Table 1.

Recent examples of functional screening strategies employed to obtain metagenome-derived biocatalysts

Screening approach	Target gene	Detection method	Inducer	Source	Host, vector	Ref.
Agar plate screening	Proteases	Phenotypical detection	1% skim-milk	Goat skin	E. coli, plasmid	[13]
Agar plate screening	Proteases	Phenotypical detection	1% skim-milk	Desert sands	E. coli, plasmid	[14]
Agar plate screening	Proteases	Phenotypical detection	AZCL-casein	Deciduous forest soil	E. coli, plasmid	[15]
Agar plate screening	Esterases	Phenotypical detection	1% Tributyrin	Marine mud	E. coli, plasmid	[16]
Agar plate screening	Esterases	Phenotypical detection	X-caprylate	Vegetable soil	E. coli, plasmid	[17]
Agar plate screening	Esterases	Phenotypical detection	α-Naphtyl-acetate, fast blue RR	Salted shrimp	E. coli, plasmid	[18]
Agar plate screening	Esterases	Phenotypical detection	1% Tributyrin	Alluvial soil	E. coli, plasmid	[19]
Agar plate screening	Esterases	Phenotypical detection	Dimethyl phthalate	Biofilm waste treatment plant	E. coli, fosmid	[20]
Agar plate screening	Lipase	Phenotypical detection	1% Tributyrin	Cymbastela concentrica, etc.	E. coli, fosmid	[21]
Agar plate screening	Lipase	Phenotypical detection	1% Tributyrin	Marine sponge (Haliclona simulans)	E. coli, fosmid	[22]
Agar plate screening	Lipase	Phenotypical detection	1% Tributyrin	Marine sponge (Ircinia sp.)	E. coli, plasmid	[23]
Agar plate screening	Lipase	Phenotypical detection	1% Tributyrin	Biomass	E. coli, cosmid	[24]
Agar plate screening	Cellulase	Phenotypical detection	Carboxymethyl cellulose	Coral (Siderastrea stellata)	E. coli, fosmid	[25]
Agar plate screening	Cellulase	Phenotypical detection	AZCL-HE-cellulase	Brown alga (Ascophyllum nodosum)	Yeast, plasmid	[26]
Agar plate screening	Starch hydrolyzing enzyme	Phenotypical detection	Starch, Lugol solution	Acid mine drainage	E. coli, plasmid	[27]
Agar plate screening	β-Glycosidases	Phenotypical detection	X-gal	Baltic Sea water	E. coli, plasmid	[28]
Agar plate screening	β-Glycosidases	Phenotypical detection	4-Nitorphenyl-β-d-glucoside	Alkaline polluted soil (Guangxi)	E. coli, plasmid	[29]
Agar plate screening	β-Glycosidases	Phenotypical detection	AZCL-xylan, xyloglucan	Cow dung	E. coli, phage	[30]
Agar plate screening	Pectinases	Phenotypical detection	Pectin	Forest soil (Western Ghats, India)	E. coli, plasmid	[31]
Agar plate screening	Tannase	Phenotypical detection	X-caprylate	Cotton field soil	E. coli, plasmid	[32]
Agar plate screening	Nuclease	Heterologous complementation	Hydrogen peroxide	Soil (Joao, Brazil)	E. coli, plasmid	[33]
Agar plate screening	RNase H	Heterologous complementation		Leaf and branch compost	E. coli, plasmid	[34]
Agar plate screening	Dioxygenases	Phenotypical detection	Indole	Aromatic compounds polluted soil	P. putida, phage	[35]
Agar plate screening	Dioxygenases	Phenotypical detection	Catechol	Activated sludge	E. coli, plasmid	[36]
Agar plate screening	Di-chlorophenol hydroxylase	Phenotypical detection	3,5-Dichlorocatehol	Polychlorinated biphenyl contaminated soil	E. coli, plasmid	[37]
Agar plate screening	Polyhydroxyalkanoate synthase	Heterologous complementation		Sandy loam surface soil	S. meliloti, cosmid	[38]
Agar plate screening	Laccase	Phenotypical detection	2,6-DMP, etc.	Mangrove soil	E. coli, plasmid	[39]
Agar plate screening	DNA polymerase	Heterologous complementation	Cold sensitive mutant strain	Glacial ice	E. coli, fosmid	[40]
Agar plate screening	Hydrogenase	Heterologous complementation	Freshwater enrichment	Not stated	E. coli, plasmid	[41]
Agar plate screening	Genes resistant to toxic elements	Phenotypical detection	pH 1.8	Acidic water (Tinto river)	E. coli, plasmid	[42]
Agar plate screening	Genes resistant to toxic elements	Phenotypical detection	Different number of antibiotics	Human fecal	E. coli, fosmid	[43]
Agar plate screening	Genes resistant to toxic elements	Phenotypical detection	Different number of antibiotics	Soil	E. coli, plasmid	[44]
Agar plate screening	Genes resistant to toxic elements	Phenotypical detection	Several antibiotics	Dairy cow manure	E. coli, fosmid	[45]
Agar plate screening	Genes resistant to toxic elements	Phenotypical detection	Several antibiotics	Cheese food matrix	E. coli, fosmid	[46]
Agar plate screening	Genes resistant to toxic elements	Phenotypical detection	Chloride salts	Surface water (Mississippi River)	E. coli, fosmid	[47]
Agar plate screening	Genes resistant to toxic elements	Heterologous complementation	Acrylate	Wastewater treatment plant	E. coli, cosmid	[48]
Microtiter plate screening	Cellulase	Absorbance measurement	Dinitrophenol-cellobioside	Soil, Buffalo rumen, etc.	E. coli, fosmid	[49]
Microtiter plate screening	Esterase	Absorbance measurement	Nitrophenyl acetate	Oil reservoir	Not stated, fosmid	[50]
Microtiter plate screening	Plant polymer decomposing enzymes	Absorbance measurement	Multiple substrates	Leaf compost	E. coli, fosmid	[51]
Microtiter plate screening	Laccase, exochitinase, etc.	Absorbance measurement	ABTS, methylumbelliferone	Forest soil (Morvan, France)	Not stated	[52]
SIGEX-FACS	Aromatic hydrocarbon catabolic operons	Fluorescence	Benzoate, naphthalene	Ground water contaminated with crude oil	E. coli, plasmid	[53]
SIGEX-FACS	Transcriptional regulators	Fluorescence	Salicylate, etc.	Ground water contaminated with crude oil	E. coli, plasmid	[54]
SIGEX-FACS	Aromatic hydrocarbon induced genes	Fluorescence	Salicylate Benzoate, etc.	Soil contaminated with polyaromatic hydrocarbon	E. coli, plasmid	[55]
GESS-FACS	Phenol generating enzymes	Fluorescence	p-Nitrophenyl	Sea tidal flat sediments	E. coli, plasmid	[56]
GESS-FACS	Lipase, cellulase, etc.	Fluorescence	p-Nitrophenyl acetate, etc.	Ocean tidal flat sediment	E. coli, fosmid	[57]
GESS-FACS	Phosphatase	Fluorescence	p-Nitrophenyl phosphate	Ocean tidal flat sediments	E. coli, fosmid	[58]
GMD	Lipolytic enzymes	Fluorescence	Fluorescein dicaprylate	Soil (Quercus serrata forest)	E. coli, plasmid	[59]
GMD, FACS	Screening for antibiotics	Fluorescence	S. aureus	3 strains of Staphylococcus obtained from an ARS culture collection	E. coli S. cerevisiae, plasmid	[60]
Microfluidics (water in oil droplets), FACS	Hydrolases	Fluorescence	Sulfate monoester Phosphate triester	Variety of sources (soil, degraded plant material, cow rumen)	E. coli, plasmid	[61]

Note: AZCL, azurine-cross-linked; AZCL-HE, azurine-cross-linked hydroxyl-ethylcellulose; DMP, dimethoxyphenol; ABTS, 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate); GESS, genetic enzyme screening system; GMD, gel micro-droplet; FACS, fluorescence-activated cell sorting; SIGEX, substrate induced gene expression; ARS, agriculture research service.