Phosphorus cycling in urban aquatic ecosystems: connecting biological processes and water chemistry to sediment P fractions in urban stormwater management ponds

Phosphorus (P) dynamics in urban landscapes may differ from that in natural landscapes due to different P sources and unique environmental conditions. However, many aspects of P cycles in urban areas, especially within engineered aquatic ecosystems, remain largely unknown. Through this work, we aim to contribute to better understanding of P cycling in urban aquatic ecosystems by investigating P fractions in sediment and their relationship with ambient chemistry in surface water from six urban stormwater management ponds located in Ontario, Canada. We found that organic P contributed up to 75% of total P in pond sediment, but this percentage decreased significantly between our two sampling events in June and September 2012. This decrease coincided with increased rates of extracellular enzyme (especially phosphatase) activities, which is indicative of fast mineralization processes in these ecosystems. Moreover, the decreased sediment organic P was matched by increased water column P concentration. This inverse relationship suggests that the large organic P pool in pond sediment, and its fast decomposition, contributed to internal release of P from sediment and increased water column P concentrations. The dominance of organic P in sediment and the putative role of relevant biological processes (i.e., decomposition and productivity) in urban ponds found in this study strongly contrast with classic water management expectations of physicochemically controlled P dynamics and long-term P storage in sediment of aquatic ecosystems. This difference suggests that urban stormwater ponds may perform poorly in terms of P retention and thereby contribute to poor water quality in terms of P pollution to downstream urban watersheds. Thus, stormwater pond design and future management strategies should consider these biogeochemical features of urban ponds, including internal P release, to help prevent eutrophication of downstream ecosystems.     

Phosphorus accumulates faster than nitrogen globally in freshwater ecosystems under anthropogenic impacts

Combined effects of cumulative nutrient inputs and biogeochemical processes that occur in freshwater under anthropogenic eutrophication could lead to myriad shifts in nitrogen (N):phosphorus (P) stoichiometry in global freshwater ecosystems, but this is not yet well‐assessed. Here we evaluated the characteristics of N and P stoichiometries in bodies of freshwater and their herbaceous macrophytes across human‐impact levels, regions and periods. Freshwater and its macrophytes had higher N and P concentrations and lower N : P ratios in heavily than lightly human‐impacted environments, further evidenced by spatiotemporal comparisons across eutrophication gradients. N and P concentrations in freshwater ecosystems were positively correlated and N : P was negatively correlated with population density in China. These results indicate a faster accumulation of P than N in human‐impacted freshwater ecosystems, which could have large effects on the trophic webs and biogeochemical cycles of estuaries and coastal areas by freshwater loadings, and reinforce the importance of rehabilitating these ecosystems.     

How humans alter dissolved organic matter composition in freshwater: relevance for the Earth’s biogeochemistry

Dissolved organic matter (DOM) is recognized for its importance in freshwater ecosystems, but historical reliance on DOM quantity rather than indicators of DOM composition has led to an incomplete understanding of DOM and an underestimation of its role and importance in biogeochemical processes. A single sample of DOM can be composed of tens of thousands of distinct molecules. Each of these unique DOM molecules has their own chemical properties and reactivity or role in the environment. Human activities can modify DOM composition and recent research has uncovered distinct DOM pools laced with human markers and footprints. Here we review how land use change, climate change, nutrient pollution, browning, wildfires, and dams can change DOM composition which in turn will affect internal processing of freshwater DOM. We then describe how human-modified DOM can affect biogeochemical processes. Drought, wildfires, cultivated land use, eutrophication, climate change driven permafrost thaw, and other human stressors can shift the composition of DOM in freshwater ecosystems increasing the relative contribution of microbial-like and aliphatic components. In contrast, increases in precipitation may shift DOM towards more relatively humic-rich, allochthonous forms of DOM. These shifts in DOM pools will likely have highly contrasting effects on carbon outgassing and burial, nutrient cycles, ecosystem metabolism, metal toxicity, and the treatments needed to produce clean drinking water. A deeper understanding of the links between the chemical properties of DOM and biogeochemical dynamics can help to address important future environmental issues, such as the transfer of organic contaminants through food webs, alterations to nitrogen cycling, impacts on drinking water quality, and biogeochemical effects of global climate change.

     

Key ecological research questions for Central European forests

Forests are under pressure from accelerating global change. To cope with the multiple challenges related to global change but also to further improve forest management we need a better understanding of (1) the linkages between drivers of ecosystem change and the state and management of forest ecosystems as well as their capacity to adapt to ongoing global environmental changes, and (2) the interrelationships within and between the components of forest ecosystems. To address the resulting challenges for the state of forest ecosystems in Central Europe, we suggest 45 questions for future ecological research. We define forest ecology as studies on the abiotic and biotic components of forest ecosystems and their interactions on varying spatial and temporal scales. Our questions cover five thematic fields and correspond to the criteria selected for describing the state of Europe’s forests by policy makers, i.e. biogeochemical cycling, mortality and disturbances, productivity, biodiversity and biotic interactions, and regulation and protection. We conclude that an improved mechanistic understanding of forest ecosystems is essential for the further development of ecosystem-oriented multifunctional forest management in the face of accelerating global change.     

The role of micro-organisms in the ecological connectivity of running waters

1. Riparian zones hold a central place in the hydrological cycle, owing to the prevalence of surface and groundwater interactions. In riparian transition zones, the quality of exfiltrating water is heavily influenced by microbial activities within the bed sediments. This paper reviews the role of micro-organisms in biogeochemical cycling in the riparian-hyporheic ecotone. 2. The production of organic substances, such as cellulose and lignin, by riparian vegetation is an important factor influencing the pathways of microbial processing in the riparian zone. For example, anaerobic sediment patches, created by entrainment of allochthonous organic matter, are focal sites of microbial denitrification. 3. The biophysical structure of the riparian zone largely influences in-stream microbial transformations through the retention of organic matter. Particulate and dissolved organic matter (POM and DOM) is retained effectively in the hyporheic zone, which drives biofilm development and associated microbial activity. 4. The structure of the riparian zone, the mechanisms of POM retention, the hydrological linkages to the stream and the intensity of key biogeochemical processes vary greatly along the river continuum and in relation to the geomorphic setting. However, the present state of knowledge of organic matter metabolism in the hyporheic zone suggests that lateral ecological connectivity is a basic attribute of lotic ecosystems. 5. Due to their efficiency in transforming POM into heterotrophic microbial biomass, attached biofilms form an abundant food resource for an array of predators and grazers in the interstitial environments of rivers and streams. The interstitial microbial loop, and the intensity of microbial production within the bed sediments, may be a primary driver of the celebrated high productivity and biodiversity of the riparian zone. 6. New molecular methods based on the analysis of the low molecular weight RNA (LMW RNA) allow unprecedented insights into the community structure of natural bacterial assemblages and also allow identification and study of specific strains hitherto largely unknown. 7. Research is needed on the development and evaluation of sampling methods for interstitial micro-organisms, on the characterization of biofilm structure, on the analysis of the biodegradable matter in the riparian-hyporheic ecotone, on the regulation mechanisms exerted on microbiota by interstitial predators and grazers, and on measures of microbial respiration and other key activities that influence biogeochemical cycles in running waters. 8. Past experiences from large-scale alterations of riparian zones by humans, such as the River Rhine in central Europe, undeniably demonstrate the detrimental consequences of disconnecting rivers from their riparian zones. A river management approach that uses the natural services of micro-organisms within intact riparian zones could substantially reduce the costs of clean, sustainable water supplies for humans.     

基于生态系统服务的城市生态基础设施:现状、问题与展望

城市生态基础设施是城市可持续发展的重要基础,也是建设生态城市的重要保证。生态系统服务是城市生态基础设施建设的核心与关键。在快速城市化的背景下,保障生态基础设施的结构完整性和功能完善性尤为重要。在阐述生态系统服务的基础上,对生态基础设施的概念与类型进行了概述;从城市湿地生态基础设施、绿地生态基础设施以及城市地表硬化的生态工程改造3个方面对城市生态基础设施研究现状进行综述;对生态基础设施结构与功能评估方法进行了总结,对基于生态系统服务的城市生态基础设施研究进行了综合评述,首次提出了城市表面生态学的概念与研究展望,为城市生态系统服务的强化与调控提供了方法论指导。城市生态基础设施与表面生态学的整合研究将对城市水文效应(内涝)、灰霾效应(PM2.5)、热岛效应、水体污染与富营养化等备受关注的重大问题提供新的解决思路与科学方法。     

Ecosystem thresholds with hypoxia

Hypoxia is one of the common effects of eutrophication in coastal marine ecosystems and is becoming an increasingly prevalent problem worldwide. The causes of hypoxia are associated with excess nutrient inputs from both point and non-point sources, although the response of coastal marine ecosystems is strongly modulated by physical processes such as stratification and mixing. Changes in climate, particularly temperature, may also affect the susceptibility of coastal marine ecosystems to hypoxia. Hypoxia is a particularly severe disturbance because it causes death of biota and catastrophic changes in the ecosystem. Bottom water oxygen deficiency not only influences the habitat of living resources but also the biogeochemical processes that control nutrient concentrations in the water column. Increased phosphorus fluxes from sediments into overlying waters occur with hypoxia. In addition, reductions in the ability of ecosystems to remove nitrogen through denitrification and anaerobic ammonium oxidation may be related to hypoxia and could lead to acceleration in the rate of eutrophication. Three large coastal marine ecosystems (Chesapeake Bay, Northern Gulf of Mexico, and Danish Straits) all demonstrate thresholds whereby repeated hypoxic events have led to an increase in susceptibility of further hypoxia and accelerated eutrophication. Once hypoxia occurs, reoccurrence is likely and may be difficult to reverse. Therefore, elucidating ecosystem thresholds of hypoxia and linking them to nutrient inputs are necessary for the management of coastal marine ecosystems. Finally, projected increases in warming show an increase in the susceptibility of coastal marine ecosystems to hypoxia such that hypoxia will expand. Guest editors: J. H. Andersen & D. J. Conley Eutrophication in Coastal Ecosystems: Selected papers from the Second International Symposium on Research and Management of Eutrophication in Coastal Ecosystems, 20–23 June 2006, Nyborg, Denmark     

微生物生态学理论框架

微生物是生态系统的重要组成部分,直接或间接地参与所有的生态过程。微生物生态学是基于微生物群体的科学,利用微生物群体DNA/RNA等标志物,重点研究微生物群落构建、组成演变、多样性及其与环境的关系,在生态学理论的指导和反复模型拟合下由统计分析得出具有普遍意义的结论。其研究范围从基因尺度到全球尺度。分子生物学技术的发展,使人们可以直接从基因水平上考查其多样性,从而使得对微生物空间分布格局及其成因的深入研究成为可能。进而可以从方法学探讨微生物生物多样性、分布格局、影响机制及其对全球变化的响应等。在微生物生态学研究中,群落构建与演化、分布特征(含植物-微生物相互关系)、执行群体功能的机理(生物地球化学循环等)、对环境变化的响应与反馈机理是今后需要关注的重点领域。概述了微生物生态学的概念,并初步提出其理论框架,在对比宏观生态学基础理论和模型的基础上,分析微生物多样性的研究内容、研究方法和群落构建的理论机制,展望了今后研究的重点领域。     

Differential response of high-elevation planktonic bacterial community structure and metabolism to experimental nutrient enrichment

Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA) to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate) caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient limitation, and emphasize that evaluation of eutrophication in these habitats should incorporate heterotrophic microbial communities and processes.     

Environmental and stoichiometric controls on microbial carbon-use efficiency in soils

Carbon (C) metabolism is at the core of ecosystem function. Decomposers play a critical role in this metabolism as they drive soil C cycle by mineralizing organic matter to CO(2) . Their growth depends on the carbon-use efficiency (CUE), defined as the ratio of growth over C uptake. By definition, high CUE promotes growth and possibly C stabilization in soils, while low CUE favors respiration. Despite the importance of this variable, flexibility in CUE for terrestrial decomposers is still poorly characterized and is not represented in most biogeochemical models. Here, we synthesize the theoretical and empirical basis of changes in CUE across aquatic and terrestrial ecosystems, highlighting common patterns and hypothesizing changes in CUE under future climates. Both theoretical considerations and empirical evidence from aquatic organisms indicate that CUE decreases as temperature increases and nutrient availability decreases. More limited evidence shows a similar sensitivity of CUE to temperature and nutrient availability in terrestrial decomposers. Increasing CUE with improved nutrient availability might explain observed declines in respiration from fertilized stands, while decreased CUE with increasing temperature and plant C?:?N ratios might decrease soil C storage. Current biogeochemical models could be improved by accounting for these CUE responses along environmental and stoichiometric gradients.     

Sulphate reduction and calcite precipitation in relation to internal eutrophication of groundwater fed alkaline fens

Although in Europe atmospheric deposition of sulphur has decreased considerably over the last decades, groundwater pollution by sulphate may still continue due to pyrite oxidation in the soil as a result of excessive fertilisation. Inflowing groundwater rich in sulphate can change biogeochemical cycling in nutrient-poor wetland ecosystems. Incoming sulphate loads may induce internal eutrophication as well as the accumulation of dissolved sulphide, which is phytotoxic. We, however, argue that upwelling sulphate rich groundwater may also promote the conservation of rare and threatened alkaline fens, since excessive fertilisation and pyrite oxidation also produces acidity, which invokes calcite dissolution, and increased alkalinity and hardness (Ca²⁺ + Mg²⁺) of the inflowing groundwater. Our observations in a very species-rich wetland nature reserve show that sulphate is reduced and effectively precipitates as iron sulphides when this calcareous and sulphate rich groundwater flows upward through the organic soil of the investigated nature reserve. Furthermore, we show that sulphate reduction coincides with an increase in alkalinity production, which in our case results in active calcite precipitation in the soil. In spite of the occurring sulphate reduction we found no evidence for internal eutrophication. Extremely low phosphorous concentration in the pore water could be attributed to a high C:P ratio of soil organic matter and co-precipitation with calcite. Our study shows that seepage dependent alkaline fen ecosystems can be remarkably resilient to fertilisation and pyrite oxidation induced groundwater quality changes.     

Ecoenzymatic stoichiometry of microbial nutrient acquisition in tropical soils

The relative activities of soil enzymes involved in mineralizing organic carbon (C), nitrogen (N), and phosphorus (P) reveal stoichiometric and energetic constraints on microbial biomass growth. Although tropical forests and grasslands are a major component of the global C cycle, the effects of soil nutrient availability on microbial activity and C dynamics in these ecosystems are poorly understood. To explore potential microbial nutrient limitation in relation to enzyme allocation in low latitude ecosystems, we performed a meta-analysis of acid/alkaline phosphatase (AP), β-1,4-glucosidase (BG), and β-1,4-N-acetyl-glucosaminidase (NAG) activities in tropical soils. We found that BG:AP and NAG:AP ratios in tropical soils are significantly lower than those of temperate ecosystems overall. The lowest BG:AP and NAG:AP ratios were associated with old or acid soils, consistent with greater biological phosphorus demand relative to P availability. Additionally, correlations between enzyme activities and mean annual temperature and precipitation suggest some climatic regulation of microbial enzyme allocation in tropical soils. We used the results of our analysis in conjunction with previously published data on soil and biomass C:N:P stoichiometry to parameterize a biogeochemical equilibrium model that relates microbial growth efficiency to extracellular enzyme activity. The model predicts low microbial growth efficiencies in P-limited soils, indicating that P availability may influence C cycling in the highly weathered soils that underlie many tropical ecosystems. Therefore, we suggest that P availability be included in models that simulate microbial enzyme allocation, biomass growth, and C mineralization.     

Development, maintenance and role of riparian vegetation in the river landscape

1. Riparian structure and function were considered from a longitudinal perspective in order to identify multiscale couplings with adjacent ecosystems and to identify research needs. 2. We characterized functional zones (with respect to vegetation development in association with various biogeochemical processes) within geomorphological settings using a delineation based upon erosional, transitional and depositional properties. 3. Vegetation dynamics within the riparian corridor are clearly influenced substantially by hydrological disturbance regimes. In turn, we suggest that vegetation productivity and diversity may widely influence riverine biogeochemical processes, especially as related to the consequences of changing redox conditions occurring from upstream to downstream. 4. However, surface and groundwater linkages are the predominant controls of landscape connectivity within riparian systems. 5. The importance of riparian zones as sources and sinks of matter and energy was examined in context of structural and functional attributes, such as sequestering or cycling of nutrients in sediments, retention of water in vegetation, and retention, diffusion or dispersal of biota. 6. The consequences of interactions between different communities (e.g. animals and plants, micro-organisms and plants) on biogeochemical processes are notably in need of research, especially with respect to control of landscape features. Multiscale approaches, coupling regional and local factors in all three spatial dimensions, are needed in order to understand more synthetically and to model biogeochemical and community processes within the river-riparian-upland landscape of catchments.     

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world’s most productive ecosystems. They store vast amounts of organic carbon, as ‘blue carbon’ reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.     

Winter climate change effects on soil C and N cycles in urban grasslands

Despite growing recognition of the role that cities have in global biogeochemical cycles, urban systems are among the least understood of all ecosystems. Urban grasslands are expanding rapidly along with urbanization, which is expected to increase at unprecedented rates in upcoming decades. The large and increasing area of urban grasslands and their impact on water and air quality justify the need for a better understanding of their biogeochemical cycles. There is also great uncertainty about the effect that climate change, especially changes in winter snow cover, will have on nutrient cycles in urban grasslands. We aimed to evaluate how reduced snow accumulation directly affects winter soil frost dynamics, and indirectly greenhouse gas fluxes and the processing of carbon (C) and nitrogen (N) during the subsequent growing season in northern urban grasslands. Both artificial and natural snow reduction increased winter soil frost, affecting winter microbial C and N processing, accelerating C and N cycles and increasing soil : atmosphere greenhouse gas exchange during the subsequent growing season. With lower snow accumulations that are predicted with climate change, we found decreases in N retention in these ecosystems, and increases in N₂O and CO₂ flux to the atmosphere, significantly increasing the global warming potential of urban grasslands. Our results suggest that the environmental impacts of these rapidly expanding ecosystems are likely to increase as climate change brings milder winters and more extensive soil frost.     

Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota

Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.     

Coastal eutrophication research: a new awareness

An analysis of the contents and conclusions of the papers contained in this issue (Hydrobiologia Volume xxx) suggests that a new vision is taking shape that may correspond to an emerging new paradigm in the way we understand and manage coastal eutrophication. This new paradigm emphasizes its global dimension and the connections with other global environmental pressures, and re-evaluates the targets of remedial actions and policies. Eutrophication research must evolve toward a more integrative, ecosystem perspective which requires that it be extended to include impacts beyond primary producers and to examine possible cascading effects and feedbacks involving other components of the ecosystem. A quantitative framework that incorporates the interacting top-down and bottom-up effects in eutrophication models must be urgently developed to guide diagnostics and establish targets to mitigate coastal eutrophication. The required macroscopic view must also be extended to the managerial and policy frameworks addressing eutrophication, through the development of policies that examine activities in the environment in an integrative, rather than sectorial, manner. Recent evidence of complex responses of coastal ecosystems to nutrient reduction requires that management targets, and the policies that support them, be reconsidered to recognize the complexities of the responses of coastal ecosystems to reduced nutrient inputs, including non-linear responses and associated thresholds. While a predictive framework for the complex trajectories of coastal ecosystems subject to changes in nutrient inputs is being developed, the assessment of managerial actions should be reconsidered to focus on the consideration of the status achieved as the outcome of nutrient reduction plans against that possibly derived from a ‘do nothing’ scenario. A proper assessment of eutrophication and the efforts to mitigate it also requires that eutrophication be considered as a component of global change, in addressing both its causes and its consequences, and that the feedbacks between other components of global change (e.g., climate change, overfishing, altered biogeochemical cycles, etc.) be explicitly considered in designing eutrophication research and in managing the problem. Guest editors: J. H. Andersen & D. J. Conley Eutrophication in Coastal Ecosystems: Selected papers from the Second International Symposium on Research and Management of Eutrophication in Coastal Ecosystems, 20–23 June 2006, Nyborg, Denmark     

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro-ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate-binding modules. These results demonstrate that virus-encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.     

The microbial nitrogen cycle

This special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen-fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite-dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.