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

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.

Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia

“…Although the sampling sites are characterized by even climatic conditions, this trend can be further substantiated, documenting high-resolution short-term temporal dynamics of the bacterial community composition in future studies. Accordingly, the bacterial community composition, including the methanotrophs, can be profoundly influenced by the soil physico-chemical parameters and land use [25,[68][69][70][71], also shown here (Fig. 3), with land use exerting a stronger impact specifically on the methanotrophs [72].…”

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

“…Aerobic methanotrophs use CH 4 for both carbon and energy requirements, and key representatives in soil belong to the type I Gammaproteobacteria family Methylococcaceae, type II Alphaproteobacteria families Methylocystaceae and Beijerinckiaceae, and Methylacidiphilaceae of the Verrucomicrobia (13). Soil pH is one of many factors influencing methanotroph activity, and type I and type II methanotrophs can dominate activity in neutral and acidic pH soils, respectively (18). In addition, a wide variety of nonmethanotrophic methylotrophs utilize methanol produced and excreted by methanotrophs, and together methanotrophic and other methylotrophic…”

Asymmetric response of soil methane uptake rate to land degradation and restoration: Data synthesis

“…Meanwhile, soil BD was significantly increased by land degradation and decreased by land restoration (Figure 1), and hence the response of soil CH 4 uptake to land degradation and restoration was negative and positive to some levels, respectively. Soil pH has been regarded as one of the main environmental factors to affect soil CH 4 uptake (Lafuente et al., 2019; Zhao, Cai, & Jia, 2020). The relationships between the response of soil CH 4 uptake and soil pH under land degradation and restoration were both negative (Figure 6c).…”