title: The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method.
abstract: Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature.
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
authors.forename: Takashi
authors.initials: T
authors.lastname: Narihiro
authors.forename: Aya
authors.initials: A
authors.lastname: Suzuki
authors.forename: Kazuaki
authors.initials: K
authors.lastname: Yoshimune
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Hori
authors.forename: Tamotsu
authors.initials: T
authors.lastname: Hoshino
authors.forename: Isao
authors.initials: I
authors.lastname: Yumoto
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yokota
authors.forename: Nobutada
authors.initials: N
authors.lastname: Kimura
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kamagata
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D058491:Bacterial Load; D001483:Base Sequence; D020562:Betaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D044822:Biodiversity; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D000068536:Bacillota / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D065928:Forests; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D008049:Lipase / Q000737:chemistry / Q000378:metabolism; D008066:Lipolysis; D056186:Metagenomics; D016296:Mutagenesis; D009821:Oils / Q000378:metabolism; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D009821:Oils; D012336:RNA, Ribosomal, 16S; D012987:Soil; D008049:Lipase