Structure, function and resilience to desiccation of methanogenic microbial communities in temporarily inundated soils of the Amazon rainforest (Cunia Reserve, Rondonia)

Abstract

Summary The floodplain of the Amazon River is a large source for the greenhouse gas methane, but the soil microbial communities and processes involved are little known. We studied the structure and function of the methanogenic microbial communities in soils across different inundation regimes in the Cunia Reserve, encompassing nonflooded forest soil (dry forest), occasionally flooded Igapo soils (dry Igapo), long time flooded Igapo soils (wet Igapo) and sediments from Igarape streams (Igarape). We also investigated a Transect (four sites) from the water shoreline into the dry forest. The potential and resilience of the CH4 production process were studied in the original soil samples upon anaerobic incubation and again after artificial desiccation and rewetting. Bacterial and archaeal 16S rRNA genes and methanogenic mcrA were always present in the soils, except in dry forest soils where mcrA increased only upon anaerobic incubation. NMDS analysis showed a clear effect of desiccation and rewetting treatments on both bacterial and archaeal communities. However, the effects of the different sites were less pronounced, with the exception of Igarape. After anaerobic incubation, methanogenic taxa became more abundant among the Archaea, while there was only little change among the Bacteria. Contribution of hydrogenotrophic methanogenesis was usually around 40%. After desiccation and rewetting, we found that Firmicutes, Methanocellales and Methanosarcinaceae became the dominant taxa, but rates and pathways of CH4 production stayed similar. Such change was also observed in soils from the Transects. The results indicate that microbial community structures of Amazonian soils will in general be strongly affected by flooding and drainage events, while differences between specific field sites will be comparatively minor.

Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments

“…It is likely that those microbes may present protection against oxidative stress, as already reported for methanogens (Angle et al, 2017; Lyu, Shao Akinyemi, & Whitman, 2018). According to Hernández et al (2019), the abundance of methanogens could be an indication of the flooding history of the Amazon floodplain. In a microcosm experiment, the authors observed the survival of the methanogenic populations to short, but not to long periods of desiccation.…”

“…A few studies have attempted to describe these communities (Conrad, Klose, Claus & Enrich-Prast, 2010; Conrad et al, 2011; Ji et al, 2016; Sawakuchi et al, 2016). Recently, using a microcosm experiment, Hernández et al (2019) showed that methanogens are present in high abundance in Amazonian floodplain sediments regardless of the incubation conditions, while their abundance in upland forest soils increases only upon anaerobic incubation. Nevertheless, to date, there was no effort to characterise the seasonal dynamics of the methanogenic and methanotrophic groups in situ .…”

Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation

“…Thus, we expected that more frequently drained soil environments exhibit smaller population changes than permanently flooded environments upon drainage or permanently dry environments upon flooding. We distinguished four categories: (1) permanently flooded lake sediments [ 69 , 70 ]; (2) annually flooded rice field soils or river floodplains [ 71 , 72 , 73 ]; (3) irregularly flooded soils (rice crop rotation) [ 74 , 75 , 76 ]; and (4) upland soils (including desert soils) [ 39 , 62 , 72 , 73 , 74 , 77 ]. We checked the potential of CH 4 production, the abundance of bacterial and archaeal microbiota, and the community composition of methanogenic archaea and (fermenting) bacteria.…”

“…The relative insensitivity of the methanogens to O 2 is consistent with the observations that dry and occasionally flooded soil environments were dominated by methanogens belonging to the genera Methanosarcina and Methanocella , which both belong to the O 2 -tolerant class II [ 68 ]. Methanosarcina and Methanocella species also increased in relative abundance after desiccation of permanently or frequently flooded soil environments, which, however, also contained O 2 -sensitive methanogens of class I (e.g., Methanosaetaceae , Methanobacteriales ) [ 71 , 73 ]. Hence, the abundance and composition of methanogen communities was consistent with theoretical expectations concerning O 2 sensitivity.…”

Methane, Microbes and Models in Amazonian Floodplains: State of the Art and Perspectives

“…Alluvial plains are environments adapted to variations in water level, and it seems that microbial communities can be adapted to these fluctuations and remain in a state of latency until the next flood. Hernández et al [61] demonstrated that in Amazon forest soils the propensity to produce CH 4 (at the laboratory) was best observed in relation to the duration of the lag phase. Soils that were never flooded (dry forest) presented this phase for a longer time than sites that were permanently flooded.…”