Table 2.
Multiple host‐vector systems for metagenomic DNA cloning and functional screening
| Library vector | Origin type/Vector type | Vector size | Relevant characteristics | Average insert size | Environment | Screening hosts | Library size (Mb or Gb)/Number of clones | Gene/function target | References |
|---|---|---|---|---|---|---|---|---|---|
| pLF61 | Shuttle/plasmid | 5.4 kb | PGK promoter; URA3 gene; origins from yeast 2 μm plasmid E. coli vector pUC19 | 1–3 kb | Soil eukaryote organisms (metatranscriptome) | S. cerevisiae W303 | 1.75 × 106 | Oligopeptide transporters | Damon et al. (2011) |
| pMM436 | Shuttle/cosmid | Not shown | ColE1 origin for E. coli and integrative attB for S. lividans; PacI restriction site flanking attB integration site for recovering metagenomic DNA | 30–40 kb | Libraries I and II different soil samples |
S. lividans
∆act ∆red |
I) 367.5 Mb/10 500 II) 2485 Mb/71 000 |
I) Haemolytic activity II) Pigmentation producing |
McMahon et al. (2012) |
| pCT3FK | Shuttle/fosmid | 11.6 kb | RK2 origin, pyr (chromosomal surroundings of the pyr locus allow homologous recombination in T. thermophilus), KmR | 35–40 kb | Water, sediment, biofilm from hot springs | T. thermophilus BL03, E. coli EPI300 | ~8000 | Esterase‐active enzymes | Leis et al. (2015) |
| pCT3FK | Shuttle/fosmid | 11.6 kb | RK2 origin, pyr (chromosomal surroundings of the pyr locus were inserted in the vector to allow homologous recombination in T. thermophilus), KmR | 50 kb | S. thermophila (genomic library) | E. coli K12 and T. thermophilus HB27 | 2.9 Mb/192 | Xylanase activity | Angelov et al. (2009) |
| pLAFR3 | Broad‐host‐range/cosmid | 22 kb | pLAFR1 with HaeII fragment (MCS and a‐complementation for ß‐galactosidase activity), TcR, cos site, RK2 origin | 25 kb | Wastewater treatment plant anaerobic sludge digestor | E. coli and R. leguminosarum bv. Viciae | 2750 Mb/110 000 | Dehydrogenase genes | Wexler et al. (2005) |
| pGNS‐BAC‐1 | Shuttle/BAC | 11.9 kb | Two origins of replication (i.e. F and RK2), oriV origin, arabinose‐inducible plasmid copy number, CmR. | 80 kb | Forest soil | Clones from E. coli were electroporated into S. marcescens, V. cholerae, E. nimipressuralis | Not shown | Not shown | Kakirde et al. (2011) |
| pOS700I | Shuttle/cosmid | Not shown | AmpR, cos sequence, pOS700I integrative in S. lividans via attB site and int gene from the Streptomyces integrative element pSAM2, allowing site‐specific integration of pOS700I in many Streptomyces species | 50 kb | Soil from an arable field | E. coli/S. lividans (only to check phenotypes found in E. coli) | 250 Mb/5000 | Polyketide synthase genes | Courtois et al. (2003) |
| pWEB436 | Shuttle/cosmid | Not shown | ColE1 origin, cos site, AmpR, ΦC31 integration system for integration in Streptomyces, ApraR, oriT from the lncP plasmid | 40–50 kb | Texas desert soil | Streptomyces albus | 1.5 million | Polyketide synthase genes | Iqbal et al. (2016) |
| pSrpsL14 | Shuttle/BAC | Not shown | ColE1 origin, pSG5 origin of Streptomyces; AmpR (E. coli); ThioR (Streptomyces); GmR (E. coli and Streptomyces) | 50–100 kb | Soil | S. lividans ∆act ∆red, P. putida MBD1 | Not shown | Antibacterial and antifungal activities | Martinez et al. (2004) |
| pKS13S | Broad‐host‐range/cosmid | 21.7 kb | RK2, TcR, cos site, RK2 oriT. | 25 kb | Oil‐contaminated soil | P. putida G7K2 and KTSK2 | 294 Mb/24 000 | Naphthalene‐catabolic genes | Ono et al. (2007) |
| pJWC1 | Broad‐host‐range/cosmid | 14 kb | trfA, RK2 oriT, RK2, TcR, ApR, RK2 stability locus (0.8 kb). | High‐molecular weight | Deciduous forest topsoil, creek bed mud/sediment and sand/clay‐covered cold desert soil | Agrobacterium tumefaciens LBA4404, Burkholderia graminis C4D1M, Caulobacter vibrioides CB15, Escherichia coli EC100, Pseudomonas putida KT2440, Ralstonia metallidurans CH34 | 750 000 | Pigmentation producing and antibacterial activity | Craig et al. (2010) |
| pJWC1 | Broad‐host‐range/cosmid | 14 kb | trfA, oriT (RK2 origin of transfer), RK2, TcR, ApR, RK2 stability locus (0.8 kb) | High‐molecular weight | Soil | Ralstonia metallidurans CH34 | 575 000 | Metabolites from pigmented compounds and antibacterial | Craig et al. (2010) |
| pKS13S | Broad‐host‐range/cosmid | 21.7 kb | RK2 origin, TcR, cos site, RK2 oriT | 25 kb | Artificially polluted soil (with biphenyl, phenanthrene, carbazole and 3‐chlorobenzoate) | P. putida KTSK2 and P. putida G7NAD2 | 5.2 Gb/208 000 | Oxygenase genes | Nagayama et al. (2015) |
| pJC8 | Broad‐host‐range/cosmid | 13 kb | TcR, GmR, Rk2, oriT, Gateway attL sites used for recombination transfer of cosmid inserts into other destination vectors | 33 kb | Soil from the wheat field | P. putida PpUW2 (PHA‐) | 362 Gb/9 × 106 | Polyhydroxy‐alkanoate synthases genes | Cheng and Charles (2016) |
| pRS44 | Broad‐host‐range/fosmid and BAC | 10.3 kb | CmR, KmR, stabilization element parDE (from RK2), oriT, Lac system for blue/white screening, ori2 origin (from the F plasmid) oriV from RK2 | 35 kb | Marine sediment | Pseudomonas fluorescens and Xanthomonas campestris | 20 000 | Not shown | Aakvik et al. (2009) |