Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities

Abstract

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH 4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH 4 emissions across floodplain areas. Here, we report the in situ composition of CH 4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH 4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH 4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH 4 emissions in the region.

Active methane processing microbes and the disproportionate role of NC10 phylum in methane mitigation in Amazonian floodplains

“…The results of these ecological metrics were not generalizable over all soil layers, sampling sites and seasons. Gontijo et al (2021) also observed resistance of methanogenic and methanotrophic microbial communities inhabiting floodplain soils to dramatic environmental changes that occur between seasons in white (Amazonas river) and clear (Tapajós river) water floodplains in the Amazon. However, variations in both occurrence and abundance of methanogenic and methanotrophic microbial taxa between soil layers, FOR and TFS sites, and non-flooded and flooded periods, can be related to metabolic flexibility and physiological adaptations of the microorganisms that may allow them to endure under changing environmental conditions (Ye et al 2018).…”

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities

“…Members of both the Methanoperedenaceae and Methylomirabilaceae families have been previously co-enriched ( Raghoebarsing et al, 2006 ), and in the absence of ammonia, which would inhibit anaerobic ammonia oxidation (anammox) activity and NO 2 – consumption, the dominant microbial consortium in an anaerobic bioreactor fed with CH 4 and NO 3 – was that of the archaeon Candidatus Methanoperdens nitroreducens and the bacterium Candidatus Methylomirabilis oxyfera ( Haroon et al, 2013 ), which were also detected in this floodplain ( Gabriel et al, 2020 ; Bento et al, 2021 ; Gontijo et al, 2021 ).…”

“…− was that of the archaeon Candidatus Methanoperdens nitroreducens and the bacterium Candidatus Methylomirabilis oxyfera (Haroon et al, 2013), which were also detected in this floodplain (Gabriel et al, 2020;Bento et al, 2021;Gontijo et al, 2021).…”

Metagenomes from Eastern Brazilian Amazonian Floodplains in the Wet and Dry Seasons

“…Floodplains and wetlands constitute 14% of the total area of the Amazon basin ( 1 ) and are considered the largest natural geographic source of methane (CH 4 ) in the tropics ( 2 ). Therefore, several studies have investigated the CH 4 -producing and -consuming microbial communities in these sediments and their responses to a range of environmental factors using 16S rRNA amplicon sequencing ( 3 – 5 ). However, their overall microbial taxonomic and functional diversity remains little explored.…”

“…Metagenomic libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, Inc., Ipswich, MA) and paired-end sequenced (2 × 150 bp) on an Illumina HiSeq 2500 instrument (Illumina, Inc., San Diego, CA) at Novogene Co., Ltd. (Beijing, China). Detailed information about the study sites, sampling, sediment physicochemical properties, and DNA extraction and quantification have been described previously ( 5 ).…”