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Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant
Open accessAbstract
Plant–microbe interactions play crucial roles in species invasions but are rarely investigated at the intraspecific level. Here, we study these interactions in three lineages of a globally distributed plant, Phragmites australis. We use field surveys and a common garden experiment to analyze bacterial communities in the rhizosphere of P. australis stands from native, introduced, and Gulf lineages to determine lineage-specific controls on rhizosphere bacteria. We show that within-lineage bacterial communities are similar, but are distinct among lineages, which is consistent with our results in a complementary common garden experiment. Introduced P. australis rhizosphere bacterial communities have lower abundances of pathways involved in antimicrobial biosynthesis and degradation, suggesting a lower exposure to enemy attack than native and Gulf lineages. However, lineage and not rhizosphere bacterial communities dictate individual plant growth in the common garden experiment. We conclude that lineage is crucial for determination of both rhizosphere bacterial communities and plant fitness.
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Invasive alien plants alter microbial communities.
“and altering microbial communities (Bowen et al., 2017).”
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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116
The diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063
Invasive Species, Environmental Change and Management, and Health
Pyšek, P., & Richardson, D. M. (2010) · Annual Review of Environment and Resources · doi:10.1146/annurev-environ-033009-095548 · Cited by 1,406
Genetic and environmental control of host-gut microbiota interactions
Org, E., Parks, B. W., Joo, J. W. J., Emert, B., Schwartzman, W., Kang, E. Y., Mehrabian, M., Pan, C., Knight, R., Gunsalus, R., et al. (2015) · Genome Research · doi:10.1101/gr.194118.115 · Cited by 381
Flagged first, then by citations
Research works printed but not linked: 63
- Burke, D. J., Hamerlynck, E. P. & Hahn, D. Interactions between the salt marsh grass Spartina patens, arbuscular mycorrhizal fungi, and sediment bacteria during the growing season. Soil Biol. Biochem. 35, 501–511 (2003). · DOI
- Bever, J. D., Platt, T. G. & Morton, E. R. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu. Rev. Microbiol. 66, 265–283 (2012). · DOI
- Brucker, R. M. & Bordenstein, S. R. The roles of host evolutionary relationships (Genus: Nasonia) and development in structuring microbial communities. Evolution 66, 349–362 (2012). · DOI
- Davenport, E. R. Elucidating the role of the host genome in shaping microbiome composition. Gut Microbes 7, 178–184 (2016). · DOI
- Horton, M. W. et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat. Comm. 5, 5320 (2014). · DOI
- Peiffer, J. A. et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl Acad. Sci. USA 110, 6548–6553 (2013). · DOI
- Micallef, S. A., Shiaris, M. P. & Colón-Carmona, A. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J. Exp. Bot. 60, 1729–1742 (2009). · DOI
- Mahoney, A. K., Yin, C. & Hulbert, S. H. Community structure, species variation, and functional characterization of rhizosphere-associated bacteria of different winter wheat (Triticum aestivum) cultivars. Front. Plant Sci. 8, 132 (2017). · DOI
- Aira, M., Gómez-Brandón, M., Lazcano, C., Bååth, E. & Domínguez, J. Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities. Soil. Biol. Biochem. 42, 2276–2281 (2010). · DOI
- Bouffaud, M.-L. et al. Is diversification history of maize influencing selection of soil bacteria by roots? Mol. Ecol. 21, 195–206 (2012). · DOI
- Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA 112, E911–E920 (2015). · DOI
- Shakya, M. et al. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoids trees. PLoS ONE 8, e76382 (2013). · DOI
- Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, e2001793 (2017). · DOI
- Reinhart, K. O. & Callaway, R. M. Soil biota and invasive plants. New. Phytol. 170, 445–457 (2006). · DOI
- Blossey, B. & Notzold, R. Evolution of increased competitive ability in invasive nonindigenous plants: a hypothesis. J. Ecol. 83, 887–899 (1995). · DOI
- Hulme, P. E. et al. Bias and error in understanding plant invasion impacts. Trends Ecol. Evol. 28, 212–218 (2013). · DOI
- Meyerson, L. A., Cronin, J. T. & Pyšek, P. Phragmites australis as a model organism for studying plant invasions. Biol. Invasions 9, 2421–2431 (2016). · DOI
- Lambertini, C. et al. Tracing the origin of Gulf Coast Phragmites (Poaceae): a story of long-distance dispersal and hybridization. Am. J. Bot. 99, 538–551 (2012). · DOI
- Saltonstall, K. Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proc. Natl Acad. Sci. USA 99, 2445–2449 (2002). · DOI
- Hauber, D. P., White, D. A., Powers, S. P. & DeFrancesch, F. R. Isozyme variation and correspondence with unusual infrared reflectance pattern in Phragmites australis (Poaceae). Plant Syst. Evol. 178, 1–9 (1991). · DOI
- Pellgrin, D. & Hauber, D. P. Isozyme variation among populations of the clonal species Phragmites australis (Cav.) Trin. ex Steudel. Aquat. Bot. 63, 241–259 (1999). · DOI
- Saltonstall, K. A rapid method for identifying the origin of North American Phragmites populations using RFLP analysis. Wetlands 23, 1043–1047 (2003). · DOI
- Saltonstall, K. & Hauber, D. Notes on Phragmites australis (Poaceae: Arundinoideae) in North America. J. Bot. Res. Inst. Texas 1, 385–388 (2007).
- Hauber, D. P., Saltonstall, K., White, D. A. & Hood, C. S. Genetic variation in the common reed Phragmites australis in the Mississippi River Delta marshes: evidence for multiple introductions. Estuar. Coasts 34, 851–862 (2011). · DOI
- Colin, R. & Eguiarte, L. E. Phylogeographic analyses and genetic structure illustrate the complex evolutionary history of Phragmites australis in Mexico. Am. J. Bot. 103, 876–887 (2016). · DOI
- Meyerson, L. A., Lambert, A. M. & Saltonstall, K. A tale of three lineages: expansion of common reed (Phragmites australis) in the US Southwest and Gulf Coast. Invasive Plant Sci. Manag. 3, 515–520 (2010). · DOI
- Ma, B., Lv, X., Warren, A. & Gong, J. Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China. Antonie Van Leeuwenhoek 104, 759–768 (2013). · DOI
- Borruso, L., Bacci, G., Mengoni, A., DePhilippis, R. & Brusetti, L. Rhizosphere effect and salinity competing to shape microbial communities in Phragmites australis (Cav.) Trin. ex-Steud. FEMS Microbiol. Lett. 359, 193–200 (2014). · DOI
- Shipley, B. Confirmatory path analysis in a generalized multilevel context. Ecology 90, 363–368 (2009). · DOI · Paper page
- Grace, J. B. et al. Guidelines for a graph-theoretic implementation of structural equation modeling. Ecosphere 3, 1–44 (2012). · DOI
- Lefcheck, L. piecewiseSEM: Piecewise structural equation modeling in R for ecology, evolution, and systematics. Methods Ecol. Evol. 573, 573–579 (2015).
- Allen, W. J., Meyerson L. A., Flick, A. J. & Cronin J. T. Indirect effects of plant-soil feedbacks on competition between native and invasive wetland plants. Preprint at http://www.biorxiv.org/content/early/2017/07/07/160523 (2017).
- Hansen, R. Shasta ground sloth food habits, Ramparts Cave, Arizona. Paleobiology. 4, 302–319 (1978). · DOI
- Orson, R. A. A paleoecological assessment of Phragmites australis in New England tidal marshes: changes in plant community structure during the last few millennia. Biol. Invasions 1, 149–158 (1999). · DOI
- Nelson, E. B. & Karp, M. Soil pathogen communities associated with native and non-native Phragmites australis, populations in freshwater wetlands. Ecol. Evol. 3, 5254–5267 (2013). · DOI
- Yarwood, S. A., Baldwin, A. H., Mateu, M. G. & Buyer, J. S. Archaeal rhizosphere communitites differ between the native and invasive lineages of the wetland plant Phragmites australis (common reed) in a Chesapeake Bay subestuary. Biol. Invasions 18, 2717–2728 (2016). · DOI
- Klironomos, J. N. Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417, 67–70 (2002). · DOI
- Maron, J. L., Luo, W., Callaway, R. M. & Pal, R. W. Do exotic plants lose resistance to pathogenic soil biota from their native range? A test with Solidago gigantea. Oecologia 179, 447–454 (2015). · DOI
- Kulmatiski, A., Beard, K. H., Stevens, J. R. & Cobbold, S. M. Plant-soil feedbacks: a meta-analytical review. Ecol. Lett. 11, 980–992 (2008). · DOI
- Maron, J. L. et al. Staged invasions across disparate grasslands: effects of seed provenance, consumers and disturbance on productivity and species richness. Ecol. Lett. 17, 499–507 (2014). · DOI
- Elton, C. S. The Ecology of Invasions by Animals and Plants (University of Chicago Press, 1958). · DOI
- Keane, R. M. & Crawley, M. J. Exotic plant invasions and the enemy release hypothesis. Trends Ecol. Evol. 17, 164–170 (2002). · DOI
- Martiny, J. B. et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006). · DOI
- Pejchar, L. & Mooney, H. A. Invasive species, ecosystem services, and human well-being. Trends Ecol. Evol. 24, 497–504 (2009). · DOI
- Kearns, P. J. et al. Nutrient enrichment induces high rates of dormancy and decreases diversity of active bacterial taxa in salt marshes. Nat. Commun. 7, 12881 (2016). · DOI
- Cronin, J. T., Bhattarai, G. P., Allen, W. J. & Meyerson, L. A. Biogeography of a plant invasion: plant–herbivore interactions. Ecology 96, 1115–1127 (2015). · DOI
- Doane, T. A. & Horwath, W. R. Spectrophotometric determination of nitrate with a single reagent. Anal. Lett. 36, 2713–2722 (2003). · DOI
- Weatherburn, M. W. Phenol-hypochlorite reaction for determination of ammonia. Anal. Chem. 39, 971–974 (1967). · DOI · Paper page
- Mettel, C., Kim, Y., Shrestha, P. M. & Liesack, W. Extraction of mRNA from soil. Appl. Environ. Microbiol. 76, 5995–6000 (2010). · DOI
- Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of seuqences per sample. Proc. Natl Acad. Sci. USA 108, 4516–4522 (2011). · DOI
- Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012). · DOI · Paper page
- Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Meth. 10, 57–59 (2013). · DOI
- Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Meth. 7, 335–336 (2010). · DOI · Paper page
- Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010). · DOI
- DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006). · DOI · Paper page
- Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494–504 (2011). · DOI
- Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2001).
- Blankenberg, D. et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Prot. Mol. Biol. 89:19.10 19.10.1–19.10.21 (2010). · DOI
- Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005). · DOI
- Goecks, J. et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010). · DOI
- Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012). · DOI
- Pinheiro, J. C. & Bates, D. M. Mixed-effects models in S and S-PLUS (Springer, 2000). · DOI · Paper page
- Lenth, R. V. Least-squares means: the R package Lsmeans. J. Stat. Softw. 69, 1–33 (2016). · DOI · Paper page
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Scientists' warning on invasive alien species
Pyšek, P., Hulme, P. E., Simberloff, D., Bacher, S., Blackburn, T. M., Carlton, J. T., Dawson, W., Essl, F., Foxcroft, L. C., Genovesi, P., et al. (2020) · Biological Reviews · doi:10.1111/brv.12627 · Cited by 2,234
Self-citation
Metadata
- Authors
- Bowen, J. L., Kearns, P. J., Byrnes, J. E. K., Wigginton, S., Allen, W. J., Greenwood, M., Tran, K., Yu, J., Cronin, J. T., & Meyerson, L. A.
- Affiliations
- Northeastern University (US)
- University of Massachusetts Boston (US)
- University of Rhode Island (US)
- Louisiana State University (US)
- Corresponding author
- Bowen, Jennifer L.
- ORCID
- Venue
- Nature Communications
- Published
- 2017-09-05
- Volume
- 8
- Issue
- 1
- Pages
- 433-433
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5585233
- OpenAlex
- W2752264965
- Cited by
- 124
- References
- 5
- Citations by year
- 2026: 3 · 2025: 9 · 2024: 16 · 2023: 10 · 2022: 18 · 2021: 25 · 2020: 18 · 2019: 16 · 2018: 9
- FWCI
- 11.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Civil War Book Review (submittedVersion)
- Journal of Media Literacy Education (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Lincoln University Research Archive (Lincoln University) (submittedVersion, cc-by)
- Funders
- National Science Foundation (1050084, 1501775, 1350491, 1049914)
- University of Massachusetts Boston
- MIT Sea Grant, Massachusetts Institute of Technology
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Nature and Landscape Conservation › Ecology and Vegetation Dynamics Studies
- Keywords
- Phragmites australis, rhizosphere bacterial community, plant lineages, invasive plants, plant-microbe interactions, host-associated microbiome, plant fitness, common garden experiment
- MeSH terms
- Bacteria, Environment, Poaceae, Models, Biological, Phylogeny, Rhizosphere, Introduced Species, Microbiota
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