Distributions and environmental drivers of archaea and bacteria in paddy soils
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The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.
Materials and methods
Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.
Results and discussion
Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.
In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.
KeywordsArchaea Bacteria Distribution Putative functional groups Paddy soil
This work was financially supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15020201), the National Natural Science Foundation of China (41601239), the China Postdoctoral Science Foundation (2016M600644), the “Pearl River Talents” Postdoctoral Program of Guangdong Province, the National Key Research and Development Program of China (2016YFD0800703), and the High-level Leading Talent Introduction Program of GDAS.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Barton NH, Briggs DEG, Eisen JA, Goldstein DB, Patel NH (2007) Evolution. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
- Chapin FS, Matson PA, Mooney HA (2002) Principles of terrestrial ecosystem ecology. Springer, New YorkGoogle Scholar
- Hu H-W, Zhang L-M, Yuan C-L, Zheng Y, Wang J-T, Chen D, He J-Z (2015) The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors. Frontier Microbiol 6:938Google Scholar
- Kelly DP, Wood AP, Stackebrandt E (2015) Thiobacillus, Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd, LondonGoogle Scholar
- Koops H-P, Pommerening-Röser A (2015) The lithoautotrophic ammonia-oxidizing bacteria. In: Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd. https://doi.org/10.1002/9781118960608.bm00013
- Kuever J, Rainey FA, Widdel F (2015) Desulfuromonas, Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd, HobokenGoogle Scholar
- Lane D (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, p 133Google Scholar
- Liesack W, Finster K (2015) Desulfuromusa. In: Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd. https://doi.org/10.1002/9781118960608.gbm01040
- Loeppert RH, Inskeep WP (1996) Iron. In: Sparks DL, Page AL, Helmke PA, Loeppert RH (eds) Methods of soil analysis Part 3—Chemical methods, SSSA Book Series. Soil Science Society of America, American Society of Agronomy, Madison, pp 639–664Google Scholar
- Lovley DR, Holmes DE, Nevin KP (2004) Dissimilatory Fe(III) and Mn(IV) reduction, advances in microbial physiology. Academic Press, Cambridge, pp 219–286Google Scholar
- Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B, Quero JL, García-Gómez M, Gallardo A, Ulrich W, Bowker MA, Arredondo T, Barraza-Zepeda C, Bran D, Florentino A, Gaitán J, Gutiérrez JR, Huber-Sannwald E, Jankju M, Mau RL, Miriti M, Naseri K, Ospina A, Stavi I, Wang D, Woods NN, Yuan X, Zaady E, Singh BK (2015) Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci U S A 112:15684–15689Google Scholar
- McDonald JH (2014) Handbook of biological statistics. Sparky House, BaltimoreGoogle Scholar
- Schink B (2015) Pelobacter, Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd, HobokenGoogle Scholar
- Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefGoogle Scholar
- Spieck E, Bock E (2015a) Nitrifying Bacteria. In: Bergey’s manual of systematics of archaea and Bacteria. John Wiley & Sons, Ltd, HobokenGoogle Scholar
- Spieck E, Bock E (2015b) The lithoautotrophic nitrite-oxidizing bacteria. In: Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd, HobokenGoogle Scholar
- Tiedje JM (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. John Wiley and Sons, Inc., New York, pp 179–244Google Scholar
- Yuan C, Zhang L, Hu H, Wang J, Shen J, He J (2018) The biogeography of fungal communities in paddy soils is mainly driven by geographic distance. J Soils Sediments. https://doi.org/10.1007/s11368-018-1924-4
- Zhang W, Ding Y, Wang L, Rui W (2007) The significance of paddy ecosystems in environmental health and sustainable development of economy in the regions around Tai Lake. Sci Technol Rev 25:24–29 (in Chinese)Google Scholar
- Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, Qin Y, Xue K, Wu L, He Z, Voordeckers JW, Nostrand JDV, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Yang Y, Brown JH (2016) Temperature mediates continental-scale diversity of microbes in forest soils. Nat Commun 7:12083CrossRefGoogle Scholar