Abstract
Acidiferrobacter spp. are facultatively anaerobic acidophiles that belong to a distinctive Acidiferrobacteraceae family, which are similar to Ectothiorhodospiraceae phylogenetically, and are closely related to Acidithiobacillia class/subdivision physiologically. The limited genome information has kept them from being studied on molecular taxonomy and environmental adaptation in depth. Herein, Af. thiooxydans ZJ was isolated from acid mine drainage (AMD), and the complete genome sequence was reported to scan its genetic constitution for taxonomic and adaptative feature exploration. The genome has a single chromosome of 3,302,271 base pairs (bp), with a GC content of 63.61%. The phylogenetic tree based on OrthoANI highlighted the unique position of Af. thiooxydans ZJ, which harbored more unique genes among the strains from Ectothiorhodospiraceae and Acidithiobacillaceae by pan-genome analysis. The diverse mobile genetic elements (MGEs), such as insertion sequence (IS), clustered regularly interspaced short palindromic repeat (CRISPR), prophage, and genomic island (GI), have been identified and characterized in Af. thiooxydans ZJ. The results showed that Af. thiooxydans ZJ may effectively resist the infection of foreign viruses and gain functional gene fragments or clusters to shape its own genome advantageously. This study will offer more evidence of the genomic plasticity and improve our understanding of evolutionary adaptation mechanisms to extreme AMD environment, which could expand the potential utilization of Af. thiooxydans ZJ as an iron and sulfur oxidizer in industrial bioleaching.
Highlights
The type strain Acidiferrobacter thiooxydans m-1 was initially reported as “Thiobacillus ferrooxidans” owing to its ironoxidizing capability, which was isolated from coal spoil refuse in Missouri, United States, over 35 years ago (Harrison, 1982)
Researchers renamed the strain as Af. thiooxydans and confirmed that it was closely related with the members of the family Ectothiorhodospiraceae, order Chromatiales, including typically alkaliphilic and halophilic bacteria that could not oxidize iron and sulfur (Hallberg et al, 2011)
The iron and sulfur oxidizer Af. thiooxydans ZJ was isolated from acid mine drainage (AMD), yielding a complete genome with 3,302,271 bp with a high GC content of 63.61%
Summary
The type strain Acidiferrobacter thiooxydans m-1 was initially reported as “Thiobacillus ferrooxidans” owing to its ironoxidizing capability, which was isolated from coal spoil refuse in Missouri, United States, over 35 years ago (Harrison, 1982). The strain Af. thiooxydans m-1 harbored a higher chromosomal GC content and the analysis of partial 16S rRNA sequences revealed that it was quite distantly related to other acidophilic bacteria. Researchers renamed the strain as Af. thiooxydans and confirmed that it was closely related with the members of the family Ectothiorhodospiraceae, order Chromatiales, including typically alkaliphilic and halophilic bacteria that could not oxidize iron and sulfur (Hallberg et al, 2011). Another member within the genus, Acidiferrobacter sp. The calculated ANI relatedness between SPIII/3 and m1 was lower than 95%, implying that they could not be assigned to the same species obviously
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