Elevated CO2 promotes long‐term nitrogen accumulation only in combination with nitrogen addition

Biogeochemical models that incorporate nitrogen (N) limitation indicate that N availability will control the magnitude of ecosystem carbon uptake in response to rising CO₂. Some models, however, suggest that elevated CO₂ may promote ecosystem N accumulation, a feedback that in the long term could circumvent N limitation of the CO₂ response while mitigating N pollution. We tested this prediction using a nine‐year CO₂xN experiment in a tidal marsh. Although the effects of CO₂ are similar between uplands and wetlands in many respects, this experiment offers a greater likelihood of detecting CO₂ effects on N retention on a decadal timescale because tidal marshes have a relatively open N cycle and can accrue soil organic matter rapidly. To determine how elevated CO₂ affects N dynamics, we assessed the three primary fates of N in a tidal marsh: (1) retention in plants and soil, (2) denitrification to the atmosphere, and (3) tidal export. We assessed changes in N pools and tracked the fate of a ¹⁵N tracer added to each plot in 2006 to quantify the fraction of added N retained in vegetation and soil, and to estimate lateral N movement. Elevated CO₂ alone did not increase plant N mass, soil N mass, or ¹⁵N label retention. Unexpectedly, CO₂ and N interacted such that the combined N+CO₂ treatment increased ecosystem N accumulation despite the stimulation in N losses indicated by reduced ¹⁵N label retention. These findings suggest that in N‐limited ecosystems, elevated CO₂ is unlikely to increase long‐term N accumulation and circumvent progressive N limitation without additional N inputs, which may relieve plant–microbe competition and allow for increased plant N uptake.     

Ecosystem model parameterization and adaptation for sustainable cellulosic biofuel landscape design

Renewable fuel standards in the US and elsewhere mandate the production of large quantities of cellulosic biofuels with low greenhouse gas (GHG) footprints, a requirement which will likely entail extensive cultivation of dedicated bioenergy feedstock crops on marginal agricultural lands. Performance data for such systems is sparse, and non‐linear interactions between the feedstock species, agronomic management intensity, and underlying soil and land characteristics complicate the development of sustainable landscape design strategies for low‐impact commercial‐scale feedstock production. Process‐based ecosystem models are valuable for extrapolating field trial results and making predictions of productivity and associated environmental impacts that integrate the effects of spatially variable environmental factors across diverse production landscapes. However, there are few examples of ecosystem model parameterization against field trials on both prime and marginal lands or of conducting landscape‐scale analyses at sufficient resolution to capture interactions between soil type, land use, and management intensity. In this work we used a data‐diverse, multi‐criteria approach to parameterize and validate the DayCent biogeochemistry model for upland and lowland switchgrass using data on yields, soil carbon changes, and soil nitrous oxide emissions from US field trials spanning a range of climates, soil types, and management conditions. We then conducted a high‐resolution case study analysis of a real‐world cellulosic biofuel landscape in Kansas in order to estimate feedstock production potential and associated direct biogenic GHG emissions footprint. Our results suggest that switchgrass yields and emissions balance can vary greatly across a landscape large enough to supply a biorefinery in response to variations in soil type and land‐use history, but that within a given land base both of these performance factors can be widely modulated by changing management intensity. This in turn implies a large sustainable cellulosic biofuel landscape design space within which a system can be optimized to meet economic or environmental objectives.     

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

Synechococcus sp. represents an ecologically diverse group of cyanobacteria found in numerous environments, including hot-spring microbial mats, where they are spatially distributed along thermal, light and oxygen gradients. These thermophiles engage in photosynthesis and aerobic respiration during the day, but switch to fermentative metabolism and nitrogen fixation at night. The genome of Synechococcus OS-B′, isolated from Octopus Spring (Yellowstone National Park) contains a phn gene cluster encoding a phosphonate (Phn) transporter and a C–P lyase. A closely related isolate, Synechococcus OS-A, lacks this cluster, but contains genes encoding putative phosphonatases (Phnases) that appear to be active only in the presence of the Phn substrate. Both isolates grow well on several different Phns as a sole phosphorus (P) source. Interestingly, Synechococcus OS-B′ can use the organic carbon backbones of Phns for heterotrophic growth in the dark, whereas in the light this strain releases organic carbon from Phn as ethane or methane (depending on the specific Phn available); Synechococcus OS-A has neither of these capabilities. These differences in metabolic strategies for assimilating the P and C of Phn by two closely related Synechococcus spp. are suggestive of niche-specific constraints in the evolution of nutrient assimilation pathways and syntrophic relationships among the microbial populations of the hot-spring mats. Thus, it is critical to evaluate levels of various P sources, including Phn, in thermally active habitats and the potential importance of these compounds in the biogeochemical cycling of P and C (some Phn compounds also contain N) in diverse terrestrial environments.     

Biogeochemical Constraints on the Ecological Rehabilitation of Wetland Vegetation in River Floodplains

The European policy for river management during peak discharge periods is currently changing from exclusion strategies (reinforcement of dykes) to allowing a more natural situation by creating more floodplain space to reduce water levels during peak discharges. In addition, water retention and water storage areas have been created. The new measures are generally being combined with nature development strategies. Up till now, however, ecological targets of broadscale floodplain wetland restoration including sedge marshes, species-rich floodplain forests and carrs, riparian mesotrophic grasslands and other biodiverse riverine ecosystems, have hardly developed in these areas. Most studies on the conditions needed for sustainable ecological development of floodplains have focused on hydrological and geomorphological rather than biogeochemical issues (including nutrient availability and limitation). There are, however, large differences in the composition of river water and groundwater and in sediment quality between rivers in densely populated areas and those in more pristine areas, which serve as a reference. It is very likely that these factors, in combination with heavily altered hydrological regimes and the narrow areas confined between the dykes on both sides of the rivers, impose major constraints on sustainable ecological development of riverine areas. Another issue is that existing wetlands are generally considered to be very appropriate for water retention and conservation, although recent research has shown that this may pose a serious threat to their biodiversity. The present paper reviews the biogeochemical constraints on the combination of floodplain rehabilitation, water conservation and the conservation and development of wetlands. It is concluded that biogeochemical problems (mainly related to eutrophication) predominantly arise in less dynamic parts of the river system, to which the flood-pulse concept applies less. Sound knowledge of the biogeochemical processes involved will contribute to greater efficiency and a better prediction of the opportunities for restoration and development of riverine wetlands. This information can be directly applied in nature management, water management, policy-making and consultancy.     

Diatom aggregation in the sea: mechanisms and ecological implications

Marine snow is a ubiquitous feature of the ocean and an important agent in the transport of energy and nutrients through marine ecosystems. Diatom aggregates, which form during blooms and, to a lesser extent, by the resuspension of benthic biofilms, are a primary source of marine snow. Genera commonly found in diatom aggregates are: Nitzschia, Chaetoceros, Rhizosolenia, Leptocylindricus, Skeletonema and Thalassionema. Most fieldwork has been restricted to a limited number of locations in the Northern Hemisphere. To quantify the global impact of diatom aggregation there is a need to conduct fieldwork in a wider range of areas, particularly in the Southern Hemisphere. Aggregates form when particles collide and stick together. Collisions in the water column are affected by turbulence, differential settlement and animal feeding, whereas diatom stickiness is affected by extracellular polymeric substances (EPS). Laboratory experiments have demonstrated that diatoms produce more EPS under nutrient limitation, although little is known about how limitation by different nutrients affects the quantity and composition of EPS and subsequent stickiness. EPS form three pools in the environment: cell coatings, soluble EPS and transparent exopolymeric particles (TEP). There is a need to investigate the dynamics of conversion between the pools of EPS by both abiotic and biological processes and how these conversions affect aggregate concentration and structure. Processes governing disaggregation have been largely overlooked, although they are as important as aggregation in determining the dynamics of aggregate concentrations in the water column. The biogeochemical significance of diatom aggregates as a means of transporting carbon and other nutrients from the euphotic zone to the seabed is well established. However, the internal biogeochemistry of aggregates is not well understood. Aggregates contain anaerobic microsites and further work is required to establish whether aggregates are significant sinks for nitrogen in the water column through anaerobic denitrification. Several hypotheses have been proposed to explain diatom aggregation in the field, but many of these are flawed because the mechanisms and adaptive explanations proposed require natural selection to operate at the level of populations rather than genes or individuals.     

The dark side of the hyporheic zone: depth profiles of nitrogen and its processing in stream sediments

1. Although it is well known that sediments can be hot spots for nitrogen transformation in streams, many previous studies have confined measurements of denitrification and nitrate retention to shallow sediments (<5 cm deep). We determined the extent of nitrate processing in deeper sediments of a sand plains stream (Emmons Creek) by measuring denitrification in core sections to a depth of 25 cm and by assessing vertical nitrate profiles, with peepers and piezometers, to a depth of 70 cm. 2. Denitrification rates of sediment slurries based on acetylene block were higher in shallower core sections. However, core sections deeper than 5 cm accounted for 68% of the mean depth‐integrated denitrification rate. 3. Vertical hydraulic gradient and vertical profiles of pore water chloride concentration suggested that deep ground water upwelled through shallow sediments before discharging to the stream channel. The results of a two‐source mixing model based on chloride concentrations suggested that the hyporheic zone was very shallow (<5 cm) in Emmons Creek. 4. Vertical profiles showed that nitrate concentration in shallow ground water was about 10–60% of the nitrate concentration of deep ground water. The mean nitrate concentrations of deep and shallow ground water were 2.17 and 0.73 mg NO₃‐N L^?1, respectively. 5. Deep ground water tended to be oxic (6.9 mg O₂ L^?1) but approached anoxia (0.8 mg O₂ L^?1) after passing through shallow, organic carbon‐rich sediments, which suggests that the decline in the nitrate concentrations of upwelling ground water was because of denitrification. 6. Collectively, our results suggest that there is substantial nitrate removal occurring in deep sediments, below the hyporheic zone, in Emmons Creek. Our findings suggest that not accounting for nitrate removal in deep sediments could lead to underestimates of nitrogen processing in streams and catchments.     

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

Viruses contribute to the mortality of marine microbes, consequentially altering biological species composition and system biogeochemistry. Although it is well established that host cells provide metabolic resources for virus replication, the extent to which infection reshapes host metabolism at a global level and the effect of this alteration on the cellular material released following viral lysis is less understood. To address this knowledge gap, the growth dynamics, metabolism and extracellular lysate of roseophage-infected Sulfitobacter sp. 2047 was studied using a variety of techniques, including liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based metabolomics. Quantitative estimates of the total amount of carbon and nitrogen sequestered into particulate biomass indicate that phage infection redirects ∼75% of nutrients into virions. Intracellular concentrations for 82 metabolites were measured at seven time points over the infection cycle. By the end of this period, 71% of the detected metabolites were significantly elevated in infected populations, and stable isotope-based flux measurements showed that these cells had elevated metabolic activity. In contrast to simple hypothetical models that assume that extracellular compounds increase because of lysis, a profile of metabolites from infected cultures showed that >70% of the 56 quantified compounds had decreased concentrations in the lysate relative to uninfected controls, suggesting that these small, labile nutrients were being utilized by surviving cells. These results indicate that virus-infected cells are physiologically distinct from their uninfected counterparts, which has implications for microbial community ecology and biogeochemistry.     

Systems approaches in global change and biogeochemistry research

Systems approaches have great potential for application in predictive ecology. In this paper, we present a range of examples, where systems approaches are being developed and applied at a range of scales in the field of global change and biogeochemical cycling. Systems approaches range from Bayesian calibration techniques at plot scale, through data assimilation methods at regional to continental scales, to multi-disciplinary numerical model applications at country to global scales. We provide examples from a range of studies and show how these approaches are being used to address current topics in global change and biogeochemical research, such as the interaction between carbon and nitrogen cycles, terrestrial carbon feedbacks to climate change and the attribution of observed global changes to various drivers of change. We examine how transferable the methods and techniques might be to other areas of ecosystem science and ecology.