Abstract
Organic matter inputs positively affect soil fertility and quality but management effects on the soil and plant microbiome are less understood. Therefore, we studied the response of microbial colonization of the East African highland banana cultivar “Mpologoma” (AAA genome) under different mulch and manure treatments on three representative smallholder farms in Uganda. In general, the gammaproteobacterial community appeared stable with no significant response to organic matter inputs after 24 months of treatment. Significant differences (p < 0.05) in the plant-associated carpo-, phyllo-, and rhizosphere microbial community composition and diversity were found among individual sampled farms, independent of added soil inputs. Across farms, banana fruit harbored a richer and more balanced gammaproteobacterial community than the rhizo- and endospheres. Gammaproteobacterial beta diversity was shaped by the microenvironment (44%) as well as the sampling site (4%). Global effects of treatments in the rhizosphere analyzed using linear discriminant analysis effect size showed significantly enriched genera, such as Enterobacter, under manure and mulch treatments. As shown in previous works, bunch size and total yield were highly increased with manure and mulch, however, our results highlight general short-term microbial stability of Ugandan banana cropping systems with increases in the gammaproteobacterial community.
Highlights
The plant and its highly diverse plant-associated microbial community, including bacteria, archaea, fungi, and protists, are nowadays recognized as holobiont (Vandenkoornhuyse et al, 2015)
We identified a highly site-specific microbiome fingerprint: the lowest alpha diversity was observed in RB sampling sites (p < 0.001; Figure 2B)
The combination of mulch and manure increases the gammaproteobacterial diversity in comparison to the control (Supplementary Figure S2)
Summary
The plant and its highly diverse plant-associated microbial community, including bacteria, archaea, fungi, and protists, are nowadays recognized as holobiont (Vandenkoornhuyse et al, 2015). Essential functions are outsourced to symbiotic microbiota partners, and plant-associated microbiomes play a key role in plant survival and health (Gilbert et al, 2012; Guttman et al, 2014). The species- and habitat-specific plant microbiota contribute to multiple aspects in functioning of the plant holobiont, such as (i) seed germination and growth, (ii) nutrient supply, (iii) resistance against biotic and abiotic stress factors, and (iv) production of bioactive metabolites (Berg et al, 2016, 2020). In addition to microbial inoculants, an extensive list of microbiome management strategies and products were developed in agriculture including (i) microbiome transplants (straw dung, manure, mulch, and biodynamic additives), (ii) microbial and plant extracts as well as (iii) methods to change environmental conditions (Berg et al, 2020, 2021; French et al, 2021). Many parts of the underlying mechanisms are yet not fully understood
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