Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact

Abstract

Lonar Lake is a unique saline and alkaline ecosystem formed by meteor impact in the Deccan basalts in India around 52 000 years ago. To investigate the role of methylotrophy in the cycling of carbon in this unusual environment, stable-isotope probing (SIP) was carried out using the onecarbon compounds methane, methanol and methylamine. Denaturing gradient gel electrophoresis fingerprinting analyses performed with heavy 13 C-labelled DNA retrieved from sediment microcosms confirmed the enrichment and labelling of active methylotrophic communities. Clone libraries were constructed using PCR primers targeting 16S rRNA genes and functional genes. Methylomicrobium, Methylophaga and Bacillus spp. were identified as the predominant active methylotrophs in methane, methanol and methylamine SIP microcosms, respectively. Absence of mauA gene amplification in the methylamine SIP heavy fraction also indicated that methylamine metabolism in Lonar Lake sediments may not be mediated by the methylamine dehydrogenase enzyme pathway. Many gene sequences retrieved in this study were not affiliated with extant methanotrophs or methylotrophs. These sequences may represent hitherto uncharacterized novel methylotrophs or heterotrophic organisms that may have been cross-feeding on methylotrophic metabolites or biomass. This study represents an essential first step towards understanding the relevance of methylotrophy in the soda lake sediments of an unusual impact crater structure.

Targeted metagenomics of active microbial populations with stable-isotope probing

“…Examples demonstrating the wide-range of applications of DNA-SIP include methane assimilation in landfill cover soil [13] and peatlands [14], methanol 70 assimilation in coastal sea water [15] and soda lake sediments [16] studies have focused on pmoA and mmoX for methanotrophs [13], mxaF and mauA for methylotrophs [15], arrA for bacterial respiration of As(V) [17], nirK and nirS for denitrifiers Despite the widespread use of DNA-SIP for targeting active microorganisms, the limitations of this method include the potential for cross-feeding of label from primary 85 consumers to other microbes, low recovery of heavy DNA, non-availability and high costs associated with the purchase of isotopically labeled substrates, and the requirement for relatively high concentrations of substrate for efficient labeling of DNA [35]. In order to help circumvent these weaknesses, careful experimental design with different incubation times can help detect and minimize cross-feeding [36,37].…”

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions

“…Because methanol is produced in the periplasm and therefore can diffuse out of the cell (29), it is reasonable to suggest that methanol might be cross-fed to nonmethanotrophic methylotrophs involved in community-based methane utilization (18,30,31). However, Kalyuzhnaya and colleagues (32) have demonstrated a novel form of fermentation-based methanotrophy that releases compounds such as formate, acetate, or hydrogen as additional possible carbon and energy sources for nonmethanotrophic heterotrophs.…”

Phylogenetic Study of Methanol Oxidizers from Chilika-Lake Sediments Using Genomic and Metagenomic Approaches

“…Chilika, slowly but steadily transforming into a lagoon, is an attractive and unparalleled fusion of marine, river, and estuarine habitat that supports unique assemblage of marine, brackish water and freshwater microbes [2], presents a challenge to physiologists and biochemists [3]. Biological effects of siltation and salinity, overall biodiversity loss due to the changes in phytoplankton communities, and degradation of lake ecosystem owing to the freshwater invasive species thereby declining the overall productivity, have been profoundly documented in recent times [2,3,5,7,8].…”

“…Due to their specific properties, for instance, haloalkaliphilic methanotrophs could be of use in modern biotechnology [4]. Methylotrophs have been reported from diverse aquatic niches, such as, Washington Lake, USA [5], Mono Lake, USA [6], Lonar Lake, India [7], Weyerhaeuser [8], Warm pool, China [9], Colne Estuary, UK [10], Brackish marsh, Portugal [11], and as a marine symbiont [12]. There is increasing evidence for the striving methanotrophs in various ecogeographical regions including the saline and alkaline aquatic environments.…”