Benthivorous fish bioturbation reduces methane emissions,but increases total greenhouse gas emissions

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Bacterial community dynamics during reduction of odorous compounds in aerated pig manure slurry

Aims:  To study the microbial community responsible for the reduction of the polluting load during aerobic digestion of pig slurry.
Methods and Results:  We analysed bacterial succession by nonculture-based methods and determined the physicochemical parameters and polluting substances during 6 days of aerobic digestion. The bacterial subpopulations evolved by aeration, predominantly Bacillus spp., degraded organic matter and vigorously consumed oxygen, as indicated by low oxidation–reduction potential (ORP). In this phase, the volatile fatty acid (VFA) levels drastically decreased, and VFAs were almost depleted on day 4. Simultaneously, the ammonia concentration decreased to its lowest level on day 4; thereafter, it increased until the end of the process. After the decrease in the total organic carbon content in the supernatant of the decomposed slurry, the ORP increased (∼0 mV), and the microbial community showed an abundance of lineages belonging to the phylum Proteobacteria.
Conclusions:  Bacillus was the predominant member of the bacterial community driving the VFA-removal process. Their predominance was related to the presence of available carbon, including VFAs and changes in ORP.
Significance and Impact of the Study:  Information on the relationships among the involved microbes, polluting materials and physicochemical parameters will aid process design and retrofitting of the process.     

The contribution of trees to ecosystem methane emissions in a temperate forested wetland

Wetland‐adapted trees are known to transport soil‐produced methane (CH₄), an important greenhouse gas to the atmosphere, yet seasonal variations and controls on the magnitude of tree‐mediated CH₄ emissions remain unknown for mature forests. We examined the spatial and temporal variability in stem CH₄ emissions in situ and their controls in two wetland‐adapted tree species (Alnus glutinosa and Betula pubescens) located in a temperate forested wetland. Soil and herbaceous plant‐mediated CH₄ emissions from hollows and hummocks also were measured, thus enabling an estimate of contributions from each pathway to total ecosystem flux. Stem CH₄ emissions varied significantly between the two tree species, with Alnus glutinosa displaying minimal seasonal variations, while substantial seasonal variations were observed in Betula pubescens. Trees from each species emitted similar quantities of CH₄ from their stems regardless of whether they were situated in hollows or hummocks. Soil temperature and pore‐water CH₄ concentrations best explained annual variability in stem emissions, while wood‐specific density and pore‐water CH₄ concentrations best accounted for between‐species variations in stem CH₄ emission. Our study demonstrates that tree‐mediated CH₄ emissions contribute up to 27% of seasonal ecosystem CH₄ flux in temperate forested wetland, with the largest relative contributions occurring in spring and winter. Tree‐mediated CH₄ emissions currently are not included in trace gas budgets of forested wetland. Further work is required to quantify and integrate this transport pathway into CH₄ inventories and process‐based models.     

Oxidative mitigation of aquatic methane emissions in large Amazonian rivers

The flux of methane (CH₄) from inland waters to the atmosphere has a profound impact on global atmospheric greenhouse gas (GHG) levels, and yet, strikingly little is known about the dynamics controlling sources and sinks of CH₄ in the aquatic setting. Here, we examine the cycling and flux of CH₄ in six large rivers in the Amazon basin, including the Amazon River. Based on stable isotopic mass balances of CH₄, inputs and outputs to the water column were estimated. We determined that ecosystem methane oxidation (MOX) reduced the diffusive flux of CH₄ by approximately 28–96% and varied depending on hydrologic regime and general geochemical characteristics of tributaries of the Amazon River. For example, the relative amount of MOX was maximal during high water in black and white water rivers and minimal in clear water rivers during low water. The abundance of genetic markers for methane‐oxidizing bacteria (pmoA) was positively correlated with enhanced signals of oxidation, providing independent support for the detected MOX patterns. The results indicate that MOX in large Amazonian rivers can consume from 0.45 to 2.07 Tg CH₄ yr^?1, representing up to 7% of the estimated global soil sink. Nevertheless, climate change and changes in hydrology, for example, due to construction of dams, can alter this balance, influencing CH₄ emissions to atmosphere.     

Methane emissions from Amazonian Rivers and their contribution to the global methane budget

Methane (CH₄) fluxes from world rivers are still poorly constrained, with measurements restricted mainly to temperate climates. Additional river flux measurements, including spatio‐temporal studies, are important to refine extrapolations. Here we assess the spatio‐temporal variability of CH₄ fluxes from the Amazon and its main tributaries, the Negro, Solimões, Madeira, Tapajós, Xingu, and Pará Rivers, based on direct measurements using floating chambers. Sixteen of 34 sites were measured during low and high water seasons. Significant differences were observed within sites in the same river and among different rivers, types of rivers, and seasons. Ebullition contributed to more than 50% of total emissions for some rivers. Considering only river channels, our data indicate that large rivers in the Amazon Basin release between 0.40 and 0.58 Tg CH₄ yr^?1. Thus, our estimates of CH₄ flux from all tropical rivers and rivers globally were, respectively, 19–51% to 31–84% higher than previous estimates, with large rivers of the Amazon accounting for 22–28% of global river CH₄ emissions.     

Impact of forest plantation on methane emissions from tropical peatland

Tropical peatlands are a known source of methane (CH₄) to the atmosphere, but their contribution to atmospheric CH₄ is poorly constrained. Since the 1980s, extensive areas of the peatlands in Southeast Asia have experienced land‐cover change to smallholder agriculture and forest plantations. This land‐cover change generally involves lowering of groundwater level (GWL), as well as modification of vegetation type, both of which potentially influence CH₄ emissions. We measured CH₄ exchanges at the landscape scale using eddy covariance towers over two land‐cover types in tropical peatland in Sumatra, Indonesia: (a) a natural forest and (b) an Acacia crassicarpa plantation. Annual CH₄ exchanges over the natural forest (9.1 ± 0.9 g CH₄ m^?2 year^?1) were around twice as high as those of the Acacia plantation (4.7 ± 1.5 g CH₄ m^?2 year^?1). Results highlight that tropical peatlands are significant CH₄ sources, and probably have a greater impact on global atmospheric CH₄ concentrations than previously thought. Observations showed a clear diurnal variation in CH₄ exchange over the natural forest where the GWL was higher than 40 cm below the ground surface. The diurnal variation in CH₄ exchanges was strongly correlated with associated changes in the canopy conductance to water vapor, photosynthetic photon flux density, vapor pressure deficit, and air temperature. The absence of a comparable diurnal pattern in CH₄ exchange over the Acacia plantation may be the result of the GWL being consistently below the root zone. Our results, which are among the first eddy covariance CH₄ exchange data reported for any tropical peatland, should help to reduce the uncertainty in the estimation of CH₄ emissions from a globally important ecosystem, provide a more complete estimate of the impact of land‐cover change on tropical peat, and develop science‐based peatland management practices that help to minimize greenhouse gas emissions.     

Effect of biofuel co-products in pig diets on the excretory patterns of N and C and on the subsequent ammonia and methane emissions from pig effluent

This study was conducted to investigate the effects of incorporation into pig diets of 20% of different co-products from the biofuel industries, which are rich in fibre, on animal growth performance, on nitrogen (N) and carbon (C) excretions, and on the subsequent ammonia volatilisation and methane production during the storage of slurry. Five experimental diets mainly based on wheat and soyabean meal were formulated: two control diets, a control high-protein (CHP) diet with 17.5% of crude protein (CP) and a control low-protein (CLP) diet with 14.0% of CP and three experimental diets with 20% of (i) dried distiller's grain with solubles (DDGS), (ii) sugar beet pulp (SBP) or (iii) fatty rapeseed meal (FRM). The animals used (20 castrated males) were housed individually in metabolism cages and fed one of the five diets (i.e. four pigs per diet). Urine and faeces were collected separately from each pig in order to measure nutrient digestibility and the excretory patterns of N and C. For each diet, ammonia volatilisation was measured from samples of slurry subsequently produced, over a 16-day storage period in a laboratory pilot scale system. The ultimate methane potential (B0, expressed in litres CH4/kg organic matter (OM)) was measured from the same slurry, for each diet, in anaerobic storage conditions over 100 days. The addition of sources of fibres to the diet decreased (P < 0.05) the animal growth performance by 13% and increased (P < 0.05) the amount of faeces excreted by 100%, whereas the amount of urine was not affected. For the high-fibre diets, there was a shift of N partitioning from urine to faeces, resulting in a much higher faecal N excretion (10 v. 5 g N/pig per day). Concurrently, the fibre enrichment in diets significantly increased (P < 0.05) the C content of the faeces by 68%. Ammonia emission from slurry was significantly reduced (P < 0.05) by 19% to 33% for the high-fibre diets, compared to the CHP diet. Ammonia emission was also reduced (P < 0.05) by 33% for the CLP compared to the CHP diet. B0 values ranged from 428 to 484 l CH4/kg OM. When these are expressed per pig and per day, the B0 from slurry was, on average, 70 l for the two control diets, and 121, 91 and 130 l for the slurry originating from the DDGS, SBP and FRM diets, respectively.     

Warming of subarctic tundra increases emissions of all three important greenhouse gases – carbon dioxide,methane, and nitrous oxide

Rapidly rising temperatures in the Arctic might cause a greater release of greenhouse gases (GHGs) to the atmosphere. To study the effect of warming on GHG dynamics, we deployed open‐top chambers in a subarctic tundra site in Northeast European Russia. We determined carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) fluxes as well as the concentration of those gases, inorganic nitrogen (N) and dissolved organic carbon (DOC) along the soil profile. Studied tundra surfaces ranged from mineral to organic soils and from vegetated to unvegetated areas. As a result of air warming, the seasonal GHG budget of the vegetated tundra surfaces shifted from a GHG sink of ?300 to ?198 g CO₂–eq m^?2 to a source of 105 to 144 g CO₂–eq m^?2. At bare peat surfaces, we observed increased release of all three GHGs. While the positive warming response was dominated by CO₂, we provide here the first in situ evidence of increasing N₂O emissions from tundra soils with warming. Warming promoted N₂O release not only from bare peat, previously identified as a strong N₂O source, but also from the abundant, vegetated peat surfaces that do not emit N₂O under present climate. At these surfaces, elevated temperatures had an adverse effect on plant growth, resulting in lower plant N uptake and, consequently, better N availability for soil microbes. Although the warming was limited to the soil surface and did not alter thaw depth, it increased concentrations of DOC, CO_2, and CH₄ in the soil down to the permafrost table. This can be attributed to downward DOC leaching, fueling microbial activity at depth. Taken together, our results emphasize the tight linkages between plant and soil processes, and different soil layers, which need to be taken into account when predicting the climate change feedback of the Arctic.     

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics

Algal blooms are a worldwide phenomenon and the biological interactions that underlie their regulation are only just beginning to be understood. It is established that algal microorganisms associate with many other ubiquitous, oceanic organisms, but the interactions that lead to the dynamics of bloom formation are currently unknown. To address this gap, we used network approaches to investigate the association patterns among microeukaryotes and bacterioplankton in response to a natural Scrippsiella trochoidea bloom. This is the first study to apply network approaches to bloom dynamics. To this end, terminal restriction fragment (T‐RF) length polymorphism analysis showed dramatic changes in community compositions of microeukaryotes and bacterioplankton over the blooming period. A variance ratio test revealed significant positive overall associations both within and between microeukaryotic and bacterioplankton communities. An association network generated from significant correlations between T‐RFs revealed that S. trochoidea had few connections to other microeukaryotes and bacterioplankton and was placed on the edge. This lack of connectivity allowed for the S. trochoidea sub‐network to break off from the overall network. These results allowed us to propose a conceptual model for explaining how changes in microbial associations regulate the dynamics of an algal bloom. In addition, key T‐RFs were screened by principal components analysis, correlation coefficients, and network analysis. Dominant T‐RFs were then identified through 18S and 16S rRNA gene clone libraries. Results showed that microeukaryotes clustered predominantly with Dinophyceae and Perkinsea while the majority of bacterioplankton identified were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. The ecologi‐cal roles of both were discussed in the context of these findings.     

Changes in microbial community structure and function during vermicomposting of pig slurry

Most studies investigating the effects of earthworms on microorganisms have focused on the changes before and after vermicomposting rather than those that occur throughout the process. In the present study, we designed continuous feeding reactors in which new layers of pig slurry (1.5 and 3 kg) were added sequentially to form an age gradient inside the reactors in order to evaluate the impact of the earthworm species Eisenia fetida on microbial community structure and function. The activity of earthworms greatly reduced the bacterial and fungal biomass and microbial diversity relative to the control values. However, the pronounced presence of earthworms in the younger layers stimulated microbial activity and as such increased carbon mineralization probably due to the fact that the microorganisms may have been less resource-limited as a result of earthworm activity, as indicated by the ratio of monounsaturated to saturated PLFAs.     

Quantification of Alternaria,Cladosporium, Fusarium and Penicillium verrucosum in Conventional and Organic Grains by qPCR

We analysed the levels of Alternaria, Cladosporium, Fusarium and Penicillium verrucosum in grain samples harvested in 2011 and 2012 from conventional and organic farms using qPCR. In general, both Alternaria and Cladosporium occurred in all cereal grains in the highest quantities, followed by P. verrucosum and Fusarium. Alternaria, Cladosporium and P. verrucosum had the highest levels in crop mixtures, barley and rye and lower levels in wheat, while Fusarium levels were the highest in crop mixtures and wheat. The levels of Alternaria and P. verrucosum were higher in organic rye and wheat than conventional grains. Although the level of Fusarium was higher in conventional than organic rye, opposite results were obtained for crop mixtures. A positive correlation was found between Alternaria, Cladosporium and P. verrucosum, indicating that similar factors might affect the distribution of these fungi in grains.     

Seasonal effects on the survival characteristics of Salmonella Typhimurium and Salmonella Derby in pig slurry during storage

AIMS: Studies were carried out to investigate the survival of Salmonella Typhimurium and Salmonella Derby in pig slurry during summer and winter seasons. METHODS AND RESULTS: Pig slurry samples collected from a commercial fattening house were inoculated with a broth culture of Salmonella Typhimurium and Salmonella Derby, each at a level of log(10) 5.0 CFU ml(-1) and log(10) 2.0 CFU ml(-1). At the higher inoculum level, S. Typhimurium and S. Derby survived for 34 and 23 days, respectively in the summer, and 58 and 46 days, respectively in the winter. Survival at the lower inoculum level for S. Typhimurium and S. Derby was 19 and 16 days, respectively, in the summer and 24 days for both in the winter. CONCLUSIONS: The survival of S. Typhimurium and S. Derby observed in this study indicates that a 2-month holding period of pig slurry, prior to land spreading, may be adequate if separate storage facilities are provided. SIGNIFICANCE AND IMPACT OF THE STUDY: Despite difficulties correlating laboratory studies with on-farm conditions, pig slurry may not represent a major source of transmission of Salmonella spp. in the farm environment in Ireland.     

Dynamic energy budget modeling reveals the potential of future growth and calcification for the coccolithophore Emiliania huxleyi in an acidified ocean

Ocean acidification is likely to impact the calcification potential of marine organisms. In part due to the covarying nature of the ocean carbonate system components, including pH and CO₂ and CO₃^2? levels, it remains largely unclear how each of these components may affect calcification rates quantitatively. We develop a process‐based bioenergetic model that explains how several components of the ocean carbonate system collectively affect growth and calcification rates in Emiliania huxleyi, which plays a major role in marine primary production and biogeochemical carbon cycling. The model predicts that under the IPCC A2 emission scenario, its growth and calcification potential will have decreased by the end of the century, although those reductions are relatively modest. We anticipate that our model will be relevant for many other marine calcifying organisms, and that it can be used to improve our understanding of the impact of climate change on marine systems.     

Toward understanding the contribution of waterbodies to the methane emissions of a permafrost landscape on a regional scale—A case study from the Mackenzie Delta,Canada

Waterbodies in the arctic permafrost zone are considered a major source of the greenhouse gas methane (CH₄) in addition to CH₄ emissions from arctic wetlands. However, the spatio‐temporal variability of CH₄ fluxes from waterbodies complicates spatial extrapolation of CH₄ measurements from single waterbodies. Therefore, their contribution to the CH₄ budget of the arctic permafrost zone is not yet well understood. Using the example of two study areas of 1,000 km² each in the Mackenzie Delta, Canada, we approach this issue (i) by analyzing correlations on the landscape scale between numerous waterbodies and CH₄ fluxes and (ii) by analyzing the influence of the spatial resolution of CH₄ flux data on the detected relationships. A CH₄ flux map with a resolution of 100 m was derived from two aircraft eddy‐covariance campaigns in the summers of 2012 and 2013. We combined the CH₄ flux map with high spatial resolution (2.5 m) waterbody maps from the Permafrost Region Pond and Lake Database and classified the waterbody depth based on Sentinel‐1 SAR backscatter data. Subsequently, we reduced the resolution of the CH₄ flux map to analyze if different spatial resolutions of CH₄ flux data affected the detectability of relationships between waterbody coverage, number, depth, or size and the CH₄ flux. We did not find consistent correlations between waterbody characteristics and the CH₄ flux in the two study areas across the different resolutions. Our results indicate that waterbodies in permafrost landscapes, even if they seem to be emission hot spots on an individual basis or contain zones of above average emissions, do currently not necessarily translate into significant CH₄ emission hot spots on a regional scale, but their role might change in a warmer climate.     

Carbon emissions performance of commercial logging in East Kalimantan,Indonesia

Adoption of reduced‐impact logging (RIL) methods could reduce CO₂ emissions by 30–50% across at least 20% of remaining tropical forests. We developed two cost effective and robust indices for comparing the climate benefits (reduced CO₂ emissions) due to RIL. The indices correct for variability in the volume of commercial timber among concessions. We determined that a correction for variability in terrain slope was not needed. We found that concessions certified by the Forest Stewardship Council (FSC, N = 3), when compared with noncertified concessions (N = 6), did not have lower overall CO₂ emissions from logging activity (felling, skidding, and hauling). On the other hand, FSC certified concessions did have lower emissions from one type of logging impact (skidding), and we found evidence of a range of improved practices using other field metrics. One explanation of these results may be that FSC criteria and indicators, and associated RIL practices, were not designed to achieve overall emissions reductions. Also, commonly used field metrics are not reliable proxies for overall logging emissions performance. Furthermore, the simple distinction between certified and noncertified concessions does not fully represent the complex history of investments in improved logging practices. To clarify the relationship between RIL and emissions reductions, we propose the more explicit term ‘RIL‐C’ to refer to the subset of RIL practices that can be defined by quantified thresholds and that result in measurable emissions reductions. If tropical forest certification is to be linked with CO₂ emissions reductions, certification standards need to explicitly require RIL‐C practices.     

Metabolite changes during the life history of Porphyra haitanensis

Plant metabolomics is essentially the comprehensive analysis of complex metabolites of plant extracts. Metabolic fingerprinting is an important part of plant metabolomics research. In this study, metabolic fingerprinting of different stages of the life history of the red alga Porphyra haitanensis was performed. The stages included conchocelis filaments, sporangial branchlets, conchosporangia, discharged conchospores and conchosporangial branchlets after conchospore discharge. Metabolite extracts were analysed with ultra‐performance liquid chromatography coupled with electrospray ionisation quadrupole‐time of flight mass spectrometry. Analyses profiles were subjected to principal components analysis and orthogonal projection to latent structures discriminant analysis using the SIMCA‐P software for biomarker selection and identification. Based on the MS/MS spectra and data from the literature, potential biomarkers, mainly of phosphatidylcholine and lysophosphatidylcholine, were identified. Identification of these biomarkers suggested that plasma membrane phospholipids underwent major changes during the life history of P. haitanensis. The levels of phosphatidylcholine and lysophosphatidylcholine increased in sporangial branchlets and decreased in discharged conchospores. Moreover, levels of sphingaine (d18:0) decreased in sporangial branchlets and increased in discharged conchospores, which indicates that membrane lipids were increasingly synthesised as energy storage in sporangial branchlets, while energy was consumed in sporangial branchlets to discharged conchospores. A metabolomic study of different growth phases of P. haitanensis will enhance our understanding of its physiology and ecology.     

Non‐native mangroves support carbon storage,sediment carbon burial,and accretion of coastal ecosystems

Mangrove forests play an important role in climate change adaptation and mitigation by maintaining coastline elevations relative to sea level rise, protecting coastal infrastructure from storm damage, and storing substantial quantities of carbon (C) in live and detrital pools. Determining the efficacy of mangroves in achieving climate goals can be complicated by difficulty in quantifying C inputs (i.e., differentiating newer inputs from younger trees from older residual C pools), and mitigation assessments rarely consider potential offsets to CO₂ storage by methane (CH₄) production in mangrove sediments. The establishment of non‐native Rhizophora mangle along Hawaiian coastlines over the last century offers an opportunity to examine the role mangroves play in climate mitigation and adaptation both globally and locally as novel ecosystems. We quantified total ecosystem C storage, sedimentation, accretion, sediment organic C burial and CH₄ emissions from ~70 year old R. mangle stands and adjacent uninvaded mudflats. Ecosystem C stocks of mangrove stands exceeded mudflats by 434 ± 33 Mg C/ha, and mangrove establishment increased average coastal accretion by 460%. Sediment organic C burial increased 10‐fold (to 4.5 Mg C ha^?1 year^?1), double the global mean for old growth mangrove forests, suggesting that C accumulation from younger trees may occur faster than previously thought, with implications for mangrove restoration. Simulations indicate that increased CH₄ emissions from sediments offset ecosystem CO₂ storage by only 2%–4%, equivalent to 30–60 Mg CO₂‐eq/ha over mangrove lifetime (100 year sustained global warming potential). Results highlight the importance of mangroves as novel systems that can rapidly accumulate C, have a net positive atmospheric greenhouse gas removal effect, and support shoreline accretion rates that outpace current sea level rise. Sequestration potential of novel mangrove forests should be taken into account when considering their removal or management, especially in the context of climate mitigation goals.     

The Contribution of Agriculture,Forestry and other Land Use activities to Global Warming, 1990–2012

We refine the information available through the IPCC AR5 with regard to recent trends in global GHG emissions from agriculture, forestry and other land uses (AFOLU), including global emission updates to 2012. Using all three available AFOLU datasets employed for analysis in the IPCC AR5, rather than just one as done in the IPCC AR5 WGIII Summary for Policy Makers, our analyses point to a down‐revision of global AFOLU shares of total anthropogenic emissions, while providing important additional information on subsectoral trends. Our findings confirm that the share of AFOLU emissions to the anthropogenic total declined over time. They indicate a decadal average of 28.7 ± 1.5% in the 1990s and 23.6 ± 2.1% in the 2000s and an annual value of 21.2 ± 1.5% in 2010. The IPCC AR5 had indicated a 24% share in 2010. In contrast to previous decades, when emissions from land use (land use, land use change and forestry, including deforestation) were significantly larger than those from agriculture (crop and livestock production), in 2010 agriculture was the larger component, contributing 11.2 ± 0.4% of total GHG emissions, compared to 10.0 ± 1.2% of the land use sector. Deforestation was responsible for only 8% of total anthropogenic emissions in 2010, compared to 12% in the 1990s. Since 2010, the last year assessed by the IPCC AR5, new FAO estimates indicate that land use emissions have remained stable, at about 4.8 Gt CO₂ eq yr^?1 in 2012. Emissions minus removals have also remained stable, at 3.2 Gt CO₂ eq yr^?1 in 2012. By contrast, agriculture emissions have continued to grow, at roughly 1% annually, and remained larger than the land use sector, reaching 5.4 Gt CO₂ eq yr^?1 in 2012. These results are useful to further inform the current climate policy debate on land use, suggesting that more efforts and resources should be directed to further explore options for mitigation in agriculture, much in line with the large efforts devoted to REDD+ in the past decade.