Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites

Abstract

The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; < 5%). Detailed analysis of the genes predicted to encode proteins of the abH08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes.

Fig 1

Relative abundance (%) of the most abundant α/β-hydrolase fold protein superfamilies in the four mangrove metagenomes (BrMgv01 to BrMgv04). Oil Mgv: oil-polluted mangrove site; Ant Mgv: anthropogenic polluted site; Prs: pristine mangrove site. The database was downloaded from the LED ftp website – http://www.led.uni-stuttgart.de/ – release 3.0, last update on 10 December 2009. Normalization was performed using the total number of annotated sequences (in LED) in each dataset.

Fig 2

Relative abundance (%) of the most abundant α/β-hydrolase fold protein families in four mangrove metagenomes (BrMgv01-BrMgv04). Hierarchical dendrogram and heat-mapping were performed using cluster V3.0 (Eisen et al., 1998) software. Red and green dots represent the epoxide hydrolase (EHs) and haloalkane dehalogenase (HDs) families respectively.

Fig 3

Left: principal component analysis (PCA) within the family abH08 using Canoco software v4.52 (Wageningen, the Netherlands). Right: Number of unassembled sequences annotated in the abH08.02 [epoxide hydrolases (EHs)] and abH08.05 [haloalkane dehalogenases (HDs)] families in BrMgv samples.