New framework for studying populations within complex microbial communities explored

A group of researchers from Uppsala and Stockholm University, co-led by SciLifeLab Fellow Sarahi L. Garcia, have explored the metabolic partnerships between three of the worlds’ most abundant freshwater bacterial genera. By combining network and ecological theory with empirical evidence, they have managed to birth a novel framework for studying populations within complex microbial communities. 

The complexity of aquatic life is hard to grasp. High microbial diversity, intricate relationships, interrelationships, and uneven resource allocation coupled with a plethora of different species sharing the same space creates a difficult problem for researchers to overcome when trying to understand the significance of certain aspects within these ecosystems. 

Sarahi L. Garcia together with co-leader Rhiannon Mondav and their team wanted to untangle some of the complexity by looking at a strain of so-called fastidious microbes, organisms with complex nutritional needs, common to freshwater lakes. Their results were published in the scientific journal American Society For Microbiology.

A major problem is that abundant environmental microbes can seldom be grown outside their natural environments. In part, because they are often unable to synthesize all the compounds needed for growth themselves, and to make up for any deficiencies, microbes often rely on the surrounding cohort of organisms. A cohort includes either slightly differing individuals of the same species that carries subtle alterations adapted for local variations (ecotypes), or other distantly related organisms that inhabit the same space (called communities).  

The metabolic partnerships of these genera to their surrounding communities of organisms and mode of cooperation can be either “reciprocal, nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product)”.

To approach the problem, the researchers decided to explore the ecological and evolutionary relationships between three of the most ubiquitous and abundant freshwater bacterial genera Candidatus, Ca. Planktophila, Ca. Nanopelagicus, and Ca. Fonsibacter; and explain their abundance and positions as dominant bacterioplankton living in a freshwater lake that is dimictic (the water of the lake mixes twice a year) and mesotrophic (medium levels of productivity and nutrients). To do this the researchers used a culture-dependent and a culture-independent method and managed to identify the three above-mentioned genus of actinobacteria and proteobacteria. 

“Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwater worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies.” according to the report.

The researchers found that the population abundance of the actinobacteria genus Ca. Planktophila could be explained by the interactions and cooperation between genus ecotypes and their surrounding community. This, however, diverges from the success of Ca. Nanopelagicus and Ca. Fonsibacter, that is better explained as a community by-product. Any correlation between the natural habitats of Ca. Planktophila and Ca. Fonsibacter (although still potentially complementary in laboratory settings) could not be seen.

“Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.”

The study was facilitated by the SciLifeLab National Genomics Infrastructure (NGI).

Read the Research Article here


Last updated: 2020-10-15

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