Insights into the genome
As indicated in the introduction, because S. novella was the first facultative sulfur chemolithotrophic bacterium to be isolated, many studies of its metabolic capabilities were carried out following its discovery. Several groups worked on the carbon metabolism of S. novella, which led to the discovery of an operational pentose phosphate pathway in this bacterium [69], which is also the only reported pathway of glucose metabolism in the description of S. novella [1]. However, analysis of the genome sequence revealed that in addition to a pentose phosphate pathway, S. novella also contains enzymes required for the Entner-Doudoroff pathway (Snov_2999 & Snov_3400, 2-dehydro-3-deoxyphosphogluconate aldolase; 6-phosphogluconate dehydratase; biocyc database) and the enzymes required for the Embden-Meyerhoff pathway, although this pathway appears to lack a phosphofructokinase (EC 2.7.1.11), indicating that it may only be able to be used for gluconeogenesis.
The respiratory chain of S. novella has also been studied and an aa3 type terminal oxidase was identified and characterized in some detail [70-73]. It was also discovered that the cytochrome c that interacts with this cytochrome oxidase (most likely this cytochrome is encoded by Snov_1033) has properties that are reminiscent of the mitochondrial respiratory chain cytochrome c [70-75], including a high pI and an ability to transfer electrons to the bovine cytochrome oxidase [76]. The analysis of the genome revealed a much greater diversity of respiratory chain complexes than previously recognized, including two NADH oxidases (gene regions Snov_1853 & Snov_2407), one succinate dehydrogenase (Snov_3317 gene region) and a cytochrome bc1 complex (Snov_2477 gene region). In addition to these components, the genome encodes two aa3 type cytochrome oxidases (gene regions Snov_0584 & 4240), two cytochrome bd type quinol oxidases (pfam02322, gene regions Snov_0620 & 3535), a cbb3 type cytochrome oxidase (gene region Snov_4464), and a cyoB type quinol oxidase (COG0843, cd01662, gene region Snov_1015) indicating a significant versatility of respiration in S. novella as well as the potential to grow at low oxygen tensions as both the cbb3 and bd type oxidases are known to have high affinities for oxygen, enabling growth under microaerophilic conditions. Experiments in our laboratory have shown that final OD600 values reached by cultures grown on thiosulfate (5g/l) and hydrogen carbonate (20 mM) supplemented DSMZ medium 69 were the same regardless of whether 25, 50, 100 or 200 ml of medium were used in a 250 ml flask. This clearly confirms that, as indicated by the genome data, S. novella is capable of growth under microaerophilic as well as aerobic conditions.
We also re-evaluated the range of substrates that support growth of S. novella. In the description of the genus Starkeya [1] only glucose, formate, methanol and oxalate were listed as growth-supporting substrates in addition to thiosulfate and tetrathionate. An early paper reporting a test of the heterotrophic potential of S. novella was published in 1969 by Taylor and Hoare [4] in which they identified 16 potential growth substrates (Table no. 7 in [4]) including all of the above except oxalate, which was identified subsequently by [5] who were seeking to evaluate the C1 compound metabolism of S. novella and also identified formamide as a potential substrate. It is unclear why the description of the genus Starkeya did not list all of the 16 growth substrates identified by Taylor and Hoare. To confirm the earlier data, we carried out a growth substrate screen using the Biolog system (GN2 assay plates) as well as an api20NE test for bacterial identification. Some substrates that are not part of this Biolog GN2 plate (e.g. oxalate, fructose, succinate etc.) were independently tested in the laboratory for their ability to support growth. In the API20NE test, in addition to a positive oxidase response, S. novella tested positive for ESC/Fecit and p-nitrophenyl hydrolysis, glucose, mannitol and gluconate utilization. The Biolog assay clearly showed that the heterotrophic potential of this bacterium is greater than previously identified, with a total of 28 growth-supporting substrates being identified in the screen (Table 5). The metabolic profile could not be identified as such, and was most closely related to that of Ancylobacter aquaticus (SIM: 0.45, Dist: 8.96), which supports the phylogenetic placement of S. novella in the Ancylobacter subgroup of the Xanthobacteriaceae. When combining all the data from the various studies, there are now 39 substrates that have been identified as supporting heterotrophic growth of S. novella. In addition to sugars such as glucose, fructose and arabinose, several sugar alcohols and amino acids as well as some organic acids can be used as growth substrates (Table 5). This reasonably large range of growth substrates is reflected in the size and the diversity of metabolic pathways present in the S. novella genome which, with a size of 4.6 Mb, is comparable to the genomes of e.g., Escherichia coli and Rhodopseudomonas palustris.
Table 5  Growth substrates utilized by S. novella  Results are combined from work done for this paper and [4-6]+ = substrate utilized, - = substrate not utilized, (+) = weak growth supported or ambiguous results in growth tests, italics = different results obtained in growth studies by different authors.  Although the analyses presented above are limited, they clearly illustrate that while the genome data confirm many of the results from early studies of the physiology of this bacterium, the metabolic capabilities of S. novella as indicated by the genome data clearly exceed those previously published in the literature and suggest that the versatility and adaptability to changing environments likely is a significant factor for its survival.