Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments

Abstract

Arthrobacter spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.

Keywords: Antarctica; Arthrobacter spp.; adaptation; metalotolerant; plasmid; psychrotolerant.

Figure 1

Phylogenetic tree for 16S rDNA sequences of Arthrobacter spp. The tree was constructed by applying the Maximum Likelihood method based on the Tamura-Nei model. Statistical support for the internal nodes was determined by 1,000 bootstrap replicates and values of ≥50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 91 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1,121 positions in the final dataset. The 16S rDNA sequence of Micrococcus antarcticus T2 was used as an outgroup. GenBank accession numbers of the 16S rDNA sequences used for the phylogenetic analysis are given in brackets. The strains analyzed in this study are in bold text. Clusters I–III, distinguished by colored backgrounds, contain the ANT strains. The IA and IB subclusters are within the cluster I. Strains containing plasmids were indicated by black dots. Number of dots corresponds to the number of plasmids found within the particular strain.

Figure 2

Linear maps showing the genetic structure and organization of the circular plasmids of Antarctic Arthrobacter spp. Arrows indicate genes and their transcriptional orientation. Predicted genetic modules are indicated by colored boxes: ARM, aromatic compound utilization; COP, copper resistance; CYT, cytochrome biogenesis; EFX, drug-specific efflux; LAM, laminarinase; LIP, lipoprotein export system; MFS, major facilitator transporter; MOB, mobilization for conjugal transfer; PAR, partitioning; RE, type IV restriction enzyme; REP, replication; RM, restriction-modification; TA, toxin-antitoxin; TNP, transposition; SLP, sulfate transport; SUL, sulfur metabolism; TAU, taurine transport; TCT, tricarboxylate transport; TER, tellurium resistance; TRA, conjugal transfer; UMU, UV-damage protection/repair; XER, recombination. Potentially active transposable elements were distinguished and the location of their IR sequences is marked by black dots. A red triangle indicates the gene that was disrupted in the plasmid pA44BH1, but is intact within pA48BH1.

Figure 3

Phylogenetic tree of partitioning proteins (ParAs) encoded within the Arthrobacter plasmids. The analysis was based on 39 sequences of the ParA proteins (122 amino acid positions) encoded within the Arthrobacter plasmids. Additionally, 23 reference ParA sequences of other bacteria, previously used by Mihasan (2015), were included in this analysis. The unrooted tree was constructed using the Maximum Likelihood method based on the Le and Gascuel model (Le and Gascuel, 2008). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Statistical support for the internal nodes was determined by 1,000 bootstrap replicates and values of ≥50% are shown. Accession numbers of the protein sequences used for the analysis are given in brackets. Clusters I–IV group ParA proteins of Arthrobacter plasmids, with reference to previously proposed clustering (Mihasan, 2015). The names of plasmids analyzed in this work are in bold text.