Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern

Abstract

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

Emerging Strategies in Polyethylene Terephthalate Hydrolase Research for Biorecycling

“…It should be noted that two genes obtained by a metagenomic approach from different sources have higher sequence identity than those of thermophilic actinomycetes, although LC-cutinase has a protein structure homologous to thermophilic cutinases from actinomycetes. As Chloroflexi was identified as one of the dominant members in the communities of the compost samples, [38] the origin of LC-cutinase may be from Chloroflexi rather than actinomycetes, as shown in Figure 1. Interestingly, both LC-cutinase and BhrPETase are closer to thermophilic cutinases from actinomycetes than to the PETase homolog group.…”

Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern

“…We acknowledge support by the Open Access Publication Funds of the University of Göttingen. A version of the manuscript is available as preprint (Lu et al, 2021).…”