Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH4 ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions.

/pdf/higher-yields-and-lower-methane-emissions-with-new-rice-10cyoxszds.pdf

Higher yields and lower methane emissions with new rice cultivars.

The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2. Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

https://www.pnas.org/content/pnas/116/17/8515.full.pdf

Widespread soil bacterium that oxidizes atmospheric methane.

Microbiological and environmental significance of metal-dependent anaerobic oxidation of methane.

Silver nanoparticles (AgNPs) are the most common materials in nanotechnology-based consumer products globally. Because of the wide application of AgNPs, their potential environmental impact is currently a highly topical focus of concern. Nitrification is one of the processes in the nitrogen cycle most susceptible to AgNPs but the specific effects of AgNPs on nitrification in aquatic environments are not well understood. We report the influence of AgNPs on nitrification and associated nitrous oxide (N2O) production in estuarine sediments. AgNPs inhibited nitrification rates, which decreased exponentially with increasing AgNP concentrations. The response of nitrifier N2O production to AgNPs exhibited low-dose stimulation ( 100% at low doses of AgNPs. This result was confirmed by metatranscriptome studies showing up-regulation of nitric oxide reductase (norQ) gene expression in the low-dose treatment. Isotopomer analysis revealed that hydroxylamine oxidation was the main N2O production pathway, and its contribution to N2O emission was enhanced when exposed to low-dose AgNPs. This study highlights the molecular underpinnings of the effects of AgNPs on nitrification activity and demonstrates that the release of AgNPs into the environment should be controlled because they interfere with nitrifying communities and stimulate N2O emission.

Effects of silver nanoparticles on nitrification and associated nitrous oxide production in aquatic environments

Straw incorporation is a common long-term practice to improve soil fertility in croplands worldwide. However, straw amendments often increase methane (CH4) emissions from rice paddies, one of the main sources of anthropogenic CH4. Intergovernmental Panel on Climate Change (IPCC) methodologies to estimate CH4 emissions from rice agriculture assume that the effect of straw addition remains constant over time. Here, we show through a series of experiments and meta-analysis that these CH4 emissions acclimate. Effects of long-term (>5 years) straw application on CH4 emissions were, on average, 48% lower than IPCC estimates. Long-term straw incorporation increased soil methanotrophic abundance and rice root size, suggesting an increase in CH4 oxidation rates through improved O2 transport into the rhizosphere. Our results suggest that recent model projections may have overestimated CH4 emissions from rice agriculture and that CH4 emission estimates can be improved by considering the duration of straw incorporation and other management practices.

Acclimation of methane emissions from rice paddy fields to straw addition

Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this 'high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane.

/pdf/conventional-methanotrophs-are-responsible-for-atmospheric-1k83eeufmt.pdf

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils.

DNA-based stable isotope probing (DNA-SIP) was employed to establish direct link between methane oxidation activity and the taxonomic identity of active methanotrophs in three rice field soils from Jian-San-Jiang (one baijiang origin soil, JB and one meadow origin soil, JM) and Qing-An (meadow origin soil, QA) districts in Northeastern China. Following microcosm incubation under 1% v/v13CH4 condition, soil organic 13C atom percent significantly increased from background 1.08 to 1.21% in average, indicating the biomass synthesis supported by methanotrophy. Real-time PCR analysis of methanotroph-specific biomarker pmoA genes of the buoyant density for DNA gradient, following the ultracentrifugation of the total DNA extracted from SIP microcosms, indicated an enrichment of methanotroph genomes in 13C-labeled DNA. It suggested propagation of microbial methane oxidizers in soils. High-throughput sequencing of 16S rRNA and pmoA genes from 13C-labeled DNA further revealed a diverse guild of both type I and II methanotrophs in all three soils. Specifically, Methylobacter-affiliated type I methanotrophs dominated the methanotrophic activity in JB and JM soils, whereas Methylocystis-affiliated type II methanotrophs dominated QA soil. This implied the physiological diversification of soil methanotrophs that might be due to constant environmental fluctuations in paddies.

Stable isotope probing of active methane oxidizers in rice field soils from cold regions

. Soil pH is considered one of the main determinants of the
assembly of globally distributed microorganisms that catalyze the
biogeochemical cycles of carbon (C) and nitrogen (N). However, direct
evidence for niche specialization of microorganisms in association with soil
pH is still lacking. Using methane-oxidizing bacteria (methanotrophs) as a
model system of C cycling, we show that pH is potentially the key driving
force selecting for canonical γ (type I) and α (type II)
methanotrophs in rice paddy soils. DNA-based stable isotope probing
(DNA-SIP) was combined with high-throughput sequencing to reveal the
taxonomic identities of active methanotrophs in physiochemically contrasting
soils from six different paddy fields across China. Following microcosm
incubation amended with 13CH4 , methane was primarily consumed by Methylocystis-affiliated
type II methanotrophs in soils with a relatively low pH (5.44–6.10), whereas
Methylobacter- or Methylosarcina-affiliated type I methanotrophs dominated methane consumption in soils
with a high pH (7.02–8.02). Consumption of 13CH4 contributed
0.203 % to 1.25 % of soil organic C, but no significant difference was
observed between high-pH and low-pH soils. The fertilization of ammonium
nitrate resulted in no significant changes in the compositions of
 13C -labeled methanotrophs in the soils, although significant inhibition
of methane oxidation activity was consistently observed in low-pH soils.
Mantel analysis further validated that soil pH, rather than other parameters
tested, had significant correlation to the variation in active
methanotrophic compositions across different rice paddy soils. These results
suggest that soil pH might have played a pivotal role in mediating the niche
differentiation of ecologically important aerobic methanotrophs in
terrestrial ecosystems and imply the importance of such niche specialization
in regulating methane emissions in paddy fields following increasingly
intensified input of anthropogenic N fertilizers.

/pdf/the-ph-based-ecological-coherence-of-active-canonical-2lmwjj2kmb.pdf

Yuanfeng Cai

Papers

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils.

Stable isotope probing of active methane oxidizers in rice field soils from cold regions

The pH-based ecological coherence of active canonical methanotrophs in paddy soils