Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics

Abstract

Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.

Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines

“…However, flavin-binding monooxygenase genes, known to be involved in the breakdown of long-chain molecules 54 were rare across samples except for Lake Assale, suggesting limited capability to decompose long-chain carbon molecules (+32C) in these ecosystems. The diversity and abundance of GH genes increased with salinity-chaotropicity, especially in the WCLs (Extended Data Fig.8), suggesting that these extremely halophilic archaea and possibly also bacteria 55 degrade a broad range of hydrocarbons 56 , mirroring observations in Ethiopian soda lakes 57 . In addition, Danakil MAGs contained genes for carbon storage, such as polyhydroxybutyrate biosynthesis genes (phbC), a common trait in many haloarchaea 58 .…”

“…The diversity and abundance of GH genes increased with salinitychaotropicity, especially in the WCLs (Extended Data Fig. 8), suggesting that these extremely halophilic archaea and possibly also bacteria 55 degrade a broad range of hydrocarbons 56 , mirroring observations in Ethiopian soda lakes 57 . In addition, Danakil MAGs contained genes for carbon storage, such as polyhydroxybutyrate biosynthesis genes (phbC), a common trait in many haloarchaea 58 .…”

A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation

“…In our preceding research 37 , we constructed metagenomic libraries from Ethiopian Soda lakes, which underwent a functional screening process targeting hydrolytic enzymes, including β-glucosidase activity. Subsequent to the screening, clones demonstrating positive results were chosen for sequencing.…”

“…Based on our previous study, the aim of this study was to investigate and characterize the enzymatic properties of a gene (CelGH3_f17) previously identified in a metagenomic library from an Ethiopian soda lake 37 , to elucidate its potential application in industrial processes. This included the cloning and expression of the gene, to study the properties and stability of the encoded β-glucosidase enzyme under extreme industrial conditions, such as high temperatures and varying pH levels.…”

Microbiology of Big Soda Lake, a multi‐extreme meromictic volcanic crater lake in the Nevada desert

“…It also exhibits some of the fastest growing tufas in the world (Medina Ferrer et al, 2022; Rosen et al, 2004), that is, stromatolite‐like structures hypothesised to emerge from a combination of abiotic and microbial processes (Cousin & Stackebrandt, 2010; Ford & Pedley, 1996), and constituting promising targets for recovering historical biosignatures (Hays et al, 2017; Potter‐McIntyre et al, 2016; Westall et al, 2021). These features make BSL a fascinating system for studying the boundaries of life's adaptations, for understanding life on early Earth and potentially on other planets, for recovering novel deeply rooted taxa, and for discovering biotechnologically useful strains and enzymes (Horikoshi, 1999; Jeilu, Simachew, et al, 2022; Mohamed et al, 2023). LSL constitutes an interesting but much less studied comparison to BSL: Despite its spatial proximity to BSL and their shared geological history, LSL does not exhibit a strong halo‐ or chemocline, likely due to its smaller depth (about 12 m in the centre).…”