Enzymology and ecology of the nitrogen cycle

The nitrogen cycle describes the processes through which nitrogen is converted between its various chemical forms. These transformations involve both biological and abiotic redox processes. The principal processes involved in the nitrogen cycle are nitrogen fixation, nitrification, nitrate assimilation, respiratory reduction of nitrate to ammonia, anaerobic ammonia oxidation (anammox) and denitrification. All of these are carried out by micro-organisms, including bacteria, archaea and some specialized fungi. In the present article, we provide a brief introduction to both the biochemical and ecological aspects of these processes and consider how human activity over the last 100?years has changed the historic balance of the global nitrogen cycle.     

Evolved physiological responses of phytoplankton to their integrated growth environment

Phytoplankton growth and productivity relies on light, multiple nutrients and temperature. These combined factors constitute the 'integrated growth environment'. Since their emergence in the Archaean ocean, phytoplankton have experienced dramatic shifts in their integrated growth environment and, in response, evolved diverse mechanisms to maximize growth by optimizing the allocation of photosynthetic resources (ATP and NADPH) among all cellular processes. Consequently, co-limitation has become an omnipresent condition in the global ocean. Here we focus on evolved phytoplankton populations of the contemporary ocean and the varied energetic pathways they employ to solve the optimization problem of resource supply and demand. Central to this discussion is the allocation of reductant formed through photosynthesis, which we propose has the following three primary fates: carbon fixation, direct use and ATP generation. Investment of reductant among these three sinks is tied to cell cycle events, differentially influenced by specific forms of nutrient stress, and a strong determinant of relationships between light-harvesting (pigment), photosynthetic electron transport and carbon fixation. Global implications of optimization are illustrated by deconvolving trends in the 10-year global satellite chlorophyll record into contributions from biomass and physiology, thereby providing a unique perspective on the dynamic nature of surface phytoplankton populations and their link to climate.     

Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation

With rising energy prices and concern over the environmental impact of fossil fuel consumption, the push to develop biomass derived fuels has increased significantly. Although most global carbon fixation occurs via the Calvin Benson Bassham cycle, there are currently five other known pathways for carbon fixation; the goal of this study was to determine the thermodynamic efficiencies of all six carbon fixation pathways for the production of biomass using flux balance analysis. The three chemotrophic pathways, the reductive acetyl-CoA pathway, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, were found to be more efficient than photoautotrophic carbon fixation pathways. However, as hydrogen is not freely available, the energetic cost of hydrogen production from sunlight was calculated and included in the overall energy demand, which results in a 5 fold increase in the energy demand of chemoautotrophic carbon fixation. Therefore, when the cost of hydrogen production is included, photoautotrophic pathways are more efficient. However, the energetic cost for the production of 12 metabolic precursors was found to vary widely across the different carbon fixation pathways; therefore, different pathways may be more efficient at producing products from a single precursor than others. The results of this study have significant impact on the selection or design of autotrophic organisms for biofuel or biochemical production. Overall biomass production from solar energy is most efficient in organisms using the reductive TCA cycle, however, products derived from one metabolic precursor may be more efficiently produced using other carbon fixation pathways.     

基于功能基因的微生物碳循环分子生态学研究进展

碳循环是生态系统中重要的生物地球化学元素循环之一。微生物参与碳固定、甲烷代谢、碳降解等多个重要的碳循环过程,深入了解微生物群落在碳循环过程中的功能和作用,有助于获悉微生物对全球气候变化的响应、适应和反馈机制,这也是微生物生态学研究的关键问题之一。传统的研究多集中于微生物分离培养技术,无法覆盖绝大部分未培养微生物,并且无法深入解析碳循环过程中微生物群落的结构和功能,宏基因组学技术的出现克服了这些缺陷,成为研究微生物群落结构和功能的有效手段。本文对目前宏基因组学的主要技术——定量PCR、DNA分子指纹图谱、基因芯片、克隆文库和高通量测序等技术进行了简要介绍,着重介绍了参与碳固定、甲烷生成和氧化、碳降解等主要碳循环过程的关键功能基因的研究现状,最后对碳循环过程中微生物宏基因组学研究的未来发展进行了总结与展望。     

Feedback of carbon and nitrogen cycles enhances carbon sequestration in the terrestrial biosphere

The efforts to explain the ‘missing sink’ for anthropogenic carbon dioxide (CO₂) have included in recent years the role of nitrogen as an important constraint for biospheric carbon fluxes. We used the Nitrogen Carbon Interaction Model (NCIM) to investigate patterns of carbon and nitrogen storage in different compartments of the terrestrial biosphere as a consequence of a rising atmospheric CO₂ concentration, in combination with varying levels of nitrogen availability. This model has separate but closely coupled carbon and nitrogen cycles with a focus on soil processes and soil–plant interactions, including an active compartment of soil microorganisms decomposing litter residues and competing with plants for available nitrogen. Biological nitrogen fixation is represented as a function of vegetation nitrogen demand. The model was validated against several global datasets of soil and vegetation carbon and nitrogen pools. Five model experiments were carried out for the modeling periods 1860–2002 and 2002–2100. In these experiments we varied the nitrogen availability using different combinations of biological nitrogen fixation, denitrification, leaching of soluble nitrogen compounds with constant or rising atmospheric CO₂ concentrations. Oversupply with nitrogen, in an experiment with nitrogen fixation, but no nitrogen losses, together with constant atmospheric CO₂, led to some carbon sequestration in organismic pools, which was nearly compensated by losses of C from soil organic carbon pools. Rising atmospheric CO₂ always led to carbon sequestration in the biosphere. Considering an open nitrogen cycle including dynamic nitrogen fixation, and nitrogen losses from denitrification and leaching, the carbon sequestration in the biosphere is of a magnitude comparable to current observation based estimates of the ‘missing sink.’ A fertilization feedback between the carbon and nitrogen cycles occurred in this experiment, which was much stronger than the sum of separate influences of high nitrogen supply and rising atmospheric CO₂. The demand‐driven biological nitrogen fixation was mainly responsible for this result. For the modeling period 2002–2100, NCIM predicts continued carbon sequestration in the low range of previously published estimates, combined with a plausible rate of CO₂‐driven biological nitrogen fixation and substantial redistribution of nitrogen from soil to plant pools.     

The carbon balance of tropical, temperate and boreal forests

Forest biomes are major reserves for terrestrial carbon, and major components of global primary productivity. The carbon balance of forests is determined by a number of component processes of carbon acquisition and carbon loss, and a small shift in the magnitude of these processes would have a large impact on the global carbon cycle. In this paper, we discuss the climatic influences on the carbon dynamics of boreal, temperate and tropical forests by presenting a new synthesis of micrometeorological, ecophysiological and forestry data, concentrating on three case-study sites. Historical changes in the carbon balance of each biome are also reviewed, and the evidence for a carbon sink in each forest biome and its likely behaviour under future global change are discussed. We conclude that there have been significant advances in determining the carbon balance of forests, but there are still critical uncertainties remaining, particularly in the behaviour of soil carbon stocks.     

Bacteria and archaea as the sources of traits for enhanced plant phenotypes

Rising global demand for food and population increases are driving the need for improved crop productivity over the next 30 years. Plants have inherent metabolic limitations on productivity such as inefficiencies in carbon fixation and sensitivity to environmental conditions. Bacteria and archaea inhabit some of the most inhospitable environments on the planet and possess unique metabolic pathways and genes to cope with these conditions. Microbial genes involved in carbon fixation, abiotic stress tolerance, and nutrient acquisition have been utilized in plants to enhance plant phenotypes by increasing yield, photosynthesis, and abiotic stress tolerance. Transgenic plants expressing bacterial and archaeal genes will be discussed along with emerging strategies and tools to increase plant growth and yield.     

Carbon and nitrogen metabolism in ectomycorrhizal fungi and ectomycorrhizas

The literature concerning the metabolism of carbon and nitrogen compounds in ectomycorrhizal associations of trees is reviewed. The absorption and translocation of mineral ions by the mycelia require an energy source and a reductant which are both supplied by respiratory catabolism of carbohydrates produced by the host plant. Photosynthates are also required to generate the carbon skeletons for amino acid and carbohydrate syntheses during the growth of the mycelia. Competition for photosynthates occurs between the fungal cells and the various vegetative sinks in the host tree. The nature of carbon compounds involved in these processes, their routes of metabolism, the mechanisms of control and the partitioning of metabolites between the various sites of utilization are only poorly understood. Both ascomycetous and basidiomycetous ectomycorrhizal fungi synthesize and some, if not all, accumulate mannitol, trehalose and triglycerides. The fungal strains employ the Embden--Meyerhof pathway of glucose catabolism and the key enzymes of the pentose phosphate pathway (6-phosphogluconate dehydrogenase, glucose-6-phosphate dehydrogenase, transaldolase and transketolase). Anaplerotic CO2 fixation, via pyruvate carboxylase and/or phosphoenolpyruvate carboxykinase, provides high pools of amino acids. This process could be important in the recapture and assimilation of respired CO2 in the rhizosphere. The ectomycorrhizas are thought to contain the Embden--Meyerhof pathway, the pentose phosphate pathway and the tricarboxylic acid cycle, which provide the carbon skeletons for the assimilation of ammonia into amino acids. The main route of assimilation of ammonia appears to be through the glutamine synthetase-glutamate synthase cycle in the ectomycorrhizas. Glutamate dehydrogenase plays a minor role in this process. Glutamate dehydrogenase and glutamine synthetase are present in free-living ectomycorrhizal fungi and they participate in the assimilation of ammonia and the synthesis of amino acids through the glutamate dehydrogenase/glutamine synthetase sequence. In both in vitro cultures of fungi and ectomycorrhizas, the assimilated nitrogen accumulates in glutamine. Glutamine, but also ammonia, are thought to be exported from the fungal tissues to the host cells. Studies on the metabolism of ectomycorrhizas and ectomycorrhizal fungi have focused on the metabolic pathways and compounds which accumulate in the symbiotic tissues. Studies on regulation of the overall process, and the control of enzyme activity in particular, are still fragmentary.(ABSTRACT TRUNCATED AT 400 WORDS)     

大尺度森林碳循环过程模拟模型综述

森林生态系统碳循环是全球陆地生态系统碳循环的重要组成部分,而碳循环模型已经成为研究森林碳循环的必要手段。森林碳循环模型可以分为统计模型和过程模型,其中过程模型以其完整的理论框架、严谨的结构分析和清晰的过程机理,逐渐占据了主导地位。从地球化学过程模型、陆面物理过程模型和生物过程模型等3个方面综述区域尺度到全球尺度(本文称为大尺度)森林碳循环过程模型研究进展,论述了各类模型的主要特征、优缺点以及应用现状,探讨了森林碳循环模拟研究中存在的问题,并讨论了森林碳循环过程模型的主流研究方向。可为不同空间尺度下森林生态系统碳循环模拟模型的选择提供参考,以及为森林碳循环研究提供借鉴。     

Potential response of dark carbon fixation to global warming in estuarine and coastal waters

Dark carbon fixation (DCF), through which chemoautotrophs convert inorganic carbon to organic carbon, is recognized as a vital process of global carbon biogeochemical cycle. However, little is known about the response of DCF processes in estuarine and coastal waters to global warming. Using radiocarbon labelling method, the effects of temperature on the activity of chemoautotrophs were investigated in benthic water of the Yangtze estuarine and coastal areas. A dome-shaped thermal response pattern was observed for DCF rates (i.e., reduced rates at lower or higher temperatures), with the optimum temperature (T_opt) varying from about 21.9 to 32.0°C. Offshore sites showed lower T_opt values and were more vulnerable to global warming compared with nearshore sites. Based on temperature seasonality of the study area, it was estimated that warming would accelerate DCF rate in winter and spring but inhibit DCF activity in summer and fall. However, at an annual scale, warming showed an overall promoting effect on DCF rates. Metagenomic analysis revealed that the dominant chemoautotrophic carbon fixation pathways in the nearshore area were Calvin-Benson-Bassham (CBB) cycle, while the offshore sites were co-dominated by CBB and 3-hydroxypropionate/4-hydroxybutyrate cycles, which may explain the differential temperature response of DCF along the estuarine and coastal gradients. Our findings highlight the importance of incorporating DCF thermal response into biogeochemical models to accurately estimate the carbon sink potential of estuarine and coastal ecosystems in the context of global warming.     

城市系统碳循环:特征、机理与理论框架

城市是地表受人类活动影响最深刻的区域,城市系统碳循环在全球和区域碳过程中具有重要的地位和作用.提出了城市“自然-社会”二元碳循环的概念,探讨了城市系统碳循环的一般特征;分析了城市系统碳循环的内部机理,主要包括:城市系统碳储量和碳输入/输出通量的主要过程和途径、城市系统碳储量、碳通量和碳流通的生命周期分析、城市系统碳输入和碳输出的类型划分等;提出了基于系统层次划分和碳流通过程的城市系统碳循环的研究框架,分析了城市自然系统和城市经济系统的主要碳流通过程和环节,构建了城市系统碳循环研究的思路和理论框架;最后提出了城市系统碳循环领域未来的研究重点.     

Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage

Autotrophic carbon fixation was characterized in representative members of the three lineages of the bacterial phylum Aquificae. Enzyme activity measurements and the detection of key genes demonstrated that Aquificae use the reductive tricarboxylic acid (TCA) cycle for autotrophic CO(2) fixation. This is the first time that strains of the Hydrogenothermaceae and 'Desulfurobacteriaceae' have been investigated for enzymes of autotrophic carbon fixation. Unexpectedly, two different mechanisms of citrate cleavage could be identified within the Aquificae. Aquificaceae use citryl-CoA synthetase and citryl-CoA lyase, whereas Hydrogenothermaceae and 'Desulfurobacteriaceae' use ATP citrate lyase. The first mechanism is likely to represent the ancestral version of the reductive TCA cycle. Sequence analyses further suggest that ATP citrate lyase formed by a gene fusion of citryl-CoA synthetase and citryl-CoA lyase and subsequently became involved in a modified version of this pathway. However, rather than having evolved within the Aquificae, our phylogenetic analyses indicate that Aquificae obtained their ATP citrate lyase through lateral gene transfer. Aquificae play an important role in biogeochemical processes in a variety of high-temperature habitats. Thus, these findings substantiate the hypothesis that autotrophic carbon fixation through the reductive TCA cycle is widespread and contributes significantly to biomass production particularly in hydrothermal habitats.     

Complete ammonia oxidization in agricultural soils: High ammonia fertilizer loss but low N2O production

The contribution of agriculture to the sustainable development goals requires climate-smart and profitable farm innovations. Increasing the ammonia fertilizer applications to meet the global food demands results in high agricultural costs, environmental quality deterioration, and global warming, without a significant increase in crop yield. Here, we reported that a third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is contributing to a significant ammonia fertilizer loss (41.9 ± 4.8%) at the rate of 3.53 ± 0.55 mg N kg⁻¹ day⁻¹ in agricultural soils around the world. The contribution of comammox to ammonia fertilizer loss, occurring mainly in surface agricultural soil profiles (0–0.2 m), was equivalent to that of bacterial ammonia oxidation (48.6 ± 4.5%); both processes were significantly more important than archaeal ammonia oxidation (9.5 ± 3.6%). In contrast, comammox produced less N₂O (0.98 ± 0.44 μg N kg⁻¹ day⁻¹, 11.7 ± 3.1%), comparable to that produced by archaeal ammonia oxidation (16.4 ± 4.4%) but significantly lower than that of bacterial ammonia oxidation (72.0 ± 5.1%). The efficiency of ammonia conversion to N₂O by comammox (0.02 ± 0.01%) was evidently lower than that of bacterial (0.24 ± 0.06%) and archaeal (0.16 ± 0.04%) ammonia oxidation. The comammox rate increased with increasing soil pH values, which is the only physicochemical characteristic that significantly influenced both comammox bacterial abundance and rates. Ammonia fertilizer loss, dominated by comammox and bacterial ammonia oxidation, was more intense in soils with pH >6.5 than in soils with pH <6.5. Our results revealed that comammox plays a vital role in ammonia fertilizer loss and sustainable development in agroecosystems that have been previously overlooked for a long term.     

Nitrous oxide production by ammonia oxidizers: Physiological diversity,niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia‐based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂O production, vary within and between ammonia‐oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow‐release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂O emissions.     

Biological Nitrogen Fixation in Sugar Cane: A Key to Energetically Viable Biofuel Production

The advantages of producing biofuels to replace fossil energy sources are derived from the fact that the energy accumulated in the biomass is captured directly from photosynthesis and is thus renewable, and that the cycle of carbon dioxide fixation by the crop, followed by burning of the fuel makes no overall contribution to atmospheric CO₂ or, consequently, to global warming. However, these advantages are negated if large quantities of fossil fuels need to be used to grow or process the biofuel crop. In this regard, the Brazilian bioethanol program, based on the fermentation/distillation of sugar cane juice, is particularly favorable, not only because the crop is principally hand harvested, but also because of the low nitrogen fertilizer use on sugar cane in Brazil. Recent ¹⁵N and N balance studies have shown that in some Brazilian cane varieties, high yields are possible without N fertilization because the plants are able to obtain large contributions of nitrogen from plant-associated biological N₂ fixation (BNF). The N₂-fixing acid-tolerant bacterium Acetobacter diazotrophicus was first found to occur within roots, stems, and leaves of sugar cane. Subsequently, two species of Herbaspirillum also have been found to occur within the interior of all sugar cane tissues. The discovery of these, and other N₂-fixing bacteria that survive poorly in soil but thrive within plant tissue (endophytic bacteria), may account for the high BNF contributions observed in sugar cane. Further study of this system should allow the gradual elimination of N fertilizer use on sugar cane, at least in Brazil, and opens up the possibility of the extension of this efficient N₂-fixing system to cereal and other crops with consequent immense potential benefits to tropical agriculture.     

Ammonia Assimilation in Rumen Bacteria: A Review

In the rumen bacteria, ammonia as the end product of nitrogen is incorporated into carbon skeleton (α-ketoglutarate) to yield glutamine and glutamate which are important nitrogen donors in nitrogenous compounds metabolism in cells. The enzymes glutamine synthetase, glutamate synthetase, and glutamate dehydrogenase are involved in these processes. Some experimental results have proven that the global nitrogen regulation system may participate in the regulation of assimilation of ammonia in rumen bacteria. This review offers a current perspective on the pathways and key enzymes of ammonia assimilation in rumen bacteria with the possible molecular regulation strategy, while points out the further research direction.     

氮输入对滨海盐沼湿地碳循环关键过程的影响及机制

滨海盐沼湿地是缓解全球变暖的有效蓝色碳汇, 但是近岸海域富营养化导致的大量氮输入对盐沼湿地稳定性和碳汇功能构成严重威胁。潮汐作用下大量氮输入对盐沼湿地植物光合碳输入、植物-土壤碳分配和土壤碳输出等碳循环关键过程产生深刻影响, 进而影响盐沼湿地碳汇功能评估的准确性。该文从植物光合固碳、植物-土壤系统碳分配、土壤有机碳分解、土壤可溶性有机碳释放、盐沼湿地土壤碳库5个方面综述了氮输入对盐沼湿地碳循环关键过程的影响。在此基础上, 针对当前研究的不足, 提出今后的研究中, 需要进一步探究氮输入对盐沼湿地植物光合固碳及碳分配过程的影响、盐沼湿地土壤有机碳分解的微生物机制、盐沼湿地土壤可溶性有机碳产生和横向流动的影响、以及氮类型对盐沼湿地土壤碳库的影响。以期为揭示氮输入对盐沼湿地碳汇形成过程与机制提供基础资料和理论依据, 为评估未来近岸海域水体富营养化影响下滨海盐沼湿地碳库的潜在变化提供新思路。     

Energy requirements and environmental impacts associated with the production of short rotation willow (Salix sp.) chip in Ireland

Willow Salix sp. is currently cultivated as a short rotation forestry crop in Ireland as a source of biomass to contribute to renewable energy goals. The aim of this study is to evaluate the energy requirements and environmental impacts associated with willow (Salix sp.) cultivation, harvest, and transport using life cycle assessment (LCA). In this study, only emissions from the production of the willow chip are included, end‐use emissions from combustion are not considered. In this LCA study, three impact categories are considered; acidification potential, eutrophication potential and global warming potential. In addition, the cumulative energy demand and energy ratio of the system are evaluated. The results identify three key processes in the production chain which contribute most to all impact categories considered; maintenance, harvest and transportation of the crop. Sensitivity analysis on the type of fertilizers used, harvesting technologies and transport distances highlights the effects of these management techniques on overall system performance. Replacement of synthetic fertilizer with biosolids results in a reduction in overall energy demand, but raises acidification potential, eutrophication potential and global warming potential. Rod harvesting compares unfavourably in comparison with direct chip harvesting in each of the impact categories considered due to the additional chipping step required. The results show that dedicated truck transport is preferable to tractor‐trailer transport in terms of energy demand and environmental impacts. Finally, willow chip production compares favourably with coal provision in terms of energy ratio and global warming potential, while achieving a higher energy ratio than peat provision but also a higher global warming potential.