Progress 05/01/15 to 08/31/17
Outputs
Target Audience:Scientists interested in microbial interactions and their effect on the functioning of complex microbial communities such as those in soil. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One graduate student was trained. How have the results been disseminated to communities of interest?Results were disseminated through publications and scientific presentations. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Manipulation of soil microbial communities is an exciting frontier with the potential to substantially reduce the use of chemical fertilizers and pesticides, to expand the types of soils and climates suitable for agriculture, and to counter the gradual decrease in soil quality associated with intensive agriculture. To advance our understanding of how microbial communities assemble and our ability to manipulate communities, we established a platform for systematically studying the relationship between ecological interactions and dynamics in multi-species communities of soil bacteria. We performed a tournament between soil bacteria in which bacteria from different species try to defend their territory against invaders or invade territory dominated by bacteria from another species. To date, little has been empirically determined about the structure of natural competitive networks, and our findings differ markedly from long-standing assumptions. Conventional wisdom is that species can be ordered according to their competitive ability if they occupy the same ecological niche, coexist if they occupy different niches, or perhaps enter into relationships of cyclic dominance, such as paper-scissor-rock-games, if they participate in niche construction activities. In sharp contrast, we found that: 1. It is impossible to rank species based on their competitive ability (aka survival of the fittest) even when they are competing in simple well-defined environments, while at the same time loops of cyclic dominance are extremely rare. 2. There is a strong tendency for species that are already abundant in the environment to hold their ground (aka-survival of the common), which results in alternative stable states for even the simplest two-species microbial communities. Instead of a single winner, our tournament resulted in multiple dominant species that could exclude each other depending on their initial abundances. These findings have several immediate implications for how we view the assembly, structuring and diversity of microbial communities. They indicate that pairwise interactions inherently predispose communities toward multiple stable states. This makes microbial communities intrinsically sensitive to initial conditions during community assembly but, at the same time, makes them more resistant to change once they are established. These results suggest that high inocula would be typically needed to establish a novel beneficial microbe in soil, but a successful treatment would not have to be repeated every year. In addition, we measured the antibiotic interactions within the panel of microbial strains. We determined that antibiotic interactions promote the bistability that we observed. These results were published in Nature Communications. Monitoring community dynamics relied on multiplexing hundreds of samples in a single Illumina run. An unexpected technical limitation we encountered was the high level of cross-talk between different multiplexed samples. In view of the widespread use of multiplexing by researchers, we performed dedicated experiments investigating cross-talk errors and came up with an effective solution, which was submitted for publication. Elimination of cross-talk overcomes a major obstacle to obtaining accurate quantitative information on effective ecological interactions and community dynamics in a scalable fashion. Finally, DNA-barcoded streptomyces strains were used to quantify and analyze the population dynamics of streptomyces strains that germinate and colonize a habitat. We found a very strong variance in reporductive success between different individuals from the same strain. The distribution of descendants that arise from individual bacteria is heavy-tailed, with a few cells effectively "winning the jackpot" to become a disproportionately large fraction of the population. The implication of these results is that in soil systems with feast and famine cycles in which microbes form spores and germinate, beneficial mutations will be much easier to spread in the population relative to the predictions of classical population genetics. This results can help us understand the fast evolution of microbes in soil. Our work also provides a general, scalable methodology for quantifying genetic drift in soil communities.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2018
Citation:
Erik S. Wright and Kalin Vetsigian. Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations. In review in eLife. Available as pre-print at: https://www.biorxiv.org/content/early/2018/01/11/246629 .
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Scientists interested in microbial interactions and their affect on the functioning of complex microbial communities such as those in soil. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project contributed to the training and professional development of a graduate student and an undergraduate student. How have the results been disseminated to communities of interest?The main findings were submitted to Nature Communications and a Methodology developed was submitted to BMC Genomics. What do you plan to do during the next reporting period to accomplish the goals?We will finish our study of communities containing more than two species and test if the ecological dynamics in the multi-species communities can be predicted based on the pairwise interactions.
Impacts
What was accomplished under these goals?
Manipulation of soil microbial communities is an exciting frontier with the potential to substantially reduce the use of chemical fertilizers and pesticides, to expand the types of soils and climates suitable for agriculture, and to counter the gradual decrease in soil quality associated with intensive agriculture. To advance our understanding of how microbial communities assemble and our ability to manipulate communities, we established a platform for systematically studying the relationship between ecological interactions and dynamics in multi-species communities of soil bacteria. We performed a tournament between soil bacteria in which bacteria from different species try to defend their territory against invaders or invade territory dominated by bacteria from another species. To date, little has been empirically determined about the structure of natural competitive networks, and our findings differ markedly from long-standing assumptions. Conventional wisdom is that species can be ordered according to their competitive ability if they occupy the same ecological niche, coexist if they occupy different niches, or perhaps enter into relationships of cyclic dominance, such as paper-scissor-rock-games, if they participate in niche construction activities. In sharp contrast, we found that: 1. It is impossible to rank species based on their competitive ability (aka survival of the fittest) even when they are competing in simple well-defined environments, while at the same time loops of cyclic dominance are extremely rare. 2. There is a strong tendency for species that are already abundant in the environment to hold their ground (aka-survival of the common), which results in alternative stable states for even the simplest two-species microbial communities. Instead of a single winner, our tournament resulted in multiple dominant species that could exclude each other depending on their initial abundances. These findings have several immediate implications for how we view the assembly, structuring and diversity of microbial communities. They indicate that pairwise interactions inherently predispose communities toward multiple stable states. This makes microbial communities intrinsically sensitive to initial conditions during community assembly but, at the same time, makes them more resistant to change once they are established. These results suggest that high inocula would be typically needed to establish a novel beneficial microbe in soil, but a successful treatment would not have to be repeated every year. In addition, we measured the antibiotic interactions within the panel of microbial strains. We determined that antibiotic interactions promote the bistability that we observed. These results were published in Nature Communications. Monitoring community dynamics relied on multiplexing hundreds of samples in a single Illumina run. An unexpected technical limitation we encountered was the high level of cross-talk between different multiplexed samples. In view of the widespread use of multiplexing by researchers, we performed dedicated experiments investigating cross-talk errors and came up with an effective solution, which was submitted for publication. Elimination of cross-talk overcomes a major obstacle to obtaining accurate quantitative information on effective ecological interactions and community dynamics in a scalable fashion. Lastly, we started performing experiments with multi-species communities that will be submitted for publication in 2017.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Erik S. Wright and Kalin Vetsigian. Inhibitory interactions promote frequent bistability among competing bacteria. Nature Communications 7, Article number: 11274 (2016).
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Progress 05/01/15 to 09/30/15
Outputs
Target Audience:Scientists interested in microbial interactions and their affect on the functioning of complex microbial communities such as those in soil. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project contributed to the training and professional development of a graduate student. How have the results been disseminated to communities of interest?Methodology we developed was published in the journal of Bioinformatics.The mainfindings have been submitted as a seperate publication (see Products section). What do you plan to do during the next reporting period to accomplish the goals?Antibiotic interactions among the panel ofmicrobial strains will be characterizedto determine their role inshaping the microbial competitive networks and promoting the bistability (survival of the common) that we identified. We will then proceed to study communities of more than two species.
Impacts
What was accomplished under these goals?
Manipulation of soil microbial communities is an exciting frontier with the potential to substantially reduce the use of chemical fertilizers and pesticides, to expand the types of soils and climates suitable for agriculture, and to counter the gradual decrease in soil quality associated with intensive agriculture. To advance our understanding of how microbial communities assemble and our ability to manipulate communities, we established a platform for systematically studying the relationship between ecological interactions and dynamics in multi-species communities of soil bacteria. We performed a tournament between soil bacteria in which bacteria from different species try to defend their territory against invaders or invade territory dominated by bacteria from another species. To date, little has been empirically determined about the structure of natural competitive networks, and our findings differ markedly from long-standing assumptions. Conventional wisdom is that species can be ordered according to their competitive ability if they occupy the same ecological niche, coexist if they occupy different niches, or perhaps enter into relationships of cyclic dominance, such as paper-scissor-rock-games, if they participate in niche construction activities. In sharp contrast, we found that: 1. It is impossible to rank species based on their competitive ability (aka survival of the fittest) even when they are competing in simple well-defined environments, while at the same time loops of cyclic dominance are extremely rare. 2. There is a strong tendency for species that are already abundant in the environment to hold their ground (aka-survival of the common), which results in alternative stable states for even the simplest two-species microbial communities. Instead of a single winner, our tournament resulted in multiple dominant species that could exclude each other depending on their initial abundances. These findings have several immediate implications for how we view the assembly, structuring and diversity of microbial communities. They indicate that pairwise interactions inherently predispose communities toward multiple stable states. This makes microbial communities intrinsically sensitive to initial conditions during community assembly but, at the same time, makes them more resistant to change once they are established. These results suggest that high inocula would be typically needed to establish a novel beneficial microbe in soil, but a successful treatment would not have to be repeated every year. To accomplish these goals, we also developed a novel methodology for quickly and cheaply determining the type of a bacterial strains. This methodology (described in DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures, Erik S. Wright, Kalin H. Vetsigian, Bioinformatics 2016) can be useful for many different applications, and can potentially be harnessed to monitor pathogens in food and thus improve food safety.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures
Erik S. Wright; Kalin H. Vetsigian
Bioinformatics 2016; doi: 10.1093/bioinformatics/btw047
- Type:
Journal Articles
Status:
Submitted
Year Published:
2016
Citation:
Erik S. Wright; Kalin H. Vestigial. Inhibitory interactions promote frequent bistability among competing bacteria
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