A hydrogen-based subsurface microbial community dominated by methanogens.

The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.     

Isolation of an autotrophic ammonia-oxidizing marine archaeon

For years, microbiologists characterized the Archaea as obligate extremophiles that thrive in environments too harsh for other organisms. The limited physiological diversity among cultivated Archaea suggested that these organisms were metabolically constrained to a few environmental niches. For instance, all Crenarchaeota that are currently cultivated are sulphur-metabolizing thermophiles. However, landmark studies using cultivation-independent methods uncovered vast numbers of Crenarchaeota in cold oxic ocean waters. Subsequent molecular surveys demonstrated the ubiquity of these low-temperature Crenarchaeota in aquatic and terrestrial environments. The numerical dominance of marine Crenarchaeota--estimated at 10(28) cells in the world's oceans--suggests that they have a major role in global biogeochemical cycles. Indeed, isotopic analyses of marine crenarchaeal lipids suggest that these planktonic Archaea fix inorganic carbon. Here we report the isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite--the first observation of nitrification in the Archaea. The autotrophic metabolism of this isolate, and its close phylogenetic relationship to environmental marine crenarchaeal sequences, suggests that nitrifying marine Crenarchaeota may be important to global carbon and nitrogen cycles.     

Potential methane reservoirs beneath Antarctica

Once thought to be devoid of life, the ice-covered parts of Antarctica are now known to be a reservoir of metabolically active microbial cells and organic carbon. The potential for methanogenic archaea to support the degradation of organic carbon to methane beneath the ice, however, has not yet been evaluated. Large sedimentary basins containing marine sequences up to 14?kilometres thick and an estimated 21,000 petagrams (1?Pg equals 10(15)?g) of organic carbon are buried beneath the Antarctic Ice Sheet. No data exist for rates of methanogenesis in sub-Antarctic marine sediments. Here we present experimental data from other subglacial environments that demonstrate the potential for overridden organic matter beneath glacial systems to produce methane. We also numerically simulate the accumulation of methane in Antarctic sedimentary basins using an established one-dimensional hydrate model and show that pressure/temperature conditions favour methane hydrate formation down to sediment depths of about 300?metres in West Antarctica and 700?metres in East Antarctica. Our results demonstrate the potential for methane hydrate accumulation in Antarctic sedimentary basins, where the total inventory depends on rates of organic carbon degradation and conditions at the ice-sheet bed. We calculate that the sub-Antarctic hydrate inventory could be of the same order of magnitude as that of recent estimates made for Arctic permafrost. Our findings suggest that the Antarctic Ice Sheet may be a neglected but important component of the global methane budget, with the potential to act as a positive feedback on climate warming during ice-sheet wastage.     

Archaeal dominance in the mesopelagic zone of the Pacific Ocean

The ocean's interior is Earth's largest biome. Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean. But quantitative data on the abundance of specific microbial groups in the deep sea are lacking. Here we report a year-long study of the abundance of two specific archaeal groups (pelagic euryarchaeota and pelagic crenarchaeota) in one of the ocean's largest habitats. Monthly sampling was conducted throughout the water column (surface to 4,750 m) at the Hawai'i Ocean Time-series station. Below the euphotic zone (> 150 m), pelagic crenarchaeota comprised a large fraction of total marine picoplankton, equivalent in cell numbers to bacteria at depths greater than 1,000 m. The fraction of crenarchaeota increased with depth, reaching 39% of total DNA-containing picoplankton detected. The average sum of archaea plus bacteria detected by rRNA-targeted fluorescent probes ranged from 63 to 90% of total cell numbers at all depths throughout our survey. The high proportion of cells containing significant amounts of rRNA suggests that most pelagic deep-sea microorganisms are metabolically active. Furthermore, our results suggest that the global oceans harbour approximately 1.3 x 10(28) archaeal cells, and 3.1 x 10(28) bacterial cells. Our data suggest that pelagic crenarchaeota represent one of the ocean's single most abundant cell types.     

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.     

A possible important CO2 sink by the global water cycle

The locations, magnitudes, variations and mechanisms responsible for the global CO2 sink are uncertain and under debate. Here, we show, based on theoretical calculations and evidences from field monitoring results, that there is a possible important CO2 sink （as DIC-dissolved inorganic carbon） by the global water cycle. The sink constitutes up to 0.8013 Pg C/a （or 10.1% of the total anthropogenic CO2 emission, or 28.6% of the missing CO2 sink）, and is formed by the CO2 absorption of water and subsequent enhanced consumption by carbonate dissolution and aquatic plant photosynthesis. Of the sink, 0.5188 Pg C/a goes to sea via precipitation over sea （0.2748 Pg C/a） and continental rivers （0.244 Pg C/a）, 0.158 Pg C/a is released to the atmosphere again, and 0.1245 Pg C/a is stored in the continental aquatic ecosystem. Therefore, the net sink could be 0.6433 Pg C/a. This sink may increase with the global-warming-intensified global water cycle, the increase in CO2 and carbonate dust in atmosphere, and reforestation/afforestation, the latter increasing soil CO2, and thus the concentration of the DIC in water.     

Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea

Planktonic Bacteria, Archaea and Eukarya reside and compete in the ocean's photic zone under the pervasive influence of light. Bacteria in this environment were recently shown to contain photoproteins called proteorhodopsins, thought to contribute to cellular energy metabolism by catalysing light-driven proton translocation across the cell membrane. So far, proteorhodopsin genes have been well documented only in proteobacteria and a few other bacterial groups. Here we report the presence and distribution of proteorhodopsin genes in Archaea affiliated with the order Thermoplasmatales, in the ocean's upper water column. The genomic context and phylogenetic relationships of the archaeal and proteobacterial proteorhodopsins indicate its probable lateral transfer between planktonic Bacteria and Archaea. About 10% of the euryarchaeotes in the photic zone contained the proteorhodopsin gene adjacent to their small-subunit ribosomal RNA. The archaeal proteorhodopsins were also found in other genomic regions, in the same or in different microbial lineages. Although euryarchaeotes were distributed throughout the water column, their proteorhodopsins were found only in the photic zone. The cosmopolitan phylogenetic distribution of proteorhodopsins reflects their significant light-dependent fitness contributions, which drive the photoprotein's lateral acquisition and retention, but constrain its dispersal to the photic zone.     

Preliminary estimation of the organic carbon pool in China’s wetlands

Accurate estimation of wetland carbon pools is a prerequisite for wetland resource conservation and implementation of carbon sink enhancement plans.The inventory approach is a realistic method for estimating the organic carbon pool in China’s wetlands at the national scale.An updated data and inventory approach were used to estimate the amount of organic carbon stored in China’s wetlands.Primary results are as follows:(1) the organic carbon pool of China’s wetlands is between 5.39 and 7.25 Pg,accounting for 1.3%-3.5% of the global level;(2) the estimated values and percentages of the organic carbon contained in the soil,water and vegetation pools in China’s wetlands are 5.04-6.19 Pg and 85.4%-93.5%,0.22-0.56 Pg and 4.1%-7.7%,0.13-0.50 Pg and 2.4%-6.9%,respectively.The soil organic carbon pool of China’s wetlands is greater than our previous estimate of 3.67 Pg,but is lower than other previous estimates of 12.20 and 8-10 Pg.Based on the discussion and uncertainty analysis,some research areas worthy of future attention are presented.     

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.     

Preservation of organic matter in sediments promoted by iron

The biogeochemical cycles of iron and organic carbon are strongly interlinked. In oceanic waters, organic ligands have been shown to control the concentration of dissolved iron. In soils, solid iron phases shelter and preserve organic carbon, but the role of iron in the preservation of organic matter in sediments has not been clearly established. Here we use an iron reduction method previously applied to soils to determine the amount of organic carbon associated with reactive iron phases in sediments of various mineralogies collected from a wide range of depositional environments. Our findings suggest that 21.5?±?8.6 per cent of the organic carbon in sediments is directly bound to reactive iron phases. We further estimate that a global mass of (19-45)?×?10(15)?grams of organic carbon is preserved in surface marine sediments as a result of its association with iron. We propose that these associations between organic carbon and iron, which are formed primarily through co-precipitation and/or direct chelation, promote the preservation of organic carbon in sediments. Because reactive iron phases are metastable over geological timescales, we suggest that they serve as an efficient 'rusty sink' for organic carbon, acting as a key factor in the long-term storage of organic carbon and thus contributing to the global cycles of carbon, oxygen and sulphur.     

Annual fluxes of carbon from deforestation and regrowth in the Brazilian Amazon

The distribution of sources and sinks of carbon among the world's ecosystems is uncertain. Some analyses show northern mid-latitude lands to be a large sink, whereas the tropics are a net source; other analyses show the tropics to be nearly neutral, whereas northern mid-latitudes are a small sink. Here we show that the annual flux of carbon from deforestation and abandonment of agricultural lands in the Brazilian Amazon was a source of about 0.2 Pg Cyr(-1) over the period 1989-1998 (1 Pg is 10(15) g). This estimate is based on annual rates of deforestation and spatially detailed estimates of deforestation, regrowing forests and biomass. Logging may add another 5-10% to this estimate, and fires may double the magnitude of the source in years following a drought. The annual source of carbon from land-use change and fire approximately offsets the sink calculated for natural ecosystems in the region. Thus this large area of tropical forest is nearly balanced with respect to carbon, but has an interannual variability of +/- 0.2 PgC yr(-1).     

降水改变对樟子松人工林土壤微生物量碳及微生物商动态变化的影响

在北京大学地球环境与生态系统塞罕坝实验站樟子松（Pinus sylvestris var. mongolica）人工林内设置降水控制实验,研究地下生态系统过程的两个重要指标土壤微生物量碳和微生物商对穿透雨增加或减少30%的响应。在2007年5月到9月的生长季,土壤微生物量碳和微生物商平均值分别为260.7mg/kg和1.84%,二者随土壤深度增加呈下降趋势。总体上,穿透雨增加或减少30%对土壤微生物量碳和微生物商的生长季内平均值影响不显著,但穿透雨减少30%的土壤微生物量碳及微生物商的变幅较大,变化范围分别为243.1～354.3mg/kg和1.43%～2.16%,5月最高,7月最低,表明生长季内穿透雨减少将导致土壤微生物活动的较大波动,从而可能改变地下碳过程的季节变化规律。     

林业碳汇提升的主要原理和途径

降低大气CO₂含量、缓解气候变暖,已成为当今科学界和国际社会广泛关注的前沿热点问题。林业碳汇作为基于自然解决方案实现“碳达峰、碳中和”的一个重要途径,在应对全球气候变化方面发挥着基础性、战略性、独特的作用。林业碳汇不仅是森林碳汇,林产品碳汇也起着不可忽视的重要作用。林业碳汇潜力提升是一个森林生态系统净碳收支平衡和全产业链林产品碳汇的调控过程,主要包括无机碳的植物固定(光合过程、净生产力等)、土壤有机碳的周转与固定(动植物和微生物残体分解与黏土固定)、林产品碳的固持(林产品产量、木材转换效率、种类和使用寿命等)等3方面的调控原理。笔者从森林碳汇和林产品碳汇两个维度阐述了提升林业碳汇的主要原理、方法或途径。提升林业碳汇潜力的主要途径包括:①通过适地适树、适钙适树人工造林,以增加森林面积;②以完善森林经营措施来增加森林净生产力;③利用矿质黏土对有机碳的保护来增加森林土壤碳汇;④提升林产品产量和改进林产品用途以增加其寿命。在全球尺度上,增加森林面积或提高森林净生产力3.4%,或用可再生能源替换薪炭木材,再将薪炭木材用于制造锯材和人造板,都可以连续30 a每年增加1 Pg的碳汇量。减少全球森林火灾面积1/4或增加森林土壤有机碳含量0.23%,也可以增加碳汇1 Pg。此外,林业固碳还有巨大潜力可以挖掘。     

Effect of evaporite deposition on Early Cretaceous carbon and sulphur cycling

The global carbon and sulphur cycles are central to our understanding of the Earth's history, because changes in the partitioning between the reduced and oxidized reservoirs of these elements are the primary control on atmospheric oxygen concentrations. In modern marine sediments, the burial rates of reduced carbon and sulphur are positively coupled, but high-resolution isotope records indicate that these rates were inversely related during the Early Cretaceous period. This inverse relationship is difficult to reconcile with our understanding of the processes that control organic matter remineralization and pyrite burial. Here we show that the inverse correlation can be explained by the deposition of evaporites during the opening of the South Atlantic Ocean basin. Evaporite deposition can alter the chemical composition of sea water, which can in turn affect the ability of sulphate-reducing bacteria to remineralize organic matter and mediate pyrite burial. We use a reaction-transport model to quantify these effects, and the resulting changes in the burial rates of carbon and sulphur, during the Early Cretaceous period. Our results indicate that deposition of the South Atlantic evaporites removed enough sulphate from the ocean temporarily to reduce biologically mediated pyrite burial and organic matter remineralization by up to fifty per cent, thus explaining the inverse relationship between the burial rates of reduced carbon and sulphur during this interval. Furthermore, our findings suggest that the effect of changing seawater sulphate concentrations on the marine subsurface biosphere may be the key to understanding other large-scale perturbations of the global carbon and sulphur cycles.     

Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline

The chemical composition of the Bannock basin has been studied in some detail. We recently showed that unusual microbial populations, including a new division of Archaea (MSBL1), inhabit the NaCl-rich hypersaline brine. High salinities tend to reduce biodiversity, but when brines come into contact with fresher water the natural haloclines formed frequently contain gradients of other chemicals, including permutations of electron donors and acceptors, that may enhance microbial diversity, activity and biogeochemical cycling. Here we report a 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water. The chemocline supports some of the most biomass-rich and active microbial communities in the deep sea, dominated by Bacteria rather than Archaea, and including four major new divisions of Bacteria. Significantly higher metabolic activities were measured in the chemocline than in the overlying sea water and underlying brine; functional analyses indicate that a range of biological processes is likely to occur in the chemocline. Many prokaryotic taxa, including the phylogenetically new groups, were confined to defined salinities, and collectively formed a diverse, sharply stratified, deep-sea ecosystem with sufficient biomass to potentially contribute to organic geological deposits.     

Nitrogen limitation of microbial decomposition in a grassland under elevated CO2

Carbon accumulation in the terrestrial biosphere could partially offset the effects of anthropogenic CO2 emissions on atmospheric CO2. The net impact of increased CO2 on the carbon balance of terrestrial ecosystems is unclear, however, because elevated CO2 effects on carbon input to soils and plant use of water and nutrients often have contrasting effects on microbial processes. Here we show suppression of microbial decomposition in an annual grassland after continuous exposure to increased CO2 for five growing seasons. The increased CO2 enhanced plant nitrogen uptake, microbial biomass carbon, and available carbon for microbes. But it reduced available soil nitrogen, exacerbated nitrogen constraints on microbes, and reduced microbial respiration per unit biomass. These results indicate that increased CO2 can alter the interaction between plants and microbes in favour of plant utilization of nitrogen, thereby slowing microbial decomposition and increasing ecosystem carbon accumulation.     

北方农牧交错带草地土壤微生物量碳空间格局及驱动因素

为探究我国北方农牧交错带草地表层(0~10 cm)和次表层(10~20 cm)土壤微生物量碳的空间格局及其环境驱动力, 选择蒙辽平原、京北坝上、阴山北麓和宁陕黄土高原4个区域总计456个土壤样品(两个土层, 57个样点, 每个样点4个样方)进行调查。结果表明, 表层与次表层土壤微生物量碳的空间格局具有一致性, 均随纬度增加而增加, 随经度和海拔增加无显著变化。随着草地退化程度加剧, 次表层土壤微生物量碳的降低幅度小于表层土壤。两层土壤 pH 值的差异随草地退化程度的加剧而缩小, 表层与次表层土壤微生物量碳的差异受土壤pH值调控, 两个土层的pH值差异越小, 微生物量碳的差异越小。气候、植被和土壤因素均会影响微生物量碳的空间变异, 其中土壤因素为区域尺度微生物量碳的主要驱动力, 表层土壤微生物量碳的主要影响因素为土壤总碳, 次表层土壤微生物量碳受土壤总氮的影响最大。在气候变化和人类活动影响加剧的背景下, 研究结果对预测区域尺度土壤微生物的响应规律及退化草地生态功能的维持和修复有重要意义。     

Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria

Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. Here, using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), we provide direct quantification of live cells as defined by the presence of ribosomes. We show that a large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (> 400 m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25-22 yr, comparable to surface sediments.     

Doubling the estimate of invertebrate biomass in a rainforest canopy

Forest canopies represent the functional interface between 90% of the Earth's terrestrial biomass and the atmosphere and include some of the most threatened of all terrestrial ecosystems. However, we lack even a basic understanding of how the biomass of plants and animals is distributed throughout forest canopies, even though this information is vital for estimating energy flow, carbon cycling, resource use and the transfer of materials within this ecosystem. Here we measure the biomass of invertebrates living in a common rainforest epiphyte, describe a striking relationship between fern size and the biomass of animals within the ferns, and reveal that one large epiphyte may contain an invertebrate biomass similar to that found in the whole of the rest of the tree crown on which it is growing. Using these data, we show that including the fauna of these epiphytes--a neglected component in rainforest ecosystems--can more than double our estimate of the total invertebrate biomass in an entire rainforest canopy.