Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments

Abstract

Soda lakes constitute extreme aquatic ecosystems with remarkably high primary productivity rates, but information on the diversity and activity of methanogens in such environments is sparse. Using 16S rRNA and functional genes, we investigated the diversity of methanogens in the sediments of Lonar Lake, a unique saline and alkaline ecosystem formed by meteorite impact in the Deccan basalts. Although domain and phylum level 16S rRNA gene libraries were dominated by phylotypes related to Halobacteriales, sequences related to potentially novel Archaea within the orders Methanosarcinales and Methanomicrobiales were obtained together with a significant fraction of sequences representing uncultivated Euryarchaeota [Correction added after online publication 16 April 2012: orders 'Methanosarcina and Methanomicrobiaceae' changed to 'Methanosarcinales and Methanomicrobiales']. To identify the active methylotrophic Archaea involved in methanogenesis, mRNA transcripts of mcrA were retrieved from methanol consuming and methane emitting sediment microcosms at two different time points. Reverse-transcription PCR, qPCR, DGGE fingerprint, and clone library analysis showed that the active Archaea were closely related to Methanolobus oregonensis. To our knowledge, this is the first study identifying active methylotrophic methanogens in such an environment.

Microbiology of Lonar Lake and other soda lakes

“…Methanogenic species related to Methanosarcina, Methanocalculus and Methanoculleus have also been isolated from the Lonar Lake sediments (Thakker and Ranade, 2002;Surakasi et al, 2007). Primer sets targeting 16S rRNA genes and mcrA (encoding the a-subunit of methyl coenzyme M reductase) revealed the presence of several potentially novel methanogenic Archaea (Methanosarcinales and Methanomicrobiales) in Lonar Lake sediments (Antony et al, 2012b). Analysis of mcrA transcripts that were retrieved from methanol-consuming and methane-emitting sediment microcosms implicated Methanolobus-like organisms as the active Archaea involved in methylotrophic methanogenesis (Antony et al, 2012b).…”

“…Primer sets targeting 16S rRNA genes and mcrA (encoding the a-subunit of methyl coenzyme M reductase) revealed the presence of several potentially novel methanogenic Archaea (Methanosarcinales and Methanomicrobiales) in Lonar Lake sediments (Antony et al, 2012b). Analysis of mcrA transcripts that were retrieved from methanol-consuming and methane-emitting sediment microcosms implicated Methanolobus-like organisms as the active Archaea involved in methylotrophic methanogenesis (Antony et al, 2012b). These methanogens may be linked to the 'intermediary ecosystem metabolism' of Lonar Lake sediments, that is, the anaerobic network of trophically linked microbes that yield intermediates (for example, fatty acids and alcohols) that drive methanogenesis either directly or indirectly (McInerney and Bryant, 1981;Drake et al, 2009).…”

“…Rift valley soda lakes, Mono Lake Grant et al (1999), Humayoun et al (2003), Rees et al (2004) Investigations on methanogenesis and methanotrophy Big Soda Lake, Mono Lake, Transbaikal soda lakes Oremland et al (1982Oremland et al ( , 1993, Iversen et al (1987), Khmelenina et al (2000) Characterization of microbes associated with arsenic cycle Mono Lake, Searles Lake Reviewed in Oremland et al (2004Oremland et al ( , 2005 Characterization Antony et al (2010Antony et al ( , 2012b Investigations on nitrogen cycle and the characterization of microbes associated with this cycle Big Soda Lake, Mono Lake, Siberian soda lakes, Mongolian soda lakes, Rift valley soda lakes Oremland et al (1988Oremland et al ( , 1990, Sorokin (1998), Sorokin et al (1998Sorokin et al ( , 2001, Ward et al (2000), Carini and Joye (2008) Characterization of diversity of chemoor photoautotrophic Bacteria Mono Lake, Kulunda steppe soda lakes, Wadi al Natrun soda lakes, Soap Lake Giri et al (2004), Kovaleva et al (2011), Asao et al (2011 environments, such as Rift valley soda lakes, Lonar Lake and Mono Lake (Jones et al, 1998;LeCleir et al, 2007;Joshi et al, 2008). Halo(alkali)philic microorganisms use several different types of organic solutes as osmolytes (Ciulla et al, 1997).…”

On the diversity of fungi from soda soils

“…High densities of bacterial and archaeal blooms may even cause the coloration of water basins associated with the soda soils, for example, as in Magadi Lake (Kenya) due to massive expansion of red haloalkaliphilic Archaea (Jones et al 1998). Studies of 16S rDNA gene sequences revealed a complex phylogenetically heterogeneous structure of the bacterial communities inhabiting soda lakes (Duckworth et al 1996;Rees et al 2004;Dong et al 2006;Wani et al 2006) often with the recovery of many new bacterial species (Sorokin and Muyzer 2010;Sorokin et al 2011;Kompantseva et al 2012;Antony et al 2012). The accumulated data suggest that soda lakes in diverse geographical regions harbor alkaliphilic bacteria and Archaea from all major trophic groups (Rees et al 2004).…”

Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning

“…Previous reports used the primers designed by Luton et al (2002) producing amplicons between 464 and 491 bp, which were analyzed and consequently excised from the DGGE gel (Antony et al 2012;García-Maldonado et al 2015). Our new alternative approach, which used semi-nested PCR coupled with the construction of clone libraries, allowed the production of longer mcrA sequences (approx.…”