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Research Highlights

May 2014

Cyanobacterial Consortia Shed New Light on Phototrophic Biofilm Assembly

Model "microecosystems" used to study producer-consumer interaction networks in microbial mats

microscopy images of microbes
Scanning electron micrographs of the unicyanobacterial consortia Phormidesmis priestleyi str. ANA (top) and Phormidium sp. OSCR (bottom). Pacific Northwest National Laboratory scientists isolated these consortia from a microbial mat in a lake and characterized their membership and interactions as a step toward using these organisms in global carbon and energy cycling applications.

Results: As part of their ongoing studies of the complex world of microbial communities, scientists at Pacific Northwest National Laboratory recently isolated two bacterial consortia from a microbial mat in Hot Lake, located in north-central Washington State. They characterized each consortia's membership and metabolic function to identify the interactions thought to recruit and maintain genetic and functional diversity in the consortia over time.

The team's results shed light on the principles that govern microbial communities, principles needed for scientists to move closer to the goal of being able to predict, engineer, and manipulate microbial communities of importance to global carbon and energy cycling.

These consortia are each anchored by a single cyanobacterium—a type of autotroph—that obtains energy from sunlight through photosynthesis and uses the energy to produce sugars from carbon dioxide. In turn, the autotrophs supply many heterotrophs—organisms that consume carbon produced by other organisms—with the carbon and oxygen they need to harvest energy and produce biomass.

"Primary production by microbial autotrophs and consumption by heterotrophs are occurring everywhere," said Dr. Steve Lindemann, PNNL microbiologist and lead author of the study, which appears in Frontiers in Microbiology. "If you don't understand the interactions, you can't predict how communities will respond to changing environmental conditions or engineer them to sustainably perform a useful function; for example, making them more productive—to generate more biomass for bioenergy applications—or resilient, so they recover quickly from environmental shocks. It's a big deal."

The relative simplicity and tractability of the consortia make them useful model systems for deciphering the interspecies interactions and principles of microbial community assembly.

The PNNL scientists found that though the consortia shared all their members except for the cyanobacteria, they contained very different abundances of each member as the communities assembled into a biofilm. This suggested that specific interactions between the cyanobacteria and heterotrophs generate a different network of interactions. These networks likely create related but unique niches that support different population sizes of each heterotroph.

The scientists also found that autotroph growth rates dominated early in assembly but yielded to heterotroph growth rates late in the growth cycle. Although the heterotrophic species composition was similar in both consortia, the population dynamics of different species varied significantly as their biofilms matured. These data suggest that, although the niches provided by the cyanobacterial metabolisms are sufficiently broad to retain the same species, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions in each consortium are likely distinct.

Why It Matters: Much like members of a growing village, microbial community members occupy niches that support their own growth, but in turn also promote other members' growth; analogous, perhaps, to a microbe's "occupation" within its community. Though different microbial "villages" require similar resources for growth, the way those resources are produced and move through the community will depend upon which niche each microbe is filling and its abundance. Consequently, though similar kinds of niches may be created in each community, there will be distinctions in the numbers or specialties of members occupying those niches depending upon other members and the community's circumstances.

As Lindemann explains, "For example, while two villages will require farmers for food production, whether those farmers are growing wheat, rice, or corn will impact the roles of other members of the community—in this example, perhaps in the amounts and types of bread made by bakers. Similarly, different primary producers are likely to interact with heterotrophic consumers in similar but unique ways. These differences will then have cascading effects upon interactions between heterotrophic members."

Such disparities in the network of interactions between two microbial communities are likely to create distinct niches in each, support different population sizes of each member species, and affect a community's overall functions and properties. Comparing interactions occurring within these two consortia therefore brings scientists closer to understanding the principles governing similar interactions in the wild—and may allow them to better predict and control microbial communities.


Process for isolation and cultivation of the unicyanobacterial consortia.

Methods: The PNNL team defined the membership and examined the spatial structure and phototroph-heterotroph succession of unicyanobacterial consortia as they assembled into biofilms. Earlier studies were limited to quantifying populations of cultivable organisms and were therefore unable to estimate the diversity of potential colonizers in experimental "microecosystems."

"Next-generation sequencing has greatly expanded our ability to comprehensively characterize a community's membership, and molecular quantitation at the species level allows us to assess heterotroph abundance independent of cultivation," Lindemann said. "We can now track the dynamics of all of the community's members, whether we can grow them by themselves or not."

Interestingly, though different cyanobacteria were primary producers in each consortium, both retained the same suite of heterotrophic species.

What's Next? The team plans to subject the consortia to environmental perturbation (such as variations in salinity, light, temperature, or availability of specific nutrients) to examine how changing conditions affect the structure and composition of the assembling consortial biofilms.

Acknowledgments:

Sponsors: This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), Genomic Science Program (GSP), as part of the PNNL Foundational Scientific Focus Area. Portions of this work were performed at the DOE Joint Genome Institute (JGI), and in EMSL, a BER-sponsored national scientific user facility located at PNNL.

Research Team: Jessica K Cole, Janine R Hutchison, Ryan S Renslow, Young-Mo Kim, William B Chrisler, Heather E Engelmann, Alice Dohnalkova, Dehong Hu, Thomas O Metz, Jim K Fredrickson, and Stephen R Lindemann, all PNNL.

Research Area: Biological Systems Science

User Facilities: EMSL, JGI 

Reference: Cole JK, JR Hutchison, RS Renslow, YM Kim, WB Chrisler, HE Engelmann, A Dohnalkova, D Hu, TO Metz, JK Fredrickson, and SR Lindemann. 2014. "Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions." Frontiers in Microbiology 5:109. DOI: 10.3389/fmicb.2014.00109.

Related Research:

Light Variation Drives Community Structure of a Hypersaline Microbial Mat


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Creating Consortia

Microbial consortia are assemblages of multiple microbial species interacting with one another. They are frequently found in nature, but few have been cultivated in the laboratory. PNNL scientists cultured two consortia from Hot Lake microbial mat samples for their investigations. The microbial mat is a complex environment, subject to uncontrolled environmental variables and diverse populations of organisms, making it difficult to link the causes and effects of changes in the mat community. The cultivated consortia contain a more manageable representation of organisms from the mat, allowing scientists to more easily identify and determine the networks of interactions.

To create the consortia, the scientists streaked biomass from a sample of the green layer of the Hot Lake mat onto plates (see Methods section for the process). They cultivated two morphologically distinct cyanobacterial filaments, yielding two unicyanobacterial consortia, UCC-A and UCC-O, Phormidesmis priestleyi str. ANA and Phormidium sp. OSCR, respectively. Experimental cultures were grown in tissue culture flasks for metabolomic, composition, and real-time PCR analyses. Glass-bottom dishes were used for microscopic analysis of the biofilms.

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