Strain Su883^T (= DSM 6589 = ATCC 49978) is the type strain of the species Thermanaerovibrio acidaminovorans, which represents the type species of the two species containing genus Thermanaerovibrio [1]. Strain SU883^T is of particular interest because it is able to ferment quite a number of amino acids [2,3], and because its metabolism is greatly enhanced in the presence of the hydrogen scavenger Methanobacterium thermoautotrophicum, from which several single substrates solely hydrogen is formed as reduced fermentation product [3]. The physiological properties of the organism have been studied in detail [2,3].

Here we present a summary classification and a set of features for T. acidaminovorans strain SU883^T, together with the description of the complete genome sequencing and annotation.

Until now, strain SU883^T was the only strain known from this species. Uncultured clones with a rather high degree of 16S rRNA similarity to the sequence of strain SU883^T (AF071414) have been obtained from mesophilic and thermophilic bioreactors treating pharmaceutical wastewater [4] (AF280844, 97.5%; AF280820, 97.7%). The sequence similarities to environmental metagenomic libraries [5,6] were below 81%, indicating a rather poor representation of closely related strains in the analyses habitats (status July 2009).

Figure 1 shows the phylogenetic neighborhood of T. acidaminovorans strain Su883^T in a 16S rRNA based tree. The three 16S rRNA gene sequences in the genome of strain Su883^T differed from each other by up to three nucleotides, and by up to 29 nucleotides (2%) from the previously published 16S rRNA sequence, generated from DSM 6589 (AF071414). The significant difference between the genome data and the reported 16S rRNA gene sequence, which contains ten ambiguous base calls, is most likely due to sequencing errors in the previously reported sequence data.

Figure 1 Phylogenetic tree highlighting the position of T. acidaminovorans strain Su883T relative to the other type strains within the phylum Synergistetes. The tree was inferred from 1,333 aligned characters [7,8] of the 16S rRNA gene sequence under the maximum likelihood criterion [9], and was rooted with the type strains of the genera within the phylum ‘Thermotogae’. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Strains with a genome sequencing project registered in GOLD [10] are printed in blue; published genomes in bold.

T. acidaminovorans cells are curved rods of 0.5-0.6 × 2.5-3.0 µm in size (Table 1 and Figure 2), with round ends, occur singly, in pairs, or in long chains when grown in a complex medium [3]. The organism is Gram-negative, non-spore-forming, moderately thermophilic, motile by means of a tuft of lateral flagella at the concave side, and strictly anaerobic for growth [1]. Interestingly, it tolerates flushing with air for at least one hour, and it produces catalase [3]. While being exposed to air, strain Su883^T loses its motility [3]. Strain Su883^T is able to grow by oxidative decarboxylation of succinate to propionate. A mechanism for reductive propionate formation could be excluded [3]. Glutamate, α-ketoglutarate, histidine, arginine, ornithine, lysine, and threonine are fermented to acetate and propionate. Serine, pyruvate, alanine, glucose, fructose, xylose, glycerol and citrate are fermented to acetate. Branched-chain amino acids are converted to branched-chain fatty acids. Hydrogen is the only reduced end product [3]. The growth and the substrate conversion are strongly enhanced by co-cultivation with methanogens, e.g., M. thermoautotrophicum [3]. Strain Su883^T contains b-type cytochromes [3]. Originally, it was reported that in strain Su883^T thiosulfate, nitrite, sulfur and fumarate are not reduced [3]. However, a more recent study shows that, although elemental sulfur (1%) inhibits the growth of strain Su883^T on glucose, strain Su883^T could grow lithoheterotrophically with H₂ as electron donor, S⁰ as electron acceptor, and yeast extract as carbon source [16]. The catablolism of arginine has been studied in detail. Apparently, degradation of arginine occurs by the arginine deiminase (ADI) pathway [2]. No activity of arginase, a key enzyme of the arginase pathway, could be detected [2]. No growth was observed on glycine, aspartate, gelatin, xylose, ribose, galactose, lactose, sucrose, mannose, lactate, ethanol, methanol, acetoin, betaine, malonate, and oxalate [3]. With either succinate, α-ketoglutarate or glutamate, the following enzyme activities were measured in cell free extracts: propionyl CoA:succinate IISCoA transferase, propionate kinase, acetate kinase, glutamate dehydrogenase, pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, malate dehydrogenase, citrate lyase and hydrogenase [3]. The following enzymes were not detected: succinate thiokinase, fumarate reductase, succinate dehydrogenase, β-methylaspartase, hydroxyglutarate dehydrogenase, isocitrate dehydrogenase and formate dehydrogenase [3]. Unfortunately, no chemotaxonomic data are currently available for T. acidaminovorans strain Su883^T.

Figure 2 Scanning electron micrograph of T. acidaminovorans strain Su883T

The genome is 1,848,474 bp long and comprises one main circular chromosome with a 63.8% GC content. (Table 3, Figure 3). Of the 1,825 genes predicted, 1,765 were protein coding genes, and 60 RNAs. In addition, 27 pseudogenes were identified. The majority of genes (79.3%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Figure 3 Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.