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Anaerobic phycomycetous fungi have been isolated from rumen fluid by using the Hungate roll tube technique. Cultures on solid substrates in roll tubes can be stored for long periods, and fungal zoospores can be enumerated in roll tubes.

Ruminant methane is a major contributor to the anthropogenic greenhouse gas inventories of Australia and New Zealand. Direct intervention in the rumen offers one means for controlling ruminant methane emissions. In this respect, acetogenic bacteria (acetogens) normally present in the rumen are of interest because they have the potential to provide an alternative sink for H2, an essential intermediate in the formation of methane. Although little is known about the populations of acetogens in grazing ruminants, studies on ruminants fed diets containing concentrates or conserved forages indicate that the rumen contains a diversity of acetogens and that some of these have the potential to act as hydrogenotrophs in place of methanogens. This paper describes the current understanding of ruminal acetogens and outlines potential applications of acetogens in methane mitigation strategies. Strategies which use acetogens to outcompete and displace methanogens are considered less likely to be successful than strategies which use acetogens to maintain low H2 levels in the rumen following suppression of methanogens. However, the former cannot be completely discounted at present.

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.