Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes

Abstract

The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.

Figure 1

Traditional tillage systems. (A) Minimal tillage system ‘chiwa’ in which we can see the use of the ‘chakitaklla’ and the form of tillage on the soil. (B) Full tillage ‘barbecho’ in which we can see the use of yunta and tractor and the form of tillage on the soil. Adapted from the "The complexity of simple tillage systems" by Oswald et al., 2009, The Journal of Agricultural Science, 147(4), 399–410. Copyright 2009 by Cambridge University Press.

Figure 2

Potato soil bacterial microbiome alpha and beta diversity analyses. (A) Species richness. (B) Shannon effective numbers. (C) Simpson effective numbers. (D) Principal Coordinates Analysis using weighted UniFrac distances. (E) Dendrogram based on the Bray–Curtis dissimilarity * p-value < 0.05; n. s., not significant.

Figure 3

Bacterial taxonomic composition for traditional tillage systems (MTS: Minimal Tillage Systems, FTS: Full Tillage Systems) at the phylum (A), class (B), and genus (C) levels.

Figure 4

(A) Venn diagram of exclusive and shared bacterial species in traditional soil tillage systems. (B) Venn diagram comparing the core microbiome of this study with the potato core microbiome proposed by Pfeiffer et al. (2016).

Figure 5

Bioindicators for soil under traditional tillage systems. (A) Relative abundance of bacterial genera for proposed bioindicators. (B) Differential abundance of bacterial bioindicators (based on LEfSe Analysis, p-value < 0.05, a minimum relative abundance > 1%, LDA threshold = 3.5). (C) Correlation between bacterial genera indicator and soil physicochemical properties. * p-value < 0.05.

Figure 6

Functional profile for traditional tillage systems inferred by HUMAnN3. (A) Metabolic pathways grouped on superclass1 hierarchy. (B) Metabolic pathways grouped on superclass2 hierarchy. (C) LEfSe analysis to determine the most differentially abundant MetaCyc pathways. (D) Principal Coordinates Analysis based on MetaCyc pathways.