Host lineage matters for bacteria

Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. We show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.

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Our paper in Nature Communications can be found at: 

 It never ceases to amaze me how the process of science gets done, and how much I enjoy being wrong. The work leading to our Nature Communications paper illustrates this point.  I had never met my co-author, Laura Meyerson, until we happened to sit on the same graduate community for a PhD student at University of Rhode Island.  I drove down from Boston for a committee meeting and Laura and I struck up a conversation about what factors control microbial community structures in soils and sediments. 

Laura is a plant biologist who specializes in invasive plant species, the mechanisms underlying invasion success, and the ecosystem consequences of invasion.  My research focuses on the role that microbial communities in salt marsh sediments play in the biogeochemistry and ecosystem services provided by salt marshes.  We didn’t have a lot of common ground unifying our research programs. 

Laura asked me whether I thought individual plant genotypes would have unique microbial signatures and I said, emphatically, that I did not think they would.  It is well known that different plant species have unique microbial consortia associated with their rooting zones, but it seemed implausible to me that different genotypes of the same plant would differentially alter their soil microbial community.  My thinking on this was informed by previous work we published in Nature Communications (Kearns et al. 2016) showing that in salt marsh sediments there are annually recurring seasonal patterns that are persistent over a decade of sampling.  Surely, over a decade of sampling by multiple people, we were not collecting sediments from the same genotype and if there was a strong genotype effect, it would overwhelm the strikingly persistent seasonal patterns we observed.  But Laura was persuasive and so we decided to do some preliminary testing. 

One of the invasive species that Laura works with is the common reed Phragmites australisP. australis has both native and invasive genotypes that can occupy the same location and she was interested to know whether the microbes associated with the different lineages mattered for the success of the plant, so she set up a common garden experiment where she grew these different lineages in individual containers with homogenized potting soil. After a few months, we harvested the plants, did basic biomass assessments, and collected the rhizosphere associated soils. 

The US invasive reed Phragmites australis, grown under greenhouse conditions at the University of Rhode Island.

 Back in the lab, and supported with funds from my NSF CAREER Award to study how marsh restorations – done, in part, to remove P. australis – alter microbial ecology of marshes, we recruited a series of undergraduates to process samples and analyze the data as part of their undergraduate honors thesis. The results of the common garden experiment were so surprising (to me), we recruited colleagues from the gulf coast to send us samples and sent people far and wide to see if these patterns persisted in the field. 

To me, at least, it is utterly amazing that the effects of plant lineage are sufficiently strong in P. australis that the microbial communities associated with their soils are more similar to plants from the same lineage that are grown thousands of miles away than they are to plants from a different lineage growing in the same system.  Carl Sagan once said that astronomy was a humbling and character building experience. I would argue that microbial ecology is as well. 

We are just beginning to understand the importance of microbes in the functioning of the planet, and, at least for me, I am excited to be wrong because it means we are adding one more piece to the puzzle. 

Individual "conetainer" containing individual lineages of P. australis grown in a common soil matrix to test the effect of lineage on rhizosphere microbial communities. 

Jennifer Bowen

Associate Professor, Northeastern University