the organic matter in a marine environment. Reducing environment was favorable for organic matter accumulation and preservation in depositing and early diagenesis stage, which is an important element for the formation of high-quality marine source rocks. Paleoclimate also influences the marine source rocks formation, as humid subtropical and tropical climates are the most favorable regimes for the formation of marine source rocks. Wind transports some vascular plant materials into the marine environment. Furthermore, upwellings driven by steady wind can cause high biologic productivity, thus formingorganic-C-rich mud. Suitable sedimentation rate is beneficial for marine organic matter accumulation. Moreover, the type of the basin also plays an important role in the development of marine source rocks. Silled basins with a positive water balance often act as nutrient traps, thus enhancing both productivity and organic matter preservations, while in open oceans, organic matter enrichment in sediments has just been found in the oxygen minimum layers.     

Spectral characteristics of dissolved organic matter in sediment pore water from Pearl River Estuary

As key parts of land-sea transition zones,estuary ecosystems play a very important role in the ocean carbon cycle processes.The sources,degradation,and preservation of dissolved organic matter(DOM)in estuaries have long been the subject of intense study.To examine the aforementioned issues,this study examined three-dimensional fluorescence spectroscopy and ultraviolet-visible absorption spectroscopy to determine the spatial distribution and sources of DOM in the pore water of three sedimentary cores from the Pearl River Estuary(S1,S2 and S3,with increasing salinity).Using the parallel factor analysis(PARAFAC)method to analyze the three-dimensional fluorescence spectrum data,five fluorescent components were obtained—three humic-like components(C1,C3,and C4),and two protein-like components(C2 and C5).C2 exhibited a significant positive correlation with the sediment microbial deoxyribose nucleic acid(DNA)concentration(R~2=0.69,P<0.01),indicating that the protein-like component C2 might be derived from the catabolism of in situ microbes.C5 displayed a relatively weak correlation with DNA concentration(R~2=0.40,P<0.05),presumably due to the incorporation of phenolic compounds,which have a fluorescence peak very similar to that of protein-like components.The source of humic-like fluorescent components is extremely complex.The content at station S1 was relatively high(1.45–8.83 R.U.),which implies that terrestrial inputs had a significant influence.The three humic-like components showed similar distributions at S2 and S3,and the fluorescence intensity was rather low;this result indicates that the DOM at these two stations was more likely affected by the metabolism of algae and microorganisms.The humification index(HIX)and the fluorescence intensity of protein-like components increased and decreased,respectively,with depth.There was a significant positive correlation between the relative content of protein-like components and the spectral slope ratio(SR),which indicates that DOM transitioned from low-molecular-weight protein-like components in the surface sediment to high-molecular-weight humic-like components in the subsurface.This study provides valuable information for understanding the pore water size/reactivity(PWSR)model of DOM and its biochemical processes occurring in estuary sediments.     

Mechanisms of carbon storage and the coupled carbon,nitrogen and sulfur cycles in regional seas in response to global change

正1.Great challenges in scientific frontiers of marine carbon storage in the scenario of global change The marine carbon cycle is influenced by anthropogenic activities,affecting global climate change and casting a significant impact on ecosystems.However,the complex spatiotemporal process of the marine carbon cycle results in the uncertainty in the estimation of marine carbon budget,either     

Untangling the role that microbes play in ocean carbon cycle—A new paradigm in marine biogeochemistry

<正>An estimated amount of 3.7×10~5 petagrams(1 Pg=10~(15)g)of organic carbon is stored in marine sediments(Lipp et al.,2008),which supports an immense subsurface biosphere that contains approximately 2.9×10~(29)to 3.6×10~(30)cells of indigenous microorganisms(Kallmeyer et al.,2012;Whitman et al.,1997).The majority of that carbon is transported from surface oceans by a process called the"biological pump(BP)",which has been a prevailing doctrine in the ocean carbon cycle.     

Modeling the contribution of the microbial carbon pump to carbon sequestration in the South China Sea

The two key mechanisms for biologically driven carbon sequestration in oceans are the biological pump(BP) and the microbial carbon pump(MCP); the latter is scarcely simulated and quantified in the China seas. In this study, we developed a coupled physical-ecosystem model with major MCP processes in the South China Sea(SCS). The model estimated a SCSaveraged MCP rate of 1.55 mg C m~(-2) d~(-1), with an MCP-to-BP ratio of 1:6.08 when considering the BP at a depth of 1000 m.Moreover, the ecosystem responses were projected in two representative global warming scenarios where the sea surface temperature increased by 2 and 4°C. The projection suggested a declined productivity associated with the increased near-surface stratification and decreased nutrient supply, which leads to a reduction in diatom biomass and consequently the suppression of the BP. However, the relative ratio of picophytoplankton increased, inducing a higher microbial activity and a nonlinear response of MCP to the increase in temperature. On average, the ratio of MCP-to-BP at a 1000-m depth increased to 1:5.95 with surface warming of 4°C, indicating the higher impact of MCP in future ocean carbon sequestration.     

The geobiological formation process of the marine source rocks in the Middle Permian Chihsia Formation of South China

The Chihsia Formation is one of the four sets of regional marine hydrocarbon source rocks from South China.In the past two decades,detailed geochemical and sedimentological studies have been carried out to investigate its origination,which have demonstrated that the high primary productivity plays a primary role in the deposition of sediments enriched in the organic matter.However,the mechanism of this high productivity and the path of the deposition and burial of the organic matter have always been a mystery.Based on the previous studies on the Shangsi Section in Guangyuan City,Sichuan Province,we proposed that the development of the equatorial upwelling due to the sea level rise is responsible for the relatively high productivity in the Chihsia Formation.The sea waters with high nutrient were transported by the sub-surface currents along the equator.High organic carbon flux was deposited on the deeper shelf,and then decomposed by bacteria,leading to the occurrence of anaerobic respiration.The metabolism of the microorganisms consumed the dissolved oxygen in waters,which was in favor of the preservation of the organic matter.This suggested geobiological model integrating with paleoclimatology,paleoceanography and geomicrobiology will help us to understand the causes of this particular sedimentary sequence.     

Impacts of land-use and climate changes on ecosystem productivity and carbon cycle in the cropping-grazing transitional zone in China

Terrestrial ecosystems are both a carbon source and sink, therefore play an important role in the global carbon cycle that act as a link of interactions between human activities and climate changes[1,2]. Climate change impacts ecosystem carbon cycle through af- fecting biological processes, e.g. plant photosynthesis, respiration, and soil carbon decomposition. Land-use change directly modifies the distribution and structure of terrestrial ecosystems and hence the carbon storage and fluxes. Usi…     

Significance of Vibrio species in the marine organic carbon cycle—A review

The genus Vibrio,belonging to Gammaproteobacteria of the phylum Proteobacteria,is a genetically and ecologically diverse group of heterotrophic bacteria,that are ubiquitous in marine environments,especially in coastal areas.In particular,vibrios dominate,i.e.up to 10%of the readily culturable marine bacteria in these habitats.The distribution of Vibrio spp.is shaped by various environmental parameters,notably temperature,salinity and dissolved organic carbon.Vibriospp.may utilize a wide range of organic carbon compounds,including chitin(this may be metabolized by most Vibrio spp.),alginic acid and agar.Many Vibrio spp.have very short replication times(as short as～10 min),which could facilitate them developing into high biomass content albeit for relatively short durations.Although Vibriospp.usually comprise a minor portion(typically~1%of the total bacterioplankton in coastal waters)of the total microbial population,they have been shown to proliferate explosively in response to various nutrient pulses,e.g.,organic nutrients from algae blooms and iron from Saharan dust.Thus,Vibrio spp.may exert large impacts on marine organic carbon cycling especially in marginal seas.Genomics and related areas of investigation will reveal more about the molecular components and mechanisms involved in Vibrio-mediated biotransformation and remineralization processes.     

Characteristics of particle fluxes in the Prydz Bay polynya,Eastern Antarctica

The settling of particulate carbon in seawater is a key component of the ocean carbon cycle. We deployed a set of sediment trap in the polynya of Prydz Bay from December 2010 to December 2011 to investigate the seasonal variations in particle fluxes. There was a clear seasonal variation in the particle fluxes, with maximum and minimum fluxes recorded during the summer and winter, respectively. The average total flux over the sampling period was 193.58 mg m~(-2)d~(-1), and the average fluxes of organic carbon(C_(org)), inorganic carbon(C_(inorg)), and biogenic silica(Si_(bio)) were 721.78, 28.67, and 2382.80 μmol m~(-2) d~(-1), respectively. Si_(bio)was the main contributor to the total mass flux, and strongly correlated with C_(org). The high Si_(bio)/C_(org)molar ratios(1) suggest that C_(org)was transported to deep sea in association with Si_(bio). By comparing remote sensing data of sea ice and chlorophyll in the upper water column, we found that the dynamics of carbon fluxes were closely related to changes in sea ice. Algae in sea ice may have a key role in biological pump processes in early summer. Apart from the ice algae bloom period, variations in carbon fluxes generally corresponded with phytoplankton blooms in the upper water. The ballast effect controlled the particle settling velocity and the efficiency of the biological pump. Sea ice rafts initiated the first particle export event and enhanced the particle settling efficiency during melting period. As diatoms might become less dominant in the ice-free area, sea ice loss may cause the efficiency of the biological pump efficiency to decrease over the long term.     

Early diagenetic growth of carbonate concretions in the upper Doushantuo Formation in South China and their significance for the assessment of hydrocarbon source rock

Mineralogical and textural characteristics and organic carbon composition of the carbonate concretions from the upper Doushantuo Formation (ca. 551 Ma) in the eastern Yangtze Gorge area reveal their early diagenetic (shallow) growth in organic-rich shale. High organic carbon content (up to 10%) and abundance of framboidal pyrites in the hosting shale suggest an anoxic or euxinic depositional environment. Well-preserved cardhouse clay fabrics in the concretions suggest their formation at 0-3 m burial depth, likely associated with microbial decomposition of organic matter and anaerobic oxidation of methane. Gases through decomposition of organic matter and/or from methanogenesis created bubbles and cavities, and anaerobic methane oxidation at the sulfate reduction zone resulted in carbonate precipitation, filling in bubbles and cavities to form spherical structures of the concretions. Rock pyrolysis analyses show that the carbonate concretions have lower total organic carbon (TOC) content but higher effective carbon than those in the host rocks. This may be caused by enclosed organic matter in pores of the concretions so that organic matter was protected from further modification during deep burial and maintained high hydrocarbon generating potential even in over-matured source rock. As a microbialite sensu latu, concretions have special growth conditions and may provide important information on the microbial activities in depositional and early burial environments.     

The contribution of bacteria to organic matter in coal-measure source rocks

On the basis of GC–MS analysis, a suite of nine coal-measure source rocks(Ro 0.51%–0.63%) from the southern margin of Junggar basin was found to contain many biomarkers for bacterially-generated hydrocarbons:hopane, sesquiterpene, C₂₃+ monomethyl alkanes(even carbon predominance), and C₂₄+ alkyl cyclohexane.Rock–eval and microscope analysis indicate that vitrinite(especially desmocollinite and homocollinite) plays a significant role in the generation of hydrocarbons in coalmeasure source rocks. Vitrinite performs this role by absorbing ultramicroscopic organic matter, generally in the form of resins or bacterial plastids. C₂₃+ monomethyl alkanes(even carbon predominance) and C₂₄+ alkyl cyclohexane series compounds are derived from bacterial metabolites of higher plants. The ultramicro organic matter adsorbed by vitrinite source rocks in the study area is probably ultramicro bacterial plastids. Because the organic matter of higher plants with low hydrogen content has been transformed into organic matter rich in hydrogen by bacteria, the hydrocarbon generation capacity of source rocks is greatly improved. In other words, in coal-measure source rocks, bacteria play an important role in hydrocarbon generation.     

Coherent variations of the obliquity components in global ice volume and ocean carbon reservoir over the past 5 Ma

The Milankovi theory stresses that the summer insolation in the high northern latitudes that is dominated by the precession cycle controls the glacial/interglacial cycles in global climate change.If the climate system responds linearly to the external insolation forcing,the precession cycle of 23 or 19 ka should dominate the variations in the climatic proxy records.I performed spectral and evolutive cross spectral analyses on the high resolution benthic 18O and 13C records from the South China Sea and the North Atlantic,the proxies of global ice volume and ocean carbon reservoir respectively.I found that the obliquity instead of the eccentricity or the precession is the most marked cycle in the global ice volume and ocean carbon reservoir variations over the past 5 Ma.The analysis further reveals that only at the obliquity band instead of the eccentricity or the precession band does the global ice volume and ocean carbon reservoir display consistently high coherency and stable phase relationship over the past 5 Ma.The consistently positive or near-zero phases of the benthic 18O relative to the benthic13C at the obliquity band suggest that the global carbon cycle is involved in the polar ice sheet growth as an important internal feedback,not a determinative driving factor.The obliquity instead of the precession or the eccentricity takes the dominant role of driving the global climate change during the Pliocene and Pleistocene.     

Quantifying the sources of dissolved inorganic carbon within the sulfate-methane transition zone in nearshore sediments of Qi’ao Island,Pearl River Estuary,Southern China

The significance of the various biogeochemical pathways that drive carbon cycling and the relative fractions of dissolved inorganic carbon(DIC) produced by these reactions within the sulfate-methane transition zone(SMTZ) are still being debated. Unraveling these processes is important to our understanding of the benthic DIC sources and their contributions to the global carbon cycle. Here, we measure pore water geochemistry(chlorine, sulfate, methane, Ca~(2+), Mg~(2+), DIC and δ~(13)C-DIC) as well as solid geochemistry(sedimentary organic carbon(SOC) and δ~(13)C of SOC) in nearshore sediments from Qi'ao Island in the Pearl River Estuary of the Southern China Sea. Our analysis indicates that SOC originates from the mixing of carbon from terrestrial and marine sources, and that terrestrial materials dominate the net loss of SOC during the degradation of organic matter, especially at sites located near the river outlets. Sulfate reduction via SOC degradation is not appreciable in the upper sediment layer due to conservative mixing-dilution by freshwater. However, below this layer, the anaerobic oxidation of methane(AOM) and methanogenesis occur. Within the SMTZ, the δ~(13)C mass balance shows that the proportions of DIC derived from organoclastic SO_4~(2-) reduction(OSR) and AOM are 50.3% to 66.7% and 0.1% to 17.9%, respectively, whereas methanogenesis contributes 17.0% to 43.9%. This study reveals that the upward diffusion of DIC from ongoing methanogenesis significantly influences carbon cycling within the SMTZ in these estuarine sediments. As a result, we suggest that the plots of the ratio of change in sulfate to change in DIC in pore water should be used with caution when discriminating between sulfate reduction pathways in methane-rich sediments.     

Sediment organic matter source estimation and ecological classification in the semi-enclosed Batan Bay Estuary,Philippines

The large organic matter flow in tropical coastal areas is recognized as an important process in the global carbon(C)cycle.However,the nature of organic matter flow in semi-enclosed tropical estuaries remains unclear due to the various environmental processes(tidal change,river flow,waves from the sea,and internal circulation)and organic matter sources therein.Thus,sediment organic matter(SOM)sources,and their distribution pattern,are key to understanding ecosystem material flow.Our research in the Batan Bay Estuary,Philippines,a semi-enclosed estuary under large mangrove deforestation,was conducted to determine ecosystem properties through analysis of C and nitrogen stable isotope ratios and environmental factors.First,we determined that mangrove litter,microphytobenthos,and phytoplankton are the main SOM sources in the Batan Bay Estuary.Second,the estuary was classified into three ecological zones(the Bay zone,Back-barrier zone,and River zone).In addition,we estimated SOM source ratios using the Stable Isotope Analysis in R package and determined different organic matter sources in different zone.The high ratios of mangrove litter as SOM indicate that a large amount of terrestrial plant organic matter remains despite the heavy mangrove deforestation that has occurred since the 1980s,and that the Back-barrier zone consists of a different type of ecosystem that promotes accumulation of C from mangrove litter and microphytobenthos.     

Soil organic carbon storage and soil CO_2 flux in the alpine meadow ecosystem

High-resolution sampling,measurements of organic carbon contents and 14C signatures of selected four soil profiles in the Haibei Station situated on the northeast Tibetan Plateau,and application of 14C tracing technology were conducted in an attempt to investigate the turnover times of soil organic car-bon and the soil-CO2 flux in the alpine meadow ecosystem. The results show that the organic carbon stored in the soils varies from 22.12×104 kg C hm-2 to 30.75×104 kg C hm-2 in the alpine meadow eco-systems,with an average of 26.86×104 kg C hm-2. Turnover times of organic carbon pools increase with depth from 45 a to 73 a in the surface soil horizon to hundreds of years or millennia or even longer at the deep soil horizons in the alpine meadow ecosystems. The soil-CO2 flux ranges from 103.24 g C m-2 a-1 to 254.93 gC m-2 a-1,with an average of 191.23 g C m-2 a-1. The CO2 efflux produced from microbial decomposition of organic matter varies from 73.3 g C m-2 a-1 to 181 g C m-2 a-1. More than 30% of total soil organic carbon resides in the active carbon pool and 72.8%―81.23% of total CO2 emitted from or-ganic matter decomposition results from the topsoil horizon (from 0 cm to 10 cm) for the Kobresia meadow. Responding to global warming,the storage,volume of flow and fate of the soil organic carbon in the alpine meadow ecosystem of the Tibetan Plateau will be changed,which needs further research.