Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

Rashid, Mamoon; Stingl, Ulrich

doi:10.1016/j.biotechadv.2015.09.005

Cited by 33 publications

(31 citation statements)

References 287 publications

(239 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The number of metagenomic studies has increased in recent years [ 39 ]. Metagenomics has been used to evaluate and exploit biodiversity in many habitats, including extremophiles environments [ 40 , 41 , 42 , 43 , 44 , 45 ]. In this study, we determined the prokaryotic diversity of sulphydric hot springs in the VL caves of Tacotalpa, Tabasco, Mexico, with severe limitations or total absence of light.…”

Section: Discussionmentioning

confidence: 99%

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

D’Auria

Artacho

Rojas

et al. 2018

Genes

View full text Add to dashboard Cite

New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L−1 H2S and <0.1 mg L−1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.

show abstract

Section: Discussionmentioning

confidence: 99%

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

D’Auria

Artacho

Rojas

et al. 2018

Genes

View full text Add to dashboard Cite

show abstract

“…This approach typically involves screening hundreds of thousands of clones, and the number of biocatalytically active proteins discovered is dependent on the library size. An alternative is the in silico search for homologs of known biocatalysts in metagenomic datasets, a method we have recently employed ourselves [5], and which is comprehensively reviewed in [6]. This method uses known structural motifs to find novel enzymes in sequence databases.…”

Section: Main Textmentioning

confidence: 99%

Simple discovery of bacterial biocatalysts from environmental samples through functional metaproteomics

et al. 2017

View full text Add to dashboard Cite

Bacterial biocatalysts play a key role in our transition to a bio-based, post-petroleum economy. However, the discovery of new biocatalysts is currently limited by our ability to analyze genomic information and our capacity of functionally screening for desired activities. Here, we present a simple workflow that combines functional metaproteomics and metagenomics, which facilitates the unmediated and direct discovery of biocatalysts in environmental samples. To identify the entirety of lipolytic biocatalysts in a soil sample contaminated with used cooking oil, we detected all proteins active against a fluorogenic substrate in sample’s metaproteome using a 2D-gel zymogram. Enzymes’ primary structures were then deduced by tryptic in-gel digest and mass spectrometry of the active protein spots, searching against a metagenome database created from the same contaminated soil sample. We then expressed one of the novel biocatalysts heterologously in Escherichia coli and obtained proof of lipolytic activity.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0247-9) contains supplementary material, which is available to authorized users.

show abstract

“…However, microorganisms inhabiting and adapted to these extreme environments are hardly cultivable. With the rise of culture‐independent methods, this ‘microbial dark matter’ is now open for exploration . We identified the ADH gene adh/a1a by utilizing annotated SAGs, derived from water samples of the Atlantis II Deep Red Sea brine pool .…”

Section: Discussionmentioning

confidence: 99%

A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool

et al. 2018

View full text Add to dashboard Cite

Enzymes originating from hostile environments offer exceptional stability under industrial conditions and are therefore highly in demand. Using single‐cell genome data, we identified the alcohol dehydrogenase (ADH) gene, adh/a1a, from the Atlantis II Deep Red Sea brine pool. ADH/A1a is highly active at elevated temperatures and high salt concentrations (optima at 70 °C and 4 mKCl) and withstands organic solvents. The polyextremophilic ADH/A1a exhibits a broad substrate scope including aliphatic and aromatic alcohols and is able to reduce cinnamyl‐methyl‐ketone and raspberry ketone in the reverse reaction, making it a possible candidate for the production of chiral compounds. Here, we report the affiliation of ADH/A1a to a rare enzyme family of microbial cinnamyl alcohol dehydrogenases and explain unique structural features for halo‐ and thermoadaptation.

show abstract

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

Cited by 33 publications

References 287 publications

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

Simple discovery of bacterial biocatalysts from environmental samples through functional metaproteomics

A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool

Contact Info

Product

Resources

About