MICROBIAL DEGRADATION OF SELECTED PESTICIDES IN AGRICULTURAL SOILS FROM EDO STATE FARMLANDS AND THEIR EFFECT ON BENEFICIAL SOIL MICROFLORA

CHAPTER ONE

GENERAL INTRODUCTION

1.1 Background to the Study

This increased agricultural output in Nigeria has been coupled with a continuous rise in the use of synthetic pesticides to control the pests, diseases and weeds that plague crop production. In Edo State, agriculture is a major source of livelihood to a huge percentage of its rural communities, thus, a wide range of vegetables such as yam, cassava, plantain, maize, and leafy vegetables are grown in its three senators districts. These crops have inevitably required the extensive and often unselective use of organophosphate, organochlorine, pyrethroid and herbicide preparations, many of which remain entrenched in the soil environment after their initial purpose of application by agriculture is fulfilled.

The total spending on pesticides in agriculture still increases many times; Nigeria traditionally spends 244 million US dollars on imports of pesticides annually, and the largest percentage is occupied by herbicides, constituting 74 percent of the total amount (FutuX Agri-consult, 2024). The frequently recorded active agents in the Nigerian farmlands are atrazine, chlorpyrifos, paraquat dichloride, glyphosate, and cypermethrin (Raimi, 2022). In response to increased concerns about toxicity, the Nigeria National Agency for Food and Drug Administration and Control (NAFDAC) imposed bans on chlorpyrifos, paraquat, and atrazine with moratorium periods ranging between 2024 and 2025, an indication of how serious the pesticide contamination problem in the country is (NAFDAC, 2024).

Of special interest is how these chemicals are to be withstood in the soil matrix. On farms, when pesticides are sprayed only a small portion of them heads to the intended pest organism. The rest is deposited in the soil, surface water, groundwater as well as the atmosphere where it reacts with the physical, chemical, and biological parts of the ecosystem. Microorganisms in the soil, which have key roles such as nutrient cycling, decomposition of organic matter, fixation of nitrogen and growth promotion of plants, are highly vulnerable to pesticide perturbation. Research has also shown that the application of pesticide leads to considerable losses in microbe biomass and changes in community structure, including the inhibition of important soil enzymes such as dehydrogenases, beta-glucosidases and phosphatases, which could control nutrient cycling and rhizosphere signalling (Walder et al., 2022; Ghosh et al., 2023

However, some microbial communities have the enzymatic processes that have the capability to convert pesticides molecules to carbon or energy, a process referred to as biodegradation or mineralization. Microbial degradation of pesticides in soil ecosystems is a key and increasingly popular research topic, especially in the bioremediation of polluted arable lands (Bose et al., 2021; WSEAS, 2024). Alcaligenes faecalis, Bacillus flexus, Bacillus cereus, and Pseudomonas spp. bacteria were found to be effective degraders of chlorpyrifos, fenvalerate, and cypermethrin, respectively (Yadav et al., 2021; Mulla et al., 2017). The main issue of concern in this study is to understand the presence of which microbial taxa in the soils of Edo State farms, which pesticide substrates they can degrade, and the extent to which they can exhibit the degradation activity on the larger community of soil microorganisms.

1.2 Statement of the Problem

Although there is an increasing body of literature on pesticide biodegradation in the world, on site based investigation in the South-South geopolitical hydraulic region of Nigeria especially the Edo State is limited. In early 2023, an assessment of the organophosphate pesticide residues in nearby Delta State farmlands found dichlorvos, dimethoate, chlorpyrifos, and profenofos in almost all sampled soils, and the pesticide residues were often well beyond acceptably high limits (Yao et al., 2023). A similar study of the organochlorine pesticide residues in southern Nigerian farm soils (2024) further confirmed the presence of historically prohibited solvents such as DDT, dieldrin, transgaming-HCH, in the crop-producing farms just in Nigeria to raise significant concerns about the legacy load maintained by soil microorganisms within the area (Inyangudoh et al., 2024

The given issue is exacerbated in the Edo State due to the dependence of smallholder farmers on the use of the cocktails of pesticides without proper training and use of personal protective equipment. The survey data in Rivers State and southwest Nigeria show that formal pesticide safety training to farmers is still perceived to be a minority, and the application of the most perilous pesticides, including the organophosphates, to food products has become common (PMC, 2022; Frontiers in Agronomy, 2025). These facts indicate that the Edo State farmland soils have a high-level of pesticide load which could be negatively influencing the population of nitrogen fixing bacteria, arbuscular mycorrhizal fungi (AMF), and other useful microorganisms upon which a sustainable agricultural productivity relies.

The knowledge gap concerning the identity and activity of pesticide-degrading microorganisms in soils of farmlands within Edo State is critical as well as the metabolic pathways of pesticide degradation and the collateral effects of pesticides build-up on beneficial soil microflora diversity and function. This paper is aimed at filling these gaps.

1.3 Justification for the Study

The justification for this study is both scientific and socioeconomic. From a scientific standpoint, indigenous pesticide-degrading microorganisms from Edo State soils may harbour novel enzymatic and genetic capabilities for the breakdown of recalcitrant agrochemicals, including organophosphate hydrolases, esterases, and oxidoreductases. Characterizing these organisms and their metabolic capacities contributes to the global knowledge base on pesticide bioremediation and may yield candidates for bioaugmentation strategies in contaminated soils.

From a public health and food security perspective, the contamination of soil by persistent pesticide residues threatens not only the health of farm workers through dermal and inhalational exposure, but also that of consumers through the uptake of residues into edible plant tissues. Pesticide-induced disruption of arbuscular mycorrhizal fungi communities reduces the plant's capacity for phosphorus absorption, undermines drought tolerance, and diminishes natural disease resistance, ultimately reducing crop yields and farmer incomes (Frontiers in Soil Science, 2022). The suppression of nitrogen-fixing bacteria further compromises soil fertility and increases dependence on costly inorganic fertilizers. A thorough understanding of these dynamics in Edo State farmlands is therefore essential for designing ecologically sound pesticide management policies and introducing microbial inoculants to restore soil health.

Furthermore, the recent NAFDAC regulatory actions banning chlorpyrifos and paraquat in Nigeria create an urgent need for baseline data on the microbial ecology of Edo State soils under these compounds, which will serve as reference points for monitoring soil recovery following the implementation of the bans.

1.4 Aim and Objectives of the Study

The aim of this study is to evaluate the microbial degradation of selected pesticides in agricultural soils from Edo State farmlands and to assess the impact of this degradation and the underlying pesticide contamination on beneficial soil microflora.

The specific objectives are:

(i) To determine the physicochemical properties and pesticide residue profiles of selected Edo State farmland soils.

(ii) To isolate, characterize, and identify pesticide-degrading microorganisms from the sampled soils using morphological, biochemical, and molecular techniques.

(iii) To evaluate the biodegradation potential of isolated microorganisms against selected pesticides (chlorpyrifos, glyphosate, and cypermethrin) under laboratory conditions.

(iv) To assess the enzymatic activity (dehydrogenase, urease, and phosphatase) of soil samples as indicators of microbial function.

(v) To determine the correlation between pesticide residue concentrations and the diversity and abundance of beneficial soil microorganisms.

1.5 Research Questions

The following research questions guide this study and are aligned directly with the stated objectives:

(i) What are the physicochemical properties and pesticide residue profiles of selected Edo State farmland soils, and how do these vary across sites with different histories of pesticide use?

(ii) Which pesticide-degrading microorganisms can be isolated and identified from the sampled Edo State farmland soils using morphological, biochemical, and molecular characterization methods?

(iii) What is the biodegradation potential of the isolated microorganisms against chlorpyrifos, glyphosate, and cypermethrin under controlled laboratory conditions?

(iv) How do the activities of key soil enzymes—dehydrogenase, urease, and phosphatase differ between pesticide-contaminated and control soils, and what do these differences indicate about the functional status of the soil microbial community?

(v) What is the population density and diversity of nitrogen-fixing bacteria and arbuscular mycorrhizal fungi in pesticide-contaminated compared to control Edo State farmland soils?

(vi) Is there a significant correlation between pesticide residue concentrations and the diversity and abundance of beneficial soil microorganisms in the studied farmlands?

1.6 Research Hypotheses

H0₁: There is no significant difference in the diversity and abundance of pesticide-degrading microorganisms between pesticide-contaminated and control Edo State farmland soils.

H0₂: There is no significant relationship between pesticide residue concentrations and the population density of beneficial soil microflora in Edo State farmlands.

H0₃: Isolated pesticide-degrading microorganisms do not significantly reduce the concentration of selected pesticides under controlled laboratory conditions.

1.7 Scope of the Study

This study is limited to agricultural soils from selected Local Government Areas in Edo State, Nigeria, with varying histories of pesticide application. Three pesticides—chlorpyrifos (organophosphate), glyphosate (herbicide), and cypermethrin (pyrethroid) are selected as representative compounds based on their documented prevalence in Nigerian farmlands. Beneficial microflora to be assessed include nitrogen-fixing bacteria (Rhizobium, Azotobacter, and Azospirillum spp.) and arbuscular mycorrhizal fungi. The study does not extend to pesticide analysis in water bodies or plant tissues adjacent to the sampled farmlands.

1.8 Significance of the Study

This study will provide the first comprehensive characterization of pesticide-degrading microbial communities indigenous to Edo State farmland soils and their relationship to beneficial soil microflora. The findings will generate actionable data for agricultural extension services, enabling the formulation of evidence-based pesticide use guidelines that preserve soil biological health. Identified high-performing degrader strains may be developed into bioremediation products applicable in post-contamination soil restoration programmes across Nigeria's South-South agricultural communities. The study also contributes to the monitoring of soil recovery following the NAFDAC bans on chlorpyrifos and paraquat, and provides reference data for longitudinal assessment of pesticide policy effectiveness in Nigerian agriculture.

1.9 Definitions of Terms

The following terms are used in this study in the specific senses defined below:

Pesticide: A chemical substance or biological agent used to kill, repel, or control pests including insects, weeds, fungi, and rodents in agricultural systems. In this study, the term refers specifically to synthetic chemical compounds applied to Edo State farmlands.

Organophosphate: A class of synthetic pesticides characterized by the presence of a phosphate ester group. Organophosphates, including chlorpyrifos, act by inhibiting acetylcholinesterase and are among the most widely used insecticides in Nigerian agriculture.

Herbicide: A pesticide designed to kill or inhibit the growth of unwanted plants (weeds). Glyphosate is the herbicide studied in this research, and it functions by inhibiting the shikimate pathway in plants.

Pyrethroid: A synthetic analogue of natural pyrethrin compounds derived from chrysanthemum flowers. Pyrethroids such as cypermethrin disrupt sodium channel function in insects and are widely applied on food crops in Nigeria.

Microbial Degradation: The breakdown of chemical compounds, including pesticides, by the metabolic activities of microorganisms such as bacteria and fungi. This may occur through mineralization (complete breakdown to inorganic products) or biotransformation (partial conversion to less toxic metabolites).

Biodegradation: The biological decomposition of organic substances by living organisms, particularly microorganisms, into simpler compounds such as carbon dioxide, water, and inorganic salts. In this context, it refers specifically to the microbial decomposition of pesticide molecules in soil.

Bioremediation: A technology that uses living organisms, primarily microorganisms, to detoxify or remove pollutants from contaminated environments including soil and water. Bioremediation may be natural (intrinsic) or engineered (through bioaugmentation or biostimulation).

Bioaugmentation: A bioremediation strategy in which specific high-performing microbial strains or consortia are introduced into a contaminated environment to supplement the indigenous microbial community and accelerate pollutant degradation.

Biostimulation: A bioremediation approach involving the addition of nutrients (nitrogen, phosphorus, carbon sources) or other amendments to a contaminated environment to stimulate the growth and metabolic activity of indigenous pesticide-degrading microorganisms.

Beneficial Soil Microflora: Soil microorganisms that contribute positively to soil health and plant productivity. In this study, the term refers specifically to nitrogen-fixing bacteria (Rhizobium, Azotobacter, Azospirillum spp.) and arbuscular mycorrhizal fungi (AMF).

Nitrogen-fixing Bacteria: Microorganisms capable of converting atmospheric dinitrogen (N₂) into bioavailable ammonium (NH₄⁺) through the enzyme nitrogenase. Examples include free-living genera such as Azotobacter and Azospirillum, and symbiotic genera such as Rhizobium.

Arbuscular Mycorrhizal Fungi (AMF): Obligate symbiotic fungi of the phylum Glomeromycota that colonize the roots of approximately 80% of terrestrial plant species, forming arbuscules for nutrient exchange. AMF enhance plant phosphorus uptake, drought tolerance, and disease resistance.

Soil Enzyme Activity: A measure of the catalytic capacity of soil for specific biochemical reactions, used as an indicator of overall soil biological health. In this study, dehydrogenase, urease, and phosphatase activities are measured as proxies for microbial metabolic activity and nutrient cycling capacity.

Pesticide Residue: The quantity of a pesticide or its metabolites remaining in soil, water, or plant tissue after application. Residue concentrations are typically expressed in milligrams per kilogram (mg/kg) for soil or micrograms per litre (µg/L) for water.

Farmland Soil: Soil that has been subject to agricultural use, including tillage, fertilizer application, and pesticide treatment. In this study, farmland soils are sampled from sites in Edo State, Nigeria, with documented histories of pesticide application.