Dynamics in the mixed microbial concourse

Wintermute, Edwin H.; Silver, Pamela A.

doi:10.1101/gad.1985210

Cited by 169 publications

(146 citation statements)

References 108 publications

Supporting

Mentioning

137

Contrasting

Unclassified

Order By: Relevance

“…As a result, spatial structure could increase the effectiveness of partner discrimination, particularly for nonfilamentous microbes, where such discrimination is otherwise more difficult. Consequently, a major question is whether the stability of microbial markets depends on spatially structured environments (54).…”

Section: (V) Supply and Demand Variationmentioning

confidence: 99%

Evolution of microbial markets

Werner

Strassmann

Ivens

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

184

139

View full text Add to dashboard Cite

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions. cooperation | mutualism | trade | partner choice

show abstract

Section: (V) Supply and Demand Variationmentioning

confidence: 99%

Evolution of microbial markets

Werner

Strassmann

Ivens

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

184

139

View full text Add to dashboard Cite

show abstract

“…As we move toward a system-level understanding of community organization and function (Zengler and Palsson, 2012), the behavioral complexity increases with the number of interacting organisms (Wintermute and Silver, 2010). To that end, application of genome-scale approaches to dissect subcellular pathways and regulatory networks involved in governing interspecies interactions is dependent, at least initially, on the availability of model biological systems and genomic information (Tai et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

et al. 2014

View full text Add to dashboard Cite

We used deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities, which was manifested through the transcriptional upregulation of transport and catabolic pathways. Although growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. These hypothesized interactions were inferred from the excretion of specific amino acids (for example, alanine and methionine) by the cyanobacterium, which correlated with the downregulation of the corresponding biosynthetic machinery in Shewanella W3-18-1. In addition, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation may indicate increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.

show abstract

“…Numerous quantitative models have also been developed to describe the behavior of these multispecies systems, including those that integrate dynamics (17,18), metabolism (19)(20)(21), and spatial coordination (22). Although these efforts have led to an improved understanding of the dynamics of syntrophic pairs and the energetic and benefits of cooperativity in these simple systems (23), larger more complex syntrophic systems have yet to be explored.…”

mentioning

confidence: 99%

Syntrophic exchange in synthetic microbial communities

Mee

Collins

Church

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

507

549

View full text Add to dashboard Cite

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.synthetic ecosystem | amino acid exchange | population modeling M icrobes are abundantly found in almost every part of the world, living in communities that are diverse in many facets. Although it is clear that cooperation and competition within microbial communities is central to their stability, maintenance, and longevity, there is limited knowledge about the general principles guiding the formation of these intricate systems. Understanding the underlying governing principles that shape a microbial community is key for microbial ecology but is also crucial for engineering synthetic microbiomes for various biotechnological applications (1-3). Numerous such examples have been recently described including the bioconversion of unprocessed cellulolytic feedstocks into biofuel isobutanol using fungal-bacterial communities (4) and biofuel precursor methyl halides using yeast-bacterial cocultures (5). Other emerging applications in biosensing and bioremediation against environmental toxins such as arsenic (6) and pathogens such as Pseudomonas aeruginosa and Vibrio cholerae have been demonstrated using engineered quorum-sensing Escherichia coli (7, 8). These ...

show abstract

Dynamics in the mixed microbial concourse

Cited by 169 publications

References 108 publications

Evolution of microbial markets

Evolution of microbial markets

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

Syntrophic exchange in synthetic microbial communities

Contact Info

Product

Resources

About