Large-Data Omics Approaches in Modern Remediation
Abstract
Background
Using Omics to Track, Identify, and Assess the Extent of Site Contamination
Integration of Omics in Remediation
Omics in Electron Donor Injections
Interpretation of Omics Data
Approach | Focus | Methods | Advantages | Limitations |
---|---|---|---|---|
Genomics | Microbial community assessment, taxonomy classification, phylogeny | Amplicon sequencing: 16S, ITS, 18S | • Quick analysis • Chip methods have low biomass and abundance requirements (Liu et al. 2021) | • PCR amplification and primer bias • Chip-based methods only identify preselected organisms |
PhyloChip, GeoChip | ||||
Metagenomics | Functional potential, bioprospecting, novel gene annotation | Shotgun sequencing | • Can obtain whole genomes • Novel gene identification • Can assess functional potential if larger contigs are assembled | • Expensive • Complicated analysis • Data quality is highly dependent on sequencing depth (Hazen et al. 2013) |
Proteomics | Complete protein profile, assimilation pathways, post and substrate utilization | HP-LC/GC, mass spectrometry (MS), X-ray crystallography | • Versatile tool for differential expression • Can quantify abundance data for community • Scope for novel protein discovery | • Ambiguity of composition results depends on accurate measurement of peptide mass • Reproducibility and specificity |
Lipidomics | Quantitative profile of the lipids in a biological system, species identification | GC/LC-MS, NMR | • Biomarker discovery • Community profiling • Functional grouping | • Complicated analysis • Requires extensive computational resources |
Metabolomics | Total metabolite profile with respect to fluctuating environmental stress, | HP-LC, MS, FT-IR | • Allows quantification of cellular regulation in response to environment • Evaluation of enzymatic activity | • Highly specialized • Expensive • Measurements are nonquantitative • Requires extensive computational analysis |
Transcriptomics | Microbial activity, gene expression profiling, novel transcript prospecting | RNA-seq, DNA microarray, qPCR and RT-PCR | • Able to distinguish between active and sedentary community members • Able to provide transcript level resolution | • Sample collection is tedious • Expensive to sequence • Risk of contamination within the microbiome |
Note: FT-IR = Fourier-transform infrared; GC = gas chromatography; HP-LC = high performance liquid chromatography; ITS = internal transcribed spacer; LC = liquid chromatography; NMR = nuclear magnetic resonance; qPCR = quantitative polymerase chain reaction; RNA-seq = ribonucleic acid sequencing; and RT-PCR = reverse transcription polymerase chain reaction.