دورية أكاديمية
18S rRNA gene amplicon sequencing combined with culture-based surveys of maize rhizosphere protists reveal dominant, plant-enriched and culturable community members.
| العنوان: | 18S rRNA gene amplicon sequencing combined with culture-based surveys of maize rhizosphere protists reveal dominant, plant-enriched and culturable community members. |
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| المؤلفون: | Taerum SJ; Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, 06511, USA., Micciulla J; Department of Molecular and Cell Biology, The University of Connecticut, Storrs, Connecticut, 06269, USA., Corso G; Department of Molecular and Cell Biology, The University of Connecticut, Storrs, Connecticut, 06269, USA., Steven B; Department of Environmental Science, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, 06511, USA., Gage DJ; Department of Molecular and Cell Biology, The University of Connecticut, Storrs, Connecticut, 06269, USA., Triplett LR; Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, 06511, USA. |
| المصدر: | Environmental microbiology reports [Environ Microbiol Rep] 2022 Feb; Vol. 14 (1), pp. 110-118. Date of Electronic Publication: 2021 Dec 26. |
| نوع المنشور: | Journal Article; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Society for Applied Microbiology and Blackwell Pub Country of Publication: United States NLM ID: 101499207 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1758-2229 (Electronic) Linking ISSN: 17582229 NLM ISO Abbreviation: Environ Microbiol Rep Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [Hoboken, N.J.] : Society for Applied Microbiology and Blackwell Pub., c2009- |
| مواضيع طبية MeSH: | Rhizosphere* , Zea mays*/genetics, Eukaryota/genetics ; Genes, rRNA ; RNA, Ribosomal, 18S/genetics ; Soil Microbiology |
| مستخلص: | Protists play important roles in shaping the microbial community of the rhizosphere and defining these roles will require the study of protist isolates. However, there is still a limited understanding of how well protist isolation efforts can capture the diversity and composition of rhizosphere protistan communities. Here, we report a simultaneous isolation and 18S rRNA gene amplicon sequencing survey describing the protist diversity of maize rhizospheres in two climatically and pedologically distinct sites. We demonstrated that the maize rhizosphere exerted significant and site-dependent effects on the protistan community structure and defined a set of core and rhizosphere-enriched protists. From the same root samples, we generated a library of 103 protist isolates representing 46 18S rRNA gene sequence variants from six eukaryotic supergroups. While cultured isolates represented a small proportion of total protist diversity recovered by sequencing, they included taxa enriched in rhizosphere soils across all samples, encompassing 9% of all core sequence variants. The isolation approach also captured 17 protists not detected through 18S rRNA gene amplicon sequencing. This study demonstrated that maize roots select for distinct protistan communities, and established a diverse protist culture collection that can be used for future research linking protists to rhizosphere status and plant health. (© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.) |
| References: | Bardgett, R.D., and Van Der Putten, W.H. (2014) Belowground biodiversity and ecosystem functioning. Nature 515: 505-511. Bass, D., and del Campo, J. (2020) Microeukaryotes in animal and plant microbiomes: ecologies of disease? Eur J Protistol 76: 125719. Bass, D., Howe, A.T., Mylnikov, A.P., Vickerman, K., Chao, E.E., Edwards Smallbone, J., et al. (2009) Phylogeny and classification of Cercomonadida (protozoa, Cercozoa): Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. Nov. Protist 160: 483-521. Berg, G., and Smalla, K. (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68: 1-13. Blandenier, Q., Seppey, C.V.W., Singer, D., Vlimant, M., Simon, A., Duckert, C., and Lara, E. (2017) Mycamoeba gemmipara nov. gen., nov. sp., the first cultured member of the environmental dermamoebidae clade LKM74 and its unusual life cycle. J Eukaryot Microbiol 64: 257-265. Ceja-Navarro, J.A., Wang, Y., Ning, D., Arellano, A., Ramanculova, L., Yuan, M.M., et al. (2021) Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. Microbiome 9: 1-18. Dumack, K., Feng, K., Flues, S., Sapp, M., Schreiter, S. Grosch, R. et al. (2020) What drives the assembly of plant-associated protist microbiomes? bioRxiv. https://doi.org/10.1101/2020.02.16.951384. Dumack, K., Sapp, M., von Steimker, T., Mänz, A.T., Rose, L.E., and Bonkowski, M. (2021) A call for research: a resource of core microbial symbionts of the Arabidopsis thaliana microbiome ready and awaiting experimental exploration. Phytobiomes J, 5, 1-19. Flues, S., Bass, D., and Bonkowski, M. (2017) Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function. Environ Microbiol 19: 3297-3309. Gao, Z., Karlsson, I., Geisen, S., Kowalchuk, G., and Jousset, A. (2019) Protists: puppet masters of the rhizosphere microbiome. Trends Plant Sci 24: 165-176. Geisen, S., and Bonkowski, M. (2018) Methodological advances to study the diversity of soil protists and their functioning in soil food webs. Appl Soil Ecol 123: 328-333. Howe, A.T., Bass, D., Scoble, J.M., Lewis, R., Vickerman, K., Arndt, H., and Cavalier-Smith, T. (2011) Novel cultured protists identify deep-branching environmental DNA clades of Cercozoa: new genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia. Protist 162: 332-372. Keeling, P.J., and del Campo, J. (2017) Marine protists are not just big bacteria. Curr Biol 27: R541-R549. Kreuzer, K., Adamczyk, J., Iijima, M., Wagner, M., Scheu, S., and Bonkowski, M. (2006) Grazing of a common species of soil protozoa (Acanthamoeba castellanii) affects rhizosphere bacterial community composition and root architecture of rice (Oryza sativa L.). Soil Biol Biochem 38: 1665-1672. Krome, K., Rosenberg, K., Dickler, C., Kreuzer, K., Ludwig-Müller, J., Ullrich-Eberius, C., et al. (2010) Soil bacteria and protozoa affect root branching via effects on the auxin and cytokinin balance in plants. Plant and Soil 328: 191-201. Leach, J.E., Triplett, L.R., Argueso, C.T., and Trivedi, P. (2017) Communication in the phytobiome. Cell 169: 587-596. Mahé, F., De Vargas, C., Bass, D., Czech, L., Stamatakis, A., Lara, E., et al. (2017) Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nat Ecol Evol 1: 0091. Nuccio, E.E., Anderson-Furgeson, J., Estera, K.Y., Pett-Ridge, J., De Valpine, P., Brodie, E.L., and Firestone, M.K. (2016) Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass. Ecology 97: 1307-1318. Oliverio, A.M., Geisen, S., Delgado-Baquerizo, M., Maestre, F.T., Turner, B.L., and Fierer, N. (2020) The global-scale distributions of soil protists and their contributions to belowground systems. Sci Adv 6: 1-11. Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., et al. (2012) CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol 10: e1001419. Philippot, L., Spor, A., Hénault, C., Bru, D., Bizouard, F., Jones, C.M., et al. (2013) Loss in microbial diversity affects nitrogen cycling in soil. ISME J 7: 1609-1619. Rossmann, M., Pérez-Jaramillo, J.E., Kavamura, V.N., Chiaramonte, J.B., Dumack, K., Fiore-Donno, A.M., et al. (2020) Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiol Ecol 96: 032. Rüger, L., Feng, K., Dumack, K., Freudenthal, J., Chen, Y., Sun, R., et al. (2021) Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.). Front Microbiol 12: 1-14. Sapp, M., Ploch, S., Fiore-Donno, A.M., Bonkowski, M., and Rose, L.E. (2018) Protists are an integral part of the Arabidopsis thaliana microbiome. Environ Microbiol 20: 30-43. Sun, A., Jiao, X., Chen, Q., Trivedi, P., Li, Z., Li, F., et al. (2021) Fertilization alters protistan consumers and parasites in crop-associated microbiomes. Environ Microbiol 23: 2169-2183. Takenouchi, Y., Iwasaki, K., and Murase, J. (2016) Response of the protistan community of a rice field soil to different oxygen tensions. FEMS Microbiol Ecol 92: 1-8. Vaulot D., Geisen S., Mahé F., Bass D. (2022). pr2-primers: An 18S rRNA primer database for protists. Molecular Ecology Resources, 22(1): 168-179. https://doi.org/10.1111/1755-0998.13465. Xiong, W., Song, Y., Yang, K., Gu, Y., Wei, Z., Kowalchuk, G.A., et al. (2020) Rhizosphere protists are key determinants of plant health. Microbiome 8: 27. Zhang, L., and Lueders, T. (2017) Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. FEMS Microbiol Ecol 93: 1-11. |
| المشرفين على المادة: | 0 (RNA, Ribosomal, 18S) |
| تواريخ الأحداث: | Date Created: 20211227 Date Completed: 20220404 Latest Revision: 20220405 |
| رمز التحديث: | 20221213 |
| DOI: | 10.1111/1758-2229.13038 |
| PMID: | 34957692 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1758-2229 |
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| DOI: | 10.1111/1758-2229.13038 |