Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France)

Abstract

Permanent anoxic layers in natural freshwater basins are rare and of considerable interest to microbial ecologists because of their potential undisturbed climax microbial communities and because of their relationship to an earlier biosphere. Lake Pavin in France provides such an environment. It is unusual because the water column has been stratified for a very long period and there has been a lack of mixing (meromixis) and its anoxic zone is in steady state (2). Despite its unique character, information on the distribution of microbial communities in the anoxic water column of Lake Pavin is limited to a terminal restriction fragment length polymorphism study of populations (16). Lehours et al. (16) found that the structures of both the bacterial and archaeal communities changed with depth. The results suggested that communities at interfaces played a predominant role in the water column. To obtain detailed phylogenetic information on the diverse populations in the differing anaerobic communities, 16S rRNA genes in samples collected at three interface layers in the anoxic water column of Lake Pavin were amplified, cloned, sequenced, and analyzed. Bacterial and archaeal clone libraries were also constructed from a sample collected at a depth of 90 m adjacent to the sediment to determine whether sediment fluxes influenced lake bottom community composition.Sample collection and library construction. Samples from depths of 60 m, 70 m, and 90 m in the water column of Lake Pavin were collected in August 2004 using an 8-liter horizontal Van Dorn bottle; samples were also collected from the sediment-water interface (Inter) at a depth of 92 m using a JenkinMortimer multiple corer (21) (see reference 16 for site characteristics). Microbial samples were prepared on site from water samples (500 ml) by filtration through polycarbonate membrane filters (GTTP; Millipore) (47 mm diameter; pore size, 0.2 m) and stored at Ϫ80°C. The sites sampled in the water column are shown in Fig.

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

“…The infected hosts exhibited sheath and flat ends (Supplementary Figure S2c), similar to those typical of the methanogenic species M. concilii (Supplementary Figure S2d) (Patel and Sprott, 1990). Even if there is no certitude about the identity of the infected cell, its tentative affiliation to Methanosaeta, in addition to the morphological similarities, is supported by the data on the occurrence of members of this genus as a dominant archaeal group in the sediments of Lake Pavin (Lehours et al, 2007;Biderre-Petit et al, 2011). Methanosaeta genus is known to be widely distributed in different environments and is probably the predominant methane producer on earth (Smith and Ingram-Smith, 2007).…”

“…Qiamp DNA mini kit (Qiagen, Hilden, Germany) was used to purify viral DNA. Possible bacterial contamination was checked by PCR amplification using the 16S rDNA primers 27f and 1492r as previously described (Lehours et al, 2007).…”

Microbial Ecology of Lake Kivu

“…or hydrogenotrophic ones ( Methanocellula spp. ), agreeing with the suggested biological origin of methane in the lake (Schoell et al 1988 ;Pasche et al 2011 ) and common methanogenic phylotypes present in strati fi ed lakes (Lehours et al 2007 Takai et al 2001 ) , with yet unknown community role ( Fig. 6.2 ).…”

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

“…Until recently, this division had no cultivated strains, yet contained just over 600 full-length phylotypes in the SILVA database version 114 (Pruesse et al, 2007). Phylotypes grouping within candidate division OP10 were detected in a wide range of environments, including soil, geothermal springs, freshwater sediments and bioreactors (Bond et al, 1995;Hugenholtz et al, 1998;Lehours et al, 2007;Stott et al, 2008;Dunfield et al, 2012), suggesting a broad range of metabolic capabilities and ecological roles. The first reported cultivated strains of candidate division OP10, strains T49 T and P488, were isolated from geothermally heated soils in New Zealand (Stott et al, 2008).…”