Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities.
Journal
Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869
Informations de publication
Date de publication:
12 2019
12 2019
Historique:
received:
01
11
2018
accepted:
21
08
2019
pubmed:
9
10
2019
medline:
1
7
2020
entrez:
9
10
2019
Statut:
ppublish
Résumé
Phototrophic communities of photosynthetic algae or cyanobacteria and heterotrophic bacteria or fungi are pervasive throughout the environment
Identifiants
pubmed: 31591554
doi: 10.1038/s41564-019-0567-6
pii: 10.1038/s41564-019-0567-6
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
2184-2191Commentaires et corrections
Type : ErratumIn
Type : CommentIn
Références
Flemming, H.-C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).
pubmed: 30760902
Zuñiga, C., Zaramela, L. & Zengler, K. Elucidation of complexity and prediction of interactions in microbial communities. Microb. Biotechnol. 10, 1500–1522 (2017).
pubmed: 5658597
pmcid: 5658597
Zengler, K. & Zaramela, L. S. The social network of microorganisms—how auxotrophies shape complex communities. Nat. Rev. Microbiol. 16, 383–390 (2018).
pubmed: 6059367
pmcid: 6059367
de Vera, J.-P. et al. Survival potential and photosynthetic activity of lichens under Mars-like conditions: a laboratory study. Astrobiology 10, 215–227 (2010).
pubmed: 20402583
Prieto-Barajas, C. M., Valencia-Cantero, E. & Santoyo, G. Microbial mat ecosystems: structure types, functional diversity, and biotechnological application. Electron. J. Biotechnol. 31, 48–56 (2018).
Amin, S. A., Parker, M. S. & Armbrust, E. V. Interactions between diatoms and bacteria. Microbiol. Mol. Biol. Rev. 76, 667–684 (2012).
pubmed: 22933565
pmcid: 3429620
Insarova, I. D. & Blagoveshchenskaya, E. Y. Lichen symbiosis: Search and recognition of partners. Biol. Bull. 43, 408–418 (2016).
Hill, D. J. The growth of lichens with special reference to the modelling of circular thalli. Lichenologist 13, 265–287 (1981).
Grube, M., Cardinale, M., de Castro, J. V., Müller, H. & Berg, G. Species-specific structural and functional diversity of bacterial communities in lichen symbioses. ISME J. 3, 1105–1115 (2009).
pubmed: 19554038
Bolhuis, H., Cretoiu, M. S. & Stal, L. J. Molecular ecology of microbial mats. FEMS Microbiol. Ecol. 90, 335–350 (2014).
pubmed: 25109247
Zhalnina, K., Zengler, K., Newman, D. & Northen, T. R. Need for laboratory ecosystems to unravel the structures and functions of soil microbial communities mediated by chemistry. mBio 9, e01175-18 (2018).
pubmed: 30018110
pmcid: 6050955
Zengler, K. et al. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat. Methods 16, 567–571 (2019).
pubmed: 31227812
pmcid: 6733021
Hom, E. F. Y. & Murray, A. W. Niche engineering demonstrates a latent capacity for fungal–algal mutualism. Science 345, 94–98 (2014).
pubmed: 24994654
pmcid: 4409001
Li, T. et al. 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. Biotechnol. Biofuels 10, 55 (2017).
pubmed: 28344645
pmcid: 5360037
Zengler, K. & Palsson, B. O. A road map for the development of community systems (CoSy) biology. Nat. Rev. Microbiol. 10, 366–372 (2012).
pubmed: 22450377
Zuñiga, C. et al. Genome-scale metabolic model for the green alga Chlorella vulgaris UTEX 395 accurately predicts phenotypes under autotrophic, heterotrophic, and mixotrophic growth conditions. Plant Physiol. 172, 589–602 (2016).
pubmed: 27372244
pmcid: 5074608
Mo, M. L., Palsson, B. Ø. & Herrgard, M. J. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol. 3, 37 (2009).
pubmed: 19321003
pmcid: 2679711
Oliveira, N. M., Niehus, R. & Foster, K. R. Evolutionary limits to cooperation in microbial communities. Proc. Natl Acad. Sci. USA 111, 17941–17946 (2014).
pubmed: 25453102
Guimarães, P. R., Pires, M. M., Jordano, P., Bascompte, J. & Thompson, J. N. Indirect effects drive coevolution in mutualistic networks. Nature 550, 511–514 (2017).
pubmed: 29045396
Du, B., Zielinski, D. C., Monk, J. M. & Palsson, B. O. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proc. Natl Acad. Sci. USA 115, 11339–11344 (2018).
pubmed: 30309961
Stegman, M. R., Cottrell, M. T. & Kirchman, D. L. Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary. ISME J. 8, 2339–2348 (2014).
pubmed: 24824666
pmcid: 4992083
Dahlman, L., Persson, J., Näsholm, T. & Palmqvist, K. Carbon and nitrogen distribution in the green algal lichens Hypogymnia physodes and Platismatia glauca in relation to nutrient supply. Planta 217, 41–48 (2003).
pubmed: 12721847
Palmqvist, K., Franklin, O. & Näsholm, T. Symbiosis constraints: Strong mycobiont control limits nutrient response in lichens. Ecol. Evol. 7, 7420–7433 (2017).
pubmed: 28944027
pmcid: 5606882
Goff, L. J. (ed.). Algal symbiosis: a continuum of interaction strategies (Cambridge Univ. Press, 2011).
Jovan, S., Riddell, J., Padgett, P. E. & Nash, T. H. Eutrophic lichens respond to multiple forms of N: implications for critical levels and critical loads research. Ecol. Appl. 22, 1910–1922 (2012).
pubmed: 23210308
Navarrete, A. et al. Physiological status and community composition of microbial mats of the Ebro Delta, Spain, by signature lipid biomarkers. Microb. Ecol. 39, 92–99 (2000).
pubmed: 10790522
Zuñiga, C. et al. Predicting dynamic metabolic demands in the photosynthetic eukaryote Chlorella vulgaris. Plant Physiol. 176, 450–462 (2018).
pubmed: 28951490
Basan, M. et al. Overflow metabolism in Escherichia coli results from efficient proteome allocation. Nature 528, 99–104 (2015).
pubmed: 26632588
pmcid: 4843128
Liu, J. K. et al. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLOS Comput. Biol. 15, e1006848 (2019).
pubmed: 30845144
pmcid: 6430413
Klitgord, N. & Segrè, D. Environments that induce synthetic microbial ecosystems. PLoS Comput. Biol. 6, e1001002 (2010).
pubmed: 21124952
pmcid: 2987903
Wink, M. Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective. Phytochemistry 64, 3–19 (2003).
pubmed: 12946402
Reznik, E., Mehta, P. & Segrè, D. Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools. PLoS Comput. Biol. 9, e1003195 (2013).
pubmed: 24009492
pmcid: 3757068
Rakoff-Nahoum, S., Foster, K. R. & Comstock, L. E. The evolution of cooperation within the gut microbiota. Nature 533, 255–259 (2016).
pubmed: 27111508
pmcid: 4978124
Morris, J. J., Lenski, R. E. & Zinser, E. R. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036-12 (2012).
pubmed: 22448042
pmcid: 3315703
Ackermann, M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat. Rev. Microbiol. 13, 497–508 (2015).
pubmed: 26145732
Good, B. H., McDonald, M. J., Barrick, J. E., Lenski, R. E. & Desai, M. M. The dynamics of molecular evolution over 60,000 generations. Nature 551, 45–50 (2017).
pubmed: 29045390
pmcid: 5788700
Breslow, D. K. et al. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat. Methods 5, 711–718 (2008).
pubmed: 18622397
pmcid: 2756093
Zengler, K. et al. Cultivating the uncultured. Proc. Natl Acad. Sci. USA 99, 15681–15686 (2002).
pubmed: 12438682
Kim, Y.-M. et al. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Front. Microbiol. 6, 209 (2015).
pubmed: 25941514
pmcid: 4400912
Lynch, M. Streamlining and simplification of microbial genome architecture. Annu. Rev. Microbiol. 60, 327–349 (2006).
pubmed: 16824010
Schellenberger, J. et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6, 1290–1307 (2011).
pubmed: 3319681
pmcid: 3319681
Nagarajan, H. et al. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nat. Commun. 4, 2809 (2013).
pubmed: 24264237
Matthews, B. W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405, 442–451 (1975).
pubmed: 1180967
Henard, C. A., Guarnieri, M. T. & Knoshaug, E. P. The Chlorella vulgaris S-nitrosoproteome under nitrogen-replete and -deplete conditions. Front. Bioeng. Biotechnol. 4, 100 (2017).
pubmed: 28144611
pmcid: 5239800
Krueger, F. Trim Galore!: A Wrapper Tool Around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ (2015).
Agarwala, R. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 46, D8–D13 (2018).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 25516281