A marine microbial consortium apparently mediating anaerobic oxidation of methane

A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles, radiotracer experiments and stable carbon isotope data. But the elusive microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria. Here we provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which we identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes. In this example of a structured archaeal-bacterial symbiosis, the archaea grow in dense aggregates of about 100 cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.     

Hydrogen is an energy source for hydrothermal vent symbioses

The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.     

Methane emissions from terrestrial plants under aerobic conditions

Methane is an important greenhouse gas and its atmospheric concentration has almost tripled since pre-industrial times. It plays a central role in atmospheric oxidation chemistry and affects stratospheric ozone and water vapour levels. Most of the methane from natural sources in Earth's atmosphere is thought to originate from biological processes in anoxic environments. Here we demonstrate using stable carbon isotopes that methane is readily formed in situ in terrestrial plants under oxic conditions by a hitherto unrecognized process. Significant methane emissions from both intact plants and detached leaves were observed during incubation experiments in the laboratory and in the field. If our measurements are typical for short-lived biomass and scaled on a global basis, we estimate a methane source strength of 62-236 Tg yr(-1) for living plants and 1-7 Tg yr(-1) for plant litter (1 Tg = 10(12) g). We suggest that this newly identified source may have important implications for the global methane budget and may call for a reconsideration of the role of natural methane sources in past climate change.     

A humid climate state during the Palaeocene/Eocene thermal maximum

An abrupt climate warming of 5 to 10 degrees C during the Palaeocene/Eocene boundary thermal maximum (PETM) 55 Myr ago is linked to the catastrophic release of approximately 1,050-2,100 Gt of carbon from sea-floor methane hydrate reservoirs. Although atmospheric methane, and the carbon dioxide derived from its oxidation, probably contributed to PETM warming, neither the magnitude nor the timing of the climate change is consistent with direct greenhouse forcing by the carbon derived from methane hydrate. Here we demonstrate significant differences between marine and terrestrial carbon isotope records spanning the PETM. We use models of key carbon cycle processes to identify the cause of these differences. Our results provide evidence for a previously unrecognized discrete shift in the state of the climate system during the PETM, characterized by large increases in mid-latitude tropospheric humidity and enhanced cycling of carbon through terrestrial ecosystems. A more humid atmosphere helps to explain PETM temperatures, but the ultimate mechanisms underlying the shift remain unknown.     

A hydrothermal origin for isotopically anomalous cap dolostone cements from south China

The release of methane into the atmosphere through destabilization of clathrates is a positive feedback mechanism capable of amplifying global warming trends that may have operated several times in the geological past. Such methane release is a hypothesized cause or amplifier for one of the most drastic global warming events in Earth history, the end of the Marinoan 'snowball Earth' ice age, ～635?Myr ago. A key piece of evidence supporting this hypothesis is the occurrence of exceptionally depleted carbon isotope signatures (δ(13)C(PDB) down to -48‰; ref. 8) in post-glacial cap dolostones (that is, dolostone overlying glacial deposits) from south China; these signatures have been interpreted as products of methane oxidation at the time of deposition. Here we show, on the basis of carbonate clumped isotope thermometry, (87)Sr/(86)Sr isotope ratios, trace element content and clay mineral evidence, that carbonates bearing the (13)C-depleted signatures crystallized more than 1.6?Myr after deposition of the cap dolostone. Our results indicate that highly (13)C-depleted carbonate cements grew from hydrothermal fluids and suggest that their carbon isotope signatures are a consequence of thermogenic methane oxidation at depth. This finding not only negates carbon isotope evidence for methane release during Marinoan deglaciation in south China, but also eliminates the only known occurrence of a Precambrian sedimentary carbonate with highly (13)C-depleted signatures related to methane oxidation in a seep environment. We propose that the capacity to form highly (13)C-depleted seep carbonates, through biogenic anaeorobic oxidation of methane using sulphate, was limited in the Precambrian period by low sulphate concentrations in sea water. As a consequence, although clathrate destabilization may or may not have had a role in the exit from the 'snowball' state, it would not have left extreme carbon isotope signals in cap dolostones.     

Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink

Mud volcanism is an important natural source of the greenhouse gas methane to the hydrosphere and atmosphere. Recent investigations show that the number of active submarine mud volcanoes might be much higher than anticipated (for example, see refs 3-5), and that gas emitted from deep-sea seeps might reach the upper mixed ocean. Unfortunately, global methane emission from active submarine mud volcanoes cannot be quantified because their number and gas release are unknown. It is also unclear how efficiently methane-oxidizing microorganisms remove methane. Here we investigate the methane-emitting Haakon Mosby Mud Volcano (HMMV, Barents Sea, 72 degrees N, 14 degrees 44' E; 1,250 m water depth) to provide quantitative estimates of the in situ composition, distribution and activity of methanotrophs in relation to gas emission. The HMMV hosts three key communities: aerobic methanotrophic bacteria (Methylococcales), anaerobic methanotrophic archaea (ANME-2) thriving below siboglinid tubeworms, and a previously undescribed clade of archaea (ANME-3) associated with bacterial mats. We found that the upward flow of sulphate- and oxygen-free mud volcano fluids restricts the availability of these electron acceptors for methane oxidation, and hence the habitat range of methanotrophs. This mechanism limits the capacity of the microbial methane filter at active marine mud volcanoes to <40% of the total flux.     

Plant litter decomposition in a semi-arid ecosystem controlled by photodegradation

The carbon balance in terrestrial ecosystems is determined by the difference between inputs from primary production and the return of carbon to the atmosphere through decomposition of organic matter. Our understanding of the factors that control carbon turnover in water-limited ecosystems is limited, however, as studies of litter decomposition have shown contradictory results and only a modest correlation with precipitation. Here we evaluate the influence of solar radiation, soil biotic activity and soil resource availability on litter decomposition in the semi-arid Patagonian steppe using the results of manipulative experiments carried out under ambient conditions of rainfall and temperature. We show that intercepted solar radiation was the only factor that had a significant effect on the decomposition of organic matter, with attenuation of ultraviolet-B and total radiation causing a 33 and 60 per cent reduction in decomposition, respectively. We conclude that photodegradation is a dominant control on above-ground litter decomposition in this semi-arid ecosystem. Losses through photochemical mineralization may represent a short-circuit in the carbon cycle, with a substantial fraction of carbon fixed in plant biomass being lost directly to the atmosphere without cycling through soil organic matter pools. Furthermore, future changes in radiation interception due to decreased cloudiness, increased stratospheric ozone depletion, or reduced vegetative cover may have a more significant effect on the carbon balance in these water-limited ecosystems than changes in temperature or precipitation.     

Nodulation of legumes by members of the beta-subclass of Proteobacteria.

Members of the Leguminosae form the largest plant family on Earth, with around 18,000 species. The success of legumes can largely be attributed to their ability to form a nitrogen-fixing symbiosis with specific bacteria known as rhizobia, manifested by the development of nodules on the plant roots in which the bacteria fix atmospheric nitrogen, a major contributor to the global nitrogen cycle. Rhizobia described so far belong exclusively to the alpha-subclass of Proteobacteria, where they are distributed in four distinct phylogenetic branches. Although nitrogen-fixing bacteria exist in other proteobacterial subclasses, for example Herbaspirillum and Azoarcus from the phylogenetically distant beta-subclass, none has been found to harbour the nod genes essential for establishing rhizobial symbiosis. Here we report the identification of proteobacteria from the beta-subclass that nodulate legumes. This finding shows that the ability to establish a symbiosis with legumes is more widespread in bacteria than anticipated to date.     

农田灌溉水循环利用系统构建方法

介绍了将农田中坑塘湿地改建用于储存降雨径流和农田灌溉排水进行回用的水循环系统构建方法,在提出水循环调蓄湿地体积估算方法的基础上,构建了调蓄湿地水循环利用系统,分析了高效净污载体、微生物筛选与附着、水生植物群落配置和水动力微循环交换系统等水质净化技术,指出区域降水量和降雨历时是影响水循环调蓄湿地体积和循环水利用量的重要因素。对上海崇明水稻田循环调蓄湿地系统进行了设计与构建,循环调蓄湿地运行后共节约灌溉水量6239.9～9359.9m3。     

云南寻甸石漠化土壤易氧化碳对丛枝菌根真菌共生的响应

【目的】运用菌根技术改良石漠化土壤性状,已成为石漠化地区植被与土壤恢复的重要生物学途径。揭示丛枝菌根(AM)真菌与植物共生驱动下石漠化土壤碳库及养分状况的变化,探明石漠化土壤易氧化碳(ROC)对土壤碳库及养分变化的响应过程及机制,为石漠化土壤的微生物修复及提高石漠化治理效率提供参考。【方法】采集云南昆明寻甸石漠化土壤,以尼泊尔桤木(Alnus nepalensis)为寄主植物,分别接种摩西斗管囊霉(Funneliformis mosseae, FM)、幼套近明球囊霉(Claroideoglomus etunicatum, CE)、根内根孢囊霉(Rhizophagus intraradices, RI),并设置对照处理(无寄主植物及无AM接种),采用高锰酸钾氧化法测定不同试验处理下土壤ROC含量,探究土壤ROC与碳库组成、养分状况及植物生长之间的相互关系。【结果】不同AM真菌均具有显著的侵染与促生效应,其中RI的侵染率与菌丝侵染密度最大,相较于对照分别提高155%和100%,并显著促进桤木树高(60%)与基径(46%)生长;不同AM真菌均显著提高ROC含量,3菌种对ROC含量的提升率大小顺序为:RI(122%)> CE(78%)> FM(61%)。ROC在土壤总有机碳库中所占比例(52%)远高于微生物生物量碳(3%~6%);3种菌种对土壤养分含量的提升效应表现为:RI > CE > FM。相较于对照,RI 菌种对植物可利用性氮、微生物生物量碳、总有机碳及植物可利用性磷的提升率分别为161%、127%、110%及97%;对ROC变化具有较大贡献的土壤环境因子分别为AM真菌侵染率(96%)、植物可利用性氮(94%)、微生物生物量碳(85%)、总有机碳(78%)及植物可利用性磷(72%)。【结论】AM真菌与尼泊尔桤木共生,显著驱动石漠化土壤碳库与养分含量变化并促进植物生长,进而增加石漠化土壤易氧化碳的积累。研究结果有助于理解石漠化地区植物生长、土壤恢复及活性有机碳沉积的微生物学调控机制。     

A microbial consortium couples anaerobic methane oxidation to denitrification

Modern agriculture has accelerated biological methane and nitrogen cycling on a global scale. Freshwater sediments often receive increased downward fluxes of nitrate from agricultural runoff and upward fluxes of methane generated by anaerobic decomposition. In theory, prokaryotes should be capable of using nitrate to oxidize methane anaerobically, but such organisms have neither been observed in nature nor isolated in the laboratory. Microbial oxidation of methane is thus believed to proceed only with oxygen or sulphate. Here we show that the direct, anaerobic oxidation of methane coupled to denitrification of nitrate is possible. A microbial consortium, enriched from anoxic sediments, oxidized methane to carbon dioxide coupled to denitrification in the complete absence of oxygen. This consortium consisted of two microorganisms, a bacterium representing a phylum without any cultured species and an archaeon distantly related to marine methanotrophic Archaea. The detection of relatives of these prokaryotes in different freshwater ecosystems worldwide indicates that the reaction presented here may make a substantial contribution to biological methane and nitrogen cycles.     

“双碳”背景下山东自然保护地碳汇功能及价值

以山东省自然保护地为研究对象,系统分析了自然保护地内不同生态系统的碳汇功能及其差异性,并针对碳汇价值实现路径进行了探索研究。结果表明,山东省自然保护地的碳汇总量为2.99×10⁶ t/a,其中森林生态系统碳汇最高(1.20×10⁶ t/a),随后依次为农田生态系统(9.09×10⁵ t/a)、近海生态系统(5.22×10⁵ t/a)、滨海湿地生态系统(2.27×10⁵ t/a)、内陆湿地生态系统(1.28×10⁵ t/a)、草地生态系统(0.04×10⁴ t/a),其碳汇总价值为1.23×10⁹元,单位面积碳汇价值为7.61×10³元/hm²。鉴于自然保护地的碳汇价值,本研究从基于自然保护地生态补偿的角度对碳汇价值实现路径进行了讨论分析,提出了碳交易与生态补偿相结合的框架体系。     

Detection and classification of atmospheric methane oxidizing bacteria in soil

Well-drained non-agricultural soils mediate the oxidation of methane directly from the atmosphere, contributing 5 to 10% towards the global methane sink. Studies of methane oxidation kinetics in soil infer the activity of two methanotrophic populations: one that is only active at high methane concentrations (low affinity) and another that tolerates atmospheric levels of methane (high affinity). The activity of the latter has not been demonstrated by cultured laboratory strains of methanotrophs, leaving the microbiology of methane oxidation at atmospheric concentrations unclear. Here we describe a new pulse-chase experiment using long-term enrichment with 12CH4 followed by short-term exposure to 13CH4 to isotopically label methanotrophs in a soil from a temperate forest. Analysis of labelled phospholipid fatty acids (PLFAs) provided unambiguous evidence of methane assimilation at true atmospheric concentrations (1.8-3.6 p.p.m.v.). High proportions of 13C-labelled C18 fatty acids and the co-occurrence of a labelled, branched C17 fatty acid indicated that a new methanotroph, similar at the PLFA level to known type II methanotrophs, was the predominant soil micro-organism responsible for atmospheric methane oxidation.     

Methane-consuming archaebacteria in marine sediments

Large amounts of methane are produced in marine sediments but are then consumed before contacting aerobic waters or the atmosphere. Although no organism that can consume methane anaerobically has ever been isolated, biogeochemical evidence indicates that the overall process involves a transfer of electrons from methane to sulphate and is probably mediated by several organisms, including a methanogen (operating in reverse) and a sulphate-reducer (using an unknown intermediate substrate). Here we describe studies of sediments related to a decomposing methane hydrate. These provide strong evidence that methane is being consumed by archaebacteria that are phylogenetically distinct from known methanogens. Specifically, lipid biomarkers that are commonly characteristic of archaea are so strongly depleted in carbon-13 that methane must be the carbon source, rather than the metabolic product, for the organisms that have produced them. Parallel gene surveys of small-subunit ribosomal RNA (16S rRNA) indicate the predominance of a new archael group which is peripherally related to the methanogenic orders Methanomicrobiales and Methanosarcinales.     

Termination of global warmth at the Palaeocene/Eocene boundary through productivity feedback

The onset of the Palaeocene/Eocene thermal maximum (about 55 Myr ago) was marked by global surface temperatures warming by 5-7 degrees C over approximately 30,000 yr (ref. 1), probably because of enhanced mantle outgassing and the pulsed release of approximately 1,500 gigatonnes of methane carbon from decomposing gas-hydrate reservoirs. The aftermath of this rapid, intense and global warming event may be the best example in the geological record of the response of the Earth to high atmospheric carbon dioxide concentrations and high temperatures. This response has been suggested to include an intensified flux of organic carbon from the ocean surface to the deep ocean and its subsequent burial through biogeochemical feedback mechanisms. Here we present firm evidence for this view from two ocean drilling cores, which record the largest accumulation rates of biogenic barium--indicative of export palaeoproductivity--at times of maximum global temperatures and peak excursion values of delta13C. The unusually rapid return of delta13C to values similar to those before the methane release and the apparent coupling of the accumulation rates of biogenic barium to temperature, suggests that the enhanced deposition of organic matter to the deep sea may have efficiently cooled this greenhouse climate by the rapid removal of excess carbon dioxide from the atmosphere.     

Aerobic respiration in the Archaean?

The Earth's atmosphere during the Archaean era (3,800-2,500 Myr ago) is generally thought to have been anoxic, with the partial pressure of atmospheric oxygen about 10(-12) times the present value. In the absence of aerobic consumption of oxygen produced by photosynthesis in the ocean, the major sink for this oxygen would have been oxidation of dissolved Fe(II). Atmospheric oxygen would also be removed by the oxidation of biogenic methane. But even very low estimates of global primary productivity, obtained from the amounts of organic carbon preserved in Archaean rocks, seem to require the sedimentation of an unrealistically large amount of iron and the oxidation of too much methane if global anoxia was to be maintained. I therefore suggest that aerobic respiration must have developed early in the Archaean to prevent a build-up of atmospheric oxygen before the Proterozoic. An atmosphere that contained a low (0.2-0.4%) but stable proportion of oxygen is required.     

一株噬甲烷菌的分离鉴定及其消除煤矿瓦斯能力的初步研究

借鉴滚管法,从煤矿矿井及甲烷处理水稻田土壤中分离纯化,获得一株可在以甲烷为唯一碳源的培养基上正常生长且具有较高甲烷氧化活性的噬甲烷细菌,暂命名为ZD4,经对该菌进行形态观察、Biolog生理生化分析、G Cmol%含量分析和16SrDNA序列同源性比较,鉴定该菌为甲烷甲基单胞菌(Methylomonas capsulatus),并对ZD4菌株进行了生长量、对甲烷消除作用的分析。试验结果表明,该菌株可以使甲烷含量在一周内比初始甲烷浓度降低85%以上。利用其良好的甲烷消除能力,用于煤矿瓦斯治理是可行的。     

Biogeochemical sequestration of carbon within phytoliths of wetland plants: A case study of Xixi wetland, China

As an important long-term terrestrial carbon sequestration mechanism, biogeochemical sequestration of carbon within phytoliths may play a significant role in the global carbon cycle and climate change. The aim of this study is to explore the potential of carbon bio-sequestration within phytoliths produced by wetland plants. The results show that the occluded carbon content of phytoliths in wetland plants ranges from 0.49% to 3.97%, with a CV (coefficient of variation) value of 810%. The data also indicate that the phytolith-occluded carbon (PhytOC) content of biomass for wetland plants depends not only on the phytolith content of biomass, but also the efficiency of carbon occlusion within phytoliths during plant growth in herb-dominated fens. The fluxes of carbon bio-sequestration within phytoliths of herb-dominated fen plants range from 0.003 to 0.077 t CO2 equivalents t-e-CO2ha-1a-1 . In China, 0.04×106 to 1.05×106t CO2 equivalents per year may be sequestrated in phytoliths of herbaceous-dominated fen plants. Globally, taking a fen area of 1.48×108 ha and the largest phytolith carbon biosequestration flux (0.077 t-e-CO 2 ha-1a-1 ) for herb-dominated fen plants, about 1.14×10 7 t CO 2 equivalents per year would have been sequestrated in phytoliths of fen plants. If other wetland plants have similar PhytOC production flux with herb-dominated fen plants (0.077 t-e-CO2ha-1a-1 ), about 4.39×10 7 t-e-CO2a-1 may be sequestrated in the phytoliths of world wetland plants. The data indicate that the management of wetland ecosystems (e.g. selection of plant species) to maximize the production of PhytOC have the potential to bio-sequestrate considerable quantities of atmospheric CO2 .     

A plant receptor-like kinase required for both bacterial and fungal symbiosis

Most higher plant species can enter a root symbiosis with arbuscular mycorrhizal fungi, in which plant carbon is traded for fungal phosphate. This is an ancient symbiosis, which has been detected in fossils of early land plants. In contrast, the nitrogen-fixing root nodule symbioses of plants with bacteria evolved more recently, and are phylogenetically restricted to the rosid I clade of plants. Both symbioses rely on partially overlapping genetic programmes. We have identified the molecular basis for this convergence by cloning orthologous SYMRK ('symbiosis receptor-like kinase') genes from Lotus and pea, which are required for both fungal and bacterial recognition. SYMRK is predicted to have a signal peptide, an extracellular domain comprising leucine-rich repeats, a transmembrane and an intracellular protein kinase domain. Lotus SYMRK is required for a symbiotic signal transduction pathway leading from the perception of microbial signal molecules to rapid symbiosis-related gene activation. The perception of symbiotic fungi and bacteria is mediated by at least one common signalling component, which could have been recruited during the evolution of root nodule symbioses from the already existing arbuscular mycorrhiza symbiosis.     

Palaeoceanography: methane release in the Early Jurassic period

Dramatic global warming, triggered by release of methane from clathrates, has been postulated to have occurred during the early Toarcian age in the Early Jurassic period. Kemp et al. claim that this methane was released at three points, as recorded by three sharp excursions of delta13C(org) of up to 3 per thousand magnitude. But they discount another explanation for the excursions: namely that some, perhaps all, of the rapid excursions could be a local signature of a euxinic basin caused by recycling of isotopically light carbon from the lower water column. This idea has been proposed previously (see ref. 3, for example) and is supported by the lack evidence for negative delta13C excursions in coeval belemnite rostra. Kemp et al. dismiss this alternative, claiming that each abrupt shift would have required the recycling of about double the amount of organic carbon that is currently present in the modern ocean; however, their measurements are not from an ocean but from a restricted, epicontinental seaway and so would not require whole-ocean mixing to achieve the excursions.