Comparative genomics of 16Microbacteriumspp. that tolerate multiple heavy metals and antibiotics

Abstract

A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

“…In the case of IDBA and Velvet, performance was comparable to SPAdes when it was introduced 36 . For Megahit, an assembler for metagenomes but also working for single genomes 38 , it has been also used in recent studies, mainly related to microbial communities or particular strains 64 . More restricted works using SKESA are reported, but performance seem to be better than SPAdes and Megahit for some cases 39 .…”

Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance

“…The relatively small size of the extended core genome was obtained using a rather low blastp sequence identity threshold (80%), suggesting that the Microbacterium genus comprises species with high genetic diversity. Using 20 closely related strains and the An’vio pipeline, Learman et al (2019) obtained a bigger core genome (26%), where the main COG categories were devoted to housekeeping functions as “Cellular processing and signaling” and “Information storage and processing.” As in this study, genes of the COG category “Inorganic ion transport and metabolism” or with unassigned function were mostly part of the accessory genome. They also registered a large genomic variability corresponding to different tolerance degrees to heavy metals and antibiotics ( Learman et al, 2019 ).…”

“…Using 20 closely related strains and the An’vio pipeline, Learman et al (2019) obtained a bigger core genome (26%), where the main COG categories were devoted to housekeeping functions as “Cellular processing and signaling” and “Information storage and processing.” As in this study, genes of the COG category “Inorganic ion transport and metabolism” or with unassigned function were mostly part of the accessory genome. They also registered a large genomic variability corresponding to different tolerance degrees to heavy metals and antibiotics ( Learman et al, 2019 ). It is known that members of the Microbacteriaceae family have on average smaller core genomes compared to other Actinobacteria families like Micrococcaceae , Cellulomonadaceae , and Streptomycetaceae ( Bai et al, 2015 ).…”

“…For instance, the studies of Henson and Learman analyzed the genetic potential of Cr(VI) reducing Microbacterium spp. ( Henson et al, 2015 ; Learman et al, 2019 ). However, to the best of our knowledge, a comprehensive investigation of the genus Microbacterium has not been published yet.…”

Techniques Used for Analyzing Microplastics, Antimicrobial Resistance and Microbial Community Composition: A Mini-Review

“…Overall, research in this area has greatly expanded due to the above-mentioned technologies; however, there is a gap in analysis and modeling of microbial colonization of both MPs and NPs in different environmental settings. Change in species diversity is mostly investigated by sequencing variable regions from the conserved 16S ribosomal RNA (16S rRNA) ( Knapp et al, 2017 ; Zhao et al, 2018 ; Zhao Y. et al, 2019 ; Chen et al, 2019 ; Learman et al, 2019 ; Meier et al, 2020 ; Figure 2 ). Sequencing methods, including whole genome sequencing (WGS), are also ideal for studying effect of HMs on resistance-related genes in bacteria ( Pathak et al, 2020 ; Figure 2 ).…”