Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation
Continuous cropping of watermelon is known to result in the disruption of the rhizospheric bacteria and fungi that contribute to the occurrence of Fusarium wilt disease. However, the underlying changes in microbial composition and function as a response to mono-cropping are less studied.
In this study, differences in composition and potential function of the microbiome between healthy and diseased soils were investigated using MiSeq targeted sequencing and the functional GeoChip array, respectively.
Twenty years of continuous watermelon monoculture was found to significantly alter the soil microbial communities by increasing bacterial diversity but decreasing fungal diversity. Compare to bacterial network, fungal co-occurrence networks were less robust and less connected in the monoculture diseased soil. Identified keystone species, belonging to the Proteobacteria, Bacteroidetesand Acidobacteria, were present in both the diseased and healthy soils. Key fungal species from the healthy soil belonged solely within the Ascomycete, while in the diseased soil Basidiomycota were dominant. As such, overall variations in the composition of the soil microbiome are accompanied by changes in the identities of the keystone species when comparing healthy versus diseased soils, further suggesting that soil function may also be altered. Relative abundances of genes associated with the degradation of hemicelluloses and chitin, the Calvin circle, ammonification, stress responses, iron uptake, and nitrogen fixation were significantly higher under long-term monoculture. Particularly, Fusarium spp. relative abundance was positively correlated with the relative abundances of genes involved in adherence, cellular metabolism, and immune evasion which may facilitate pathogen infection of plant roots.
In conclusion, these results highlight the significant compositional and functional differences in microbial communities between Fusarium wilt diseased soils and healthy soils under watermelon cultivation. This provides insight into the complex array of microorganisms in soils that suffer from Fusarium disease and illustrates potential directions towards the manipulation of the soil microbiome for suppression of this disease.
KeywordsFusarium wilt of watermelon Microbial composition Microbial function Continuous monocropping GeoChip
This study was supported by the National Nature Science Foundation of China (31772398), Special Fund for Agro-scientific Research in the public Interest (201503110), China Science and Technology Ministry (2015CB150500), the Jiangsu Science and Technology Department (BK20160730), and the China Postdoctoral Science Foundation (2017 M621761 and 2018 T110510), the Fundamental Research Funds for the Central Universities (KYZ201720).
- Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. Icwsm 8:361–362Google Scholar
- Karpouzas DG, Karatasas A, Spiridaki E, Rousidou C, Bekris F, Omirou M, Ehaliotis C, Papadopoulou KK (2011) Impact of a beneficial and of a pathogenic Fusarium strain on the fingerprinting-based structure of microbial communities in tomato (Lycopersicon esculentum Milll.) rhizosphere. Eur J Soil Biol 47:400–408. https://doi.org/10.1016/j.ejsobi.2011.07.011 CrossRefGoogle Scholar
- Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefGoogle Scholar
- Shiwen W, Jing R, Ting H, Guanru Q, haihui H, Wenhui L, Wu F, Kai P (2018) Evaluation of soil enzyme activities and microbial communities in tomato continuous cropping soil treated with Jerusalem artichoke residues. Commun Soil Sci Pl An 49:2727–2740. https://doi.org/10.1080/00103624.2018.1538370 CrossRefGoogle Scholar
- Siegel-Hertz K, Edel-Hermann V, Chapelle E, Terrat S, Raaijmakers JM, Steinberg C (2018) Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Chateaurenard region. Front Microbiol 9:568. https://doi.org/10.3389/fmicb.2018.00568 CrossRefGoogle Scholar
- Steinhauser D, Krall L, Müssig C, Büssis D, Usadel B (2007) Correlation networks. In: Junker BH, Schreiber F (eds) Analysis of biological networks. John Wiley & Sons, Inc., New Jersey, pp 305–333Google Scholar
- Sun S, Li S, Avera BN, Strahm BD, Badgley BD (2017) Soil bacterial and fungal communities show distinct recovery patterns during forest ecosystem restoration. Appl Environ Microbiol 83Google Scholar
- Utkhede R (2006) Soil sickness, replant problem or replant disease and its integrated control. Allelopathy J 18:23–38Google Scholar
- Yao H, He Z, Wilson M, Campbell C (2000) Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microb Ecol 40:223–237Google Scholar
- Zhao S, Liu D, Ling N, Chen F, Fang W, Shen Q (2014) Bio-organic fertilizer application significantly reduces the Fusarium oxysporum population and alters the composition of fungi communities of watermelon Fusarium wilt rhizosphere soil. Biol Fert Soils 50:765–774. https://doi.org/10.1007/s00374-014-0898-7 CrossRefGoogle Scholar
- Zhang H, Jiang Z, Liu L, Zheng X, Li S, Zhang J, Wang J, He Q, Lv W (2015) Effects of intercropping on microbial community function and diversity in continuous watermelon cropping soil. Fresenius Environ Bull 24:3288–3294Google Scholar
- Zhou J, Kang S, Schadt CW, Garten CT, Jr. (2008) Spatial scaling of functional gene diversity across various microbial taxa. Proc Natl Acad Sci U S A 105: 7768–7773Google Scholar