Influence of rice cultivars on soil bacterial microbiome under elevated carbon dioxide
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Elevated CO2 concentration (eCO2) may stimulate plant growth and influence the soil microbial community, but questions remain for whether microbial responses to elevated CO2 would vary by different CO2-responsive plants. We thus attempted to elaborate the changes of soil microbiome to different rice cultivars under the eCO2 condition.
Materials and methods
Two rice cultivars, i.e., the CO2-tolerant cultivar, Wuyunjing23 (WYJ23), and the CO2-sensitive one, Yandao 6 (YD6), were grown under eCO2 and ambient CO2 (aCO2) conditions. The contents of dissolved organic carbon (DOC) and nitrogen (DON) in soil were measured. Real-time qualitative PCR (qPCR) and high-throughput sequencing techniques were employed to characterize the bacterial community. Furthermore, co-occurrence network analysis was applied to reveal the ecological interactions among bacterial taxa.
Results and discussion
No significant differences were found among all treatments in terms of bacterial population, alpha-diversity indices, and bacterial community structure. However, the topological parameters of ecological networks highlighted the distinct co-occurrence patterns among treatments. YD6 under eCO2 led to more links, lower modularity, and greater centralization degree compared to that under aCO2. Opposite trends of those parameters were observed for WYJ23 under eCO2 compared to that under aCO2. Besides, more Proteobacteria and Acidobacteria served as keystone taxa in the CO2-sensitive cultivar treatments, compared to those in WYJ23, implying the different influences of rice cultivars on the microbial ecological network.
Different rice cultivars under eCO2 did not influence the alpha- and beta-diversity of the soil bacterial community, but changed the co-occurrence network of the community. More attention should be paid to the assembly mechanisms of the soil microbial microbiome when evaluating the impacts of productive crops on the soil-plant ecosystem under the eCO2 condition.
Keywords16S rRNA gene Co-occurrence network Free air carbon dioxide enrichment Rice cultivar
This work was supported by the National Basic Research Program (973 Program) (grant number 2014CB954500), National Natural Science Foundation of China (grant numbers 41430859, 41671267, and 41501264), National Key R&D Program (grant number 2016YFD0200306), Youth Innovation Promotion Association, CAS (Member No. 2014271), and Research Program for Key Technologies of Sponge City Construction and Management in Guyuan City (Grant NO. SCHM-2018).
- Calfapietra C, Ainsworth EA, Beier C, De Angelis P, Ellsworth DS, Godbold DL, Hendrey GR, Hickler T, Hoosbeek MR, Karnosky DF, King J, Korner C, Leakey ADB, Lewin KF, Liberloo M, Long SP, Lukac M, Matyssek R, Miglietta F, Nagy J, Norby RJ, Oren R, Percy KE, Rogers A, Mugnozza GS, Stitt M, Taylor G, Ceulemans R, Grp E-FF (2010) Challenges in elevated CO2 experiments on forests. Trends Plant Sci 15(1):5–10CrossRefGoogle Scholar
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336CrossRefGoogle Scholar
- Drigo B, Pijl AS, Duyts H, Kielak A, Gamper HA, Houtekamer MJ, Boschker HTS, Bodelier PLE, Whiteley AS, van Veen JA, Kowalchuk GA (2010) Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2. P Natl Acad Sci USA 107(24):10938–10942CrossRefGoogle Scholar
- Edgar RC (2017) SEARCH_16S: a new algorithm for identifying 16S ribosomal RNA genes in contigs and chromosomes. bioRxiv:124131Google Scholar
- Eisenhauer N, Lanoue A, Strecker T, Scheu S, Steinauer K, Thakur MP, Mommer L (2017) Root biomass and exudates link plant diversity with soil bacterial and fungal biomass. Sci Rep 7:44641Google Scholar
- He SB, Guo LX, Niu MY, Miao FH, Jiao S, Hu TM, Long MX (2017) Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation. Sci Rep 7:3608Google Scholar
- IPCC (2014) Climate change 2013—the physical science basis: Working Group I contribution to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, CambridgeGoogle Scholar
- Johnson DV, Jain SM, Al-Khayri JM (2016) Advances in plant breeding strategies: agronomic, abiotic and biotic, vol 2. Springer, BerlinGoogle Scholar
- Liang Y, Zhao H, Deng Y, Zhou J, Li G, Sun B (2016) Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes. Front Microbiol 7:60Google Scholar
- Norby RJ, Zak DR (2011) Ecological lessons from free-air CO2 enrichment (FACE) experiments. In: Futuyma DJ, Shaffer HB, Simberloff D (eds) Annual review of ecology, evolution, and systematics, vol 42. Annual review of ecology evolution and systematics. Pp 181-203Google Scholar
- Oksanen J, Blanchet F, Kindt R, Legendre P, Minchin P, O’Hara R, Simpson G, Solymos P, Henry M, Stevens H, Wagner H (2013) Vegan: community ecology packageGoogle Scholar
- Okubo T, Liu DY, Tsurumaru H, Ikeda S, Asakawa S, Tokida T, Tago K, Hayatsu M, Aoki N, Ishimaru K, Ujiie K, Usui Y, Nakamura H, Sakai H, Hayashi K, Hasegawa T, Minamisawa K (2015) Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria. Front Microbiol 6:136CrossRefGoogle Scholar
- Core Team R (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
- Wood SA, Gilbert JA, Leff JW, Fierer N, D'Angelo H, Bateman C, Gedallovich SM, Gillikin CM, Gradoville MR, Mansor P, Massmann A, Yang N, Turner BL, Brearley FQ, McGuire KL (2017) Consequences of tropical forest conversion to oil palm on soil bacterial community and network structure. Soil Biol Biochem 112:258–268CrossRefGoogle Scholar
- Yang G, Peng M, Tian XL, Dong SL (2017) Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: an example of sea cucumber. Sci Rep 7:4778Google Scholar
- Zhou JZ, Deng Y, Luo F, He ZL, Yang YF (2011) Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. mBio 2(4):e00122–11Google Scholar