Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example

Abstract

Molecular ecology approaches are rapidly advancing our insights into the microorganisms involved in the degradation of marine oil spills and their metabolic potentials. Yet, many questions remain open: how do oil-degrading microbial communities assemble in terms of functional diversity, species abundances and organization and what are the drivers? How do the functional properties of microorganisms scale to processes at the ecosystem level? How does mass flow among species, and which factors and species control and regulate fluxes, stability and other ecosystem functions? Can generic rules on oil-degradation be derived, and what drivers underlie these rules? How can we engineer oil-degrading microbial communities such that toxic polycyclic aromatic hydrocarbons are degraded faster? These types of questions apply to the field of microbial ecology in general. We outline how recent advances in single-species systems biology might be extended to help answer these questions. We argue that bottom-up mechanistic modeling allows deciphering the respective roles and interactions among microorganisms. In particular constraint-based, metagenome-derived community-scale flux balance analysis appears suited for this goal as it allows calculating degradation-related fluxes based on physiological constraints and growth strategies, without needing detailed kinetic information. We subsequently discuss what is required to make these approaches successful, and identify a need to better understand microbial physiology in order to advance microbial ecology. We advocate the development of databases containing microbial physiological data. Answering the posed questions is far from trivial. Oil-degrading communities are, however, an attractive setting to start testing systems biology-derived models and hypotheses as they are relatively simple in diversity and key activities, with several key players being isolated and a high availability of experimental data and approaches.

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

“…In this article, we review various mathematical approaches developed for simulating microbial community dynamics. While a number of published studies have offered insightful perspectives on this subject (e.g., [12][13][14][15][16][17][18]), the present review is unique in the following aspects. First, instead of being confined to specific applications, we cover a wide range of frameworks developed for modeling diverse systems such as biofilms, biogeochemical cycling (in soil or ocean), human microbiota, biotechnology processes, etc.…”

ATP luminescence assay as a bioburden estimator of biomass accumulation in caves

“…Levels of environmental microbial ATP correlate strongly with the results of aerobic plate counts (Chen & Godwin, 2006). ATP-based methods have previously been used in environmental microbiology, for example, to measure microbial activity in aquatic environments (Hammes et al, 2010), in marine oil spills (Röling & van Bodegom, 2014), in mineral leach liquors (Okibe & Johnson, 2011) and in an orthoquartzite (quartz-cemented sandstone) cave (Barton et al, 2014). The surfaces from this cave contained a high level of microbial biomass determined by an ATPbased luminescence assay when compared to other (carbonate) cave systems (Barton et al, 2014).…”

“…Quantitative measurements of microbial cellular components give a reliable estimation of the biomass (White et al, 1997) and of community structure and functioning (Röling & van Bodegom, 2014). For example, lipid phosphate or phospholipid esterlinked fatty acids provide a quantitative measure for microbes with intact cellular membrane (Gottschalk, 2012), and lipopolysaccharides (LPS) as essential life molecules for the Gram-negative bacteria (Botos et al, 2016) are used specifically to estimate their presence in the environment (Parker et al, 1982).…”

Oil Sorbents based on Methacrylic Acid - Grafted Polypropylene Fibers: Synthesis and Characterization

“…Crude oil can be released from tankers, wells, offshore and shoreline waters. Hence, the rescue for oil spill issues, particularly marine oil spills where oil is released into the sea, ocean or coastal places, is extremely complicated, consuming a lot of manpower and material resources [10][11][12]. Using low cost oil sorbents is one of the most important approaches for recovering marine oil spills.…”