Abbas S, Ahmed I, Iida T, Lee Y-J, Busse H-J, Fujiwara T, Ohkuma M (2015) A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan. Antonie Leeuwenhoek 108:859–870

CAS  PubMed  Google Scholar 

Afzal AM, Rasool MH, Waseem M, Aslam B (2017) Assessment of heavy metal tolerance and biosorptive potential of Klebsiella variicola isolated from industrial effluents. AMB Express 7:184

PubMed  PubMed Central  Google Scholar 

Aguilar-Barajas E, Ramírez-Díaz MI, Riveros-Rosas H, Cervantes C (2010) Heavy metal resistance in Pseudomonas. In: Ramos JL, Alain F (eds) Pseudomonas: molecular microbiology, infection and biodiversity. Springer, Dordrecht, pp 255–282

Google Scholar 

Alengebawy A, Abdelkhalek ST, Qureshi SR, Wang M-Q (2021) Heavy metals and pesticides toxicity in agricultural soil and plants: ecological risks and human health implications. Toxics 9:42

CAS  PubMed  PubMed Central  Google Scholar 

Alhasawi A, Costanzi J, Auger C, Appanna ND, Appanna VD (2015) Metabolic reconfigurations aimed at the detoxification of a multi-metal stress in Pseudomonas fluorescens: Implications for the bioremediation of metal pollutants. J Biotechnol 20:38–43

Google Scholar 

Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS (2016) PHASTER: a better faster version of the PHAST phage search tool. Nucleic Acids Res 44:16–21

Google Scholar 

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75

Google Scholar 

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

CAS  PubMed  PubMed Central  Google Scholar 

Bazzi W, Abou Fayad AG, Nasser A, Haraoui L-P, Dewachi O, Abou-Sitta G et al (2020) Heavy metal toxicity in armed conflicts potentiates AMR in A. baumannii by selecting for antibiotic and heavy metal co-resistance mechanisms. Front Microbiol 11:68

PubMed  PubMed Central  Google Scholar 

Beech I, Hanjagsit L, Kalaji M, Neal AL, Zinkevich V (1999) Chemical and structural characterization of exopolymers produced by Pseudomonas sp. NCIMB 2021 in continuous culture. Microbiology 145:1491–1497

CAS  PubMed  Google Scholar 

Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA (2021) Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. Sci Rep 11:1370

CAS  PubMed  PubMed Central  Google Scholar 

Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, Brinkman FSL (2017) IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45:30–35

Google Scholar 

Bertrand RL (2019) Lag Phase Is a Dynamic, Organized, Adaptive, and Evolvable Period That Prepares Bacteria for Cell Division. J Bacteriol 201:e00697-18

PubMed  PubMed Central  Google Scholar 

Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P et al (2015) MeDuSa: a multi-draft based scaffolder. Bioinformatics 31:2443–2451

CAS  PubMed  Google Scholar 

Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ et al (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365

PubMed  PubMed Central  Google Scholar 

Bric JM, Bostock RM, Silverstone SE (1991) Rapid in situ assay for indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane. Appl Environ Microbiol 57:535–538

CAS  PubMed  PubMed Central  Google Scholar 

Burland TG (2000) DNASTAR’s lasergene sequence analysis software. In: Misener S, Krawetz SA (eds) bioinformatics methods and protocols. Humana Press, Totowa, pp 71–91

Google Scholar 

Cappuccino JG, Welsh C (2017) Microbiology a laboratory manual. Pearson, Upper Saddle River

Google Scholar 

Cappucino JC, Sherman N (1992) Microbiology: a laboratory manual. Benjamin/Cummings Publishing Company, New York

Google Scholar 

Carraro N, Sentchilo V, Polák L, Bertelli C, van der Meer JR (2020) Insights into mobile genetic elements of the biocide-degrading bacterium Pseudomonas nitroreducens HBP-1. Genes 11:930

CAS  PubMed Central  Google Scholar 

Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J (2008) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25:119–120

PubMed  PubMed Central  Google Scholar 

Challaraj Emmanuel ES, Vignesh V, Anandkumar B, Maruthamuthu S (2011) Bioaccumulation of cerium and neodymium by Bacillus cereus isolated from rare earth environments of Chavara and Manavalakurichi, India. Indian J Microbiol 51:488–495

CAS  PubMed  PubMed Central  Google Scholar 

Chellaiah ER (2018) Cadmium (heavy metals) bioremediation by Pseudomonas aeruginosa: a minireview. Appl Water Sci 8:154

Google Scholar 

Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:884–890

Google Scholar 

Chlebek D, Płociniczak T, Gobetti S, Kumor A, Hupert-Kocurek K, Pacwa-Płociniczak M (2022) Analysis of the genome of the heavy metal resistant and hydrocarbon-degrading rhizospheric Pseudomonas qingdaonensis ZCR6 strain and assessment of its plant-growth-promoting traits. Int J Mol Sci 23:214

CAS  Google Scholar 

Chong TM, Yin WF, Mondy S, Grandclément C, Dessaux Y, Chan KG (2012) Heavy-metal resistance of a France vineyard soil bacterium Pseudomonas mendocina strain S5.2 revealed by whole-genome sequencing. J Bacteriol 194:6366–6366

CAS  PubMed  PubMed Central  Google Scholar 

Choudhary S, Sar P (2009) Characterization of a metal resistant Pseudomonas sp. isolated from uranium mine for its potential in heavy metal (Ni2+, Co2+, Cu2+, and Cd2+) sequestration. Bioresour Technol 100:2482–2492

CAS  PubMed  Google Scholar 

Çolak F, Atar N, Yazıcıoğlu D, Olgun A (2011) Biosorption of lead from aqueous solutions by Bacillus strains possessing heavy-metal resistance. Chem Eng J 173:422–428

Google Scholar 

Ducret V, Gonzalez MR, Leoni S, Valentini M, Perron K (2020) The CzcCBA efflux system requires the CadA P-type ATPase for timely expression upon zinc excess in Pseudomonas aeruginosa. Front Microbiol 11:911

PubMed  PubMed Central  Google Scholar 

Euzéby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 47:590–592

PubMed  Google Scholar 

Faghihzadeh F, Anaya NM, Schifman LA, Oyanedel-Craver V (2016) Fourier transform infrared spectroscopy to assess molecular-level changes in microorganisms exposed to nanoparticles. Nanotechnol Environ Eng 1:1

Google Scholar 

Fashola MO, Ngole-Jeme VM, Babalola OO (2016) Heavy metal pollution from gold mines: environmental effects and bacterial strategies for resistance. Int J Env Res Public Health 13:1047

Google Scholar 

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

PubMed  Google Scholar 

Figueras MJ, Beaz-Hidalgo R, Hossain MJ, Liles MR (2014) Taxonomic affiliation of new genomes should be verified using average nucleotide identity and multilocus phylogenetic analysis. Genome Announc 2:e00927-00914

Google Scholar 

Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470

CAS  PubMed  PubMed Central  Google Scholar 

Gautam SS, Kc R, Leong KW, Mac Aogáin M, O’Toole RF (2019) A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens. J Biol Methods 6:e110

PubMed  PubMed Central  Google Scholar 

Giller KE, Witter E, McGrath SP (2009) Heavy metals and soil microbes. Soil Biol Biochem 41:2031–2037

CAS  Google Scholar 

Greenacre M, Hastie T (1987) The geometric interpretation of correspondence analysis. J Am Stat Assoc 82:437–447

Google Scholar 

Hamill PG, Stevenson A, McMullan PE, Williams JP, Lewis ADR, Sudharsan S et al (2020) Microbial lag phase can be indicative of or independent from cellular stress. Sci Rep 10:5948

CAS  PubMed  PubMed Central  Google Scholar 

Hassen A, Saidi N, Cherif M, Boudabous A (1998) Effects of heavy metals on Pseudomonas aeruginosa and Bacillus thuringiensis. Bioresour Technol 65:73–82

CAS  Google Scholar 

Hassen W, Neifar M, Cherif H, Najjari A, Chouchane H, Driouich RC et al (2018) Pseudomonas rhizophila S211, a new plant growth-promoting rhizobacterium with potential in pesticide-bioremediation. Front Microbiol. https://doi.org/10.3389/fmicb.2018.00034

Article  PubMed  PubMed Central  Google Scholar 

Havryliuk O, Hovorukha V, Patrauchan M, Youssef NH, Tashyrev O (2020) Draft whole genome sequence for four highly copper resistant soil isolates Pseudomonas lactis strain UKR1, Pseudomonas panacis strain UKR2, and Pseudomonas veronii strains UKR3 and UKR4. Current Research in Microbial Sciences 1:44–52

PubMed  PubMed Central  Google Scholar 

Helal M (2016) Multiple Heavy Metal and Antibiotic Resistance of Acinetobacter baumannii Strain HAF – 13 Isolated from Industrial Effluents. Am J Microbiol Res 4:26–36

Google Scholar 

Hu C, Guo J, Qu J, Hu X (2007) Photocatalytic degradation of pathogenic bacteria with AgI/TiO2 under visible light irradiation. Langmuir 23:4982–4987

CAS  PubMed  Google Scholar 

Izrael-Živković L, Beškoski V, Rikalović M, Kazazić S, Shapiro N, Woyke T et al (2019) High-quality draft genome sequence of Pseudomonas aeruginosa san ai, an environmental isolate resistant to heavy metals. Extremophiles 23:399–405

PubMed  Google Scholar 

Jadhav JP, Kalyani DC, Telke AA, Phugare SS, Govindwar SP (2010) Evaluation of the efficacy of a bacterial consortium for the removal of color, reduction of heavy metals, and toxicity from textile dye effluent. Bioresour Technol 101:165–173

CAS  PubMed  Google Scholar 

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114

PubMed  PubMed Central  Google Scholar 

Jiang C-Y, Sheng X-F, Qian M, Wang Q-Y (2008) Isolation and characterization of a heavy metal-resistant Burkholderia sp. from heavy metal-contaminated paddy field soil and its potential in promoting plant growth and heavy metal accumulation in metal-polluted soil. Chemosphere 72:157–164

CAS  PubMed  Google Scholar 

Kamran S, Shahid I, Baig DN, Rizwan M, Malik KA, Mehnaz S (2017) Contribution of zinc solubilizing bacteria in growth promotion and zinc content of wheat. Front Microbiol 8:2593

PubMed