Grinnell, J. The niche-relationships of the California thrasher. Auk 34, 427–433 (1917).
Google Scholar
Elton, C. S. Animal Ecology (Univ. Chicago Press, 2001).
Hutchinson, G. E. Concluding remarks Cold Spring Harb. Symp. Quant. Biol. 22, 415–427 (1957).
Hutchinson, G. E. An Introduction to Population Ecology (Yale Univ. Press, 1978).
Colwell, R. K. & Rangel, T. F. Hutchinson’s duality: the once and future niche. Proc. Natl Acad. Sci. USA 106, 19651–19658 (2009).
Google Scholar
Polechová, J. & Storch, D. in Encyclopedia of Ecology 2nd edn, Vol. 3 (ed Fath, B.) 72–80 (Elsevier, 2018).
Hardin, G. The competitive exclusion principle. Science 131, 1292–1297 (1960).
Google Scholar
Hutchinson, G. E. Population studies: animal ecology and demography. Bull. Math. Biol. 53, 193–213 (1991).
Google Scholar
Odum, E. P. Fundamentals of Ecology (Saunders, 1959).
Begon, M., Townsend, C. R. & JL., H. Ecology: From Individuals to Ecosystems (Wiley, 2006).
Levin, S. & Carpenter, S. The Princeton Guide to Ecology (Princeton Univ. Press, 2009).
Bruno, J. F., Stachowicz, J. J. & Bertness, M. D. Inclusion of facilitation into ecological theory. Trends Ecol. Evol. 18, 119–125 (2003).
Google Scholar
Bulleri, F., Bruno, J. F., Silliman, B. R. & Stachowicz, J. J. Facilitation and the niche: implications for coexistence, range shifts and ecosystem functioning. Funct. Ecol. 30, 70–78 (2016).
Google Scholar
Austin, M. Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecol. Modell. 157, 101–118 (2002).
Google Scholar
Soberon, J. & Peterson, A. T. Interpretation of models of fundamental ecological niches and species’ distributional areas. Biodivers. Inform. 2, 1–10 (2005).
Google Scholar
Pires, M. M. & Guimarães, P. R. Interaction intimacy organizes networks of antagonistic interactions in different ways. J. R. Soc. Interface 10, 20120649 (2013).
Google Scholar
Ashby, B., Watkins, E., Lourenço, J., Gupta, S. & Foster, K. R. Competing species leave many potential niches unfilled. Nat. Ecol. Evol. 1, 1495–1501 (2017).
Google Scholar
Pérez-Gutiérrez, R. A. et al. Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network. ISME J. 7, 487–497 (2013).
Google Scholar
Russel, J., Røder, H. L., Madsen, J. S., Burmølle, M. & Sørensen, S. J. Antagonism correlates with metabolic similarity in diverse bacteria. Proc. Natl Acad. Sci. USA 114, 10684–10688 (2017).
Google Scholar
Ricklefs, R. E. Evolutionary diversification, coevolution between populations and their antagonists, and the filling of niche space. Proc. Natl Acad. Sci. USA 107, 1265–1272 (2010).
Google Scholar
Stadler, B. & AFG, D. Ecology and evolution of aphid–ant interactions. Annu. Rev. Ecol. Evol. Syst. 107, 345–372 (2005).
Google Scholar
Thébault, E. & Fontaine, C. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853–856 (2010).
Google Scholar
Rohr, R. P., Saavedra, S. & Bascompte, J. On the structural stability of mutualistic systems. Science 345, 1253497 (2014).
Google Scholar
Hom, E. & Murray, A. Niche engineering demonstrates a latent capacity for fungal–algal mutualism. Science 345, 94–95 (2014).
Google Scholar
Klein, A. M. et al. Importance of pollinators in changing landscapes for world crops. Proc. R. Soc. B 274, 303–313 (2007).
Google Scholar
Yurtsev, E. A., Conwill, A. & Gore, J. Oscillatory dynamics in a bacterial cross-protection mutualism. Proc. Natl Acad. Sci. USA 113, 6236–6241 (2016).
Google Scholar
Pereira, F. C. & Berry, D. Microbial nutrient niches in the gut. Environ. Microbiol. 19, 1366–1378 (2017).
Google Scholar
Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 109 (2017).
Google Scholar
Goldford, J. E. et al. Emergent simplicity in microbial community assembly. Science 361, 469–474 (2018).
Google Scholar
Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).
Google Scholar
Ratzke, C. & Gore, J. Modifying and reacting to the environmental pH can drive bacterial interactions. PLoS Biol. 16, e2004248 (2018).
Google Scholar
Matthews, B., Aebischer, T., Sullam, K. E., Lundsgaard-Hansen, B. & Seehausen, O. Experimental evidence of an eco-evolutionary feedback during adaptive divergence. Curr. Biol. 26, 483–489 (2016).
Google Scholar
Hendry, A. Eco-evolutionary Dynamics (Princeton Univ. Press, 2017).
Wintermute, E. H. & Silver, P. A. Emergent cooperation in microbial metabolism. Mol. Syst. Biol. 6, 407 (2010).
Google Scholar
Giri, S. et al. Metabolic dissimilarity determines the establishment of cross- feeding interactions in bacteria. Preprint at bioRxiv https://doi.org/10.1101/2020.10.09.333336 (2020).
Preussger, D., Giri, S., Muhsal, L. K., Oña, L. & Kost, C. Reciprocal fitness feedbacks promote the evolution of mutualistic cooperation. Curr. Biol. 30, 3580–3590.e7 (2020).
Google Scholar
Stearns, S. Trade-offs in life-history evolution. Funct. Ecol. 3, 259–268 (1989).
Google Scholar
Agrawal, A. A., Conner, J. K. & Rasmann, S. in Evolution Since Darwin (eds Bell, M. A. et al.) Ch. 10 (Sinauer Associates, 2010).
González-Cabaleiro, R., Ofiţeru, I. D., Lema, J. M. & Rodríguez, J. Microbial catabolic activities are naturally selected by metabolic energy harvest rate. ISME J. 9, 2630–2641 (2015).
Google Scholar
Kassen, R. The experimental evolution of specialists, generalists, and the maintenance of diversity. J. Evol. Biol. 15, 173–190 (2002).
Google Scholar
Sexton, J. P., Montiel, J., Shay, J. E., Stephens, M. R. & Slatyer, R. A. Evolution of ecological niche breadth. Annu. Rev. Ecol. Evol. Syst. 48, 183–206 (2017).
Google Scholar
May, R. & Arthur, R. Niche overlap as a function of environmental variability. Proc. Natl Acad. Sci. USA 69, 1109–1113 (1972).
Google Scholar
Bono, L. M., Draghi, J. A. & Turner, P. E. Evolvability costs of niche expansion. Trends Genet. 36, 14–23 (2020).
Google Scholar
Treves, D. S., Manning, S. & Adams, J. Repeated evolution of an acetate-cross-feeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15, 789–797 (1998).
Google Scholar
Rozen, D. E., Schneider, D. & Lenski, R. E. Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J. Mol. Evol. 61, 171–180 (2005).
Google Scholar
Rakoff-Nahoum, S., Coyne, M. J. & Comstock, L. E. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr. Biol. 24, 40–49 (2014).
Google Scholar
Enke, T. N. et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr. Biol. 29, 1528–1535.e6 (2019).
Google Scholar
Gentile, C. L. & Weir, T. L. The gut microbiota at the intersection of diet and human health. Science 362, 776–780 (2018).
Google Scholar
Ruff, W. E., Greiling, T. M. & Kriegel, M. A. Host–microbiota interactions in immune-mediated diseases. Nat. Rev. Microbiol. 18, 521–538 (2020).
Google Scholar
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).
Google Scholar
Morris, B. E. L., Henneberger, R., Huber, H. & Moissl-Eichinger, C. Microbial syntrophy: interaction for the common good. FEMS Microbiol. Rev. 37, 384–406 (2013).
Google Scholar
D’Souza, G. et al. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat. Prod. Rep. 35, 455–488 (2018).
Google Scholar
Johnson, W. M. et al. Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities? FEMS Microbiol. Ecol. 96, 1–14 (2020).
Google Scholar
Machado, D. et al. Polarization of microbial communities between competitive and cooperative metabolism. Nat. Ecol. Evol. 5, 195–203 (2021).
Google Scholar
Bernhardsson, S., Gerlee, P. & Lizana, L. Structural correlations in bacterial metabolic networks. BMC Evol. Biol. 11, 20 (2011).
Google Scholar
Zelezniak, A. et al. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl Acad. Sci. USA 112, 6449–6454 (2015).
Google Scholar
Hester, E. R., Jetten, M. S. M., Welte, C. U. & Lücker, S. Metabolic overlap in environmentally diverse microbial communities. Front. Genet. https://doi.org/10.3389/fgene.2019.00989 (2019).
Mitri, S. & Richard Foster, K. The genotypic view of social interactions in microbial communities. Annu. Rev. Genet. 47, 247–273 (2013).
Google Scholar
Levine, J. M., Bascompte, J., Adler, P. B. & Allesina, S. Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546, 56–64 (2017).
Google Scholar
Louca, S. et al. Function and functional redundancy in microbial systems. Nat. Ecol. Evol. 2, 936–943 (2018).
Google Scholar
Vanstockem, M., Michiels, K., Vanderleyden, J. & van Gool, A. P. Transposon mutagenesis of Azospirillum brasilense and Azospirillum lipoferum: physical analysis of Tn5 and Tn5-Mob insertion mutants. Appl. Environ. Microbiol. 53, 410–415 (1987).
Google Scholar
Thomason, L. C., Costantino, N. & Court, D. L. E. coli genome manipulation by P1 transduction. Curr. Protoc. Mol. Biol. 79, 1.17.1–1.17.8 (2007).
Pande, S. et al. Metabolic cross-feeding via intercellular nanotubes among bacteria. Nat. Commun. 6, 6238 (2015).
Google Scholar
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Google Scholar
Konkol, M. A., Blair, K. M. & Kearns, D. B. Plasmid-encoded comi inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J. Bacteriol. 195, 4085–4093 (2013).
Google Scholar
Koo, B. M. et al. Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis. Cell Syst. 4, 291–305.e7 (2017).
Google Scholar
Thompson, I., Lilley, A., Ellis, R., Bramwell, P. & Bailey, M. Survival, colonization and dispersal of genetically modified Pseudomonas fluorescens SBW25 in the phytosphere of field grown sugar beet. Nat. Biotechnol. 13, 1493–1497 (1995).
Google Scholar
Rainey, P. B. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1, 243–257 (1999).
Google Scholar
Horton, R., Hunt, H., Ho, S., Pullen, J. & Pease, L. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61–68 (1989).
Google Scholar
Ditta, G., Stanfield, S., Corbin, D. & Helinski, D. R. Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl Acad. Sci. USA 77, 7347–7351 (1980).
Google Scholar
Zhang, X. X. & Rainey, P. B. Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176, 2165–2176 (2007).
Google Scholar
Lassak, J., Henche, A. L., Binnenkade, L. & Thormann, K. M. ArcS, the cognate sensor kinase in an atypical arc system of Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 76, 3263–3274 (2010).
Google Scholar
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Google Scholar
Stecher, G., Tamura, K. & Kumar, S. Molecular evolutionary genetics analysis (MEGA) for macOS. Mol. Biol. Evol. 37, 1237–1239 (2020).
Google Scholar
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).
Google Scholar
Bochner, B. R. Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 33, 191–205 (2009).
Google Scholar
Source: Ecology - nature.com
