Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides

Abstract

Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of CH DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.

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

“…The high-throughput sequencing of 16S rRNA genes resulted in a considerable number of unclassified Methylococcaceae after amended 13 CH 4 incubation. This observation was similar to our previous finding in another mangrove forest [19] in which unclassified Methylococcaceae made up more than 50% of the sequences at all sites. The mangrove forests in this present study were spatially connected to the previously-analyzed mangrove forests, so the unclassified methanotrophs in the upstream and downstream sites may also be novel methanotrophs that are important to CH 4 oxidation in the mangrove forest ecosystems [19].…”

“…In addition, the~10% of unclassified Type Ia methanotrophs at the downstream site increased to a relative abundance of 20% after amended CH 4 incubation. Because a similar observation was reported in the tidal-influenced mangrove soil in our previous study [19], the unclassified methanotrophs in this study may also be new methanotrophic bacteria adapted to highly saline environments.…”

“…In addition, Type Ia Methylobacter was the dominant methanotrophic bacterium in both upstream and downstream sites. However, results from this study and our previous study located between the two mangrove sites in the present study [19] show that there is no transitional change in compositions. In our previous study sites, Type Ia Methylosarcina and uncultured Type Ib methanotrophs in the deep-sea-5 cluster were the dominant genera and shared >50% of the relative abundance.…”

“…Almost all of these above mentioned methanotrophs possess the particulate methane monooxygenase (pMMO), which catalyzes CH 4 oxidation [ 14 , 15 ]. By using functional gene biomarkers (i.e., pmoA ), previous studies found that Type II methanotrophs often dominate CH 4 oxidation in freshwater ecosystems such as rice paddies, while Type I methanotrophs are mostly found in saline water ecosystems such as hypersaline lakes, estuaries, and coastal wetlands [ 16 , 17 , 18 , 19 , 20 , 21 ]. Recent studies further revealed niche differentiation in Type I methanotrophs at a finer resolution, demonstrating that Type Ia methanotrophs have a high tolerance to salinity (i.e., >1% NaCl), while Type Ib methanotrophs do not [ 22 , 23 ].…”

Methanotrophic Community Detected by DNA-SIP at Bertioga’s Mangrove Area, Southeast Brazil

“…Even though coastal marsh ecosystems are considered net sinks for carbon sequestration, spatial and temporal gradients promote a wide range of biogeochemical and anaerobic conditions, making them important sources of greenhouse gases to the atmosphere [4]. The prevalence of anaerobic conditions partnered with the high organic matter content favors methanogenesis by archaea.…”