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

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

Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions

Analysis of Earth’s magnetic field changes by correlation of its parameters

Changes of Earth magnetic field parameters: field intensity and its components along axes of rectangular coordinates are analyzed in space and time. Data from magnetic observatories Belsk and Hel in Poland were used. Correlation analysis of magnetic field components was applied. Influence of respective field components on changes of geomagnetic field intensity was determined. Shift of space and time factors was used to assess the influence of covariations of geomagnetic field components on changes of covariations of field intensity. Article in English Žemės magnetosferos pokyčių, taikant jos parametrų koreliaciją, analizė Straipsnyje analizuojama Žemės magnetosferos parametrų: lauko jėgos intensyvumo ir jos komponenčių pagal stačiakampių koordinačių ašis reikšmių kaita erdvėje bei laike. Tyrimams naudota Lenkijos Belsk ir Hel magnetinių observatorijų metraščių duomenys, taikyta magnetosferos lauko jėgos komponenčių koreliacinė analizė. Nustatyta atitinkamų geomagnetinio lauko jėgos komponenčių pokyčių įtaka geomagnetinio lauko jėgos intensyvumo pokyčiams. Įvertinant geomagnetinio lauko jėgos komponenčių kovariacijų įtaką lauko jėgos intensyvumo kovariacijų pokyčiams atsižvelgta į erdvės ir laiko faktorių kaitą.

Insight into heavy metal resistome of soil psychrotolerant bacteria originating from King George Island (Antarctica)

The presence of heavy metals in Antarctica is an emerging issue, especially as (bio)weathering of metal-containing minerals occurs and human influence is more and more visible in this region. Chemical analysis of three soil samples collected from the remote regions of King George Island (Antarctica) revealed the presence of heavy metals (mainly copper, mercury, and zinc) at relatively high concentrations. Physiological characterization of over 200 heavy metal-resistant, psychrotolerant bacterial strains isolated from the Antarctic soil samples was performed. This enabled an insight into the heavy metal resistome of these cultivable bacteria and revealed the prevalence of co-resistance phenotypes. All bacteria identified in this study were screened for the presence of selected heavy metal-resistance genes, which resulted in identification of arsB (25), copA (3), czcA (33), and merA (26) genes in 62 strains. Comparative analysis of their nucleotide sequences provided an insight into the diversity of heavy metal-resistance genes in Antarctic bacteria

Rola bakterii dysymilacyjnie redukujących arseniany w procesach mobilizacji i immobilizacji arsenu w środowisku

Drewniak, Łukas

Genomic Analysis of Shewanella sp. O23S—The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction

Shewanella sp. O23S is a dissimilatory arsenate reducing bacterial strain involved in arsenic transformations within the abandoned gold mine in Zloty Stok (SW Poland). Previous physiological studies revealed that O23S may not only release arsenic from minerals, but also facilitate its immobilization through co-precipitation with reduced sulfur species. Given these uncommon, complementary characteristics and the application potential of the strain in arsenic-removal technologies, its genome (~5.3 Mbp), consisting of a single chromosome, two large plasmids (pSheA and pSheB) and three small plasmid-like phages (pSheC-E) was sequenced and annotated. Genes encoding putative proteins involved in heavy metal transformations, antibiotic resistance and other phenotypic traits were identified. An in-depth comparative analysis of arsenic respiration (arr) and resistance (ars) genes and their genetic context was also performed, revealing that pSheB carries the only copy of the arr genes, and a complete ars operon. The plasmid pSheB is therefore a unique natural vector of these genes, providing the host cells arsenic respiration and resistance abilities. The functionality of the identified genes was determined based on the results of the previous and additional physiological studies, including: the assessment of heavy metal and antibiotic resistance under various conditions, adhesion-biofilm formation assay and BiologTM metabolic preferences test. This combined genetic and physiological approach shed a new light on the capabilities of O23S and their molecular basis, and helped to confirm the biosafety of the strain in relation to its application in bioremediation technologies

Rola bakterii dysymilacyjnie redukujących arseniany w procesach mobilizacji i immobilizacji arsenu w środowisku

Celem badań podjętych w ramach niniejszej rozprawy była (i) szczegółowa analiza fizjologiczna, genomiczna, i funkcjonalna dwóch szczepów DARB: Aeromonas sp. O23A i Shewanella sp. O23S wyizolowanych z kopalni złota i arsenu w Złotym Stoku, określenie (ii) roli tych szczepów w procesach mobilizacji i immobilizacji arsenu i (iii) czynników wpływających na te przemiany, oraz (iv) oszacowanie możliwości zastosowania analizowanych szczepów w systemach bioremediacji.The aim of the research described in this dissertation was: (i) a detailed genomic, physiological and functional analysis of two DARB strains: Aeromonas sp. O23A and Shewanella sp. O23S, isolated from the gold and arsenic mine in Zloty Stok, and determination of (ii) the role of these strains in the processes of mobilization and immobilization of arsenic, (iii) factors affecting these transformations, and (iv) estimation of the application potential of the analyzed strains in bioremediation systems