Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest

Abstract

Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms. For this, an in-depth survey of the taxonomic and functional microbial diversity recovered in a fosmid library (Library_Oil Mgv) constructed from oil-impacted Brazilian mangrove sediment was carried out. Fosmid DNA of the whole library was extracted and submitted to Illumina HiSeq sequencing. The resulting Library Oil_Mgv dataset was further compared with those obtained by direct sequencing of environmental DNA from Brazilian mangroves (from distinct regions and affected by distinct sources of contamination), focusing on hydrolases with potential use in biotechnological processes. The most abundant hydrolases found were proteases, esterases and amylases, with similar occurrence profile in all datasets. The main microbial groups harboring such hydrolase-encoding genes were distinct in each mangrove, and in the fosmid library these enzymes were mainly assigned to Chloroflexaceae (for amylases), Planctomycetaceae (for esterases) and Bradyrhizobiaceae (for proteases). Assembly and analysis of Library_Oil Mgv reads revealed three potentially novel enzymes, one epoxide hydrolase, one xylanase and one amylase, to be further investigated via heterologous expression assays.

Invited Review: Biodiversity of Plant Polysaccharide-Degrading Bacteria in Mangrove Ecosystem

“…In addition, several thermostable cellulases were also isolated (Kalaiselvi et al 2013;Naresh et al 2019). Meanwhile, based on metagenomic approaches, bacteria belonging to three phyla, Proteobacteria, Firmicutes and Actinobacteria were detected as cellulose-degrading bacteria, and a novel β-glucosidase and a endoglucanase were cloned and characterized (Li et al 2012;Mai et al 2014;Thompson et al 2013;Ottoni et al 2017). Besides that, Numerous genes encoding cellulose-degrading enzymes, such as, endo-1,4-D -glucanase (cellulase) and β-glucosidase were found in metagenome datasets from Matang Mangrove Forest Reserve (Priya et al 2018).…”

“…Ottoni and colleagues conducted taxonomic analysis of the hydrolase sequences including cellulase in fosmid library constructed from mangrove sediment in São Paulo state, Bertioga, Brazil (Ottoni et al 2017). As a result of the analysis, cellulase related to the families Pseudomonadaceae and Thermoanaerobacteraceae were the most abundant.…”

Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods

“…The culture-dependent method is a classical strategy for bioprospecting enzymes from environmental samples [12]. However, the necessity to reproduce requirements for microbial growth in laboratory conditions is a limitation of this approach [13]; thus, new strategies for bioprospecting have been driven by culture-independent methods, such as functional screening from metagenomic libraries constructed using environmental DNA [14]. This method favors the discovery of enzymes from uncultivated microorganisms without performing a cultivation step [15].…”

“…The present study aimed to identify genes and microorganisms from mangrove samples that were able to produce xylanases and amylases, either using approaches dependent and independent of cultivation. Based on previous studies that explored the mangrove sediments as biotechnological source [14,[19][20][21], the study hypothesized that the conditions found in mangrove areas, mainly the high salinity, could select for organisms harboring genes and enzymes of high industrial interest and these enzymes could be recovered by applying culture-dependent and cultureindependent methods.…”

Clinical Resistome Screening of 1,110 Escherichia coli Isolates Efficiently Recovers Diagnostically Relevant Antibiotic Resistance Biomarkers and Potential Novel Resistance Mechanisms

“…Functional metagenomics is a multi-step experimental approach that uses expression libraries encoding isolated DNA of mixed microbial populations for the transformation of a relevant host microorganism. Transformed clones can subsequently be selected for a broad range of phenotypes of interest, e.g., enzymatic activities such as lipo-, haemo- or hydrolytic activities (Henne et al, 2000; Rondon et al, 2000; Ottoni et al, 2017). This potentially results in the discovery of novel candidate enzymes that are encoded in the original microbial population.…”