Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China
Lin Gao
A , Rui Wang B , Jiaming Gao B , Fangming Li B , Guanghua Huang C , Guang Huo B , Zhiyu Liu B , Wei Tang B and Guoming Shen A D
+ Author Affiliations
- Author Affiliations
A Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
B Hubei Corporation of China National Tobacco Corporation, Wuhan 430000, China.
C China Tobacco Zhejiang Industrial Co. Ltd., Hangzhou 310004, China.
D Corresponding author. Email: gllg2000@126.com
Soil Research 58(1) 35-40 https://doi.org/10.1071/SR19204
Submitted: 31 July 2019 Accepted: 10 September 2019 Published: 2 October 2019
Abstract
To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.
Additional keywords: high-throughput sequencing technology, soil microbial community structure.
References
Baker K, Cook RJ (1974) ‘Biological control of plant pathogens.’ (WH Freeman and Company: New York, NY, USA)Benizri E, Piutti S, Verger S, Pages L, Vercambre G, Poessel J, Michelot P (2005) Replant diseases: bacterial community structure and diversity in peach rhizosphere as determined by metabolic and genetic fingerprinting. Soil Biology & Biochemistry 37, 1738–1746.
| Replant diseases: bacterial community structure and diversity in peach rhizosphere as determined by metabolic and genetic fingerprinting.Crossref | GoogleScholarGoogle Scholar |
Bonanomi G, Antignani V, Capodilupo M, Scala F (2010) Identifying the characteristics of organic soil amendments that suppress soil borne plant diseases. Soil Biology & Biochemistry 42, 136–144.
| Identifying the characteristics of organic soil amendments that suppress soil borne plant diseases.Crossref | GoogleScholarGoogle Scholar |
Borneman J, Becker JO (2007) Identifying microorganisms involved in specific pathogen suppression in soil. Annual Review of Phytopathology 45, 153–172.
| Identifying microorganisms involved in specific pathogen suppression in soil.Crossref | GoogleScholarGoogle Scholar | 17506652PubMed |
Brussaard L, Ruiter PCD, Brown GG (2007) Soil biodiversity for agricultural sustainability. Agriculture, Ecosystems & Environment 121, 233–244.
| Soil biodiversity for agricultural sustainability.Crossref | GoogleScholarGoogle Scholar |
Expósito RG, Bruijn ID, Postma J, Raaijmakers JM (2017) Current insights into the role of rhizosphere bacteria in disease suppressive soils. Frontiers in Microbiology 8, 25–29.
Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annual Review of Phytopathology 42, 243–270.
| Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness.Crossref | GoogleScholarGoogle Scholar | 15283667PubMed |
Gnatyuk TT, Zhitkevich NV, Gritsay RV, Patyka VF (2013) Curtobacterium flaccumfaciens pv. flaccumfaciens is the agent of bacterial disease of soybean. Mikrobiologichnii Zhurnal 6, 22–27.
Gorissen A, van Overbeek L, van Elsas J (2004) Pig slurry reduces the survival of Ralstonia solanacearum biovar 2 in soil. Canadian Journal of Microbiology 50, 587–593.
| Pig slurry reduces the survival of Ralstonia solanacearum biovar 2 in soil.Crossref | GoogleScholarGoogle Scholar | 15467784PubMed |
Hu J, Wei Z, Friman VP, Gu SH, Wang XF, Eisenhauer N, Yang TJ, Ma J, Shen QR, Xu YC, Jousset A (2016) Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. mBio 7, e01790-16
| Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression.Crossref | GoogleScholarGoogle Scholar | 27965449PubMed |
Ijaz Ashraf UT (2017) Challenges faced by farmers in crop management practices under environmental and soil degradation. Horticultural Biotechnology Research 3, 22–25.
Janvier C, Villeneuve F, Alabouvette C, Hermann VE, Mateille T, Steinberg C (2007) Soil health through soil disease suppression: which strategy from descriptors to indicators? Soil Biology & Biochemistry 39, 1–23.
| Soil health through soil disease suppression: which strategy from descriptors to indicators?Crossref | GoogleScholarGoogle Scholar |
Kinkel LL, Bakker MG, Schlatter DC (2011) A coevolutionary framework for managing disease-suppressive soils. Annual Review of Phytopathology 49, 47–67.
| A coevolutionary framework for managing disease-suppressive soils.Crossref | GoogleScholarGoogle Scholar | 21639781PubMed |
Kwak YS, Weller DM (2013) Take-all of wheat and natural disease suppression: a review. Plant Pathology Journal 29, 125–135.
| Take-all of wheat and natural disease suppression: a review.Crossref | GoogleScholarGoogle Scholar | 25288939PubMed |
Li X, Liu YX, Lu N, Cai LT, Yuan YB, Shi JX (2017) Integrated bio-control of tobacco bacterial wilt and its effect on soil microbial community structure. Turang Xuebao 54, 216–226.
Li CJ, Li DF, Zhou GS, Xu L, Xu TY, Zhao ZX (2019) Effects of different types of biochar on soil microorganism and rhizome diseases occurrence of flue-cured tobacco. Acta Agronomica Sinica 45, 289–296.
Mazzola M (2002) Mechanisms of natural soil suppressiveness to soilborne diseases. Antonie van Leeuwenhoek 81, 557–564.
| Mechanisms of natural soil suppressiveness to soilborne diseases.Crossref | GoogleScholarGoogle Scholar | 12448751PubMed |
Mazzola M (2010). Management of resident soil microbial community structure and function to suppress soilborne disease development. In ‘Climate change & crop production’. (Ed. MP Reynolds) pp. 200–218. (CAB International: Wallingford, Oxfordshire, UK)
Mazzola M, Freilich S (2017) Prospects for biological soilborne disease control: application of indigenous versus synthetic microbiomes. Phytopathology 107, 256–263.
| Prospects for biological soilborne disease control: application of indigenous versus synthetic microbiomes.Crossref | GoogleScholarGoogle Scholar | 27898265PubMed |
Mendes R, Kruijt M, Bruijn DI, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100.
| Deciphering the rhizosphere microbiome for disease-suppressive bacteria.Crossref | GoogleScholarGoogle Scholar | 21551032PubMed |
Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE (2015) Soil-borne microbiome: linking diversity to function. Microbial Ecology 70, 255–265.
| Soil-borne microbiome: linking diversity to function.Crossref | GoogleScholarGoogle Scholar | 25586384PubMed |
Meng Q, Yin J, Rosenzweig N, Douches D, Hao JJ (2012) Culture-based assessment of microbial communities in soil suppressive to potato common scab. Plant Disease 96, 712–717.
| Culture-based assessment of microbial communities in soil suppressive to potato common scab.Crossref | GoogleScholarGoogle Scholar | 30727529PubMed |
Murakami H, Nakagawa A, Hyakumachi M, Oka N, Uragami A (2012) Recent studies on the control of soil-borne diseases. Japanese Journal of Soil Science and Plant Nutrition 1, 69–73.
Sneh B, Pozniak D, Salomon D (1987) Soil suppressiveness to fusarium wilt of melon, induced by repeated croppings of resistant varieties of melons. Journal of Phytopathology 120, 347–354.
| Soil suppressiveness to fusarium wilt of melon, induced by repeated croppings of resistant varieties of melons.Crossref | GoogleScholarGoogle Scholar |
Weir BS, Johnston PR, Damm U (2012) The Colletotrichum gloeosporioides species complex. Studies in Mycology 73, 115–180.
| The Colletotrichum gloeosporioides species complex.Crossref | GoogleScholarGoogle Scholar | 23136459PubMed |
Welbaum GE, Sturz AV, Dong ZM, Nowak J (2004) Managing soil microorganisms to improve productivity of agro-ecosystems. Critical Reviews in Plant Sciences 23, 175–193.
| Managing soil microorganisms to improve productivity of agro-ecosystems.Crossref | GoogleScholarGoogle Scholar |
Zak DR, Holmes WE, White DC, Peacock AD, Tilman D (2003) Plant diversity, soil microbial communities and ecosystem function: are there any links? Ecology 84, 2042–2050.
| Plant diversity, soil microbial communities and ecosystem function: are there any links?Crossref | GoogleScholarGoogle Scholar |
Zhu ZQ (2008) Current status and prospect of tobacco leaf production and research in China. Acta Tabacaria Sinica 14, 70–73.
