Microbial Involvement in Carbon Transformation via CH4 and CO2 in Saline Sedimentary Pool

Abstract

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Rock samples (W2, W3, and W4) differed in lithology (clayey salt with veins of fibrous salt and lenses of gypsum and anhydrite; siltstone and sandstone; siltstone with veins of fibrous salt and lenses of anhydrite) and the accompanying salt type (spiza salts or green salt). Microbial communities present in the Miocene strata were studied using activity measurements and high throughput sequencing. Biological activity (i.e., carbon dioxide and methane production or methane oxidation) occurred in all of the studied clayey salt and siltstone samples but mainly under water-saturated conditions. Microcosm studies performed at elevated moisture created more convenient conditions for the activity of both methanogenic and methanotrophic microorganisms than the intact sediments. This points to the fact that water activity is an important factor regulating microbial activity in saline subsurface sediments. Generally, respiration was higher in anaerobic conditions and ranged from 36 ± 2 (W2200%t.w.c) to 48 ± 4 (W3200%t.w.c) nmol CO2 gdw−1 day−1. Methanogenic activity was the highest in siltstone and sandstone (W3, 0.025 ± 0.018 nmol CH4 gdw−1 day−1), while aerobic methanotrophic activity was the highest in siltstone with salt and anhydrite (W4, 220 ± 66 nmol CH4 gdw−1 day−1). The relative abundance of CH4-utilizing microorganisms (Methylomicrobium, Methylomonas, Methylocystis) constituted 0.7–3.6% of all taxa. Methanogens were represented by Methanobacterium (0.01–0.5%). The methane-related microbes were accompanied by a significant number of unclassified microorganisms (3–64%) and those of the Bacillus genus (4.5–91%). The stable isotope composition of the CO2 and CH4 trapped in the sediments suggests that methane oxidation could have influenced δ13CCH4, especially in W3 and W4.

Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies

“…Biodiversity analyses of microorganisms inhabiting various extreme environments like coal deposits [1,2,[18][19][20], groundwater [21][22][23], and subsurface petroleum reservoirs [24] have shown that methanotrophs are also a component of the subsurface microbiomes. Our previous research revealed that the Wieliczka Formation is the habitat of a methanotrophically active community [25][26][27]. We hypothesize that the rock surrounding the salt beds may serve as a new source of methanotrophic bacteria capable of efficiently degrading methane, thus with potential biotechnological application.…”

“…4 kg) were extracted from freshly excavated surfaces of Wieliczka Formation sediments, immediately put into sterile plastic containers, and tightly sealed. Samples used for DNA extraction and microbial enrichment were externally sterilized by UV irradiation and flaming as previously described [26,31].…”

“…Enrichment and culture of methanotrophs were performed on the basis of the environmental sample (W4), whose methanotrophic activity we demonstrated in our previous work [26]. The biologically active environmental sample obtained from this incubation was subsequently used for further laboratory analyses.…”

“…The isolation of genomic DNA from samples (environmental sample (W4); environmental sample + medium (preculture) and enrichment culture) followed the procedure described in our previous publication [26]. For this process, rock samples weighing 10 g were aseptically collected from the interior of the clumps.…”

A first insight into the Polish Bochnia Salt Mine metagenome

“…However, none of the previous studies attempted a detailed characterization of the microbial community of the environment. In the only study of Polish salt mines to use next generation sequencing (NGS) to date, Goraj et al ( 2021 ) describe the structure of the microbial community inhabiting halite and its importance for carbon transformation. In contrast, no studies have examined the brines from seepages and outflows in salt mines, nor have they assessed the biotechnological and pharmaceutical potential of the microbiota of Polish salt mines.…”