The Experts below are selected from a list of 321 Experts worldwide ranked by ideXlab platform
Karsten Zengler - One of the best experts on this subject based on the ideXlab platform.
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Synthetic microbial communities of Heterotrophs and phototrophs facilitate sustainable growth.
Nature Communications, 2020Co-Authors: Cristal Zuñiga, Michael J. Betenbaugh, Michael T. Guarnieri, Jackson Jenkins, Kerem Bingol, Young-mo Kim, Karsten ZenglerAbstract:Microbial communities comprised of phototrophs and Heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the Heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners. Successful application of microbial community for bioproduction relies on the selection of appropriate heterotroph and phototroph partners. Here, the authors construct community metabolic models to guide strain selection and experimentally validate metabolic exchanges that sustain the Heterotrophs in minimal media.
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synthetic microbial communities of Heterotrophs and phototrophs facilitate sustainable growth
Nature Communications, 2020Co-Authors: Cristal Zuñiga, Michael J. Betenbaugh, Michael T. Guarnieri, Jackson Jenkins, Kerem Bingol, Young-mo Kim, Karsten ZenglerAbstract:Microbial communities comprised of phototrophs and Heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the Heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
Sallie W. Chisholm - One of the best experts on this subject based on the ideXlab platform.
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Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria
2020Co-Authors: Sean Michael Kearney, Elaina Thomas, Allison Coe, Sallie W. ChisholmAbstract:Abstract BackgroundProchlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; Heterotrophs grow on organic carbon supplied by the photolithoautotrophs. We have maintained these cultures of Prochlorococcus and Synechococcus for 100s to 1000s of generations; they represent ideal microcosms for examining the selective pressures shaping autotroph/heterotroph interactions. ResultsWe examine the diversity of Heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. Heterotroph community composition differed between clades and ecotypes of the autotrophic ‘hosts’ but there was significant overlap in heterotroph community composition. Differences were associated with timing, location, depth, and methods of isolation, suggesting the particular conditions surrounding isolation have a persistent effect on long-term culture composition. The majority of Heterotrophs in the cultures are rare in the global ocean; enrichment conditions favor the opportunistic outgrowth of these rare bacteria. We did find a few examples, such as Heterotrophs in the family Rhodobacteraceae, that are ubiquitous and abundant in cultures and in the global oceans; their abundance in the wild is also positively correlated with that of picocyanobacteria. ConclusionsCollectively, the cultures converged on similar compositions, likely from bottlenecking and selection that happens during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.
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Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria
bioRxiv, 2020Co-Authors: Sean Michael Kearney, Allison Coe, Elaina G Thomas, Sallie W. ChisholmAbstract:Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; Heterotrophs grow on organic carbon supplied by the photolithoautotrophs. We have maintained these cultures of Prochlorococcus and Synechococcus for 100s to 1000s of generations; they represent ideal microcosms for examining the selective pressures shaping autotroph/heterotroph interactions. Here we examine the diversity of Heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. Heterotroph community composition differed between clades and ecotypes of the autotrophic ′hosts′ but there was significant overlap in heterotroph community composition. Differences were associated with timing, location, depth, and methods of isolation, suggesting the particular conditions surrounding isolation have a persistent effect on long-term culture composition. The majority of Heterotrophs in the cultures are rare in the global ocean; enrichment conditions favor the opportunistic outgrowth of these rare bacteria. We did find a few examples, such as Heterotrophs in the family Rhodobacteraceae, that are ubiquitous and abundant in cultures and in the global oceans; their abundance in the wild is also positively correlated with that of picocyanobacteria. Collectively, the cultures converged on similar compositions, likely from bottlenecking and selection that happens during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.
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Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness
mSystems, 2018Co-Authors: Steven J. Biller, Allison Coe, Sara E. Roggensack, Sallie W. ChisholmAbstract:ABSTRACT Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus , grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness—a condition that cells would experience when mixed below the ocean’s euphotic zone. More Prochlorococcus transcripts exhibited 24-h periodic oscillations in coculture than in pure culture, both over the normal diel cycle and after the shift to extended darkness. This demonstrates that biotic interactions, and not just light, can affect timing mechanisms in Prochlorococcus , which lacks a self-sustaining circadian oscillator. The transcriptomes of replicate pure cultures of Prochlorococcus lost their synchrony within 5 h of extended darkness and reflected changes in stress responses and metabolic functions consistent with growth cessation. In contrast, when grown with Alteromonas , replicate Prochlorococcus transcriptomes tracked each other for at least 13 h in the dark and showed signs of continued biosynthetic and metabolic activity. The transcriptome patterns suggest that the heterotroph may be providing energy or essential biosynthetic substrates to Prochlorococcus in the form of organic compounds, sustaining this autotroph when it is deprived of solar energy. Our findings reveal conditions where mixotrophic metabolism may benefit marine cyanobacteria and highlight new impacts of community interactions on basic Prochlorococcus cellular processes. IMPORTANCE Prochlorococcus is the most abundant photosynthetic organism on the planet. These cells play a central role in the physiology of surrounding Heterotrophs by supplying them with fixed organic carbon. It is becoming increasingly clear, however, that interactions with Heterotrophs can affect autotrophs as well. Here we show that such interactions have a marked impact on the response of Prochlorococcus to the stress of extended periods of darkness, as reflected in transcriptional dynamics. These data suggest that diel transcriptional rhythms within Prochlorococcus , which are generally considered to be strictly under the control of light quantity, quality, and timing, can also be influenced by biotic interactions. Together, these findings provide new insights into the importance of microbial interactions on Prochlorococcus physiology and reveal conditions where heterotroph-derived compounds may support autotrophs—contrary to the canonical autotroph-to-heterotroph trophic paradigm.
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Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus
The ISME Journal, 2016Co-Authors: Steven J. Biller, Allison Coe, Sallie W. ChisholmAbstract:: Microbial interactions, whether direct or indirect, profoundly affect the physiology of individual cells and ultimately have the potential to shape the biogeochemistry of the Earth. For example, the growth of Prochlorococcus, the numerically dominant cyanobacterium in the oceans, can be improved by the activity of co-occurring Heterotrophs. This effect has been largely attributed to the role of Heterotrophs in detoxifying reactive oxygen species that Prochlorococcus, which lacks catalase, cannot. Here, we explore this phenomenon further by examining how the entire transcriptome of Prochlorococcus NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002, with which it was co-cultured for years, separated and then reunited. Significant changes in the Prochlorococcus transcriptome were evident within 6 h of initiating co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48 h experiment, suggesting that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely corresponded to reduced stress conditions for Prochlorococcus, as inferred from the depletion of transcripts encoding DNA repair enzymes and many members of the 'high light inducible' family of stress-response proteins. Later, notable changes were seen in transcripts encoding components of the photosynthetic apparatus (particularly, an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes, suggesting that the introduction of the heterotroph may have induced increased production of reduced carbon compounds for export. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.
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response of prochlorococcus ecotypes to co culture with diverse marine bacteria
The ISME Journal, 2011Co-Authors: Jessie W Thompson, Daniel Sher, Nadav Kashtan, Laura R Croal, Sallie W. ChisholmAbstract:Interactions between microorganisms shape microbial ecosystems. Systematic studies of mixed microbes in co-culture have revealed widespread potential for growth inhibition among marine heterotrophic bacteria, but similar synoptic studies have not been done with autotroph/heterotroph pairs, nor have precise descriptions of the temporal evolution of interactions been attempted in a high-throughput system. Here, we describe patterns in the outcome of pair-wise co-cultures between two ecologically distinct, yet closely related, strains of the marine cyanobacterium Prochlorococcus and hundreds of heterotrophic marine bacteria. Co-culture with the collection of heterotrophic strains influenced the growth of Prochlorococcus strain MIT9313 much more than that of strain MED4, reflected both in the number of different types of interactions and in the magnitude of the effect of co-culture on various culture parameters. Enhancing interactions, where the presence of heterotrophic bacteria caused Prochlorococcus to grow faster and reach a higher final culture chlorophyll fluorescence, were much more common than antagonistic ones, and for a selected number of cases were shown to be mediated by diffusible compounds. In contrast, for one case at least, temporary inhibition of Prochlorococcus MIT9313 appeared to require close cellular proximity. Bacterial strains whose 16S gene sequences differed by 1–2% tended to have similar effects on MIT9313, suggesting that the patterns of inhibition and enhancement in co-culture observed here are due to phylogenetically cohesive traits of these Heterotrophs.
Hanqing Yu - One of the best experts on this subject based on the ideXlab platform.
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evaluation on factors influencing the heterotrophic growth on the soluble microbial products of autotrophs
Biotechnology and Bioengineering, 2011Co-Authors: Bingjie Ni, Raymond J Zeng, Fang Fang, Juan Xu, Guoping Sheng, Hanqing YuAbstract:: In this work, the heterotrophic growth on the microbial products of autotrophs and the effecting factors were evaluated with both experimental and modeling approaches. Fluorescence in situ hybridization (FISH) analysis illustrated that ammonia oxidizers (AOB), nitrite oxidizers (NOB), and Heterotrophs accounted for about 65%, 20%, and 15% of the total bacteria, respectively. The mathematical evaluation of experimental data reported in literature indicated that heterotrophic growth in nitrifying biofilm (30-50%) and granules (30%) was significantly higher than that of nitrifying sludge (15%). It was found that low influent ammonium resulted in a lower availability of soluble microbial products (SMP) and a slower heterotrophic growth, but high ammonium (>150 mg N L(-1)) feeding would lead to purely AOB dominated sludge with high biomass-associated products contained effluent, although the absolute heterotrophic growth increased. Meanwhile, the total active biomass concentration increased gradually with the increasing solids retention time, whereas the factions of active AOB, NOB, and Heterotrophs varied a lot at different solids retention times. This work could be useful for better understanding of the autotrophic wastewater treatment systems.
Michael J. Betenbaugh - One of the best experts on this subject based on the ideXlab platform.
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synthetic microbial communities of Heterotrophs and phototrophs facilitate sustainable growth
Nature Communications, 2020Co-Authors: Cristal Zuñiga, Michael J. Betenbaugh, Michael T. Guarnieri, Jackson Jenkins, Kerem Bingol, Young-mo Kim, Karsten ZenglerAbstract:Microbial communities comprised of phototrophs and Heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the Heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
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Synthetic microbial communities of Heterotrophs and phototrophs facilitate sustainable growth.
Nature Communications, 2020Co-Authors: Cristal Zuñiga, Michael J. Betenbaugh, Michael T. Guarnieri, Jackson Jenkins, Kerem Bingol, Young-mo Kim, Karsten ZenglerAbstract:Microbial communities comprised of phototrophs and Heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the Heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners. Successful application of microbial community for bioproduction relies on the selection of appropriate heterotroph and phototroph partners. Here, the authors construct community metabolic models to guide strain selection and experimentally validate metabolic exchanges that sustain the Heterotrophs in minimal media.
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Mimicking lichens: incorporation of yeast strains together with sucrose-secreting cyanobacteria improves survival, growth, ROS removal, and lipid production in a stable mutualistic co-culture production platform
Biotechnology for Biofuels, 2017Co-Authors: Tingting Li, Chien-ting Li, Kirk Butler, Stephanie G. Hays, Michael Thomas Guarnieri, George A. Oyler, Michael J. BetenbaughAbstract:BackgroundThe feasibility of heterotrophic–phototrophic symbioses was tested via pairing of yeast strains Cryptococcus curvatus, Rhodotorula glutinis, or Saccharomyces cerevisiae with a sucrose-secreting cyanobacterium Synechococcus elongatus.ResultsThe phototroph S. elongatus showed no growth in standard BG-11 medium with yeast extract, but grew well in BG-11 medium alone or supplemented with yeast nitrogen base without amino acids (YNB w/o aa). Among three yeast species, C. curvatus and R. glutinis adapted well to the BG-11 medium supplemented with YNB w/o aa, sucrose, and various concentrations of NaCl needed to maintain sucrose secretion from S. elongatus, while growth of S. cerevisiae was highly dependent on sucrose levels. R. glutinis and C. curvatus grew efficiently and utilized sucrose produced by the partner in co-culture. Co-cultures of S. elongatus and R. glutinis were sustained over 1 month in both batch and in semi-continuous culture, with the final biomass and overall lipid yields in the batch co-culture 40 to 60% higher compared to batch mono-cultures of S. elongatus. The co-cultures showed enhanced levels of palmitoleic and linoleic acids. Furthermore, cyanobacterial growth in co-culture with R. glutinis was significantly superior to axenic growth, as S. elongatus was unable to grow in the absence of the yeast partner when cultivated at lower densities in liquid medium. Accumulated reactive oxygen species was observed to severely inhibit axenic growth of cyanobacteria, which was efficiently alleviated through catalase supply and even more effectively with co-cultures of R. glutinis.ConclusionsThe pairing of a cyanobacterium and eukaryotic heterotroph in the artificial lichen of this study demonstrates the importance of mutual interactions between phototrophs and Heterotrophs, e.g., phototrophs provide a carbon source to Heterotrophs, and Heterotrophs assist phototrophic growth and survival by removing/eliminating oxidative stress. Our results establish a potential stable production platform that combines the metabolic capability of photoautotrophs to capture inorganic carbon with the channeling of the resulting organic carbon directly to a robust heterotroph partner for producing biofuel and other chemical precursors.
Bingjie Ni - One of the best experts on this subject based on the ideXlab platform.
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evaluation on factors influencing the heterotrophic growth on the soluble microbial products of autotrophs
Biotechnology and Bioengineering, 2011Co-Authors: Bingjie Ni, Raymond J Zeng, Fang Fang, Juan Xu, Guoping Sheng, Hanqing YuAbstract:: In this work, the heterotrophic growth on the microbial products of autotrophs and the effecting factors were evaluated with both experimental and modeling approaches. Fluorescence in situ hybridization (FISH) analysis illustrated that ammonia oxidizers (AOB), nitrite oxidizers (NOB), and Heterotrophs accounted for about 65%, 20%, and 15% of the total bacteria, respectively. The mathematical evaluation of experimental data reported in literature indicated that heterotrophic growth in nitrifying biofilm (30-50%) and granules (30%) was significantly higher than that of nitrifying sludge (15%). It was found that low influent ammonium resulted in a lower availability of soluble microbial products (SMP) and a slower heterotrophic growth, but high ammonium (>150 mg N L(-1)) feeding would lead to purely AOB dominated sludge with high biomass-associated products contained effluent, although the absolute heterotrophic growth increased. Meanwhile, the total active biomass concentration increased gradually with the increasing solids retention time, whereas the factions of active AOB, NOB, and Heterotrophs varied a lot at different solids retention times. This work could be useful for better understanding of the autotrophic wastewater treatment systems.