Anaerobic digestion is used with success for the treatment of solid waste, urban and industrial effluents with a concomitant energy production. The process is robust and stable, but the complexity of the microbial community involved in the process is not yet fully comprehensive. Nowadays, the study of this complex ecosystem is facilitated by the availability of different molecular tools, but it is very important to choose the adequate tool to answer specific questions. The aim of this review is to describe different molecular techniques, indicate the questions that can be addressed by each technique, enumerate their limitations and give practical advices for their use. Examples of how the molecular tools have been used to address various questions in anaerobic digestion are presented. The key point now is to apply all this information to improve anaerobic digestion. The integration of concepts of microbial-ecology, environmental-engineering, modeling and bioinformatics is currently necessary.
Chromium (Cr)-resistant bacteria isolated from a soil with 6 g kg(-1) of Cr were identified based on 16S rRNA gene sequence analysis as a Stenotrophomonas, and designated as JD1. Growth of JD1 was accompanied by transformation of Cr(VI) to Cr(III) in liquid medium initially containing 300 mg L(-1) Cr(VI), the maximum concentration allowing growth. JD1 produced the highest levels of a Cr(VI)-binding exopolysaccharide when grown in medium with 100 mg L(-1) Cr(VI). The relative exopolysaccharide monosaccharide composition was analysed by HPLC, which showed that rhamnose+galactose was the major component, and that its relative level increased when cells were grown with Cr(VI). JD1 grew as a biofilm on various inert surfaces. Biofilm macromolecular composition analysis indicated that the relative levels of exopolysaccharide and protein were more abundant in biofilms grown in 100 mg L(-1) Cr(VI), whereas relative uronic acid levels remained constant. Biofilm cells exposed to Cr(VI) were elongated, grouped in clusters and exopolysaccharide obtained from the biofilm extracellular matrix had an enhanced capacity to bind Cr(VI). Exopolysaccharide production and composition, and biofilm growth are discussed as a mechanism of protection that allows survival during Cr(VI) stress.
Cyanobacterial 16S ribosomal RNA gene diversity was examined in a benthic mat on Fildes Peninsula of King George Island (62º09'54.4''S, 58º57'20.9''W), maritime Antarctica. Environmental DNA was isolated from the mat, a clone library of PCR-amplified 16S rRNA gene fragments was prepared, and amplified ribosomal DNA restriction analysis (ARDRA) was done to assign clones to seven groups. Low cyanobacterial diversity in the mat was suggested in that 83% of the clones were represented by one ARDRA group. DNA sequences from this group had high similarity with 16S rRNA genes of Tychonema bourrellyi and T. bornetii isolates, whose geographic origins were southern Norway and Northern Ireland. Cyanobacterial morphotypes corresponding to Tychonema have not been reported in Antarctica, however, this morphotype was previously found at Ward Hunt Lake (83ºN), and in western Europe (52ºN). DNA sequences of three of the ARDRA groups had highest similarity with 16S rDNA sequences of the Tychonema group accounting for 9.4% of the clones. Sequences of the remaining three groups (7.6%) had highest similarity with 16S rRNA genes of uncultured cyanobacteria clones from benthic mats of Lake Fryxell and fresh meltwater on the McMurdo Ice Shelf.
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