Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression

Abstract

In our previous work, applying biofertilizer containing Bacillus amyloliquefaciens strain NJN-6 to a banana orchard infected by a serious Fusarium wilt disease over two consecutive years effectively controlled this soil-borne disease. In this study, deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) sequences was performed to investigate how the composition of rhizosphere microbial community responded to the application of biofertilizer (BIO), pig manure compost (PM), and chemical fertilizer (CF) and to explore the potential correlation between the microbial community composition and the Fusarium wilt disease. A total of 104,201 bacterial 16S rRNA genes and 154,953 fungal ITS sequence reads were obtained after basic quality control, and Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Ascomycota were the most abundant bacterial and fungal phyla across all samples. Compared with the PM and CF control, the alpha diversity of bacteria significantly (P<0.05) increased, whereas the value of the fungi was significantly (P<0.05) reduced following two consecutive years of biofertilizer application. Moreover, the abundance of Acidobacteria (Gp1 and Gp3), Firmicutes, Leptosphaeria, and Phaeosphaeriopsis was significantly (P < 0.05) increased, while the abundance of Proteobacteria and Ascomycota was significantly (P<0.05) decreased in the BIO treatment. Furthermore, the abundance of Fusarium, a causal pathogen for Fusarium wilt disease, was significantly (P<0.05) reduced in the BIO treatment compared with the CF control and was slightly reduced (not significant) compared with the PM control. Interestingly, the disease incidence was negatively correlated with the enriched taxa of Acidobacteria (Gp1 and Gp3) and Firmicutes, Leptosphaeria, and Phaeosphaeriopsis but positively correlated with abundance of Proteobacteria, Ascomycota, Fusarium, Cylindrocarpon, Gymnascella, Monographella, Pochonia, and Sakaguchia taxa. The results from this study suggest that 2 years of biofertilizer application manipulated the composition of rhizosphere microbial community and induced the Fusarium suppression by increasing bacterial diversity and potentially stimulating microbial consortia taxa, such as Acidobacteria (Gp1 and Gp3), Firmicutes, Leptosphaeria, and Phaeosphaeriopsis.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

“…However, fungal Shannon diversity was lower in BOF treatment than that in CK and CF treatments. These results were in agreement with the previous reports that BOF application decreased the soil fungal diversity in the rhizosphere of cucumber (Zhang et al, 2013), cotton (Luo et al, 2010), watermelon (Zhao et al, 2011) and banana (Shen et al, 2015a). The principal coordinate (PCoA) ( Figure 2 ) and permutational multivariate analysis (Supplementary Table S2) demonstrated that the fertilizer treatment was the more important factor than soil depth that influenced the soil microbial community composition.…”

“…In the current study, the application of BOF increased the bacterial richness (Chao1) which was consistent with the results of Shen et al (2015a). However, fungal Shannon diversity was lower in BOF treatment than that in CK and CF treatments.…”

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

“…Although Aspergillus did decline during fermentation, from a maximum of 91.48% on day 3 to 48.26% on day 15, Aspergillus oryzae remained a major genus throughout fermentation, indicating a high tolerance to the dry, high salt and high temperature conditions of the second step. Lichtheimia gradually declined in abundance during koji making, but increased during fermentation, from 12.26% on day 1 to 51.05% on day 15, suggesting this genus was adapted to the harsh environment, and indicating a key role in douchi fermentation [56], consistent with previous studies [60,61]. Burgess et al .…”

Soil fungal communities in tea plantation after 10 years of chemical vs . integrated fertilization

“…Likewise, the genera Fusarium and Sordariales (no rank) dominated in IF-treated soils (Figure 2b). Our results indicating the prevalence of Fusarium in subtropical tea plantations are in agreement with the finding of Shen et al (2015), who reported that Fusarium was the dominant group in the rhizosphere from a different crop, i.e. banana, with quite different soil management practices.…”

“…The genera unclassified Microascaceae, unclassified Ascomycota, and Agaricomycetes (no rank) are unique in IF-treated plots and rarely found in other two fertilizer treatments ( Figure 2b). These findings were broadly confirmed in arable soils and paddy soils at different sites, respectively (Shen et al, 2015;Chen et al, 2016), indicating that the combined applications of organic manures and chemical fertilizers resulted in the presence of a unique group of fungi in soils. This fungal community structure change may be caused by their responses to variations in soil organic C and N contents associated with integrated fertilization (Lazcano et al, 2013;Chen et al, 2016).…”