Niche Differentiation of Active Methane-Oxidizing Bacteria in Estuarine Mangrove Forest Soils in Taiwan

Abstract

Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO₂ into plant biomass. These forests often experience various levels of inundation and play an important role in CH₄ emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly ¹³C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10-15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. ¹³C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils.

Keywords: 16S rRNA gene; DNA stable isotope probing; aerobic methane oxidation; coastal mangrove soil; methanotrophs; pmoA gene.

Figure 1

Map of studied mangrove sites (black stars) in the Tamsui estuary, Taiwan. The grey star indicates the site from a previous study [19].

Figure 2

CH₄ oxidation potential in the studied upstream (Guandu) and downstream (Bali) mangrove soils. Bars with the same letters are not significantly different at p = 0.05 based on Tukey’s honestly significant difference (HSD) comparison.

Figure 3

Number of pmoA copies in the studied upstream (Guandu) and downstream (Bali) mangrove soils. Bars with the same letters are not significantly different at p = 0.05 based on Tukey’s HSD comparison. The capital letters indicate the statistical results from pmoA genes before and after incubation at one site, and the lower case letters indicate the statistical results from pmoA genes between the sites and seasons in the fresh or incubated soils.

Figure 4

Relative abundance of the pmoA gene from ¹²CH₄- and ¹³CH₄-incubated soils in upstream (Guandu) and downstream (Bali) mangrove forests in winter (a,c) and in summer (b,d) at different density fractions (fractions 2–14).

Figure 5

The relative abundance of methanotrophic communities identified with the pmoA genes in the average of triplicate fresh soils under field conditions and in ¹³C-DNA from ¹³CH₄-enriched microcosms of (a) upstream (Guandu) and (b) downstream (Bali) mangrove forest soils, Taipei, Taiwan. Two regional peak fractions of pmoA genes were found in the ¹³CH₄-amended Bali mangrove soils in one season (Figure 4), so the pmoA genes in both fractions were sequenced to identify the potential active methanotrophs.

Figure 6

The relative abundance of methanotrophic communities identified with the 16S rRNA genes in fresh and ¹³CH₄-enriched (a) upstream (Guandu) and (b) downstream (Bali) mangrove forest soils, Taipei, Taiwan. Two regional peak fractions of pmoA genes were found in the ¹³CH₄-amended Bali mangrove soils in one season (Figure 4), so the 16S rRNA in both fractions were sequenced to identify the potential active methanotrophs.

Figure 7

Canonical correspondence analysis (CCA) between methanotrophs and physiochemical properties in mangrove forests in Tamsui, Taipei, Taiwan. (S_bOC: soluble organic C; S_bON: soluble organic N; NH₄⁺: ammonium; NO₃^-: nitrate; TDN: total dissolved N; PMN: potential mineralizable N; TOC: total organic C; TN: total N.).