Modeling impacts of farming management alternatives on CO2, CH4, and N2O emissions: A case study for water management of rice agriculture of China

Since the early 1980s, water management of rice paddies in China has changed substantially, with midseason drainage gradually replacing continuous flooding. This has provided an opportunity to estimate how a management alternative impacts greenhouse gas emissions at a large regional scale. We integrated a process-based model, DNDC, with a GIS database of paddy area, soil properties, and management factors. We simulated soil carbon sequestration (or net CO2 emission) and CH4 and N2O emissions from China\u27s rice paddies (30 million ha), based on 1990 climate and management conditions, with two water management scenarios: continuous flooding and midseason drainage. The results indicated that this change in water management has reduced aggregate CH4 emissions about 40%, or 5 Tg CH4 yr−1, roughly 5–10% of total global methane emissions from rice paddies. The mitigating effect of midseason drainage on CH4 flux was highly uneven across the country; the highest flux reductions (\u3e200 kg CH4-C ha−1 yr−1) were in Hainan, Sichuan, Hubei, and Guangdong provinces, with warmer weather and multiple-cropping rice systems. The smallest flux reductions (\u3c25 kg CH4-C ha−1 yr−1) occurred in Tianjin, Hebei, Ningxia, Liaoning, and Gansu Provinces, with relatively cool weather and single cropping systems. Shifting water management from continuous flooding to midseason drainage increased N2O emissions from Chinese rice paddies by 0.15 Tg N yr−1 (∼50% increase). This offset a large fraction of the greenhouse gas radiative forcing benefit gained by the decrease in CH4 emissions. Midseason drainage-induced N2O fluxes were high (\u3e8.0 kg N/ha) in Jilin, Liaoning, Heilongjiang, and Xinjiang provinces, where the paddy soils contained relatively high organic matter. Shifting water management from continuous flooding to midseason drainage reduced total net CO2emissions by 0.65 Tg CO2-C yr−1, which made a relatively small contribution to the net climate impact due to the low radiative potential of CO2. The change in water management had very different effects on net greenhouse gas mitigation when implemented across climatic zones, soil types, or cropping systems. Maximum CH4 reductions and minimum N2O increases were obtained when the mid-season draining was applied to rice paddies with warm weather, high soil clay content, and low soil organic matter content, for example, Sichuan, Hubei, Hunan, Guangdong, Guangxi, Anhui, and Jiangsu provinces, which have 60% of China\u27s rice paddies and produce 65% of China\u27s rice harvest

Reduced methane emissions from large-scale changes in water management of China’s rice paddies during 1980-2000

Decreased methane emissions from paddy rice may have contributed to the decline in the rate of increase of global atmospheric methane (CH4) concentration over the last 20 years. In China, midseason paddy drainage, which reduces growing season CH4 fluxes, was first implemented in the early 1980s, and has gradually replaced continuous flooding in much of the paddy area. We constructed a regional prediction for China\u27s rice paddy methane emissions using the DNDC biogeochemical model. Results of continuous flooding and midseason drainage simulations for all paddy fields in China were combined with regional scenarios for the timing of the transition from continuous flooding to predominantly mid-season drainage to generate estimates of total methane flux for 1980–2000. CH4 emissions from China\u27s paddy fields were reduced over that period by ∼5 Tg CH4 yr−1

Greenhouse gas emissions from croplands of China

China possesses cropland of 1.33 million km 2. Cultivation of the cropland not only altered the biogeochemical cycles of carbon (C) and nitrogen (N) in the agroecosystems but also affected global climate. The impacts of agroecosystems on global climate attribute to emissions of three greenhouse gases, namely carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)

Greenhouse gas emission consequences of large-scale changes in water management of China’s rice paddies during 1980-2000

In China, midseason paddy drainage, which reduces growing season methane fluxes and enhances growing season nitrous oxide fluxes, was first implemented in the early 1980s, and has gradually replaced continuous flooding in much of the paddy rice area. We constructed a prediction rice paddy methane and nitrous oxide emissions in China using the DNDC biogeochemical model. Results of continuous flooding and midseason drainage simulations for all paddy fields in China (about 30 million ha) were combined with regional scenarios for the timing of the transition from continuous flooding to predominantly mid-season drainage to generate estimates of total methane (CH4) and nitrous oxide (N2O) flux for 1980-2000. By shifting from continuous flooding to midseason drainage management, we estimate that total N2O emissions from the rice paddies in China increased by about 0.17 Tg N2O-N yr−1 due to the stimulated nitri- fication and denitrification, while CH4 emissions decreased by about 4.5 Tg CH4-C yr−1 due to increased soil aeration. Simulated net carbon loss in paddy soils was about 0.65 Tg C yr−1 due to elevated decomposition. On a 100-year time frame, CH4 has a global warming potential (GWP) 23 times that of CO2, and N2O has a GWP 296 times that of CO2. The total GWP impact (2000 vs. 1980) of shifting to predominantly mid-season paddy drainage was -0.138 Pg CO2-equiv yr−1 from methane, +0.077 Pg CO2-equiv yr−1 from nitrous oxide and +0.0024 Pg CO2 yr−1 from soil C loss, for a total GWP impact of -0.059 Pg CO2-equiv yr−1 . The results imply that more than half of the GWP benefit of decreased CH4 emissions was offset, primarily by increases in N2O emissions, and to a small degree by soil C loss

Culturable prokaryotic diversity of deep, gas hydrate sediments: First use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG)

Deep subseafloor sediments may contain depressurization-sensitive, anaerobic, piezophilic prokaryotes. To test this we developed the DeepIsoBUG system, which when coupled with the HYACINTH pressure-retaining drilling and core storage system and the PRESS core cutting and processing system, enables deep sediments to be handled without depressurization (up to 25 MPa) and anaerobic prokaryotic enrichments and isolation to be conducted up to 100 MPa. Here, we describe the system and its first use with subsurface gas hydrate sediments from the Indian Continental Shelf, Cascadia Margin and Gulf of Mexico. Generally, highest cell concentrations in enrichments occurred close to in situ pressures (14 MPa) in a variety of media, although growth continued up to at least 80 MPa. Predominant sequences in enrichments were Carnobacterium, Clostridium, Marinilactibacillus and Pseudomonas, plus Acetobacterium and Bacteroidetes in Indian samples, largely independent of media and pressures. Related 16S rRNA gene sequences for all of these Bacteria have been detected in deep, subsurface environments, although isolated strains were piezotolerant, being able to grow at atmospheric pressure. Only the Clostridium and Acetobacterium were obligate anaerobes. No Archaea were enriched. It may be that these sediment samples were not deep enough (total depth 1126–1527 m) to obtain obligate piezophiles

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments

Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites (Brightlingsea [BR], Alresford [AR] and Hythe [HY]) along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridisation, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2–8 × 107 16S rRNA gene copies cm−3) than the high-salinity marine sites from BR and AR (2 × 104–2 × 107 and 4 × 106–2 × 107 16S rRNA gene copies cm−3, respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the ‘Bathyarchaeota’ (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only ‘marine’ group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

Genetic basis of hyperlysinemia

Background: Hyperlysinemia is an autosomal recessive inborn error of L-lysine degradation. To date only one causal mutation in the AASS gene encoding aminoadipic semialdehyde synthase has been reported. We aimed to better define the genetic basis of hyperlysinemia. Methods. We collected the clinical, biochemical and molecular data in a cohort of 8 hyperlysinemia patients with distinct neurological features. Results: We found novel causal mutations in AASS in all affected individuals, including 4 missense mutations, 2 deletions and 1 duplication. In two patients originating from one family, the hyperlysinemia was caused by a contiguous gene deletion syndrome affecting AASS and PTPRZ1. Conclusions: Hyperlysinemia is caused by mutations in AASS. As hyperlysinemia is generally considered a benign metabolic variant, the more severe neurological disease course in two patients with a contiguous deletion syndrome may be explained by the additional loss of PTPRZ1. Our findings illustrate the importance of detailed biochemical and genetic studies in any hyperlysinemia patient

Enzymology of the branched-chain amino acid oxidation disorders: the valine pathway

Valine is one of the three branched-chain amino acids which undergoes oxidation within mitochondria. In this paper, we describe the current state of knowledge with respect to the enzymology of the valine oxidation pathway and the different disorders affecting oxidation