Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem.

Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.

Mitigating yield-scaled greenhouse gas emissions through combined application of soil amendments: A comparative study between temperate and subtropical rice paddy soils.

Effects of different soil amendments were investigated on methane (CH4) and nitrous oxide (N2O) emissions, global warming potential (GWP) and yield scaled GWPs in paddy soils of Republic of Korea, Japan and Bangladesh. The experimental treatments were NPK only, NPK+fly ash, NPK+silicate slag, NPK+phosphogypsum(PG), NPK+blast furnace slag (BFS), NPK+revolving furnace slag (RFS), NPK+silicate slag (50%)+RFS (50%), NPK+biochar, NPK+biochar+Azolla-cyanobacteria, NPK+silicate slag+Azolla-cyanobacteria, NPK+phosphogypsum (PG)+Azolla-cyanobacteria. The maximum decrease in cumulative seasonal CH4 emissions was recorded 29.7% and 32.6% with Azolla-cyanobacteria plus phospho-gypsum amendments in paddy soils of Japan and Bangladesh respectively, followed by 22.4% and 26.8% reduction with silicate slag plus Azolla-cyanobacteria application. Biochar amendments in paddy soils of Japan and Bangladesh decreased seasonal cumulative N2O emissions by 31.8% and 20.0% respectively, followed by 26.3% and 25.0% reduction with biochar plus Azolla-cyanobacteria amendments. Although seasonal cumulative CH4 emissions were significantly increased by 9.5-14.0% with biochar amendments, however, global warming potentials were decreased by 8.0-12.0% with cyanobacterial inoculation plus biochar amendments. The maximum decrease in GWP was calculated 22.0-30.0% with Azolla-cyanobacteria plus silicate slag amendments. The evolution of greenhouse gases per unit grain yield (yield scaled GWP) was highest in the NPK treatment, which was decreased by 43-50% from the silicate slag and phosphogypsum amendments along with Azolla-cyanobacteria inoculated rice planted soils. Conclusively, it is recommended to incorporate Azolla-cyanobacteria with inorganic and organic amendments for reducing GWP and yield scaled GWP from the rice planted paddy soils of temperate and subtropical countries.

Seasonal changes of CO(2), CH(4) and N(2)O fluxes in relation to land-use change in tropical peatlands located in coastal area of South Kalimantan.

Tropical peatland could be a source of greenhouse gases emission because it contains large amounts of soil carbon and nitrogen. However these emissions are strongly influenced by soil moisture conditions. Tropical climate is characterized typically by wet and dry seasons. Seasonal changes in the emission of carbon dioxide (CO(2)), methane (CH(4)) and nitrous oxide (N(2)O) were investigated over a year at three sites (secondary forest, paddy field and upland field) in the tropical peatland in South Kalimantan, Indonesia. The amount of these gases emitted from the fields varied widely according to the seasonal pattern of precipitation, especially methane emission rates were positively correlated with precipitation. Converting from secondary forest peatland to paddy field tended to increase annual emissions of CO(2) and CH(4) to the atmosphere (from 1.2 to 1.5 kg CO(2)-C m(-2)y(-1) and from 1.2 to 1.9 g CH(4)-C m(-2)y(-1)), while changing land-use from secondary forest to upland tended to decrease these gases emissions (from 1.2 to 1.0 kg CO(2)-C m(-2)y(-1) and from 1.2 to 0.6 g CH(4)-C m(-2)y(-1)), but no clear trend was observed for N(2)O which kept negative value as annual rates at three sites.

Effect of aquatic weeds on methane emission from submerged paddy soil.

Paddy fields are one of the dominant anthropogenic sources of methane emission to the atmosphere, and the main passageway of methane from paddy soil is through the rice plant. However, the effect of aquatic weeds on methane emission from rice paddies has not been properly evaluated yet. Methane emission from weeded pots and unweeded ones with anaerobic paddy soil was measured throughout the period of rice growth. More than double the amount of methane was emitted from weeded pots compared with unweeded ones. Peroxidase activity of rice root was not different between weeded and unweeded pots. However, methanogenic bacteria populations were higher in weeded pots than in unweeded ones, while methane oxidation activity, measured by the propylene oxidation technique, was higher in unweeded pots than in weeded ones. Methane oxidation activity of roots from three typical aquatic weeds in paddy fields, Lipocarpha sp., Rotala indica, and Ludwigia epilobioides, was higher than that of rice plants, while lower stems of these aquatic plants showed similar or lower activity compared with the same areas of rice plants. These results indicate that the role of aquatic weeds in paddy soil in methane emission should not be overlooked in evaluating mitigation options for reducing methane emission from paddy fields.

Interaction between the left-handed Z-DNA and polyamine-2. The crystal structure of the d(CG)3 and spermidine complex.

This paper deals with the crystal structure of d(CG)3-spermidine complex. The DNA fragment, d(CG)3, was crystallized with N-(2-amino-propyl)-1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many intermolecular contacts between d(CG)3 and spermidine, but the binding mode of spermidine to the d(CG)3 molecule is different from that of the d(CG)3 and N-(2-amino-ethyl)-1,4-diamino-butane [PA(24)] complex: a spermidine molecule bound to the d(CG)3 and its symmetrically related neighboring d(CG)3 molecules through the water molecules with hydrogen bonds, while one PA(24) molecule connected directly to one d(CG)3 molecule, but not to its neighboring d(CG)3 molecule. In the crystal, the d(CG)3 molecule was the left-handed Z-form, and three magnesium cations and a sodium cation were observed around the d(CG)3 moiety with different binding modes from the case of the d(CG)3-PA(24) complex.

Polyamine interaction with Z-DNA.

In order to elucidate the detailed Z-DNA interaction with polyamines and also to clarify the mutual molecular recognition between the left-handed helix and the biologically important polyamine molecule, several polyamine-Z-DNA hexamer complexes were crystallized and their crystal structures were determined by X-ray diffraction. The general interaction modes found in these crystal structures were discussed in comparison with those in the complexes between polyamine and the right-handed DNA or RNA.