铁施肥促进海洋浮游植物和生物碳泵的不确定性

铁作为浮游植物所必需的微量元素,限制了全球超过三分之一海域的初级生产力,尤其是在高营养盐、低叶绿素海域(high nutrient low chlorophyll,HNLC)。长期以来海洋铁施肥被认为是一项可以降低大气二氧化碳含量的地球工程策略。然而通过13次海洋人工铁施肥(artificial ocean iron fertilization,aOIF)实验发现,铁的额外添加对海洋深层碳输出量的促进作用要显著低于预期。本文简要地总结了碳在海洋和大气中的循环过程,回顾了人工铁施肥实验对生物碳泵和碳通量等的影响,分析了从海洋铁施肥到海洋碳汇关键生物地球化学过程的影响因素。综上分析发现,科学界对生物碳泵过程及其调控机制的认识仍十分浅薄,考虑到海洋铁施肥还会对海洋生态系统带来一定的负面作用,铁施肥能否作为降低大气中CO₂的有效手段,以达到碳中和并缓解温室效应仍需进一步研究。     

Dimethylsulfide is an energy source for the heterotrophic marine bacterium Sagittula stellata

Dimethylsulfide (DMS) is a volatile organosulfur compound, ubiquitous in the oceans, that has been credited with various roles in biogeochemical cycling and in climate control. Various oceanic sinks of DMS are known - both chemical and biological - although they are poorly understood. In addition to the utilization of DMS as a carbon or a sulfur source, some Bacteria are known to oxidize it to dimethylsulfoxide (DMSO). Sagittula stellata is a heterotrophic member of the Alphaproteobacteria found in marine environments. It has been shown to oxidize DMS during heterotrophic growth on sugars, but the reasons for and the mechanisms of this oxidation have not been investigated. Here, we show that the oxidation of DMS to DMSO is coupled to ATP synthesis in S. stellata and that DMS acts as an energy source during chemoorganoheterotrophic growth of the organism on fructose and on succinate. DMS dehydrogenase (which is responsible for the oxidation of DMS to DMSO in other marine Bacteria) and DMSO reductase activities were absent from cells grown in the presence of DMS, indicating an alternative route of DMS oxidation in this organism.     

The Biogeochemical Role of Baleen Whales and Krill in Southern Ocean Nutrient Cycling

The availability of micronutrients is a key factor that affects primary productivity in High Nutrient Low Chlorophyll (HNLC) regions of the Southern Ocean. Nutrient supply is governed by a range of physical, chemical and biological processes, and there are significant feedbacks within the ecosystem. It has been suggested that baleen whales form a crucial part of biogeochemical cycling processes through the consumption of nutrient-rich krill and subsequent defecation, but data on their contribution are scarce. We analysed the concentration of iron, cadmium, manganese, cobalt, copper, zinc, phosphorus and carbon in baleen whale faeces and muscle, and krill tissue using inductively coupled plasma mass spectrometry. Metal concentrations in krill tissue were between 20 thousand and 4.8 million times higher than typical Southern Ocean HNLC seawater concentrations, while whale faecal matter was between 276 thousand and 10 million times higher. These findings suggest that krill act as a mechanism for concentrating and retaining elements in the surface layer, which are subsequently released back into the ocean, once eaten by whales, through defecation. Trace metal to carbon ratios were also higher in whale faeces compared to whale muscle indicating that whales are concentrating carbon and actively defecating trace elements. Consequently, recovery of the great whales may facilitate the recycling of nutrients via defecation, which may affect productivity in HNLC areas.     

Bacterially mediated iron cycling and associated biogeochemical processes in a subtropical shallow coastal aquifer: implications for groundwater quality

Bacterially mediated iron redox cycling exerts a strong influence on groundwater geochemistry, but few studies have investigated iron biogeochemical processes in coastal alluvial aquifers from a microbiological viewpoint. The shallow alluvial aquifer located adjacent to Poona estuary on the subtropical Southeast Queensland coast represents a redox-stratified system where iron biogeochemical cycling potentially affects water quality. Using a 300 m transect of monitoring wells perpendicular to the estuary, we examined groundwater physico-chemical conditions and the occurrence of cultivable bacterial populations involved in iron (and manganese, sulfur) redox reactions in this aquifer. Results showed slightly acidic and near-neutral pH, suboxic conditions and an abundance of dissolved iron consisting primarily of iron(II) in the majority of wells. The highest level of dissolved iron(III) was found in a well proximal to the estuary most likely a result of iron curtain effects due to tidal intrusion. A number of cultivable, (an)aerobic bacterial populations capable of diverse carbon, iron, or sulfur metabolism coexisted in groundwater redox transition zones. Our findings indicated aerobic, heterotrophic respiration and bacterially mediated iron/sulfur redox reactions were integral to carbon cycling in the aquifer. High abundances of dissolved iron and cultivable iron and sulfur bacterial populations in estuary-adjacent aquifers have implications for iron transport to marine waters. This study demonstrated bacterially mediated iron redox cycling and associated biogeochemical processes in subtropical coastal groundwaters using culture-based methods.     

Abundant and diverse bacteria involved in DMSP degradation in marine surface waters

An expanded analysis of oceanic metagenomic data indicates that the majority of prokaryotic cells in marine surface waters have the genetic capability to demethylate dimethylsulfoniopropionate (DMSP). The 1701 homologues of the DMSP demethylase gene, dmdA , identified in the (2007) Global Ocean Sampling (GOS) metagenome, are sufficient for 58% (±9%) of sampled cells to participate in this critical step in the marine sulfur cycle. This remarkable frequency of DMSP-demethylating cells is in accordance with biogeochemical data indicating that marine phytoplankton direct up to 10% of fixed carbon to DMSP synthesis, and that most of this DMSP is subsequently degraded by bacteria via demethylation. The GOS metagenomic data also revealed a new cluster of dmdA sequences (designated Clade E) that implicates marine gammaproteobacteria in DMSP demethylation, along with previously recognized alphaproteobacterial groups Roseobacter and SAR11. Analyses of G+C content and gene order indicate that lateral gene transfer is likely responsible for the wide distribution of dmdA among diverse taxa, contributing to the homogenization of biogeochemical roles among heterotrophic marine bacterioplankton. Candidate genes for the competing bacterial degradation process that converts DMSP to the climate-active gas dimethylsulfide (DMS) ( dddD and dddL ) occur infrequently in the (2007) GOS metagenome, suggesting either that the key DMS-producing bacterial genes are yet to be identified or that DMS formation by free-living bacterioplankton is insignificant relative to their demethylation activity.     

稻田土壤关键元素的生物地球化学耦合过程及其微生物调控机制

水稻土是在长期植稻下人为培育的特殊耕作土壤,是我国土壤学的特色,其研究也反映我国土壤学的国际地位。水稻土是研究土壤生物地球化学过程的理想模型。稻田土壤关键元素(碳氮磷硫铁等)的生物地球化学循环过程、耦合机理及其驱动机制研究是土壤生物学研究的核心之一。因此,以国际土壤年为契机,结合中国科学院院士工作局资助的"土壤生物学发展战略研究"项目的部分成果,以稻田关键元素(碳氮磷硫铁等)生物地球化学循环过程及其耦合的微生物驱动机制为核心,重点讨论了稻田土壤基本生物化学特征、稻田土壤碳-氮、碳-氮-磷、碳-氮-铁等多元素耦合过程及其与微生物之间的反馈机制,并由此提出了稻田土壤关键元素生物地球化学循环微生物驱动机制研究的未来重点发展方向为:1)土壤关键元素生物地球化学过程的异质性及其微生物过程的互作机制研究;2)微生物参与机制对土壤关键元素循环过程的响应、反馈机制与调控机制研究;3)土壤关键生物地球化学过程的计量学研究。     

Influence of dimethyl sulfide on the carbon cycle and biological production

Dimethyl sulfide (DMS) is a significant source of marine sulfate aerosol and plays an important role in modifying cloud properties. Fully coupled climate simulations using dynamic marine ecosystem and DMS calculations are conducted to estimate DMS fluxes under various climate scenarios and to examine the sign and strength of phytoplankton-DMS-climate feedbacks for the first time. Simulation results show small differences in the DMS production and emissions between pre-industrial and present climate scenarios, except for some areas in the Southern Ocean. There are clear changes in surface ocean DMS concentrations moving into the future, and they are attributable to changes in phytoplankton production and competition driven by complex spatially varying mechanisms. Comparisons between parallel simulations with and without DMS fluxes into the atmosphere show significant differences in marine ecosystems and physical fields. Without DMS, the missing subsequent aerosol indirect effects on clouds and radiative forcing lead to fewer clouds, more solar radiation, and a much warmer climate. Phaeocystis, a uniquely efficient organosulfur producer with a growth advantage under cooler climate states, can benefit from producing the compound through cooling effects of DMS in the climate system. Our results show a tight coupling between the sulfur and carbon cycles. The ocean carbon uptake declines without DMS emissions to the atmosphere. The analysis indicates a weak positive phytoplankton-DMS-climate feedback at the global scale, with large spatial variations driven by individual autotrophic functional groups and complex mechanisms. The sign and strength of the feedback vary with climate states and phytoplankton groups. This highlights the importance of a dynamic marine ecosystem module and the sulfur cycle mechanism in climate projections.     

INTRACELLULAR DIMETHYLSULFOXIDE (DMSO) IN UNICELLULAR MARINE ALGAE: SPECULATIONS ON ITS ORIGIN AND POSSIBLE BIOLOGICAL ROLE

Recent studies have established that aqueous phase concentrations of dimethylsulfoxide (DMSO) often exceed those of dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS). Yet, in comparison to DMSP and DMS, DMSO remains a poorly understood component of the marine sulfur cycle. Much of what is known about the mechanisms for the formation and loss for DMSO is inferred from laboratory experiments, and no explanation exists to rationalize how a large pool of DMSO is maintained. One formation pathway that, until very recently, has been ignored involves the direct synthesis of DMSO by marine phytoplankton. This review examines some of the circumstantial evidence for DMSO in marine particulate material and recent reports containing preliminary data for particulate DMSO (DMSO_p) in the marine environment. Drawing on literature from a range of scientific disciplines, speculations on the possible origins and biological functions of intracellular DMSO are also made. On the basis of its physicochemical properties, intracellular DMSO could have a potential role as a cryoprotectant, a specialist cryo-osmoregulator in extreme environments, an intracellular electrolyte modifier, and a free-radical scavenger. The review also assesses the impact of DMSO_p at both the organism and the global level. Consideration is given to the marine biogeochemical cycling of sulfur and potential links to climate control.     

Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake

Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria, and indicate the use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant, indicating that DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment.     

Characterization of Enrichment Cultures Involved in the Carbon,Sulfur and Iron Biogeochemical Cycles in French Guiana Mobile Muds

The fluidized sediment ecosystem off French Guiana is characterized by active physical reworking, diversity of electron acceptors and highly variable redox regime. It is well studied geochemically but little is known about specific microorganisms involved in its biogeochemistry. Based on the biogeochemical profiles and rate kinetics, several possible biotically mediated pathways of the carbon, sulfur and iron cycles were hypothesized. Enrichment studies were set up with a goal to culture microorganisms responsible for these pathways. Stable microbial consortia potentially capable of the following chemolithoautotrophic types were enriched from the environment and characterized: elemental sulfur/thiosulfate disproportionators, thiosulfate-oxidizing ferrihydrite and nitrate reducers, sulfide/ferrous sulfide oxidizers coupled with nitrate and microaerophilic iron oxidizers. Attempts to generate several enrichments (anoxic ammonia oxidation, and sulfide oxidizers with ferric iron or manganese oxide) were not successful. Heterotrophic sulfate and elemental sulfur reduction bacteria are prominent and dominate reductive sulfur transformations. We hypothesize that carbon dioxide fixation coupled with synthesis of organic matter happens mostly via sulfur disproportionation and sulfur species oxidation with iron oxidation playing a minor role.     

Towards a systematic understanding of structure–function relationship of dimethylsulfoniopropionate‐catabolizing enzymes

Each year, several million tons of dimethylsulfoniopropionate (DMSP) are produced by marine phytoplankton and bacteria as an important osmolyte to regulate their cellular osmosis. Microbial breakdown of DMSP to the volatile gas dimethylsulfide (DMS) plays an important role in global biogeochemical cycles of the sulphur element between land and the sea. Understanding the enzymes involved in the transformation of DMSP and DMS holds the key to a better understanding of oceanic DMSP cycles. Recent work by Shao et al. (2019) has resolved the crystal structure of two important enzymes, DmdB and DmdC, involved in DMSP transformation through the demethylation pathway. Their work represents an important step towards a systematic understanding of the structure–function relationships of DMSP‐catabolizing enzymes in marine microbes.     

红树林湿地硫酸盐还原菌的多样性及其参与驱动的元素耦合机制

红树林生态系统是热带和亚热带地区重要的滨海湿地,具有营养物质形态多样化和高效动态变化的特征,是驱动碳、氮、硫等元素循环的热区。硫酸盐还原菌(sulfate-reducing prokaryotes,SRPs)是地球最古老的微生物生命形式之一,在推动早期地球地质演化以及现代生物地球化学循环中发挥关键作用,但其在红树林湿地还缺乏全面深入研究。本文基于Genome Taxonomy Database中原核生物基因组的挖掘,系统总结了硫酸盐还原菌的类群,梳理了近年来国内外红树林中硫酸盐还原菌的分布情况及影响其分布的因素,分析了硫酸盐还原菌在红树林生态系统的碳、氮、硫及铁等元素地球化学循环中的作用,并对硫酸盐还原菌未来的研究方向进行了展望,以期为深入研究硫酸盐还原菌参与驱动的元素生物地球化学循环及其耦合机制提供参考。     

Investigating the inter-relationships between water attenuated irradiance, primary production and DMS(P)

Both solar irradiance and primary production have been proposed as independent controls on seawater dimethyl sulphide (DMS) and dimethylsulphoniopropionate (DMSP) concentrations. However, irradiance also drives photosynthesis, and thus influences a complex set of inter-related processes that modulate marine DMS. We investigate the potential inter-relationships between the rate of primary production (carbon assimilation), water-attenuated irradiance and DMS/DMSP dynamics by applying correlation analysis to a high resolution, concurrently sampled in situ data set from a range of latitudes covering multiple biogeochemical provinces from 3 of the 4 Longhurst biogeochemical domains. The combination of primary production (PP) and underwater irradiance (Iz) within a multivariate regression model is able to explain 55% of the variance in DMS concentrations from all depths within the euphotic zone and 66% of the variance in surface DMS concentrations. Contrary to some previous studies we find a variable representing biological processes is necessary to better account for the variance in DMS. We find that the inclusion of Iz accounts for variance in DMS that is independent from the variance explained by PP. This suggests an important role for solar irradiance (beyond the influence of irradiance upon primary production) in mediating the relationship between the productivity of the ecosystem, DMS/DMSP production and ambient seawater DMS concentrations.     

Marine biodiversification in response to evolving phytoplankton stoichiometry

Diversification of the marine biosphere is intimately linked to the evolution of the biogeochemical cycles of carbon, nutrients, and primary productivity. A meta-analysis of the ratio of carbon-to-phosphorus buried in sedimentary rocks during the past 3 billion years indicates that both food quantity and, critically, food quality increased through time as a result of the evolving stoichiometry (nutrient content) of eukaryotic phytoplankton. Evolving food quantity and quality was primarily a function of broad tectonic cycles that influenced not just carbon burial, but also nutrient availability and primary productivity. Increasing nutrient availability during the middle-to-Late Proterozoic culminated in the production of food (phytoplankton biomass and fresh dead organic matter) with C:P Redfield ratios sufficient to finally promote geologically-rapid biodiversification during the Proterozoic–Phanerozoic transition. This resulted in further, massive nutrient sequestration into biomass that triggered positive feedback via nutrient recycling (bioturbation, mesozooplankton grazing) on phytoplankton productivity. Increasing rates and depths of bioturbation through the Phanerozoic suggest that nutrient recycling continued to increase. Increasing bioturbation and nutrient cycling appear to have been necessary to sustain the primary productivity and “energetics” (biomass, metabolic rates, and physical activity such as predation) of the marine biosphere because of the geologically-slow input of macronutrients like phosphorus from land and the continued sequestration of nutrients into marine and terrestrial biomass.     

Formation of methylmercaptan and dimethylsulfide from methoxylated aromatic compounds in anoxic marine and fresh water sediments

Abstract Anaerobic formation of dimethylsulfide (DMS) and methylmercaptan (MSH) in anoxic sulfide-containing slurries from marine and fresh water sediments was stimulated by addition of syringate (4-hydroxy,3,5,-dimethoxybenzoate) and 3,4,5,-trimethoxybenzoate. The release of DMS and MSH occurred during the consumption of the aromatic monomers and ceased after their depletion. DMS was the dominant methylated sulfur compound in fresh water sediments, in contrast to marine sediments where MSH was predominant. No production of volatile organic sulfur compounds was observed in slurries containing gallate (3,4,5,-trihydroxybenzoate) or in autoclaved controled. About 50–65% of the methoxy carbon could be accounted for by peak accumulation of DMS and MSH. In the saline sediments, large amounts of CH₄ were formed during the period when DMS and MSH disappeared. About 65–70% of the methylcarbon of the volatile methylated sulfur compounds (VMSC) could be accounted for in the produced CH₄. This study demonstrates a previously unknown microbial process by which DMS and MSH are formed during anaerobic decomposition of methoxylated aromatic compounds in marine and freshwater sediments.     

Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches

Phytoplankton are limited by iron (Fe) in ~40% of the world's oceans including high-nutrient low-chlorophyll (HNLC) regions. While low-Fe adaptation has been well-studied in large eukaryotic diatoms, less is known for small, prokaryotic marine picocyanobacteria. This study reveals key physiological and genomic differences underlying Fe adaptation in marine picocyanobacteria. HNLC ecotype CRD1 strains have greater physiological tolerance to low Fe congruent with their expanded repertoire of Fe transporter, storage and regulatory genes compared to other ecotypes. From metagenomic analysis, genes encoding ferritin, flavodoxin, Fe transporters and siderophore uptake genes were more abundant in low-Fe waters, mirroring paradigms of low-Fe adaptation in diatoms. Distinct Fe-related gene repertories of HNLC ecotypes CRD1 and CRD2 also highlight how coexisting ecotypes have evolved independent approaches to life in low-Fe habitats. Synechococcus and Prochlorococcus HNLC ecotypes likewise exhibit independent, genome-wide reductions of predicted Fe-requiring genes. HNLC ecotype CRD1 interestingly was most similar to coastal ecotype I in Fe physiology and Fe-related gene content, suggesting populations from these different biomes experience similar Fe-selective conditions. This work supports an improved perspective that phytoplankton are shaped by more nuanced Fe niches in the oceans than previously implied from mostly binary comparisons of low- versus high-Fe habitats and populations.     

Oxidation of dimethylsulfide to tetrathionate by Methylophaga thiooxidans sp. nov.: a new link in the sulfur cycle

A new pathway of dimethylsulfide (DMS) metabolism was identified in a novel species of Gammaproteobacteria, Methylophaga thiooxidans sp. nov., in which tetrathionate (S₄O₆^2?) was the end‐product of DMS oxidation. Inhibitor evidence indicated that DMS degradation was initiated by demethylation, catalysed by a corrinoid demethylase. Thiosulfate was an intermediate, which was oxidized to tetrathionate by a cytochrome‐linked thiosulfate dehydrogenase. Thiosulfate oxidation was coupled to ATP synthesis, and M. thiooxidans could also use exogenous thiosulfate as an energy source during chemolithoheterotrophic growth on DMS or methanol. Cultures grown on a variety of substrates oxidized thiosulfate, indicating that thiosulfate oxidation was constitutive. The observations have relevance to interactions among sulfur‐metabolizing bacteria in the marine environment. The production of tetrathionate from an organosulfur precursor is previously undocumented and represents a potential step in the biogeochemical sulfur cycle, providing a ‘shunt’ across the cycle.     

Reductive dissolution of pyrite by methanogenic archaea

The formation and fate of pyrite (FeS₂) modulates global iron, sulfur, carbon, and oxygen biogeochemical cycles and has done so since early in Earth’s geological history. A longstanding paradigm is that FeS₂ is stable at low temperature and is unavailable to microorganisms in the absence of oxygen and oxidative weathering. Here, we show that methanogens can catalyze the reductive dissolution of FeS₂ at low temperature (≤38 °C) and utilize dissolution products to meet cellular iron and sulfur demands associated with the biosynthesis of simple and complex co-factors. Direct access to FeS₂ is required to catalyze its reduction and/or to assimilate iron monosulfide that likely forms through coupled reductive dissolution and precipitation, consistent with close associations observed between cells and FeS₂. These findings demonstrate that FeS₂ is bioavailable to anaerobic methanogens and can be mobilized in low temperature anoxic environments. Given that methanogens evolved at least 3.46 Gya, these data indicate that the microbial contribution to the iron and sulfur cycles in ancient and contemporary anoxic environments may be more complex and robust than previously recognized, with impacts on the sources and sinks of iron and sulfur and other bio-essential and thiophilic elements such as nickel and cobalt.Subject terms: Biogeochemistry, Water microbiology     

Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean

Bacteria and archaea in the dark ocean (>200 m) comprise 0.3–1.3 billion tons of actively cycled marine carbon. Many of these microorganisms have the genetic potential to fix inorganic carbon (autotrophs) or assimilate single-carbon compounds (methylotrophs). We identified the functions of autotrophic and methylotrophic microorganisms in a vent plume at Axial Seamount, where hydrothermal activity provides a biogeochemical hot spot for carbon fixation in the dark ocean. Free-living members of the SUP05/Arctic96BD-19 clade of marine gamma-proteobacterial sulfur oxidizers (GSOs) are distributed throughout the northeastern Pacific Ocean and dominated hydrothermal plume waters at Axial Seamount. Marine GSOs expressed proteins for sulfur oxidation (adenosine phosphosulfate reductase, sox (sulfur oxidizing system), dissimilatory sulfite reductase and ATP sulfurylase), carbon fixation (ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO)), aerobic respiration (cytochrome c oxidase) and nitrogen regulation (PII). Methylotrophs and iron oxidizers were also active in plume waters and expressed key proteins for methane oxidation and inorganic carbon fixation (particulate methane monooxygenase/methanol dehydrogenase and RuBisCO, respectively). Proteomic data suggest that free-living sulfur oxidizers and methylotrophs are among the dominant primary producers in vent plume waters in the northeastern Pacific Ocean.