scholarly journals Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Kelle C. Freel ◽  
Stephanie Fouteau ◽  
David Roche ◽  
Julien Farasin ◽  
Aline Huber ◽  
...  
Keyword(s):  
Parent Strain ◽  
Mine Drainage ◽  
Bacterial Genome ◽  
Extreme Environments ◽  
Point Mutations ◽  
Multiple Point ◽  
Content Type ◽  
Link Type ◽  
High Concentrations ◽  
Integrative And Conjugative Element

Thiomonas bacteria are ubiquitous at acid mine drainage sites and play key roles in the remediation of water at these locations by oxidizing arsenite to arsenate, favouring the sorption of arsenic by iron oxides and their coprecipitation. Understanding the adaptive capacities of these bacteria is crucial to revealing how they persist and remain active in such extreme conditions. Interestingly, it was previously observed that after exposure to arsenite, when grown in a biofilm, some strains of Thiomonas bacteria develop variants that are more resistant to arsenic. Here, we identified the mechanisms involved in the emergence of such variants in biofilms. We found that the percentage of variants generated increased in the presence of high concentrations of arsenite (5.33 mM), especially in the detached cells after growth under biofilm-forming conditions. Analysis of gene expression in the parent strain CB2 revealed that genes involved in DNA repair were upregulated in the conditions where variants were observed. Finally, we assessed the phenotypes and genomes of the subsequent variants generated to evaluate the number of mutations compared to the parent strain. We determined that multiple point mutations accumulated after exposure to arsenite when cells were grown under biofilm conditions. Some of these mutations were found in what is referred to as ICE19, a genomic island (GI) carrying arsenic-resistance genes, also harbouring characteristics of an integrative and conjugative element (ICE). The mutations likely favoured the excision and duplication of this GI. This research aids in understanding how Thiomonas bacteria adapt to highly toxic environments, and, more generally, provides a window to bacterial genome evolution in extreme environments.

scholarly journals A New Fungal Isolate, Penidiella sp. Strain T9, Accumulates the Rare Earth Element Dysprosium

2015 ◽  
Vol 81 (9) ◽  
pp. 3062-3068 ◽  
Author(s):  
Takumi Horiike ◽  
Mitsuo Yamashita
Keyword(s):  
Rare Earth ◽  
Mine Drainage ◽  
Liquid Waste ◽  
Morphological Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Cell Pellet ◽  
Acidic Conditions ◽  
High Concentrations ◽  
Rrna Gene Sequencing

ABSTRACTWith an aim to develop a highly efficient method for the recovery of rare earth elements (REEs) by using microorganisms, we attempted to isolate dysprosium (Dy)-accumulating microorganisms that grow under acidic conditions from environmental samples containing high concentrations of heavy metals. One acidophilic strain, T9, which was isolated from an abandoned mine, decreased the concentration of Dy in medium that contained 100 mg/liter Dy to 53 mg/liter Dy after 3 days of cultivation at pH 2.5. The Dy content in the cell pellet of the T9 strain was 910 μg/mg of dry cells. The T9 strain also accumulated other REEs. Based on the results of 28S-D1/D2 rRNA gene sequencing and morphological characterization, we designated this fungal strainPenidiellasp. T9. Bioaccumulation of Dy was observed on the cell surface of the T9 strain by elemental mapping using scanning electron microscopy-energy dispersive X-ray spectroscopy. Our results indicate thatPenidiellasp. T9 has the potential to recover REEs such as Dy from mine drainage and industrial liquid waste under acidic conditions.

Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Inna A. Panova ◽  
Olga Ikkert ◽  
Marat R. Avakyan ◽  
Dmitry S. Kopitsyn ◽  
Andrey V. Mardanov ◽  
...  
Keyword(s):  
Mine Drainage ◽  
Sequence Similarity ◽  
Cell Structure ◽  
Draft Genome ◽  
Electron Acceptors ◽  
Rrna Gene ◽  
Protein Coding ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0–3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0–7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum Firmicutes , class Clostridia , family Peptococcaceae , genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus Desulfosporosinus , for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В−3021T).

scholarly journals Antibacterial activity and mode of action of potassium tetraborate tetrahydrate against soft-rot bacterial plant pathogens

Microbiology ◽  
2020 ◽  
Vol 166 (9) ◽  
pp. 837-848
Author(s):  
Yingyu Liu ◽  
Melanie J. Filiatrault
Keyword(s):  
Type Species ◽  
Plant Pathogens ◽  
Point Mutations ◽  
Resistant Mutant ◽  
Soft Rot ◽  
Alternative Methods ◽  
Management Options ◽  
Content Type ◽  
Link Type ◽  
Resistant Mutants

Bacterial soft rot caused by the bacteria Dickeya and Pectobacterium is a destructive disease of vegetables, as well as ornamental plants. Several management options exist to help control these pathogens. Because of the limited success of these approaches, there is a need for the development of alternative methods to reduce losses. In this study, we evaluated the effect of potassium tetraborate tetrahydrate (PTB) on the growth of six Dickeya and Pectobacterium spp. Disc diffusion assays showed that Dickeya spp. and Pectobacterium spp. differ in their sensitivity to PTB. Spontaneous PTB-resistant mutants of Pectobacterium were identified and further investigation of the mechanism of PTB resistance was conducted by full genome sequencing. Point mutations in genes cpdB and supK were found in a single Pectobacterium atrosepticum PTB-resistant mutant. Additionally, point mutations in genes prfB (synonym supK) and prmC were found in two independent Pectobacterium brasiliense PTB-resistant mutants. prfB and prmC encode peptide chain release factor 2 and its methyltransferase, respectively. We propose the disruption of translation activity due to PTB leads to Pectobacterium growth inhibition. The P. atrosepticum PTB-resistant mutant showed altered swimming motility. Disease severity was reduced for P. atrosepticum -inoculated potato stems sprayed with PTB. We discuss the potential risk of selecting for bacterial resistance to this chemical.

scholarly journals Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
Frédéric Auvray ◽  
Alexandre Perrat ◽  
Yoko Arimizu ◽  
Camille V. Chagneau ◽  
Nadège Bossuet-Greif ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Whole Genome Sequence ◽  
Active Metabolites ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Sequence Types ◽  
Trna Locus ◽  
Integrative And Conjugative Element

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.

Pseudomarimonas arenosa gen. nov., sp. nov. isolated from marine sand

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Veeraya Weerawongwiwat ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung-Sook Lee ◽  
Ampaitip Sukhoom ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
Marine Sand ◽  
The Family ◽  
Rrna Gene Sequencing

A novel Gram-negative, aerobic, non-motile, rod-shaped, bacterial strain (CAU 1598T) was isolated from marine sand. Strain CAU 1598T grew well at 30 °C, pH 6.5–7.0 and with 3 % NaCl (w/v). Phylogeny results based on 16S rRNA gene sequencing indicated that the identified strain had the highest similarity (94.3%) to Pseudoxanthomonas putridarboris , indicating that strain CAU 1598T belongs to the family Xanthomonadaceae . Further, the fatty acid profile of the strain was primarily composed of C16:0, iso-C15 : 0, iso-C16 : 0, summed feature 3 (consisting of C16 : 1  ω7c/iso-C15 : 0 2-OH) and summed feature 9 (consisting of iso-C17 : 1  ω9c and/or C16 : 0 10-methyl), with ubiquinone-8 as the major isoprenoid quinone. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, an unidentified aminolipid and an unidentified lipid. The G+C content of the bacterial genome was 62.6 mol% and its 5.4 Mb length encompassed 144 contigs and 4236 protein-coding genes. These phenotypic, chemotaxonomic and phylogenetic data indicate that CAU 1598T belongs to a new genus and species, for which the name Pseudomarimonas arenosa gen. nov., sp. nov. is proposed. The type strain is CAU 1598T (=KCTC 82406T=MCCC 1K05673T).

scholarly journals Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1525-1530 ◽  
Author(s):  
Claire M. Grison ◽  
Stephen Jackson ◽  
Sylvain Merlot ◽  
Alan Dobson ◽  
Claude Grison
Keyword(s):  
Type Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Sulfoquinovosyl Diacylglycerol ◽  
Anthyllis Vulneraria ◽  
High Concentrations ◽  
Physiological Tests

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052T (98.4 %), Rhizobium tibeticum CCBAU 85039T (98.1 %), Rhizobium grahamii CCGE 502T (98.0 %) and Rhizobium mesoamericanum CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with R. endophyticum CCGE 2052T, R. tibeticum CCBAU 85039T, R. mesoamericanum CCGE 52T, Rhizobium grahamii CCGE 502T, Rhizobium etli CCBAU 85039T and Rhizobium radiobacter KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus Rhizobium with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).

Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3313-3318 ◽  
Author(s):  
Wakao Fukuda ◽  
Tomomi Kimura ◽  
Shigeo Araki ◽  
Yuki Miyoshi ◽  
Haruyuki Atomi ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Water Soluble ◽  
Protease Production ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
High Concentrations ◽  
Ph Range

A Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium (strain 107-E2T) was isolated from freshwater samples containing microbial mats collected at a lake in Skarvsnes, Antarctica (temporary lake name, Lake Tanago Ike). Strain 107-E2T grew between 5 and 25 °C, with an optimum of 23 °C. Moreover, colony formation was observed on agar media even at −5 °C. The pH range for growth was between 6.0 and 9.0, with an optimum of pH 7.0–8.0. The range of NaCl concentration for growth was between 0.0 and 0.5 % (w/v), with an optimum of 0.0 %. No growth was observed in media containing organic compounds at high concentrations, which indicated that strain 107-E2T was an oligotroph. In the late stationary phase, strain 107-E2T produced a dark brown water-soluble pigment. Esterase, amylase and protease production was observed. Antimicrobial-lytic activities for Gram-negative bacteria and yeast were observed. Ubiquinone-8 was the major respiratory quinone. The major fatty acids were iso-C15 : 0, iso-C17 : 1ω9c and iso-C15 : 1 at 5. The G+C content of genomic DNA was 66.1 mol%. Analysis of the 16S rRNA gene sequences revealed that strain 107-E2T belonged to the genus Lysobacter , and low DNA–DNA relatedness values with closely related species distinguished strain 107-E2T from recognized species of the genus Lysobacter . The phylogenetic situation and physiological characteristics indicated that strain 107-E2T should be classified as a representative of a novel species of the genus Lysobacter , for which the name Lysobacter oligotrophicus sp. nov. is proposed. The type strain is 107-E2T ( = JCM 18257T = ATCC BAA-2438T).

scholarly journals Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L.

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2737-2742 ◽  
Author(s):  
Jun Jie Zhang ◽  
Tian Yan Liu ◽  
Wen Feng Chen ◽  
En Tao Wang ◽  
Xin Hua Sui ◽  
...  
Keyword(s):  
Cicer Arietinum ◽  
Novel Species ◽  
Carbon Sources ◽  
Temperature Growth ◽  
Content Type ◽  
Cicer Arietinum L ◽  
Link Type ◽  
Sds Page ◽  
High Concentrations ◽  
Type Strains

Three chickpea rhizobial strains (CCBAU 83963T, CCBAU 83939 and CCBAU 83908), which were identified previously as representing a distinctive genospecies, were further studied here and compared taxonomically with related species in the genus Mesorhizobium . Results from SDS-PAGE of whole-cell soluble proteins revealed differences from closely related recognized species of the genus Mesorhizobium . Levels of DNA–DNA relatedness were 15.28–50.97 % between strain CCBAU 83963T and the type strains of recognized Mesorhizobium species (except for Mesorhizobium thiogangeticum ). Strain CCBAU 83963T contained fatty acids characteristic of members of the genus Mesorhizobium , but it possessed high concentrations of C19 : 0 cyclo ω8c and iso-C17 : 0. Strain CCBAU 83963T had phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids, and an ornithine-containing lipid, phosphatidyl-N-dimethylethanolamine and cardiolipin as minor components. Nodulation tests demonstrated the distinct symbiotic character of strain CCBAU 83963T; only Cicer arietinum, its host plant, could be invaded to form effective nitrogen-fixing nodules. The narrow spectrum of utilization of sole carbon sources, lower resistance to antibiotics, and NaCl, pH and temperature growth ranges differentiated these novel rhizobia from recognized species of the genus Mesorhizobium . Based on the data presented, the three novel rhizobial strains are considered to represent a novel species of the genus Mesorhizobium , for which the name Mesorhizobium muleiense sp. nov. is proposed. The type strain is CCBAU 83963T ( = HAMBI 3264T = CGMCC 1.11022T).

scholarly journals A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Arnoud H. M. van Vliet ◽  
Oliver J. Charity ◽  
Mark Reuter
Keyword(s):  
Type Species ◽  
Campylobacter Coli ◽  
Bacterial Populations ◽  
Content Type ◽  
Microbial Genomes ◽  
Link Type ◽  
Cas9 Protein ◽  
History Of ◽  
Integrative Conjugative Elements ◽  
Integrative And Conjugative Element

Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli . CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli . CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C . jejuni genomes and 92/1347 (6.8 %) C . coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter .

scholarly journals From cloning to mutant in 5 days: rapid allelic exchange in Staphylococcus aureus

2021 ◽  
Author(s):  
Ian R. Monk ◽  
Timothy P. Stinear
Keyword(s):  
Staphylococcus Aureus ◽  
Type Species ◽  
Point Mutations ◽  
Site Specific ◽  
Content Type ◽  
Allelic Exchange ◽  
Link Type ◽  
Foreign Dna ◽  
Time Required ◽  
A Site

In the last 10 years, the barriers preventing the uptake of foreign DNA by clinical Staphylococcus aureus isolates have been identified and powerful mutagenesis techniques such as allelic exchange are now possible in most genotypes. However, these targeted approaches can still be cumbersome, and the construction of unmarked deletions/point mutations may take many weeks or months. Here, we introduce a streamlined allelic exchange protocol using IMxxB Escherichia coli and the plasmid pIMAY-Z. With this optimized approach, a site-specific mutation can be introduced into S. aureus in 5 days, from the start of cloning to isolation of genomic DNA for confirmatory whole-genome sequencing. This streamlined protocol considerably reduces the time required to introduce a specific, unmarked mutation in S. aureus and should dramatically improve the scalability of gene-function studies.

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