Abstract
Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.
Highlights
Aquatic environments consist of a complex consortium of organisms engaged in syntrophic activities that have consequential impacts on ecosystem health and sustainability
Aquatic microorganisms are responsible for the cycling of vast pools of organic materials that make their way from land to water, and are the base of all complex aquatic foodwebs, which make them of integral importance to global ecosystem stability
The natural technical progression to functional omics approaches fills much of the void in a mechanistic, systems biology understanding of aquatic ecosystem dynamics
Summary
Aquatic environments consist of a complex consortium of organisms engaged in syntrophic activities that have consequential impacts on ecosystem health and sustainability. Though technological advancements and refined bioinformatics approaches have made such methodologies increasingly feasible, it is worth noting that there remain considerable challenges to the tandem-application approach These begin with the unavoidable biases inherent in the numerous sampling and preservation protocols, choice of nucleic acid isolation methods, and parameters of quality control and data filtering required during downstream bioinformatics analyses (Morgan et al, 2010; Brooks 2016; Pollock et al, 2018). Adding to this technical morass, is the array of environmental physicochemical factors influencing microbial community functionality and observed variability, especially in aquatic systems, which include water depth, temperature, sunlight exposure and seasonality, to list only few. Though methodology will naturally evolve with time, a focused development framework will allow for methodology uptake across the broader research community
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