18 research outputs found
Fables for All Ages
No full textTagore is a favorite author for me as a writer of poems bearing on the spiritual life. I was thus surprised to see him presented as a writer of fables. Alas, I fear that what is in this paperback book is not fables as I understand "fable." A T of C would have helped me realize that there are three longer works here, perhaps short stories or Novellen. I have to save enjoying them for a later time. For now, I include the book in the collection as a help to me and others who may expect something different from the book's title.Abanindranath Tagore, translated biy Manoshi Bhattachary
Microbial interactions and community assembly at microscales
No full textIn most environments, microbial interactions take place within microscale cell aggregates. At the scale of these aggregates (∼100μm), interactions are likely to be the dominant driver of population structure and dynamics. In particular, organisms that exploit interspecific interactions to increase ecological performance often co-aggregate. Conversely, organisms that antagonize each other will tend to spatially segregate, creating distinct micro-communities and increased diversity at larger length scales. We argue that, in order to understand the role that biological interactions play in microbial community function, it is necessary to study microscale spatial organization with enough throughput to measure statistical associations between taxa and possible alternative community states. We conclude by proposing strategies to tackle this challenge
Microbial community structure and dynamics on patchy landscapes
No full textThesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 139-156).Microbes are tiny metabolic engines with large-scale effects on industry, the environment, and human health. Understanding how the micron-scale actions (and interactions) of individual microbes give rise to macro-scale consequences remains a major challenge in microbial ecology. However, for the most part, studies employ coarsegrained sampling schemes, which average over the heterogeneous microscopic structure of microbial communities. This has limited our ability to establish mechanistic links between dynamics occurring across these disparate spatial scales. However, such links are critical for (a) making sense of the tremendous extant microbial diversity on Earth, and (b) predicting how perturbations (e.g., global climate change) may influence microbial diversity and function. In this thesis, I characterize the structure and dynamics of wild bacterial populations in the ocean at spatial scales of tens of microns. I then employ a simple, two-strain laboratory model system to link (cooperative) inter-species interactions at local scales to emergent properties at larger scales, focusing on spatially connected meta-communities undergoing range expansions into new territory. This work encompasses diverse environments (ranging from well-mixed communities in the laboratory to individual crustaceans) and approaches (including mathematical modeling, highthroughput sequencing, and traditional microbiological experiments). Altogether, we find that the microscale environment inhabited by a microbe - that is, "what the neighborhood is like" and "who lives next to whom" - shapes the structure and dynamics of wild microbial populations at local scales. Moreover, these local interactions can drive patterns of biodiversity and function, even at spatial scales much larger than the length of an individual cell. Thus, our work represents a small step toward developing mechanistic theories for how microbes shape our planet's ecosystems.by Manoshi Sen Datta.Ph. D
Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids
No full textInactivation of β‐lactam antibiotics by resistant bacteria is a ‘cooperative’ behavior that may allow sensitive bacteria to survive antibiotic treatment. However, the factors that determine the fraction of resistant cells in the bacterial population remain unclear, indicating a fundamental gap in our understanding of how antibiotic resistance evolves. Here, we experimentally track the spread of a plasmid that encodes a β‐lactamase enzyme through the bacterial population. We find that independent of the initial fraction of resistant cells, the population settles to an equilibrium fraction proportional to the antibiotic concentration divided by the cell density. A simple model explains this behavior, successfully predicting a data collapse over two orders of magnitude in antibiotic concentration. This model also successfully predicts that adding a commonly used β‐lactamase inhibitor will lead to the spread of resistance, highlighting the need to incorporate social dynamics into the study of antibiotic resistance.National Science Foundation (U.S.). Graduate Research Fellowship (Grant 0645960)Massachusetts Institute of Technology. Undergraduate Research Opportunities ProgramAmerican Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi
Range expansion promotes cooperation in an experimental microbial metapopulation
No full textNatural populations throughout the tree of life undergo range expansions in response to changes in the environment. Recent theoretical work suggests that range expansions can have a strong effect on evolution, even leading to the fixation of deleterious alleles that would normally be outcompeted in the absence of migration. However, little is known about how range expansions might influence alleles under frequency- or density-dependent selection. Moreover, there is very little experimental evidence to complement existing theory, since expanding populations are difficult to study in the natural environment. In this study, we have used a yeast experimental system to explore the effect of range expansions on the maintenance of cooperative behaviors, which commonly display frequency- and density-dependent selection and are widespread in nature. We found that range expansions favor the maintenance of cooperation in two ways: (i) through the enrichment of cooperators at the front of the expanding population and (ii) by allowing cooperators to “outrun” an invading wave of defectors. In this system, cooperation is enhanced through the coupling of population ecology and evolutionary dynamics in expanding populations, thus providing experimental evidence for a unique mechanism through which cooperative behaviors could be maintained in nature.National Cancer Institute (U.S.) (Cancer Center Support Grant P30CCA14051)United States. Dept. of Defense (National Defense Science and Engineering Graduate Fellowship Program)MIT Department of Physics Pappalardo Program (Fellowship)Massachusetts Institute of Technology. Undergraduate Research Opportunities ProgramNational Institutes of Health (U.S.) (R00 Pathways to Independence Award GM085279-02)National Science Foundation (U.S.) (Career Award PHY-1055154)Pew Charitable Trusts (Fellowship 2010-000224-007)Alfred P. Sloan Foundation (Fellowship BR2011-066)National Institutes of Health (U.S.) (New Innovator Award DP2
Microbial interactions lead to rapid micro-scale successions on model marine particles
No full textIn the ocean, organic particles harbour diverse bacterial communities, which collectively digest and recycle essential nutrients. Traits like motility and exo-enzyme production allow individual taxa to colonize and exploit particle resources, but it remains unclear how community dynamics emerge from these individual traits. Here we track the taxon and trait dynamics of bacteria attached to model marine particles and demonstrate that particle-attached communities undergo rapid, reproducible successions driven by ecological interactions. Motile, particle-degrading taxa are selected for during early successional stages. However, this selective pressure is later relaxed when secondary consumers invade, which are unable to use the particle resource but, instead, rely on carbon from primary degraders. This creates a trophic chain that shifts community metabolism away from the particle substrate. These results suggest that primary successions may shape particle-attached bacterial communities in the ocean and that rapid community-wide metabolic shifts could limit rates of marine particle degradation.American Society for Engineering Education. National Defense Science and Engineering Graduate FellowshipNational Science Foundation (U.S.) (CAREER Award PHY-1055154)European Research Council (Starting Grant 336938)National Science Foundation (U.S.). Division of Ocean Sciences (Award 14359930
Cross-Kingdom Chemical Communication Drives a Heritable, Mutually Beneficial Prion-Based Transformation of Metabolism
No full textIn experimental science, organisms are usually studied in isolation, but in the wild they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast
from using other carbon sources in the presence of glucose. [GAR[superscript +]], a protein-based epigenetic element, allows yeast to circumvent this glucose repression and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR[superscript +]]. [GAR[superscript +]] is advantageous to bacteria because yeast cells make less ethanol, and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This crosskingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR[superscript +]] presents a unique example of Lamarckian inheritance.G. Harold and Leila Y. Mathers FoundationHoward Hughes Medical Institut
Evolution: ‘Snowed’ In with the Enemy
No full textSummaryExplaining the origins and maintenance of cooperation in nature is a key challenge in evolutionary biology. A recent study demonstrates two novel mechanisms through which the natural ecology of sinking ocean aggregates — colloquially called ‘marine snow’ — promotes cooperation
Rapid, inexpensive measurement of synthetic bacterial community composition by Sanger sequencing
No full textAbstractSimple synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. For instance, while next-generation amplicon sequencing can be very accurate, high costs (>30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we introduce a new approach for quantifying composition in synthetic bacterial communities based on Sanger sequencing. First, for a given community, we PCR-amplify a universal marker gene (here, the 16S rRNA gene), which yields a mixture of amplicons. Second, we sequence this amplicon mixture in a single Sanger sequencing reaction, which produces a “mixed” electropherogram with contributions from each community member. We also sequence each community member’s marker gene individually to generate “individual” electropherograms. Third, we fit the mixed electropherogram as a linear combination of time-warped individual electropherograms, thereby allowing us to estimate the fractional amplicon abundance of each strain within the community. Importantly, our approach accounts for retention-time variability in electrophoretic signals, which is crucial for accurate compositional estimates. Using synthetic communities of marine bacterial isolates, we show that this approach yields accurate and reproducible abundance estimates for two-, four-, and seven-strain bacterial communities. Furthermore, this approach can provide results within one day and costs ~5 USD per sample. We envision this approach will enable new insights in microbial ecology by increasing the number of samples that can be analyzed and enabling faster iteration between experiments and theory. We have implemented our method in a free and open-source R package called CASEU (“Compositional Analysis by Sanger Electropherogram Unmixing”), available at https://bitbucket.org/DattaManoshi/caseu.</jats:p
