•  
  •  
 

Bulletin of Chinese Academy of Sciences (Chinese Version)

Keywords

soil microbiome; strategic outline; scientific question; vision perspective

Document Type

Article

Abstract

In the past three decades, soil microbiology has emerged as a hotspot for transdisciplinary integration of earth science and life science. The remarkable diversity and vast number of microbes in soil are termed microbial engine being primarily responsible for the global cycling of the key elements on earth. Ironically, it is estimated that the majority of these tiny organisms remains unknown, and these untapped resources are defined as microbial dark matters. Collectively, these countless microbes and their physiochemical soil environments are considered as soil microbiome, which has attracted huge attention across a wide range of fields including sustainable agriculture, high-tech industry, environment protection, and medicine science. In fact, soil microbiome is being recognized as one of the strategic high ground of a new round of science and technology revolution. This review summarizes the progress of soil microbiome, outlines the key scientific questions, synthesizes the major advances of China Soil Microbiome Initiative, highlights the challenges and opportunities ahead of soil microbiomes in China, and concludes with capacity building through various pathways to advance soil microbiomes researches.

First page

554

Last Page

565

Language

Chinese

Publisher

Bulletin of Chinese Academy of Sciences

References

Jones M D, Crandell D W, Singleton D R, et al. Stableisotope probing of the polycyclic aromatic hydrocarbondegrading bacterial guild in a contaminated soil. Environmental Microbiology, 2011, 13(10): 2623-2632.

Peng J, Zhang Y, Su J, et al. Bacterial communities predominant in the degradation of 13C 4-4, 5, 9, 10-pyrene during composting. Bioresource Technology, 2013, 143: 608-614.

Zhu Y G, Yoshinaga M, Zhao F J, et al. Earth abides arsenic biotransformations. Annual Review of Earth and Planetary Sciences, 2014, 42(1): 443-467.

Jia Y, Huang H, Zhu Y G, et al. Arsenic uptake by rice is influenced by microbe-mediated arsenic redox changes in the rhizosphere. Environmental Science & Technology, 2014, 48(2):1001-1007.

Jia Y, Huang H, Zhong M, et al. Microbial Arsenic Methylation in Soil and Rice Rhizosphere. Environmental Science & Technology, 2013, 47(7): 3141-3148.

沈仁芳, 赵学强.土壤微生物在植物获得养分中的作用.生态学报, 2015, 35(20): 6584-6591.

Wall D H, Nielsen U N, Six J. Soil biodiversity and human health. Nature, 2015, 528(7580): 69-76.

Harvey A L, Edrada-Ebel R, Quinn R J. The re-emergence of natural products for drug discovery in the genomics era. Nature Reviews Drug Discovery, 2015, 14(2): 111-129.

Hamamoto H, Urai M, Ishii K, et al. Lysocin E is a new antibiotic that targets menaquinone in the bacterial membrane. Nature Chemical Biology, 2015, 11(2): 127-168.

Ling L L, Schneider T, Peoples A J, et al. A new antibiotic kills pathogens without detectable resistance. Nature, 2015, 517: 455-455.

Taylor P L, Rossi L, Pascale G, et al. A forward chemical screen identifies antibiotic adjuvants in Escherichia coli. ACS Chemical Biology, 2012, 7(9): 1547-1555.

Hanski I, Hertzen L, Fyhrquist N, et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(21): 8334-8339.

宋长青, 吴金水, 陆雅海, 等.中国土壤微生物学研究10年回顾.地球科学进展, 2013, 28(10): 1087-1105.

Shen C, Liang W, Shi Y, et al. Contrasting elevational diversity patterns between eukaryotic soil microbes and plants. Ecology, 2014, 95(11): 3190-3202.

Ge Y, He J Z, Zhu Y G, et al. Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? The ISME Journal, 2008, 2(3): 254-264.

Feng Y, Grogan P, Caporaso J G, et al. pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils. Soil Biology and Biochemistry, 2014, 74: 193-200.

Shen C, Xiong J, Zhang H, et al. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biology and Biochemistry, 2013, 57:204-211.

Xiang X, Gibbons S M, Yang J, et al. Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance. Plant and Soil, 2015, 397(1): 347-356.

Liang Y, Jiang Y, Wang F, et al. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. The ISME journal, 2015, 9(12):2561-2572.

Chu H, Sun H, Tripathi B M, et al. Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau. Environmental Microbiology, 2016, 18(5):1523-1533.

Zhang X, Johnston E R, Liu W, et al. Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes. Global Change Biology, 2016, 22(1): 198-207.

Wang C, Wang, X, Liu D, et al. Aridity threshold in controlling ecosystem nitrogen cycling in arid and semi-arid grasslands. Nature Communications, 2014, 5: 4799.

Wang G, Liu J, Yu Z, et al. Unique distribution of cyanobacterial podoviruses and their potential hosts in a paddy field of northeast China. FEMS Microbiology Ecology, 2014, 90(1): 331-334.

Zhu G, Wang S, Wang W, et al. Hotspots of anaerobic ammonium oxidation at land-freshwater interfaces. Nature Geoscience, 2013, 6(2): 103-107.

Nie S A, Li H, Yang X, et al. Nitrogen loss by anaerobic oxidation of ammonium in rice rhizosphere. The ISME Journal, 2015, 9(9): 2059-2067.

Yang X R, Li H, Nie S A, et al. Potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Applied and Environmental Microbiology, 2015, 81(3): 938-947.

Ding L J, Su J Q, Xu H J, et al. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA- 13C-acetate probing coupled with pyrosequencing. The ISME Journal, 2015, 9(3): 721-734.

Zhu Y G, Su J Q, Cao Z, et al. A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation. Science Bulletin, 2016, 61(13): 1052-1060.

Cai Y, Zheng Y, Bodelier P L E, et al. Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nature Communications, 2016, 7: 11728.

Gao J, Ma A, Zhuang X, et al. An N-acyl homoserine lactone synthase in the ammonia-oxidizing bacterium nitrosospira multiformis. Applied and Environmental Microbiology, 2014, 80(3): 951-958.

Sun L, Lu Y, Yu F, et al. Biological nitrification inhibition by rice root exudates and its relationship with nitrogen-use efficiency. New Phytologist, 2016.

Jiang Y, Jin C, Sun B. Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil. Environmental Microbiology, 2014, 16(10): 3083-3094.

Lin J, Zhu B, Cheng W. Decadally cycling soil carbon is more sensitive to warming than faster-cycling soil carbon. Global Change Biology, 2015, 21(12): 4602-4612.

Xu P, Liang L Z, Dong X Y, et al. Response of soil phosphorus required for maximum growth of asparagus officinalis l. to inoculation of arbuscular mycorrhizal fungi. Pedosphere, 2014, 24(6): 776-782.

Liang L Z, Qi H J, Xu P, et al. High phosphorus at seedling stage decreases the post-transplanting fertiliser requirement of cucumber ( Cucumis sativus L.). Scientia Horticulturae, 2015, 190: 98-103.

He Y, Wu J, Lv B, et al. Involvement of 14-3-3 protein GRF9 in root growth and response under polyethylene glycol-induced water stress. Journal of Experimental Botany, 2015, 66(8): 2271-2281.

Li X, Zhao J, Tan Z, et al. GmEXPB2, a cell wall β-expansin, affects soybean nodulation through modifying root architecture and promoting nodule formation and development. Plant Physiology, 2015, 169(4): 2640-2653.

Zhu C Q, Zhu X F, Hu A Y, et al. Differential effects of nitrogen forms on cell wall phosphorus remobilization are mediated by nitric oxide, pectin content, and phosphate transporter expression. Plant Physiology, 2016, 171(2): 1407-1417.

Zhu X F, Zhu C Q, Zhao X S, et al. Ethylene is involved in root phosphorus remobilization in rice ( Oryza sativa) by regulating cell-wall pectin and enhancing phosphate translocation to shoots. Annals of Botany, 2016.

Download
Request a Copy

Share

COinS