The Adaptive Genome of Desulfovibrio vulgaris Hildenborough

April 18, 2018 eJournal Highlight: 2017 Glimpses at the Adaptive Genome Watch Team (martine [at] minst [dot] org)

Kuwahara H, 2017 reported the uncultured bacterium Candidatus Desulfovibrio trichonymphae "lacks genes for mannose permease, which are commonly found in the genomes of desulfovibrios (Santana M, 2006)".
Poosarla VG, 2017 referenced to Santana M, 2006 for supporting the statement that sulfate-reducing bacteria "are major culprits in microbiologically influenced corrosion".  Even though Santana M, 2006 did not discuss corrosion by sulfate-reducing bacteria, it is interesting to recall the late Professor John R. Postgate's account that the Hildenborough strain of Desulfovibrio vulgaris was isolated in 1946 from a specimen of Wealden clay, which was associated with a corroding water pipe that was being excavated at Hildenborough (2006 personal communication to M. Crasnier-Mednansky).   

May 2, 2013 eJournal Highlight: A Glimpse at the Adaptive Genome Watch Team (martine [at] minst [dot] org)

Zapata-Peņasco I, 2013 further reinforced the contention Desulfovibrio has an adaptive genome by stating "Desulfovibrio is a remarkably versatile taxon in metabolic pathways among the SRB [Sulfate Reducing Bacteria]; for instance, it is capable of bidirectional transmigration and adaptation to both water and terrestrial environments due to its adaptive genome (Santana M, 2006)".

May 17, 2006 eJournal Highlight: Adaptation and bacterial IQ: Looking at Bacterial Genomes beyond the Tip of the Iceberg
M. Crasnier-Mednansky, Ph.D., D.Sc. (martine [at] minst [dot] org)
Copyright © 2006 Mednansky Institute, Inc.

Integrating the vast amount of data released by sequencing bacterial genomes and metagenomes is a colossal task.  Currently the avalanche of information is classified and analyzed by automatic means however a need exists for manual search.  The latter allows pieces of the 'genomic puzzle' to be assembled while focusing on specific features of interest.

Santana M, 2006 manually analyzed the genome of Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough by assimilating data in relation to the presence of genes encoding proteins belonging to the phosphotransferase system (Kundig W, 1964; Postma PW, 1993).  As a result the metabolic diversity and adaptive character of the sulfate reducer Desulfovibrio vulgaris were emphasized.

Bacterial adaptation has been quantified by defining an adaptability index or 'bacterial IQ' (Galperin MY, 2005).  The IQ was determined by specifically looking for the presence of signal transduction proteins in bacterial and archaeal proteomes derived from 167 genome sequences.  Despite the conscientious perspective by the author, that "better ways to evaluate bacterial IQ are needed", the deductive proposal that Desulfovibrio vulgaris Hildenborough has an adaptive genome is in agreement with his IQ-derived classification.  Indeed, D. vulgaris Hildenborough appears as the fourth most 'intelligent' organisms among the 167 analyzed (Table 1 in Galperin MY, 2005).  In contrast, the model organism Escherichia coli, as well as other members of the Enterobacteriaceae family, are reported as being 'dumb'.

Among the 'bacterial leaders' was found, second on the list, Geobacter sulfurreducens, a metal reducer which, like the sulfate reducer Desulfovibrio vulgaris Hildenborough, belongs to the delta subdivision of Proteobacteria (Caccavo F Jr, 1994).  Interestingly, both organisms are classified as strict anaerobes, in contrast with findings that G. sulfurreducens can grow in the presence of oxygen (Lin WC, 2004), and a close relative of D. vulgaris, is equipped with the necessary components to live aerobically (Lemos RS, 2001).  In addition, D. vulgaris can efficiently protect itself against oxygen exposure (Voordouw JK, 1998; Fournier M, 2003).  Undoubtedly, the ability to cope with oxygen is a distinct advantage especially for adapting to environments whose oxygen content is fluctuating (Cypionka H, 2000), a situation likely to occur in the habitats of these two 'intelligent' bacteria.

Professor John R. Postgate, F.R.S., illuminated the remarkable versatility of the sulfate reducer group of bacteria as he wrote "… they have, so to speak, grown from a couple of microbiological eccentrics to a positive menageries of species, comprising a variety of physiologies, but all strict anaerobes".  Could this versatility be accounted for by their adaptive genomes?  Bacterial genomes are dynamic after all, and the existence of unique strain-specific genes within bacterial genomes may reveal their hosts not-too-distant past.

SENTRA (D'Souza M, 2007) for genome analysis of prokaryotic signal transduction proteins

Desulfovibrio vulgaris Hildenborough at SENTRA (no longer maintained), see NCBI

Comprehensive Microbial Resources for bacterial genomes released by JCVI

JCVI Comprehensive Microbial Resource for genome annotation and analyses

Desulfovibrio vulgaris Hildenborough genome page at JCVI

HAMAP: High-quality Automated and Manual Annotation of Microbial Proteomes at ExPASy

Desulfovibrio vulgaris Hildenborough proteome at HAMAP

GOLD for monitoring complete and ongoing genome projects worldwide