Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage

MSystems
Liangzhi LiHuaqun Yin

Abstract

Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions.IMPORTANCE Ex...Continue Reading

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Methods Mentioned

BETA
amplicon sequencing
nucleic acid recovery

Software Mentioned

CRISPRCasFinder
ISfinder
Cytoscape
IslandViewer
Muscle
OrthoVenn2
SMRT Link
MEGA
CoNet
PosiGene

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