Abstract
Abstract. 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.
Highlights
Rice paddy fields are one of the major sources of the potent greenhouse gas methane, contributing approximately 10 %–25 % of global methane emissions (Kögel-Knabner et al, 2010)
During SIP microcosm’s incubation, a fraction of 13C-CH4 was converted to soil organic matter (SOM) by MOB through cell biomass synthesis, and it was assessed as the changes in the 13C atom percent of the soil Total organic carbon (TOC)
The lowered methane oxidation rate following fertilization might suffer from decreased oxygen concentration at the later stage of the microcosm incubation, especially for the low-pH soil incubations that lasted more than 30 d
Summary
Rice paddy fields are one of the major sources of the potent greenhouse gas methane, contributing approximately 10 %–25 % of global methane emissions (Kögel-Knabner et al, 2010). Despite coexistence of type I and II methanotrophs in these ecosystems, their activity and contribution to methane oxidation has often been observed to vary largely depending on different environmental conditions and the predominant activity of either type I or type II methanotrophs (Chen et al, 2008a; Daebeler et al, 2014; He et al, 2012; Liebner and Wagner, 2007; Lin et al, 2004) This might be due to some major physiological differences that exist between these two groups. Adaptation to slightly acidic pH values (growth optima 5.0–6.0) is characteristic for type IIb (Methylocella and Methylocapsa) and some Methylocystis type Ia MOB strains (Belova et al, 2013; Dedysh et al, 2000, 2007) These and other physiological traits of type I and II methanotrophs may be important in partitioning their specialized niches in different ecosystems
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