Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism

Abstract

Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained results indicate that Aeromonas sp. O23A is well-adapted to the extreme environmental conditions occurring in the Zloty Stok mine. The analysis of genome encoded traits allowed for a better understanding of the mechanisms of adaptation of the strain, also with respect to its presumable role in colonization and remediation of arsenic-contaminated waters, which may never have been discovered based on physiological analyses alone.

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

“…We assessed the performance of PlasFlow using the recently published Aeromonas sp. O23A genome, which contains four plasmids with size ranging from 4 to 60 kb ( 35 ). Preliminary genome assembly was performed using SPAdes, resulting in 240 scaffolds, which were further filtered to exclude all sequences shorter than 1 kb.…”

“…Applicability of presented software to newly sequenced genomic data was assessed using recently published Aeromonas sp. 023A ( 35 ), assembled using SPAdes, and draft genomic sequences available in the Refseq database, matching following criteria: (i) the genome was marked as the ‘representative genome’; (ii) the genome was at the assembly level ‘Scaffold’ or ‘Contig’ and (iii) for a given species, only the most up-to-date sequence was downloaded. An additional test was performed using a set of 42 bacterial genomes that contained a various number of plasmids, which has been described in Arredondo-Alonso et al.…”

Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine

“…O23A and Shewanella sp. O23S), which are among the dominant dissimilatory arsenate reducing strains in this environment, were thoroughly examined, together with their prophages [ 12 , 13 ].…”

In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2

“…The strain was tested for growth in divalent heavy metals such as 1 mM of Cd 2+ , Co 2+ , Cu 2+ , Ni 2+ , Zn 2+ , Mn 2+ and Pb 2+ ions and 0.1 mM of Hg 2+ . A growth of OD > 0.2 was considered as metal resistant for that treatment (Uhrynowski et al 2017).…”