Gram-Negative Bacteria from Organic and Conventional Agriculture in the Hydrographic Basin of Loja: Quality or Pathogen Reservoir?

Darío Cruz,Jhoan Peña,Rodrigo Cisneros,Wilson Zúñiga-Sarango,Heriberto Fernández,Andrea Jaramillo,Ángel Benítez

doi:10.3390/agronomy11112362

Abstract

Organic and conventional agriculture are vital for the development of human society; however, the use of contaminated water and the inappropriate use of organic chemical fertilizers can lead to an increase in the microbial load (potentially pathogenic) of the normal microbiota of the agricultural soil. In this context, the aim of our study was to isolate Gram-negative bacteria from the superficial soil layer and irrigation water of agricultural areas (11 organic farms and nine conventional farms) and consider their potential ecological and health risk importance. Through culture isolation using three bacterial media (TSA) trypticase soy agar (general nutritive media); MacConkey Gram-negative bacteria and (EMB) eosin methylene blue agar (selective for Enterobacteriaceae) and classical biochemical tests, we recorded a total of 12 bacterial species, most belonging to the Enterobacteriaceae family, such as Enterobacter, Escherichia, Klebsiella, Salmonella and Shigella, which can be pathogenic for humans and animals. In contrast, bacteria such as Pantoea agglomerans, Pseudomonas aeruginosa, P. fluorescens and Burkholderia mallei could facultatively work as diazotrophic or plant growth-promoting rhizobacteria. Soil bacteria richness detected with the media applied was significantly higher than water bacteria, but we found no significant differences between organic and conventional agriculture. We conclude that the isolated bacteria in water and soil mostly belongs to enteropathogenic bacteria which could be pathogenic to animals and humans. While other bacteria like Pseudomonas aeruginosa could be viewed as useful by improving nutrient availability in agricultural soil.

Highlights

Agriculture is of vital importance for the development of human societies and has an enormous impact in the soil functional system [1], since almost 40% of the total land area is used for food production through agriculture [2]
Conventional agriculture is characterized by the usage of chemicals during its production [5]; on the contrary, organic agriculture is based on the effective natural management of plant-soil nutrition cycling [6] and makes use of natural organic compounds such as manure, compost and homemade fertilizers from animal waste such as chicken manure to compensate for nutrient deficiencies [5]
From pure isolates (40 in total), 12 bacterial species were identified according to their biochemical reaction, out of which two were identified to genus level (Table 1)

Summary

Introduction

Agriculture is of vital importance for the development of human societies and has an enormous impact in the soil functional system [1], since almost 40% of the total land area is used for food production through agriculture [2]. In Ecuador and especially Loja, the smallholder farmers lack scientific knowledge regarding the correct soil management in agricultural practices [7]. Jimenez et al [7] indicate that the most common practice in the Loja province is manual tillage (57%), including the incorporation of crop residues and animal manure to improve the soil production. This production in Ecuador and Loja province mainly corresponds to crops like maize, oats, vetch, potatoes, onion and beans [7,8]. The correct applications of this traditional knowledge could help “conservation agriculture” as was experimented with in small-scale farming in Ecuador’s highlands [8]

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