Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes

Abstract

The advent of genomic‐, transcriptomic‐ and proteomic‐based approaches has revolutionized our ability to describe marine microbial communities, including biogeography, metabolic potential and diversity, mechanisms of adaptation, and phylogeny and evolutionary history. New interdisciplinary approaches are needed to move from this descriptive level to improved quantitative, process‐level understanding of the roles of marine microbes in biogeochemical cycles and of the impact of environmental change on the marine microbial ecosystem. Linking studies at levels from the genome to the organism, to ecological strategies and organism and ecosystem response, requires new modelling approaches. Key to this will be a fundamental shift in modelling scale that represents micro‐organisms from the level of their macromolecular components. This will enable contact with omics data sets and allow acclimation and adaptive response at the phenotype level (i.e. traits) to be simulated as a combination of fitness maximization and evolutionary constraints. This way forward will build on ecological approaches that identify key organism traits and systems biology approaches that integrate traditional physiological measurements with new insights from omics. It will rely on developing an improved understanding of ecophysiology to understand quantitatively environmental controls on microbial growth strategies. It will also incorporate results from experimental evolution studies in the representation of adaptation. The resulting ecosystem‐level models can then evaluate our level of understanding of controls on ecosystem structure and function, highlight major gaps in understanding and help prioritize areas for future research programs. Ultimately, this grand synthesis should improve predictive capability of the ecosystem response to multiple environmental drivers.

Hybrid datasets: integrating observations with experiments in the era of macroecology and big data

“…, Mock et al. ). Hence, the hybridization strategy proposed here can also be implemented to increase the scope and causal inferential strength of studies that make extensive use of DNA‐sequencing techniques, which are amongst the most important contemporary sources of “big data” in ecology.…”

“…Opportunities arise with studies examining the molecular mechanisms regulating the response of organism to stress. For example, recent studies on microbes and corals have integrated observational and experimental approaches to evaluate the effects of global warming on gene expression (Barshis et al 2013, Mock et al 2016. Hence, the hybridization strategy proposed here can also be implemented to increase the scope and causal inferential strength of studies that make extensive use of DNA-sequencing techniques, which are amongst the most important contemporary sources of "big data" in ecology.…”

Competition between Silicifiers and Non-silicifiers in the Past and Present Ocean and Its Evolutionary Impacts

“…This has been complemented by the discovery of new silicifying species (Ichinomiya et al, 2011), most notably silicon accumulation in some strains of the hugely ecologically important cyanobacteria Synechococcus (Baines et al, 2012). Combined with metagenomic surveys and geochemical monitoring (Mutsuo et al, 2015;Sunagawa et al, 2015) it will be possible to gain a much deeper knowledge of the role of different marine groups in silicon biogeochemistry and how competitive interactions govern their ecology, distribution and response to changing climatic conditions (Mock et al, 2016).…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…Microbial species dominate the ocean numerically and the majority of marine primary production is microbial in origin, produced by cyanobacteria and microalgae (Duarte and Cebrian, 1996;DeLong, 2009;Amaral-Zettler et al, 2010). Microorganisms may act as sentinels of system ecological status because they respond rapidly to natural and anthropogenic environmental pressures in terms of diversity, physiology, and function (Mock and Kirkham, 2012;Nogales et al, 2011;Mock et al, 2015). They hold promise as ecosystem indicators with regard to measures of biodiversity, toxic species, pathogens, and metabolic properties that indicate ecosystem health, such as biodegradation capacity and resistance to metals and antibiotics (Ininbergs et al, 2015;Tan et al, 2015;Caruso et al, 2016).…”

“…The Global Ocean Sampling expedition helped establish DNA sequencing as a fundamental tool in marine ecosystem research (Rusch et al, 2007;Dupont et al, 2015). Potential benefits of DNA sequencing of microbial communities to marine assessment programs include characterization of food webs, assessing responses to disruption and stress, and detection of sensitive, rare, threatened, toxic, or invasive taxa (Hulme, 2006;Kudela et al, 2010;Mock and Kirkham, 2012;Lindeque et al, 2013;Muller-Karger et al, 2014;Pawlowski et al, 2014;Chown et al, 2015;Mock et al, 2015;Tan et al, 2015;Zaiko et al, 2015;Bowers et al, 2016;Bucklin et al, 2016).…”