Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

Sheri L Simmons; Genevieve DiBartolo; Vincent J Denef; Daniela S. Aliaga Goltsman; Michael P Thelen; Jillian F Banfield

doi:10.1371/journal.pbio.0060177

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

PLoS Biology ◽

10.1371/journal.pbio.0060177 ◽

2008 ◽

Vol 6 (7) ◽

pp. e177 ◽

Cited By ~ 90

Author(s):

Sheri L Simmons ◽

Genevieve DiBartolo ◽

Vincent J Denef ◽

Daniela S. Aliaga Goltsman ◽

Michael P Thelen ◽

...

Keyword(s):

Acid Mine Drainage ◽

Mine Drainage ◽

Genomic Analysis ◽

Strain Variation ◽

Acid Mine ◽

Population Genomic ◽

Group Ii

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Genomic Analysis of a Newly Isolated Acidithiobacillus ferridurans JAGS Strain Reveals Its Adaptation to Acid Mine Drainage

Minerals ◽

10.3390/min11010074 ◽

2021 ◽

Vol 11 (1) ◽

pp. 74

Author(s):

Jinjin Chen ◽

Yilan Liu ◽

Patrick Diep ◽

Radhakrishnan Mahadevan

Keyword(s):

Acid Mine Drainage ◽

Mine Drainage ◽

Genomic Structure ◽

Evolutionary Relationship ◽

Genomic Analysis ◽

Protein Coding ◽

Acid Mine ◽

Inorganic Ion ◽

Unique Genes ◽

Core Genes

Acidithiobacillus ferridurans JAGS is a newly isolated acidophile from an acid mine drainage (AMD). The genome of isolate JAGS was sequenced and compared with eight other published genomes of Acidithiobacillus. The pairwise mutation distance (Mash) and average nucleotide identity (ANI) revealed that isolate JAGS had a close evolutionary relationship with A. ferridurans JCM18981, but whole-genome alignment showed that it had higher similarity in genomic structure with A. ferrooxidans species. Pan-genome analysis revealed that nine genomes were comprised of 4601 protein coding sequences, of which 43% were core genes (1982) and 23% were unique genes (1064). A. ferridurans species had more unique genes (205–246) than A. ferrooxidans species (21–234). Functional gene categorizations showed that A. ferridurans strains had a higher portion of genes involved in energy production and conversion while A. ferrooxidans had more for inorganic ion transport and metabolism. A high abundance of kdp, mer and ars genes, as well as mobile genetic elements, was found in isolate JAGS, which might contribute to its resistance to harsh environments. These findings expand our understanding of the evolutionary adaptation of Acidithiobacillus and indicate that A. ferridurans JAGS is a promising candidate for biomining and AMD biotreatment applications.

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Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) Bacteria in Acid Mine Drainage Biofilms

Applied and Environmental Microbiology ◽

10.1128/aem.02943-08 ◽

2009 ◽

Vol 75 (13) ◽

pp. 4599-4615 ◽

Cited By ~ 130

Author(s):

Daniela S. Aliaga Goltsman ◽

Vincent J. Denef ◽

Steven W. Singer ◽

Nathan C. VerBerkmoes ◽

Mark Lefsrud ◽

...

Keyword(s):

Acid Mine Drainage ◽

Carbon Fixation ◽

Mine Drainage ◽

Conjugative Plasmid ◽

Rrna Gene ◽

Group Iii ◽

Acid Mine ◽

Core Proteins ◽

Proteomic Analyses ◽

Group Ii

ABSTRACT We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.

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