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.

Influence of elevated carbon dioxide and temperature on belowground carbon allocation and enzyme activities in tropical flooded soil planted with rice.

Changes in the soil labile carbon fractions and soil biochemical properties to elevated carbon dioxide (CO2) and temperature reflect the changes in the functional capacity of soil ecosystems. The belowground root system and root-derived carbon products are the key factors for the rhizospheric carbon dynamics under elevated CO2 condition. However, the relationship between interactive effects of elevated CO2 and temperature on belowground soil carbon accrual is not very clear. To address this issue, a field experiment was laid out to study the changes of carbon allocation in tropical rice soil (Aeric Endoaquept) under elevated CO2 and elevated CO2 + elevated temperature conditions in open top chambers (OTCs). There were significant increase of root biomass by 39 and 44 % under elevated CO2 and elevated CO2 + temperature compared to ambient condition, respectively. A significant increase (55 %) of total organic carbon in the root exudates under elevated CO2 + temperature was noticed. Carbon dioxide enrichment associated with elevated temperature significantly increased soil labile carbon, microbial biomass carbon, and activities of carbon-transforming enzyme like ß-glucosidase. Highly significant correlations were noticed among the different soil enzymes and soil labile carbon fractions.

Relationship between CH4 and N2O flux from soil and their ambient mixing ratio in a riparian rice-based agroecosystem of tropical region.

Temporal variations of the ambient mixing ratio of greenhouse gas (CH(4) and N(2)O) in a riparian rice-based agro-ecosystem of tropical region were studied during 2005-2006 in coastal Odisha. The endeavour was made with the hypothesis that the ambient mixing ratio of CH(4) and N(2)O depends on the changes in the flux of CH(4) and N(2)O from the rice fields in the riparian rice ecosystems. A higher ambient mixing ratio of CH(4) was recorded during the tillering to grain filling stages of the rice crop, during both dry and wet seasons. The higher ambient mixing ratio of CH(4) during the wet season may attribute to the higher CH(4) emission from the rice field. The average mixing ratio of CH(4) was recorded as 1.84 ± 0.05 ppmv and 1.85 ± 0.06 ppmv during 2005 and 2006, respectively. The ambient CH(4) mixing ratio was recorded negatively correlated with the average ambient temperature. The N(2)O mixing ratio ranged from 261.57 to 399.44 ppbv with an average of 330.57 ppbv during 2005. However, the average mixing ratio of N(2)O was recorded as 318.83 ± 20.00 ppbv during 2006. The N(2)O mixing ratio was recorded to be negatively correlated with rainfall and average ambient temperature. Significant negative correlation (r = -0.209) of N(2)O with sunshine hours may attribute to the photochemical break down of N(2)O. The temporal variation of N(2)O flux from the rice field does not affect the ambient mixing ratio of N(2)O in the same way as in the case of the ambient mixing ratio of CH(4). However, the higher mixing ratio of N(2)O during the fallow period of the post monsoon period may attribute to the N(2)O flux from soil. Results indicate that intensively cultivated coastal ecosystems can be a major source of ambient greenhouse gas.

Nitrous oxide and methane emission from a flooded rice field as influenced by separate and combined application of herbicides bensulfuron methyl and pretilachlor.

Combination of divergent active principles to achieve broad-spectrum control is gaining popularity to manage the weed menace in intensive agriculture. However, such application could have non-target impacts on the soil processes affecting soil ecology and environmental interactions. A field experiment was conducted to investigate the impact of separate and combined applications of herbicides bensulfuron methyl and pretilachlor on the emission of N(2)O and CH(4), and related soil and microbial parameters in a flooded alluvial field planted to rice cv Lalat. Single application of the herbicide bensulfuron methyl or pretilachlor resulted in a significant reduction of N(2)O and CH(4) emissions while the combination of these two herbicides distinctly increased N(2)O and CH(4) emissions. Cumulative N(2)O emissions (kg N(2)O-N) followed the order of bensulfuron methyl (0.35 kg ha(-1))

Interaction effects of elevated CO2 and temperature on microbial biomass and enzyme activities in tropical rice soils.

The impacts of elevated CO(2) and temperature on microbial biomass and soil enzyme activities in four physicochemically different types of tropical rice soils (Aeric Endoaquept, Aeric Tropoaquept, Ultic Haplustalf and Udic Rhodostalf) were investigated in a laboratory incubation study. Soil samples were incubated under 400, 500 and 600 µmol mol(-1) CO(2) concentration at 25°C, 35°C and 45°C for 2 months. Elevated CO(2) significantly increased the mean microbial biomass carbon (MBC) content, across the soils, over control by 6.2%, 38.0% and 49.2% at 400, 500 and 600 µmol mol(-1) CO(2) concentration, respectively. Soil enzyme activities (fluorescein diacetate hydrolase, dehydrogenase, ß-glucosidase, urease, alkaline and acid phosphatases) also increased significantly ranging from 1.3% (urease) to 53.2% (alkaline phosphatase) under high CO(2) in the soils studied. Both MBC and soil enzyme activities were further stimulated at high temperatures suggesting elevated CO(2) and high temperature interaction accelerated the general turnover of the organic C fractions of the soil and through increase in microbially mediated processes.

Dynamics of changes in methanogenesis and associated microflora in a flooded alluvial soil following repeated application of dicyandiamide, a nitrification inhibitor.

Influence of repeated application of the nitrification inhibitor dicyandiamide (DCD), on CH(4) production and associated microflora in a flooded alluvial soil, was investigated in a laboratory incubation study. Application of DCD at the time of soil incubation resulted in a substantial reduction in CH(4) production (31% over that of untreated control). Second repeat application of DCD, on the contrary, annulled the inhibitory effect on CH(4) production, restoring it to the level of unamended soil. Application of the third dose of DCD maintained CH(4) production almost to the same extent as that of second application. The alleviation of the initial inhibitory effect of DCD on CH(4) production was linked to the enhanced degradation of DCD following its repeated application to the flooded soil. Admittedly, abatement of the initial inhibitory effect of DCD on CH(4) production in soil repeatedly amended with DCD was also related to the inhibition of CH(4)-oxidizing bacterial population and noticeable stimulation of heterotrophic bacterial population. Results suggest that repeat application of DCD with fertilizer-N to flooded rice soils might not be effective in controlling CH(4) production under field condition.

Development of methane emission factors for Indian paddy fields and estimation of national methane budget.

A state-wise assessment of methane (CH(4)) budget for Indian paddies, based on a decadal measurement data across India is presented for the calendar year (CY) 1994, the base year for India's Initial National Communication (NATCOM) to the United Nations Framework Convention on Climate Change (UNFCCC), along with national trend from CY 1979 to 2006. The NATCOM CH(4) emission factors (EFs) for Indian paddy cultivation areas, generally having less than 0.7% of soil organic carbon (SOC), have been estimated as 17.48+/-4 g m(-2) for irrigated continuously flooded (IR-CF), 6.95+/-1.86 g m(-2) for rain-fed drought prone (RF-DP), 19+/-6 g m(-2) for rain-fed flood prone (RF-FP) and deep-water (DW), 6.62+/-1.89 g m(-2) for irrigated intermittently flooded single aeration (IR-IF-SA) and 2.01+/-1.49 g m(-2) for IR-IF multiple aeration (MA) paddy water regimes. The state-wise study for 1994 has indicated national CH(4) budget estimate of 4.09+/-1.19 Tg y(-1) and the trend from 1979 to 2006 was in the range of 3.62+/-1 to 4.09+/-1.19 Tg y(-1). Four higher emitting or "hot spot" states (West Bengal, Bihar, Madhya Pradesh and Uttar Pradesh) have accounted for 53.9% of total CH(4) emission with RF-FP paddy water regime as the major contributor. CH(4) emissions were enhanced by factors such as SOC ( approximately 1.5 times due to increase in SOC by approximately 1.8 times), paddy cultivars (approximately 1.5 times), age of seedlings (approximately 1.4 times), and seasons (approximately 1.8 times in Kharif or monsoon than in Rabi or winter season).

Methane oxidation in an intensively cropped tropical rice field soil under long-term application of organic and mineral fertilizers.

Methane (CH4) oxidation is the only known biological sink process for mitigating atmospheric and terrestrial emissions of CH4, a major greenhouse gas. Methane oxidation in an alluvial soil planted to rice (Oryza sativa L.) under long-term application of organic (compost with a C/N ratio of 21.71), and mineral fertilizers was measured in a field-cum-laboratory incubation study. Oxidation rates were quantified in terms of decrease in the concentration of CH4 in the headspace of incubation vessels and expressed as half-life (t(1)2) values. Methane oxidation rates significantly differed among the treatments and growth stages of the rice crop. Methane oxidation rates were high at the maximum tillering and maturity stages, whereas they were low at grain-filling stage. Methane oxidation was low (t(1)2) = 15.76 d) when provided with low concentration of CH4. On the contrary, high concentration of CH4 resulted in faster oxidation (t(1)2) = 6.67 d), suggesting the predominance of "low affinity oxidation" in rice fields. Methane oxidation was stimulated following the application of mineral fertilizers or compost implicating nutrient limitation as one of the factors affecting the process. Combined application of compost and mineral fertilizer, however, inhibited CH4 oxidation probably due to N immobilization by the added compost. The positive effect of mineral fertilizer on CH4 oxidation rate was evident only at high CH4 concentration (t(1)2 = 4.80 d), while at low CH4 concentration their was considerable suppression (t(1) = 17.60 d). Further research may reveal that long-term application of fertilizers, organic or inorganic, may not inhibit CH4 oxidation.

Butachlor inhibits production and oxidation of methane in tropical rice soils under flooded condition.

In laboratory incubation experiments, application of a commercial formulation of the herbicide butachlor (N-butoxymethyl-2-chloro-2',6'-diethyl acetanilide) to three tropical rice soils, widely differing in their physicochemical characteristics, under flooded condition inhibited methane (CH4) production. The inhibitory effect was concentration dependent and most remarkable in the alluvial soil. Thus, following application of butachlor at 5, 10, 50 and 100 microg g(-1) soil, respectively, cumulative CH4 production in the alluvial soil was inhibited by 15%, 31%, 91% and 98% over unamended control. Since CH4 production was less pronounced in the sandy loam and acid sulfate soil, the impact of amendment with butchalor, albeit inhibitory, was less extensive than the alluvial soil. Inhibition of CH4 production in butachlor-amended alluvial soil was related to the prevention in the drop in redox potential as well as low methanogenic bacterial population especially at high concentrations of butachlor. CH4 oxidation was also inhibited in butachlor-amended alluvial soil with the inhibitory effect being more prevalent under flooded condition. Inhibition in CH4 oxidation was related to a reduction in the population of soluble methane monooxygenase producing methanotrophs. Results demonstrate that butachlor, a commonly used herbicide in rice cultivation, even at very low concentrations can affect CH4 production and its oxidation, thereby influencing the biogeochemical cycle of CH4 in flooded rice soils.

Influence of salinity on methanogenesis and associated microflora in tropical rice soils.

In a laboratory incubation study, methane (CH4) production in two saline soils and a nonsaline soil sample was investigated under flooded conditions. Mean CH4 production was remarkable (630.86 ng CH4/g) in nonsaline alluvial soil, but low (12.97 ng CH4/g) in acid sulfate saline (Pokkali) soil which was attributed to the high sulfate content of the later. CH4 production was also low in the coastal saline (Canning) soil (142.36 ng CH4/g) but increased upon leaching the soil of its salt content. Addition of salts to the nonsaline alluvial soil at 4, 8, 16 and 20 dS/m progressively decreased CH4 production. The inhibition of CH4 production was related to low microbial activities as reflected by decreased microbial biomass C and low soil microbial population including that of methanogens.

Influence of heavy metals on methane oxidation in tropical rice soils.

In a laboratory incubation study, the effect of select heavy metals on methane (CH4) oxidation in two rice soils was investigated under two moisture regimes. Heavy metals differed in their effect on CH4 oxidation in both soils under the two water regimes. Cr significantly inhibited CH4 oxidation in the alluvial soil at 60% moisture holding capacity, while Cu stimulated the process. On the contrary, Zn inhibited CH4 oxidation in both alluvial and laterite soils only under flooded conditions. Application of rice straw alleviated the inhibitory effect of heavy metals on CH4 oxidation and CO2 production. Inhibition of CH4 oxidation in the alluvial soil was related to the methanotrophic bacterial population in Cr- and Zn-amended alluvial soil.

Effects of heavy metals on methane production in tropical rice soils.

In a laboratory incubation study, the effect of select heavy metals on methane (CH(4)) production in three rice soils was investigated under flooded conditions. Heavy metals behaved differently in their effect on methanogenesis in different soils and methane-producing bacteria. Cd, Cu, and Pb inhibited CH(4) production in all the soils. Zn stimulated CH(4) production in the alluvial soil, but inhibited it in laterite and acid sulfate soils. Cr effectively inhibited CH(4) production in the alluvial soil, but stimulated it in laterite and acid sulfate soils. The stimulatory effect of Zn and the inhibitory effect of Cr on methanogenesis in alluvial soil were attributed to their stimulation or inhibition of methanogenic bacterial population.

Novel polypeptides induced by the insecticide lindane (gamma-hexachlorocyclohexane) are required for its biodegradation by a Sphingomonas paucimobilis strain.

When exposed to the potent insecticide gamma-hexachlorocyclohexane or lindane, a Sphingomonas paucimobilis strain rapidly synthesized 7 novel polypeptides and concomitantly gained the ability to degrade lindane. Synthesis of these proteins was switched-off subsequent to the disappearance of lindane from the medium. Treatments which induced the synthesis of identical proteins also conferred on cells the ability to degrade lindane. In contrast, cells blocked in protein synthesis could not be induced to degrade lindane. The close correspondence observed between expression of lindane-induced proteins and gamma-hexachlorocyclohexane catabolism strongly implicates these novel proteins in lindane biodegradation.

Effect of herbicides on nitrogen fixation (C2H2 reduction) associated with rice rhizosphere.

In a field study nitrogenase activity associated with rice rhizosphere was differently influenced by the applied herbicides. Pretilachlor at two application levels had no effect on nitrogenase activity while butachlor and benthiocarb exerted marginal stimulation. Cinmethylin consistently stimulated nitrogenase activity throughout the plant growth period. Anilofos when applied singly had no substantial effect on nitrogenase activity but in combination with 2,4-D the activity was enhanced. Populations of anaerobic nitrogen-fixing bacteria and Azospirillum sp. and Azotobacter sp. were stimulated in such a combination.