Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.

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Abundance of mobile genetic elements in an Acinetobacter lwoffii strain isolated from Transylvanian honey sample

Scientific Reports ◽

10.1038/s41598-020-59938-9 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Alexandra Veress ◽

Tibor Nagy ◽

Tímea Wilk ◽

János Kömüves ◽

Ferenc Olasz ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Rapid Evolution ◽

Mobile Genetic Elements ◽

Metal Resistance ◽

Honey Sample ◽

Common Pattern ◽

Is Elements ◽

Genetic Elements ◽

Resistance Determinants ◽

Close Relatives

AbstractBased on phylogenetic analyses, strain M2a isolated from honey, an unexpected source of acinetobacters, was classified as Acinetobacter lwoffii. The genome of this strain is strikingly crowded with mobile genetic elements. It harbours more than 250 IS elements of 15 IS-families, several unit and compound transposons and 15 different plasmids. These IS elements, including 30 newly identified ones, could be classified into at least 53 IS species. Regarding the plasmids, 13 of the 15 belong to the Rep-3 superfamily and only one plasmid, belonging to the “Low-GC” family, possesses a seemingly complete conjugative system. The other plasmids, with one exception, have a mobilization region of common pattern, consisting of the divergent mobA/mobL-family and mobS-, mobC- or traD-like genes separated by an oriT-like sequence. Although two plasmids of M2a are almost identical to those of A. lwoffi strains isolated from gold mine or Pleistocene sediments, most of them have no close relatives. The presence of numerous plasmid-borne and chromosomal metal resistance determinants suggests that M2a previously has also evolved in a metal-polluted environment. The numerous, possibly transferable, plasmids and the outstanding number of transposable elements may reflect the high potential of M2a for rapid evolution.

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Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

Applied and Environmental Microbiology ◽

10.1128/aem.01746-17 ◽

2017 ◽

Vol 84 (2) ◽

Cited By ~ 14

Author(s):

Roman Pantůček ◽

Ivo Sedláček ◽

Adéla Indráková ◽

Veronika Vrbovská ◽

Ivana Mašlaňová ◽

...

Keyword(s):

Antibiotic Resistance ◽

New Species ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Novel Species ◽

Extreme Environments ◽

Mobile Genetic Elements ◽

Whole Genome ◽

Content Type ◽

Genetic Elements

ABSTRACT Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources comprising stone fragments and sandy soil in James Ross Island, Antarctica. Here, we describe properties of a novel species of the genus Staphylococcus that has a 16S rRNA gene sequence nearly identical to that of Staphylococcus saprophyticus. However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85% and inferred DNA-DNA hybridization of <30%. It forms a separate branch in the S. saprophyticus phylogenetic clade as confirmed by multilocus sequence analysis of six housekeeping genes, rpoB, hsp60, tuf, dnaJ, gap, and sod. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbors. In contrast to S. saprophyticus subsp. saprophyticus, the novel strains are pyrrolidonyl arylamidase and β-glucuronidase positive and β-galactosidase negative, nitrate is reduced, and acid produced aerobically from d-mannose. Whole-genome sequencing of the 2.69-Mb large chromosome revealed the presence of a number of mobile genetic elements, including the 27-kb pseudo-staphylococcus cassette chromosome mec of strain P5085T (ψSCCmec P5085), harboring the mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environments, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidime, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactam producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085T (= CCM 8730T = DSM 104441T). IMPORTANCE The description of Staphylococcus edaphicus sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The genomic characteristics presented here elucidate the evolutionary relationships in the Staphylococcus genus with a special focus on antimicrobial resistance, pathogenicity, and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome, shaped by horizontal gene transfer. Thus, S. edaphicus can act not only as a reservoir of antibiotic resistance in a natural environment but also as a mediator for the spread and evolution of resistance genes.

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Genome Sequence of Listeria monocytogenes Plasmid pLM-C-273 Carrying Genes Related to Stress Resistance

Genome Announcements ◽

10.1128/genomea.01125-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 2

Author(s):

Lindsay Liang ◽

Saravanamuttu Gnaneshan ◽

Rafael A. Garduño ◽

Gustavo V. Mallo

Keyword(s):

Antibiotic Resistance ◽

Listeria Monocytogenes ◽

Genome Sequence ◽

Resistance Genes ◽

Stress Resistance ◽

Clinical Sample ◽

Mobile Genetic Elements ◽

Metal Resistance ◽

Genetic Elements

Mobile genetic elements in bacteria, such as plasmids, act as important vectors for the transfer of antibiotic resistance, virulence, and metal resistance genes. Here, we report the genome sequence of a new plasmid pLM-C-273, identified in a Listeria monocytogenes strain isolated from a clinical sample in Ontario, Canada.

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Bacterial isolates harboring antibiotics and heavy-metal resistance genes co-existing with mobile genetic elements in natural aquatic water bodies

Saudi Journal of Biological Sciences ◽

10.1016/j.sjbs.2020.06.002 ◽

2020 ◽

Vol 27 (10) ◽

pp. 2660-2668

Author(s):

Insha Sultan ◽

Asghar Ali ◽

Firdoos A. Gogry ◽

Irfan A. Rather ◽

Jamal S.M. Sabir ◽

...

Keyword(s):

Heavy Metal ◽

Resistance Genes ◽

Mobile Genetic Elements ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Water Bodies ◽

Bacterial Isolates ◽

Genetic Elements

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Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa390 ◽

2020 ◽

Vol 76 (1) ◽

pp. 101-109 ◽

Cited By ~ 1

Author(s):

Markus H K Johansson ◽

Valeria Bortolaia ◽

Supathep Tansirichaiya ◽

Frank M Aarestrup ◽

Adam P Roberts ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Salmonella Enterica ◽

Sequence Data ◽

Sequence Similarity ◽

Mobile Genetic Elements ◽

Metal Resistance ◽

Animal Origin ◽

Genetic Elements ◽

Antimicrobial Resistance Genes

Abstract Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.

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MrdH, a Novel Metal Resistance Determinant of Pseudomonas putida KT2440, Is Flanked by Metal-Inducible Mobile Genetic Elements

Journal of Bacteriology ◽

10.1128/jb.00465-09 ◽

2009 ◽

Vol 191 (19) ◽

pp. 5976-5987 ◽

Cited By ~ 19

Author(s):

Adhikarla Haritha ◽

Korripally Prem Sagar ◽

Anand Tiwari ◽

Patnala Kiranmayi ◽

Agnes Rodrigue ◽

...

Keyword(s):

Pseudomonas Putida ◽

Mobile Genetic Elements ◽

Metal Resistance ◽

Resistance Determinant ◽

Nickel Resistance ◽

Pseudomonas Putida Kt2440 ◽

Domain Organization ◽

Genetic Elements ◽

Reverse Transcription Pcr ◽

Metal Efflux

ABSTRACT We report here the identification and characterization of mrdH, a novel chromosomal metal resistance determinant, located in the genomic island 55 of Pseudomonas putida KT2440. It encodes for MrdH, a predicted protein of ∼40 kDa with a chimeric domain organization derived from the RcnA and RND (for resistance-nodulation-cell division) metal efflux proteins. The metal resistance function of mrdH was identified by the ability to confer nickel resistance upon its complementation into rcnA mutant (a nickel- and cobalt-sensitive mutant) of Escherichia coli. However, the disruption of mrdH in P. putida resulted in an increased sensitivity to cadmium and zinc apart from nickel. Expression studies using quantitative reverse transcription-PCR showed the induction of mrdH by cadmium, nickel, zinc, and cobalt. In association with mrdH, we also identified a conserved hypothetical gene mreA whose encoded protein showed significant homology to NreA and NreA-like proteins. Expression of the mreA gene in rcnA mutant of E. coli enhanced its cadmium and nickel resistance. Transcriptional studies showed that both mrdH and mreA underwent parallel changes in gene expression. The mobile genetic elements Tn4652 and IS1246, flanking mrdH and mreA were found to be induced by cadmium, nickel, and zinc, but not by cobalt. This study is the first report of a single-component metal efflux transporter, mrdH, showing chimeric domain organization, a broad substrate spectrum, and a location amid metal-inducible mobile genetic elements.

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