Skip to main content

Table 1 Bacterial strains used in this study

From: Genetic optimisation of bacteria-induced calcite precipitation in Bacillus subtilis

Strain

Relevant characteristicsa

Source/Constructionb

DH5α

Escherichia coli DH5α

Laboratory stock

DSM 33

Wild-type Sporosarcina pasteurii DSM 33

DSMZ

ATCC 9945a

Wild-type Bacillus paralicheniformis ATCC 9945a

ATCC

W168

Wild-type Bacillus subtilis W168

Laboratory stock

NCIB3610

Wild-type Bacillus subtilis NCIB3610

Laboratory stock

HB13321

W168 ytpB::MLSr

[58]

WΔ

(SGB666)

W168 ureABC::kanr

LFH: kanr amplified from pDG780 using primers SG0144/SG0145; upstream and downstream gene fragments amplified from W168 gDNA using primers SG0510/SG0511 and SG0512/SG0513. W168 transformed with PCR products joined using primers SG0510/SG0513. Correct gene deletion checked with primers SG0532/SG0147 and SG0533/SG0146

WΔ-SpU (SGB739)

W168 ureABC::kanr, lacA::PxylA-ureABCEFGDSp-MLSr

pBS2E-PxylA-ureABCEFGDSp → SGB666

W-SpU

(SGB740)

W168 lacA::PxylA-ureABCEFGDSp-MLSr

pBS2E-PxylA-ureABCEFGDSp → W168

WΔ-U

(SGB823)

W168 ureABC::kanr, amyE::PxylA-UTBp-catr

pBS1C-PxylA-UTBp → SGB666

WΔ-H

(SGB824)

W168 ureABC::kanr, amyE::PxylA-ureHBp-cat

pBS1C-PxylA-ureHBp → SGB666

WΔ-U-H

(SGB825)

W168 ureABC::kanr, amyE::PxylA-UTBp-ureHBp-cat

pBS1C-PxylA-UTBp-ureHBp → SGB666

WΔ-U-BpU (SGB826)

W168 ureABC::kanr, amyE::PxylA-UTBp-catr, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB823

WΔ-H-BpU (SGB827)

W168 ureABC::kanr, amyE::PxylA-ureHBp-catr, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB824

WΔ-U-H-BpU (SGB828)

W168 ureABC::kanr, amyE::PxylA-UTBp-ureHBp-catr, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB825

WΔ-BpU (SGB844)

W168 ureABC::kanr, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB666

NΔ

(SGB905)

NCIB3610 ureABC::kanr

SPP1 transduction SGB666 → NCIB3610

NΔ-U

(SGB912)

NCIB3610 ureABC::kanr, amyE::PxylA-UTBp-cat

SPP1 transduction SGB823 → SGB905

NΔ-H

(SGB913)

NCIB3610 ureABC::kanr, amyE::PxylA-ureHBp-cat

SPP1 transduction SGB824 → SGB905

NΔ-U-H

(SGB914)

NCIB3610 ureABC::kanr, amyE::PxylA-UTBp-ureHBp-cat

SPP1 transduction SGB825 → SGB905

NΔ-BpU

(SGB915)

NCIB3610 ureABC::kanr, thrC:: PxylA-ureABCEFGDBp-spcr

SPP1 transduction SGB844 → SGB905

NΔ-U-BpU

(SGB921)

NCIB3610 ureABC::kanr, amyE::PxylA-UTBp-cat, thrC:: PxylA-ureABCEFGDBp-spcr

SPP1 transduction SGB844 → SGB912

NΔ-H-BpU

(SGB922)

NCIB3610 ureABC::kanr, amyE::PxylA-ureHBp-ca.r, thrC:: PxylA-ureABCEFGDBp-spcr

SPP1 transduction SGB844 → SGB913

NΔ-U-H-BpU

(SGB923)

NCIB3610 ureABC::kanr, amyE::PxylA-UTBp-ureHBp-cat, thrC:: PxylA-ureABCEFGDBp-spcr

SPP1 transduction SGB844 → SGB914

W-Δd

(SGB926)

W168 dltABCDE::zeor

LFH: zeor amplified from pBS1Z using primers SG0526/SG0527, upstream and downstream gene fragments amplified from W168 gDNA using primers SG0891/SG0892 and SG0893/SG0894. W168 transformed with PCR products joined using primers SG0891/SG0894. Correct gene deletion checked with primers SG0895/SG0527 and SG0526/SG0896

WΔ-Δd

(SGB985)

W168 ureABC::kanr, ΔdltABCDE::zeor

gDNA SGB926 → SGB666

WΔ-Δd-H

(SGB987)

W168 ureABC::kanr, amyE::PxylA-ureHBp-cat, dltABCDE::zeor

gDNA SGB926 → SGB824

WΔ-Δd-H-BpU

(SGB988)

W168 ureABC::kanr, amyE::PxylA-ureHBp-ca.r, dltABCDE::zeor, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB987

WΔ-Δe-H

(SGB992)

W168 ureABC::kanr, amyE::PxylA-ureHBp-cat, epsH::MLSr

LFH: MLS amplified from HB13321 using primers SG0634/SG0635, upstream and downstream gene fragments amplified from W168 gDNA using primers SG1009/SG1010 and SG1011/SG1012. SGB824 transformed with PCR products joined using primers SG1009/SG1012. Correct gene deletion checked with primers SG1021/SG0635 and SG0634/SG1022

WΔ-Δt-H

(SGB993)

W168 ureABC::kanr, amyE::PxylA-ureHBp-cat, tasA::MLSr

LFH: MLS amplified from HB13321 using primers SG0634/SG0635, upstream and downstream gene fragments amplified from W168 gDNA using primers SG1013/SG1014 and SG1015/SG1016. SGB824 transformed with PCR products joined using primers SG1013/SG1016. Correct gene deletion checked with primers SG1023/SG0635 and SG0634/SG1024

WΔ-Δe-H-BpU

(SGB995)

W168 ureABC::kanr, amyE::PxylA-ureHBp-cat, epsH::MLSr, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB992

WΔ-Δt-H-BpU

(SGB996)

W168 ureABC::kanr, amyE::PxylA-ureHBp-cat, tasA::MLSr, thrC:: PxylA-ureABCEFGDBp-spcr

pXT-PxylA-ureABCEFGDBp → SGB993

  1. a Relevant characteristics are listed. Antibiotic resistance cassettes are denoted as follows: Kan: kanamycin resistance; cat: chloramphenicol resistance; spc: spectinomycin resistance; MLS: erythromycin and lincomycin resistance; zeo: zeocin (phleomycin D1) resistance
  2. b The direction of strain construction is indicated by an arrow, transferring with plasmid/genomic/PCR DNA via transformation or phage (SPP1) transduction into recipients using standard techniques. Plasmids referred to are given in Table 2, primers in Additional file 5. ATCC: American type culture collection; DSMZ: German collection of microorganisms and Cell cultures GmbH; LFH: long flanking homology mutagenesis; gDNA: genomic DNA