Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane

Abstract

Agriculture has marked impacts on the production of carbon dioxide (CO 2 ) and consumption of methane (CH 4 ) by microbial communities in upland soils-Earth's largest biological sink for atmospheric CH 4 . To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, we conducted molecular surveys of CH 4 -oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH 4 and CO 2 at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH 4 consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH 4 consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH 4 consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO 2 emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH 4 oxidation, as compared with processes driven by widely distributed metabolic processes, like CO 2 production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.

Microbial minorities modulate methane consumption through niche partitioning

“…Microbial BEF studies use DNA-based molecular diversity assessment techniques bearing no diagnostic means to determine which of the species is contributing to the observed function (Bell et al, 2009). Positive BEF relationships are most often observed with narrow functions (e.g., methane oxidation (Levine et al, 2011), polymer degradation (Wohl et al, 2004;Peter et al, 2011) or pesticide degradation (Monard et al, 2011)), where species are brought together to determine which all contribute to the specific function in the respective experimental setup. Hence, BEF studies in microbial ecosystems where species that are actively contributing to ecosystem functioning cannot be pinpointed will give biased results, often concluding functional redundancy to be occurring which actually is either a lack of niche heterogeneity or cumulative counting of 'seed bank' species that are not actively contributing to the measured function.…”

“…chemical process catalyzed. Recently, a strong link between diversity of microbes consuming atmospheric methane and soil methane uptake was demonstrated (Levine et al, 2011) for high-affinity methanotrophs in upland soils. In combination with our results on low-affinity MOB in wetland habitats, it can be concluded that microbial diversity and microbial traits are important regulating factors in the global methane budget.…”

Greenhouse gas emissions from a soil cultivated with wheat (Triticum spp. L.) and amended with castor bean (Ricinus communis L.) or Jatropha curcas L. seed cake: A greenhouse experiment

“…An agricultural soil is often a sink for CH 4 (Levine et al 2011), but not in the first weeks of this experiment. Organic material application and plant growth might stimulate CH 4 emissions from soil.…”

Microbial biomass in sediments affects greenhouse gas effluxes in Poyang Lake in China

“…It should be noted that we examined anaerobic CH 4 oxidation in our study which was often ignored in CH 4 oxidation. The PLFAs method cannot differentiate the methanogenic biomass, but previous studies found that CH 4 efflux was positively correlated with methanogenic biomass (Radl et al 2007;Gutierrez et al 2013;Narvaez et al 2013;Urbanov a et al 2013) but negatively with methanotrophic biomass (Levine et al 2011;Nazaries et al 2013). In fact, the CH 4 efflux at the airÀwater interface is the balance between CH 4 production in the sediment and CH 4 oxidation in the process of transport from the sediment to the atmosphere.…”

“…For example, Urbanov a et al (2013) found that CH 4 efflux was positively associated with methanogenic biomass in Mountain Peatlands, Central Europe. Levine et al (2011) reported that CH 4 efflux was negatively correlated with methanotrophic biomass in agricultural soil. In addition, Balser and Firestone (2005) have reported that the biomass of gram-negative bacteria was specifically related to the N 2 O efflux in an annual grassland and a mixedconifer forest in California.…”