Isolation and Molecular Characterization of Potential Plant Growth-Promoting Bacteria from Groundnut and Maize

Abstract

Exploring microbial resources from coastal environments is crucial for enhancing food security; however, current knowledge remains limited. This study aimed to isolate and molecularly characterize bacteria associated with maize and groundnut, and to evaluate their potential as plant growth-promoting (PGP) agents. Rhizobacteria were isolated from rhizospheric soil, and endophytic bacteria were obtained from surface-sterilized and macerated plant roots. One gram of each sample was suspended in sterile distilled water in test tubes, serially diluted, and plated on nutrient agar. After incubation, distinct colonies were sub-cultured to obtain pure cultures for biochemical tests, screening for PGP traits, assessment of pH and salt tolerance, optimal growth conditions, bioinoculation potential, and molecular analysis. Out of sixty isolated bacteria, five potent strains, BS1-BS5, were identified. BS3 showed the highest mannanase activity, with a 2.3 cm zone of clearance, while BS2 exhibited high indole-3-acetic acid (IAA) and phosphate solubilization activities of 10.92 µg/mL and 10.78 mg/L. BS1 and BS4 demonstrated high drought tolerance, 0.94 and 0.98 at 10% PEG, with BS1 also showing maximum salt tolerance of 0.76. At 6.0 g and 2.0 g supplementation, BS1 and BS2 utilized 100% lactose and fructose. BS3 exhibited the highest percentage of antifungal activity, with a 30.12% inhibition rate. BS4 and BS5 promoted shoot lengths of 55.00 cm and 49.80 cm, respectively. Although the bacterial species isolated are generally considered pathogenic, their positive effects contributed significantly to maize growth.

1. Introduction

Growing staple food crops is a key driver of food security worldwide, especially in coastal environments [1]. Nigeria plays a critical role in this context due to its diverse agricultural resources [2]. Harnessing coastal microbial resources offers promising potential to boost agricultural productivity [3]. Microbes inhabiting plant rhizosphere compartments are particularly important because of their ability to enhance plant nutrition to improve crop yields [4,5]. Raising awareness about the ecological roles of plant and soil microbes through academic programs can help connect researchers with local farmers [3]. Such collaboration can encourage farmers to adopt eco-friendly practices, including the use of biological agents to enhance the production of crops like groundnut and maize.

Traditional agriculture often relies heavily on agrochemicals, which can degrade soil health over time [6]. In contrast, plant and soil microbes offer a sustainable alternative by naturally improving soil fertility and promoting plant growth without environmental harm [7]. Research into rhizosphere and endosphere bacteria is of great interest to the scientists [4,5]. This aims to develop biorational applications of bioinoculants to sustain soil conditions in the Ayeka, Igbobini, Igodan, Okitipupa, and Okunmo regions. Although efforts to bridge the researchers and farmers through the practical application of bioinoculants in these regions are ongoing, testing their effectiveness and adaptability for possible scalability is essential to reduce dependence on harmful chemicals and support sustainable farming practices [8]. Despite the limited information in the literature regarding the use of bioinoculants in these areas, this research will be valuable in boosting agricultural productivity along the coastline.

The rhizosphere compartments of groundnut and maize harbor unique bacterial strains adapted to local environmental conditions [9,10]. Exploring these strains can uncover new bacteria with applications in agriculture, advancing scientific knowledge, and local innovation [11]. Such bacteria can help address challenges like climate-induced stress, soil degradation, nutrient deficiencies, and pest or disease pressures [12]. They can also enhance crop resilience, improve soil health, and increase productivity while reducing crop loss [13,14].

Groundnut and maize are staple crops globally, and improving their yield and disease resistance benefits both food security and local economies [15]. However, in the study areas, water scarcity during the dry season can limit plant growth and crop productivity [8]. Multifunctional bacteria with diverse growth-promoting and drought-tolerance mechanisms offer promising solutions [16]. Bacteria in the rhizosphere and endosphere of these crops can significantly enhance sustainable productivity, especially in drought-prone regions with unpredictable rainfall [17].

This research could lead to the development of commercial bio-products, such as bioinoculants or biofertilizers designed specifically for groundnuts and maize growth enhancement. Such products have the potential to create new markets, stimulate local economic development, and support agricultural startups through job creation. Although prior studies have highlighted the benefits of endophytic and rhizobacteria in enhancing plant nutrition [18,19,20]. There is limited information on bacterial strains from groundnut and maize rhizo-endosphere in the study areas. In particular, molecular characterization of plant growth-promoting bacteria (PGPB) from the Nigerian coastal rhizo-endosphere of maize and groundnut remains scarce. This gap motivates the current study to focus on identifying and understanding local bacterial strains. Investigating these bacteria aims to highlight their role in promoting environmental sustainability and diverse agricultural applications [21].

Studying agriculturally important bacteria from the rhizosphere and endosphere of groundnut and maize has immensely contributed to enhancing agricultural productivity [8]. It also provides valuable insights into global scientific knowledge on bioprospecting endophytic and rhizobacteria for plant health and eco-friendly agriculture. This work serves as a model for broader efforts aimed at developing sustainable agricultural systems. Therefore, the specific aim of this study is to isolate, characterize, and evaluate the PGP potential of bacterial strains from the rhizosphere and endosphere of groundnut and maize in selected communities within Okitipupa and Ese-Odo Local Government Areas of Ondo State, Nigeria. Furthermore, this study will expand scientific understanding of locally adapted beneficial bacteria and their role in enhancing crop productivity and resilience in these underexplored agroecological zones. We hypothesize that native bacterial strains from the rhizosphere of these crops possess distinct growth-promoting and stress-tolerance traits suitable for bioinoculant development. Additionally, this study provides information on the functional overlap of pathogenic bacteria as plant growth enhancers, which could serve as models for plant–microbe interactions and benchmarks in establishing a safety threshold for managing microbial risks within agricultural systems.

2. Materials and Methods

2.1. Collection of Plant Samples from Agricultural Farmlands

The groundnut samples were collected from agricultural farmlands in Igodan (IGD -6°45′34.578″ N Latitude and 4°77′70.879″ E Longitude), and Okunmo (OKM—6°44′54.304″ N Latitude and 4°77′04.179″ E Longitude), while maize samples were obtained from farmlands in Ayeka (AYK—6°38′45.58188″ N Latitude and 4°46′31.23012″ E Longitude), Igbobini (IGB—6°30′57.51648″ N Latitude and 4°52′25-56372″ E Longitude), and Okitipupa (KTP—6°30′46″ N Latitude and 4°46′46″ E and 174° S Longitude). Ayeka, Igodan, Okitipupa, and Okunmo are located in Okitipupa Local Government Area, while Igbobini is in Ese-Odo Local Government Area of Ondo State, Nigeria. The climatic conditions of this region are characterized by two distinct seasons: a wet (rainy) season from April to October, and a dry season from November to March (Ondo State Profile). The average annual rainfall typically exceeds 2000 mm, and the mean annual temperature remains around 27 °C. These favorable agro-climatic conditions support the cultivation of staple food crops, such as maize, and oilseed crops, such as groundnut. The region is also increasingly engaged in intensified agricultural practices and agribusiness activities. The uprooted plants with adhering soils were carefully collected in triplicate, labeled, and placed inside sterile plastic bags before being transported to the Microbiology Laboratory for microbiological and other analyses.

2.2. Sample Preparation and Microbial Analysis

Surface sterilization of the collected plant roots was carried out by sequentially soaking them in 70% ethanol for 3 min, followed by 3% sodium hypochlorite for 3 min, then 70% ethanol for 30 s. The roots were subsequently rinsed five times with sterile distilled water and cut into small, uniform segments. A sterility check was performed by culturing the surface-sterilized roots on a nutrient agar to confirm the absence of external contaminants. Thereafter, 1 g each of macerated root tissue and rhizospheric soil was separately weighed and dispensed into test tubes to prepare stock solutions. The samples were serially diluted up to 10⁻⁶. An aliquot of 0.1 mL from dilutions, 10⁻³ and 10⁻⁵, was aseptically pipetted into sterile Petri dishes, followed by pour plating with sterilized nutrient agar (RDM-NA-01, Chaitanya Agro Biotech PVT. Ltd., Malkapur, India). The inoculated plates, prepared in triplicate, were incubated at 37 °C for 24 h. Resulting colonies were counted, recorded, and purified by streaking onto fresh nutrient agar plates to obtain pure cultures. The pure isolates were stored in 25% sterile glycerol in Eppendorf tubes and kept in a laboratory freezer at −20 °C. Various biochemical tests, including Gram staining, catalase, indole production, hydrogen sulphide production, and sugar fermentation, were performed to primarily characterize the bacterial isolates.

2.3. Screening of Rhizo- and Endophytic Bacteria for Plant Growth Promotion

After obtaining pure cultures of rhizospheric and endophytic bacterial isolates, plant growth-promoting tests were conducted in triplicate [8].

2.3.1. Indole Acetic Acid (IAA) Production

From the initial screening, a total of 36 and 24 bacterial isolates from maize and groundnut, respectively, were tested for their ability to produce IAA using L-tryptophan as a substrate. Briefly, the bacterial isolates were inoculated into nutrient broth supplemented with 0.1% L-tryptophan (substrate) and broth without the substrate (as a control), and incubated in test tubes on a rotary shaker at 180 rpm for 48 h. After incubation, the cultures were centrifuged at 8000 rpm for 10 min. To 2 mL of the resulting supernatant, 3 drops of orthophosphoric acid and 4 mL of Salkowski reagent were added, followed by incubation in the dark for 30 min. The development of a pink coloration indicated a positive result for IAA production. The quantity of IAA in the substrate-supplemented medium was measured using a spectrophotometer (INESA, Shanghai, China) at 535 nm. The IAA concentration was recorded in µg/mL using a corresponding IAA standard curve.

2.3.2. Exopolysaccharides Production

Exopolysaccharide production by the bacterial isolates was assessed using nutrient broth supplemented with 10% sucrose, adjusted to pH 7.0, and sterilized at 121 °C for 15 min. Sterile Whatman filter paper discs (3 mm diameter) were gently placed on the surface of the solidified medium in Petri plates. A 24 h old bacterial culture was inoculated directly onto the filter paper discs, and the plates were incubated at 30 °C for 24 h. The formation of a mucoid appearance on the filter paper indicated a positive test for exopolysaccharide production. Un-inoculated Petri plate served as a control.

2.3.3. Hydrogen Cyanide Production

The bacterial isolates were evaluated for hydrogen cyanide (HCN) production using sterile nutrient broth amended with glycine (4.4 g/L). Ten milliliters of the liquid medium were dispensed into test tubes and sterilized at 121 °C for 15 min. After cooling, the tubes were inoculated with bacterial isolates and allowed to stand. Sterile rectangular Whatman filter papers soaked in a solution of 2% sodium carbonate and 0.05% picric acid (yellow color) were placed inside the test tubes without touching the liquid medium. The tubes were then plugged with sterile cotton wool and incubated at 30 °C for 4 days. A color change in the filter paper from yellow to brown or dark brown indicated a positive result for HCN production. Un-inoculated tube served as a control.

2.3.4. Ammonia Production

Ammonia production was assessed by inoculating bacterial isolates into 10 mL of sterilized peptone water, followed by incubation at 30 °C for 48 h on a rotary shaker. After incubation, 0.5 mL of Nessler′s reagent was added to each test tube and allowed to stand for 5 min. A color change from slight yellow to brown indicated a positive reaction. Un-inoculated tube served as a control.

2.3.5. Nitrogen Fixation Production

The nitrogen fixation ability of the bacterial isolates was assessed on Jensen′s medium composed of 20 g sucrose, 0.5 g NaCl, 0.5 g MgSO₄·7H₂O, 1.0 g K₂HPO₄, 0.005 g Na₂MoO₄, 2.0 g CaCO₃, 0.1 g FeSO₄·7H₂O, and 15 g agar per 1000 mL sterile distilled water, adjusted to pH 7.2. The medium was sterilized at 121 °C for 15 min, allowed to cool, and poured into Petri plates. The plates were inoculated with the bacterial isolates and incubated at 30 °C for 5 days. Growth of bacteria on the plates indicated a positive result for nitrogen fixation. Un-inoculated plate served as a control.

2.3.6. Phosphate Solubilization

For phosphate solubilization, Pikovskaya agar composed of 0.2 g KCl, 10 g glucose, 0.1 g MgSO₄·7H₂O, 0.5 g yeast extract, 5 g Ca₃(PO₄)₂, 0.002 g FeSO₄·7H₂O, 0.5 g (NH₄)₂SO₄, 0.2 g NaCl, 0.002 g MnSO₄·H₂O, 15 g agar, and 1000 mL sterile distilled water was used. The medium was sterilized at 121 °C for 15 min, allowed to cool, and poured into plates. The Petri plates were spot-inoculated at the center with the selected isolates and incubated at 35 °C for 3–5 days. The formation of clear zones around the colonies indicated positive phosphate solubilization, while an uninoculated plate served as a control. For quantitative screening, bacterial isolates were inoculated into sterilized Pikovskaya broth supplemented with tricalcium phosphate and incubated at 35 °C for 72 h. The cultures were centrifuged at 6000 rpm for 10 min, and the optical density of the supernatant was measured at 882 nm using a spectrophotometer (INESA, Shanghai, China). The phosphate solubilization ability was calculated using a standard curve.

2.4. Other Tests

For other tests performed, detailed methodologies are provided in the Supplementary Material S1–S4. Briefly, extracellular enzyme screening was conducted using appropriate substrates: mannanase (locust bean gum and other components), cellulase (carboxymethyl cellulose and other components), amylase (soluble starch and other components), and lipase (peanut oil emulsion and other components), as described by Adeleke et al. [22] (Supplementary Material S1.1–S1.4). Additionally, bacterial growth measurements were carried out in nutrient broth with varying salt concentrations (Supplementary Material S2.0), at different pH levels (S3.1), and with carbon (Supplementary Material S3.2) and nitrogen (Supplementary Material S3.3) supplementation under optimized nutrient source conditions, as described by Fasusi et al. [23] and Agunbiade et al. [24]. The antagonistic potential of the screened drought-tolerant bacterial isolates was also evaluated using a dual plate assay (Supplementary Material S4.0).

2.5. Identification of Isolated Bacteria by Molecular Techniques

After the initial screening, five bacterial isolates -two from maize roots, one from maize rhizosphere soil, and two from groundnut rhizosphere soil—showing the most plant growth-promoting attributes across the sampling sites were selected for molecular analysis. Bacterial DNA was extracted using commercial DNA extraction kits specific for bacteria/fungi (Zymo Research, Irvine, CA, USA). A NanoDrop spectrophotometer (Thermo Scientific™, Waltham, MA, USA) was used to accurately quantify the extracted DNA at A260/280 nm. The amplification of the 16S rRNA gene was conducted using primers 27F/1492R. The integrity of the PCR products was assessed by electrophoresis on 1% agarose gel and visualized using a gel documentation system (E-BOX, Vilber Lourmat, Pavia, Italy). Post-PCR purification was performed using the enzymatic method (ExoSAP), and PCR products were further purified using the ZR-96 DNA Sequencing Clean-up Kit™ (Zymo Research, Irvine, CA, USA). Sequencing was carried out using the Nimagen Brilliant Dye™ Terminator Cycle Sequencing Kit V3.1, BRD3-100/1000, according to the manufacturer’s instructions. The resulting sequencing data were analyzed using BioEdit software (version 7.2.5) and aligned using ClustalW. A Basic Local Alignment Search Tool (BLAST Version 2.17.0, 2025) search was performed on the National Center for Biotechnology Information (NCBI) database to generate consensus sequences [25]. After identification, the bacteria were cultured in a growth medium (i.e., nutrient broth) for inoculum preparation and standardization of cell suspension for maize seed and seedling inoculation. The detailed methodology is provided in the Supplementary Material S5.0.

2.6. Statistical Analysis

The data obtained from the study, conducted in triplicate, were analyzed using analysis of variance (ANOVA), followed by Duncan’s Multiple Range Test (DMRT) using the Statistical Package for the Social Sciences (SPSS), version 16.0. A confidence level of p < 0.05 was considered statistically significant. Results were presented as mean ± standard deviation. Summary data for individual variables were illustrated using simple and clustered bar graphs, showing the mean values of the control and treatment groups.

3. Results

3.1. Bacterial Plate Cellular Morphology and Biochemical Tests

The macro- and microscopic characterization of the bacterial strains, along with their biochemical traits, is presented in

Table 1. Morphological and Microscopic Characterization of the Bacterial Strains and Their Biochemical Traits.

Entity Features	BSI	BS2	BS3	BS4	BS5
Cell Morphology
Size	Big	Thin	Big	Big	Big
Gram reaction	-	+	-	-	-
Surface	Smooth	Smooth	Smooth	Smooth	Smooth
Shape	Regular	Irregular	Irregular	Circular	Circular
Colour	Creamy	Creamy	Creamy	Creamy	Milky
Cellular shape	Rod	Rod	Rod	Rod	Rod
Elevation	Long/Raised	Flat	Flat	Flat	Flat
Optical density	Opaque	Opaque	Opaque	Opaque	Opaque
Margin	Entire	Entire	Entire	Lobate	Entire
Consistency	Mucoid	Mucoid	Mucoid	Mucoid	Fibrous
Arrangement	Chains	Chains	Single	Chains	Chains
Biochemical tests
CT	+	+	+	+	+
HSP	+	+	+	+	+
Indole	-	-	+	-	+
SH	+	+	+	+	+
Nitrate	+	+	+	+	+
Sugar fermentation
Glucose	(++)	(++)	(++)	(++)	(++)
Fructose	(+)	(++)	(++)	(++)	(++)
Sucrose	(++)	(++)	(++)	(+)	(++)
Lactose	(+)	(++)	(++)	(+)	(++)
Maltose	(+)	(++)	(++)	(++)	(++)
Sample source	IGB	AYK	OKM	IGD	KTP
Isolation sources	Maize root endosphere	Groundnut rhizosphere soil	Maize root endosphere	Maize rhizosphere soil	Groundnut rhizosphere soil

Key: + = positive, - = negative, CT—Catalase, HSP—Hydrogen Sulphide Production, SH—Starch Hydrolysis, (+)—Acid Production, Colour Changes/no Gas Production, (++)—Acid Production, Colour Changes/Gas Production, IGB—Igbobini, AYK—Ayeka, OKM—Okunmo, IGD—Igodan, KTP—Okitipupa.

. The bacteria exhibited diverse morphological features. Most colonies on the cultured plates were large, except for strain BS2, which was isolated from groundnut rhizosphere soil in Ayeka. All bacterial isolates had smooth surfaces and irregular shapes, except strains BS4, isolated from maize rhizosphere soil in Igbobini, and BS5, isolated from groundnut rhizosphere soil in Okitipupa, which were circular. Only strain BS5 appeared milky, while strain BS1 exhibited a long, raised elevation. All bacterial strains were mucoid, except BS5. The cellular morphology of the bacteria was rod-shaped, and they appeared Gram-positive after staining. All strains fermented sugars.

3.2. Qualitative and Quantitative Screening of Plant Growth-Promoting Rhizo- and Endophytic Bacteria

Table 2. Qualitative screening of plant growth-promoting bacteria.

PGP Screening		Isolates
	BSI	BS2	BS3	BS4	BS5
IAA	+	+	+	+	+
EXP	+	+	+	+	+
HCN	+	+	+	+	+
AP	+	+	+	+	+
NF	+	+	+	+	+
PS	+	+	+	+	+
Drought	+	+	+	+	+
Enzymes
Amylase	+	+	+	+	+
Cellulase	+	+	+	+	+
Mannanase	+	+	+	+	+
Lipase	+	+	+	+	+

Key: +—positive; IAA—Indole Acetic Acid; EXP—Exopolysaccharide; HCN—Hydrogen cyanide; AP—Ammonia Production; NF—Nitrogen Fixation; PS—Phosphate solubilization.

and

Table 3. Enzyme screening and quantitative screening of plant growth-promoting bacteria.

PGP Screening			Isolates
	Control	BSI	BS2	BS3	BS4	BS5
Amylase (cm)	0.00 ± 0.00 a	2.50 ± 0.00 c	2.10 ± 0.00 c	1.30 ± 0.00 b	2.30 ± 0.00 c	1.90 ± 0.00 c
Cellulase (cm)	0.00 ± 0.00 a	1.10 ± 0.00 c	1.60 ± 0.00 c	0.90 ± 0.00 b	1.70 ± 0.00 c	2.10 ± 0.00 c
Mannanase (cm)	0.00 ± 0.00 a	0.70 ± 0.00 b	1.50 ± 0.00 c	2.30 ± 0.00 c	0.90 ± 0.00 b	1.40 ± 0.00 c
Lipase (cm)	0.00 ± 0.00 a	0.70 ± 0.00 b	1.80 ± 0.00 b	1.10 ± 0.00 c	0.90 ± 0.00 b	0.50 ± 0.00 b
IAA supplemented with TRP (µg/mL)	2.10 ± 0.01 a	4.72 ± 0.01 b	10.92 ± 0.02 d	9.36 ± 0.02 c	4.41 ± 0.02 b	10.51 ± 0.02 d
IAA supplemented with TRP and 10% PEG (µg/mL)	2.06 ± 0.02 a	3.47 ± 0.02 b	5.30 ± 0.00 d	3.11 ± 0.01 b	2.90 ± 0.00 a	4.15 ± 0.02 c
PS (µg/mL)	1.16 ± 0.01 a	5.46 ± 0.01 c	10.78 ± 0.02 e	2.86 ± 0.01 b	5.62 ± 0.01 c	8.53 ± 0.02 d
HCN	0.20 ± 0.00 a	0.34 ± 0.02 a	0.55 ± 0.01 a	1.01 ± 0.01 a	0.43 ± 0.02 a	0.87 ± 0.03 a
NF	1.93 ± 0.02 a	2.47 ± 0.02 a	2.22 ± 0.01 a	2.79 ± 0.03 a	2.50 ± 0.00 a	2.36 ± 0.02 a

Key: TRP—tryptophan; IAA—Indole Acetic Acid; HCN—Hydrogen cyanide; NF—Nitrogen Fixation; PS—Phosphate solubilization. Values are represented as mean ± standard deviation of triplicate readings. The superscript (small alphabets) across the same row represent a significant difference.

present the qualitative and quantitative assessment of plant growth-promoting rhizospheric and endophytic bacteria. All isolates responded positively to the assays, although with varying levels of activity (Table 2). Strain BS1 exhibited the highest zone of clearance for amylase activity (2.5 cm), while the activities of the other isolates showed no significant difference compared to the control. Strains BS2 and BS5 demonstrated high IAA production, with concentrations of 10.92 µg/mL and 10.51 µg/mL, respectively, in media supplemented with tryptophan, relative to the control. No significant differences were observed among the bacterial isolates in nitrogen-fixing ability and hydrogen cyanide production. The standard curves for IAA and phosphate solubilization are shown in Figures S1 and S2, respectively. The identification of bacterial strains based on 16S rRNA gene sequencing is presented in

Table 4. Bacteria Identification Based on 16S rRNA Gene Sequencing.

Isolates	AN	QC	E-Value	% SM	QL	BICS	Source
BS1	MT263025.1	100%	0.0	98.27	1500	Enterobacter cloacae	MR-IGB
BS2	KT074456.1	98%	0.0	98.84	749	Bacillus cereus	GS-AYK
BS3	KR094121.1	100%	0.0	93.10	1508	Morganella morganii	MR-OKM
BS4	MN636438.1	100%	0.0	98.26	979	Serratia marcescens	MS-IGD
BS5	KU749295.1	100%	0.0	98.73	132	Wohlfahrtiimonas chitiniclastica	GR-KTP

Key: AN—accession numbers; QC—query cover; SM—similarity; QL—query length; BICS—Blast ID closest species; MR-IGB—maize root Igbobini; GS-AYK—groundnut soil Ayeka; MR-OKM—maize root Okunmo; MS-IGD—maize soil Igodan; GR-KTP—groundnut root Okitipupa.

. The identified strains include Enterobacter cloacae BS1, Bacillus cereus BS2, Morganella morganii BS3, Serratia marcescens BS4, and Wohlfahrtiimonas chitiniclastica BS5. Based on the sample sources and the design of the study, it is important to note that several of the isolated strains are recognized human pathogens. These include Enterobacter cloacae, Bacillus cereus, Morganella morganii, and Serratia marcescens. Additionally, Wohlfahrtiimonas chitiniclastica is a known zoonotic bacterium associated with bacteremia, myiasis, and soft tissue infections. According to South African regulations on hazardous biological agents (South Africa: Consolidated Regulations: Regulations for Hazardous Biological Agents. https://www.saflii.org/za/legis/consol_reg/rfhba405/ (accessed, 3 September 2025)), these bacteria are classified as potentially pathogenic. However, it should be emphasized that the identification of these pathogens was incidental and not the primary objective of this study.

3.3. Drought Tolerance Screening

The drought screening test was conducted on the isolated bacterial strains. In the preliminary screening using 10% PEG, E. cloacae BS1 and S. marcescens BS4 exhibited high drought tolerance, with absorbance values of 0.34 and 0.35, respectively, compared to the control (culture medium without PEG supplementation) (Figure 1). Figure 2A–E illustrate the drought tolerance of each bacterial isolate across different PEG concentrations and incubation times. At 5%, 10%, and 15% PEG concentrations, E. cloacae BS1 showed drought tolerance levels of 0.94, 0.95, and 0.54, respectively, after 72 h of incubation, relative to the control (Figure 2A). Similar trends were observed for B. cereus BS2 and M. morganii BS3 at 5% and 10% PEG concentrations after 48 and 72 h of incubation, respectively (Figure 2B,C). Drought tolerance levels of 0.98 and 1.00 were recorded for S. marcescens BS4 and W. chitiniclastica BS5, respectively, after 72 h in media supplemented with 10% PEG (Figure 2D,E).

3.4. Bacteria Subjected to Different Salt Concentrations and Varied pH

The bacterial response to different salt concentrations and varying pH levels is presented in Figure 3 and Figure 4. E. cloacae BS1 exhibited salt tolerance, with high values of 0.76, 0.74, and 0.73 compared with the control, with values of 0.21 (Figure 3). The low salt tolerance of 0.12 at 0.1g of salt was recorded in strain BS5. The bacteria showed optimal growth at pH 7.0 (Figure 4).

3.5. Optimization of Process Parameters of Nutrient Source Requirements

The percentage optimization of process parameters for carbon and nitrogen sources in the bacterial isolates is presented in

Table 5. Percentage optimization of carbon source requirements of the bacterial isolates.

Sugars	Concentration (g)	BS1	BS2	BS3	BS4	BS5
Glucose	Control	33.00 ± 0.00 a	33.00 ± 0.00 a	33.00 ± 0.00 a	33.00 ± 0.00 a	33.00 ± 0.00 a
	2.0	93.94 ± 0.01 d	81.82 ± 0.02 c	96.97 ± 0.02 d	84.84 ± 0.02 c	72.73 ± 0.01 d
	4.0	30.30 ± 0.03 b	45.45 ± 0.03 b	57.58 ± 0.03 b	63.64 ± 0.03 b	51.52 ± 0.01 b
	6.0	72.73 ± 0.01 c	81.83 ± 0.01 c	66.67 ± 0.02 c	84.85 ± 0.01 c	57.58 ± 0.02 c
Lactose	Control	24.00 ± 0.00 a	24.00 ± 0.00 a	24.00 ± 0.00 a	24.00 ± 0.00 a	24.00 ± 0.00 a
	2.0	37.50 ± 0.02 b	83.33 ± 0.03 c	79.17 ± 0.03 c	91.67 ± 0.03 d	41.67 ± 0.02 b
	4.0	37.50 ± 0.00 b	50.00 ± 0.00 b	54.17 ± 0.01 b	62.50 ± 0.02 b	70.83 ± 0.02 c
	6.0	100.00 ± 0.02 c	91.67 ± 0.01 d	83.33 ± 0.01 d	79.17 ± 0.02 c	91.67 ± 0.01 d
Maltose	Control	22.00 ± 0.00 a	22.00 ± 0.00 a	22.00 ± 0.00 a	22.00 ± 0.00 a	22.00 ± 0.00 a
	2.0	100.00 ± 0.00 d	72.73 ± 0.02 d	95.45 ± 0.03 c	81.82 ± 0.02 c	90.91 ± 0.02 d
	4.0	95.451 ± 0.02 c	68.18 ± 0.01 c	86.36 ± 0.01 b	90.91 ± 0.03 d	72.73 ± 0.01 c
	6.0	63.64 ± 0.01 b	59.09 ± 0.03 b	95.45 ± 0.03 c	77.27 ± 0.01 b	59.09 ± 0.02 b
Fructose	Control	14.00 ± 0.00 a	14.00 ± 0.00 a	14.00 ± 0.00 a	14.00 ± 0.00 a	14.00 ± 0.00 a
	2.0	78.57 ± 0.01 c	100.00 ± 0.00 c	85.71 ± 0.01 d	42.86 ± 0.02 b	85.71 ± 0.02 b
	4.0	78.57 ± 0.03 c	42.86 ± 0.02 b	71.43 ± 0.02 c	42.86 ± 0.01 b	85.71 ± 0.02 b
	6.0	71.42 ± 0.02 b	100.00 ± 0.00 c	42.86 ± 0.02 b	78.57 ± 0.02 c	85.71 ± 0.03 b

Key: BS1—E. cloacae; BS2—B. cereus; BS3—M. morganii; BS4—S. marcescens; BS5—W. chitiniclastica. Values are represented as mean ± standard deviation of triplicate readings. The superscript (small alphabets) down the column represent a significant difference.

and

Table 6. Percentage optimization of the nitrogen source requirement of the bacterial isolates.

Test	Concentration (g)	BS1	BS2	BS3	BS4	BS5
Control	Control	11.00 ± 0.00 a	11.00 ± 0.00 a	11.00 ± 0.00 a	11.00 ± 0.00 a	11.00 ± 0.00 a
PN	2.0	42.85 ± 0.01 b	66.67 ± 0.03 b	90.48 ± 0.00 d	80.95 ± 0.01 c	80.95 ± 0.01 d
	4.0	76.19 ± 0.02 c	66.67 ± 0.01 b	42.86 ± 0.01 b	100.00 ± 0.00 d	61.90 ± 0.02 c
	6.0	95.23 ± 0.02 d	90.48 ± 0.00 c	76.19 ± 0.02 c	57.14 ± 0.01 b	52.38 ± 0.00 b
Casein	Control	20.00 ± 0.00 a	20.00 ± 0.00 a	20.00 ± 0.00 a	20.00 ± 0.00 a	20.00 ± 0.00 a
	2.0	95.00 ± 0.00 d	100.00 ± 0.00 d	80.00 ± 0.01 b	80.00 ± 0.01 c	50.00 ± 0.00 b
	4.0	85.00 ± 0.01 b	75.00 ± 0.01 c	85.00 ± 0.00 c	70.00 ± 0.00 b	100.00 ± 0.00 c
	6.0	90.00 ± 0.02 c	70.00 ± 0.00 b	60.00 ± 0.00 d	70.00 ± 0.01 b	50.00 ± 0.00 b

Key: BS1—E. cloacae; BS2—B. cereus; BS3—M. morganii; BS4—S. marcescens; BS5—W. chitiniclastica. Values are represented as mean ± standard deviation of triplicate readings. The superscript (small alphabets) down the column represent a significant difference.

. In media supplemented with 2 g of glucose, M. morganii BS3 exhibited a high glucose utilization rate of 96.97%. E. cloacae BS1 showed 100% utilization of both glucose (at 6 g) and maltose (at 2 g). Similarly, B. cereus BS2 achieved 100% utilization with 2 g of fructose, compared to the control (Table 5). For nitrogen sources, media supplemented with 2 g of potassium nitrate resulted in 100% utilization by strain BS4. Additionally, a medium supplemented with 6 g of potassium nitrate yielded 95.23% utilization by strain BS1, while strain BS3 showed a much lower utilization rate of 42.86% under the same conditions, compared to the control value of 11%. Furthermore, 100% casein utilization was recorded for strains BS2 and BS5 in media supplemented with 2 g and 4 g of casein, respectively, relative to the control, which showed only 20% utilization (Table 6).

3.6. Antifungal Activities

The percentage inhibition of the isolated bacteria against the pathogenic fungus S. rolfsii is presented in Figure 5. E. cloacae BS1 exhibited a percentage inhibition of 25.30%, while W. chitiniclastica BS5 showed 26.51%, compared to the control, which had an inhibition value of 8.30%. There was no significant difference between the inhibition values of B. cereus BS2 and S. marcescens BS4, which recorded 27.71% inhibition. M. morganii BS3 demonstrated the highest percentage inhibition, at 30.12%.

3.7. Seed and Maize Inoculation

Figure 6 shows the effect of isolated bacteria on seed germination. Nine seeds germinated in the plate inoculated with strain BS3, while no significant difference was observed in the other inoculated plates compared to the control plate, with six seeds germinated. Also, the results of bacteria inoculation on maize growth, shown in Figure 7, Figure 8 and Figure 9. A high number of 30 adventitious roots were observed in maize plants inoculated with M. morganii BS3, while 11 roots were recorded in maize plants inoculated with E. cloacae BS1 (Figure 7). The highest seedling length of 55.00 cm was recorded in maize inoculated with S. marcescens BS4, followed by 49.80 cm in maize inoculated with W. chitiniclastica BS5, compared to the control, which recorded 4.90 cm and 4.20 cm, respectively (Figure 8). The highest fresh root weight of 8.30 g, shoot weight of 28.40 g, and leaf weight of 33.20 g were recorded in maize plants inoculated with M. morganii BS3, W. chitiniclastica BS5, and E. cloacae BS1, respectively, compared to the control (Figure 9).

4. Discussion

The plant rhizosphere harbors diverse microorganisms that play crucial roles in promoting environmental sustainability and enhancing crop productivity [26]. Over time, crop yields have increasingly been impacted by adverse ecological conditions that negatively affect plant growth and soil health [27]. In-depth research into plant microbial communities offers promising solutions for mitigating environmentally induced stressors and improving plant performance [4,28]. Such an approach can complement existing strategies aimed at optimizing the use of beneficial microorganisms, particularly within the context of organic farming and eco-friendly agricultural practices [6]. In this study, PGPB associated with groundnut and maize were isolated from five locations within Okitipupa metropolis: Ayeka, Igbobini, Igodan, Okitipupa, and Okunmo. The collected samples were analyzed to identify non-pathogenic bacterial strains capable of enhancing plant growth and sustainability through mechanisms such as nutrient acquisition, growth hormone production, enzyme activity, and antibiosis.

A significant number of microbes that enhance plant growth in staple food crops, such as groundnut, maize, sorghum, tomato, millet, and cowpea, have been shown to positively influence plant growth through bioinoculation under both suitable and challenging agroecosystems [29,30,31]. The selection of isolates BS1, BS2, BS3, BS4, and BS5 in this study was based on their strong plant growth-promoting traits and drought tolerance, chosen from a total of sixty screened bacterial isolates. Several notable bacterial genera, including Bradyrhizobium, Burkholderia, Flavobacterium, Klebsiella, Methylotenera, and Paenibacillus, are recognized for their role in improving soil health within the endo-rhizosphere regions of various plants [32,33,34,35].

The different morphological features of the bacterial isolates likely reflect their unique physiological traits [22]. For example, the smooth surface of some isolates may facilitate their adaptation to varying environmental conditions [36]. The circular colonies of BS4 and BS5, which differed from those of other isolates, could indicate distinct genetic characteristics. Additionally, the smooth texture and circular shape of these bacterial colonies might suggest specific mechanisms of colony development, possibly related to biofilm formation or cellular organization [37]. Supporting this, Sondang et al. [38] reported circular colony morphology in Bacillus and Pseudomonas species isolated from the endosphere and rhizosphere of healthy maize plants. The mucoid consistency observed in some colonies is often associated with the production of exopolysaccharides [39], a trait common in biofilm-forming bacteria that enhances their colonization of plant root zones. Moreover, the chain-like arrangement seen in some isolates may be linked to cellular communication and adaptive strategies such as quorum sensing [40]. In contrast, the single-cell arrangement observed in BS3 stands out and may reflect specific metabolic or genetic adaptations crucial for plant–microbe interactions. Finally, the ability of the bacterial isolates to ferment sugars demonstrates their metabolic flexibility [41].

Sugar fermentation by endophytic and rhizosphere bacteria in maize and groundnut is crucial for root colonization, as these microbes utilize plant-derived sugars both as energy sources and signaling molecules. These sugars not only fuel microbial metabolism but also trigger key colonization behaviors such as chemotaxis, adhesion, and biofilm formation [22]. For example, Sun et al. [42] demonstrated that exposure to maize sugars enhanced the motility and biofilm formation of B. velezensis S3-1, improving its establishment in the rhizosphere. Moreover, the dynamic sugar profile of root exudates during plant growth influences the structure of microbial communities and their colonization success [43]. The glucose transporter gene ptsG, identified in the genome of B. cereus, has been reported to enhance sugar uptake and effective colonization, underscoring the importance of sugar transport mechanisms [44]. Additionally, the endophyte Herbaspirillum seropedicae′s ability to utilize sugars, organic acids, and phenolics from root exudates contributes to root colonization, nutrient uptake, and stress resilience [45].

Certain genera of endophytic bacteria, such as Bacillus, Pantoea, Curtobacterium, Enterobacter, Flavobacterium, Microbacterium, and Xanthomonas, isolated from maize grown under greenhouse conditions, have been documented to exhibit plant growth-promoting properties [46,47]. Chen et al. [48] reported that Enterobacter cloacae, isolated from maize roots, is capable of solubilizing phosphate and enhancing plant growth, while M. morganii was isolated from the potato rhizosphere in Tanzania [49]. To date, there have been no reports of isolating the endophytic bacterium W. chitiniclastica from groundnut roots, making this study the first to document its presence. Further research is needed to validate its potential use in agriculture for improved crop yield. Additionally, maize rhizobacterium S. marcescens and Bacillus cereus inhabiting groundnut soils have also been reported to contribute to plant growth and resilience to various environmental stresses [50,51].

It should be noted that several bacterial strains isolated in this study, E. cloacae BS1, B. cereus BS2, M. morganii BS3, and S. marcescens BS4, have been classified as pathogenic according to international and national biosafety regulations (South Africa: Consolidated Regulations: Regulations for Hazardous Biological Agents. https://www.saflii.org/za/legis/consol_reg/rfhba405/ (accessed, 3 September 2025)). Additionally, W. chitiniclastica BS5 is known as an emerging zoonotic pathogen associated with bacteremia, myiasis, and soft tissue infections [52,53]. While these strains demonstrated potential plant growth-promoting (PGP) traits, their pathogenic nature raises significant biosafety concerns. According to recent medical literature and regulatory guidelines, such bacteria may pose health risks to agricultural workers, with the possibility of transmission to consumers through contaminated agricultural products [53].

The primary aim of this study was to explore these identifiable bacteria as plant growth promoters, despite their incidental classification as human pathogens. This highlights the critical importance of rigorous biosafety screening before any consideration of their use in agriculture [54]. The presence of pathogenic bacteria in sampled soils and plants can be attributed to various environmental and anthropogenic factors. A significant source is livestock defecation, as many of the identified pathogens are commensal inhabitants of the gastrointestinal tracts of animals, including cattle [55]. When these animals graze or are reared near agricultural fields, their fecal matter can contaminate the soil, introducing enteric bacteria such as E. cloacae, M. morganii, S. marcescens, and other pathogens [56]. This natural contamination results in a soil microbiome containing both beneficial and potentially harmful bacterial species [55].

Furthermore, human defecation in or near agricultural areas—often due to inadequate sanitation infrastructure—can lead to the direct release of pathogenic bacteria into the environment [55], adding more human-associated pathogens to the soil microbial community. Both animal and human sources increase the likelihood of pathogenic bacteria′s presence in soil and plant samples. Interestingly, these bacteria may also contribute to soil health and plant growth, especially in regions where open grazing or insufficient waste management practices are common [53].

It is important to recognize that soil is a complex and dynamic ecosystem harboring a diverse microbial population [3]. The coexistence of pathogens with plant growth-promoting bacteria reflects the multifaceted nature of soil microbiota, where bacteria with different ecological roles, from beneficial symbionts to opportunistic pathogens, can be present simultaneously [48]. This complexity underscores the need for careful screening and evaluation when selecting bacterial strains for agricultural applications to ensure both safety and efficacy.

Nevertheless, this study confirmed the functionality of these bacteria as plant growth promoters. The identified strains hold great promise for diverse applications, including enhancing plant growth, boosting plant resilience to drought, reclaiming heavy metal-polluted soils, controlling phytopathogens, producing secondary metabolites, biodegrading organic debris through enzymatic activity, and synthesizing nano-products [32,51]. They exhibited multifunctional plant growth traits essential for improving plant growth and nutrition under harsh conditions [57].

Exopolysaccharide production by the isolated bacteria may play a key role in enhancing plant resilience to abiotic stresses while supporting overall growth [58]. Their potential to produce indole-3-acetic acid (IAA) can stimulate the development of root architecture, including root elongation and lateral root formation, thereby improving water and nutrient uptake [59]. Additionally, IAA mediates plant development by promoting cell division and elongation, acting as a signaling molecule involved in plant growth, organ formation, and chlorophyll synthesis in photosynthetic plants [60].

Phosphorus and nitrogen are vital nutrients in the soil for plant growth [10,27]. However, their immobilized forms often render them inaccessible to plants [61]. Soil microorganisms play a crucial role in converting these nutrients into accessible forms [62]. The bacterial isolates screened in this study demonstrated phosphate solubilization and nitrogen fixation capabilities. Moreover, ammonia production by these bacteria significantly contributes to improving soil structure, root development, nutrient solubilization, and suppression of phytopathogens [63].

The survival of some bacterial isolates in PEG-6000-supplemented media over time indicates their adaptive mechanisms for enhancing drought resilience in maize [24]. These drought-tolerant bacterial strains isolated from maize have been shown to improve the plant′s ability to withstand drought stress [24]. The optimal growth of the bacterial cultures occurred at pH 7.0, although changes in pH can influence microbial behavior, energy requirements, and metabolic rates [22]. Nonetheless, the plant growth-promoting activities of these bacteria, both in the presence and absence of drought conditions, demonstrate their effectiveness in supporting plant growth under normal and drought stress environments [24].

The interaction between microbial substrate preferences and plant root exudates determines the success of bacterial colonization and the functional benefits these microbes provide, including enzyme-mediated nutrient mobilization and growth promotion [43]. The ability of these bacteria to utilize sugars indicates a strong metabolic capacity for glucose catabolism, a key trait for rhizobacteria thriving in the maize rhizosphere, where root exudates typically supply simple sugars like glucose as primary energy sources [64]. Moderate glucose consumption supports essential microbial functions such as nutrient cycling, plant growth promotion, and stress alleviation in plants [65].

Previous studies reported lactose utilization efficiencies ranging from 40% to 60% by Bacillus species isolated from groundnut rhizospheres [66]. Similarly, maltose utilization by maize-associated Pseudomonas species generally ranges between 50% and 65% [67]. Azospirillum brasilense strains from maize roots have demonstrated fructose utilization rates between 55% and 70% [68]. The results from this study exceed those reported by Rao et al. [69], who found 65% fructose utilization by groundnut-associated rhizobacteria, indicating potentially higher metabolic efficiency in the tested strains.

Potassium nitrate serves as a critical inorganic nitrogen source for many rhizobacteria. The ability to utilize nitrate supports bacterial growth, nitrogen cycling, and can enhance plant nutrient availability [70]. Rhizobacteria from maize rhizospheres, including Pseudomonas and Bacillus species, have been shown to effectively utilize nitrate, with utilization rates typically ranging from 40% to 70%, depending on the strain and environmental conditions [71]. Similarly, groundnut-associated rhizobacteria have demonstrated nitrate utilization efficiencies of approximately 45% to 60%, supporting nitrogen fixation and overall plant growth promotion [72]. Casein, a proteinaceous organic nitrogen source, requires bacteria to produce extracellular proteases for its degradation [22]. The high utilization rate of 80% for 0.6 g casein by W. chitiniclastica, isolated from groundnut roots, suggests enhanced proteolytic activity, which correlates with improved plant growth and biocontrol potential [73]. This protease activity may also contribute to pathogen suppression and nutrient mobilization in the rhizosphere [74].

The results of the antifungal activity assay indicated that the isolates possess bioactive properties capable of suppressing fungal growth, demonstrating significant antifungal effects [75]. This suggests that BS3 is metabolically versatile and may exhibit strong rhizosphere competence. Kalai-Grami et al. [76] reported that certain E. cloacae strains exhibited antifungal activity with inhibition zones ranging from 1.5 to 2.1 cm against Fusarium spp., closely aligning with the 1.9 cm zone observed in this study. Additionally, the inhibition of Alternaria solani, A. alternata, and Curvularia lunata has been attributed to the antifungal effects of endophytic E. cloacae strains [75]. The in vitro antifungal activity of root-derived E. cloacae isolated from cucumber against Pythium aphanidermatum further confirms the broad-spectrum efficacy of endophytic E. cloacae strains [77].

The highest antifungal activity observed in Morganella species colonizing maize soil can be linked to the expression of specific functional traits that mediate their ecological role and survival in diverse environments [78]. Like other Morganella species, M. morganii is a Gram-negative, straight rod-shaped, facultative anaerobe commonly found as a commensal in the intestinal tracts of organisms [79]. Despite their known pathogenic nature, recent studies have reported the plant growth-promoting potential of Morganella species in enhancing jute growth and their dual role in controlling Fusarium oxysporum in banana [2,79], suggesting their potential for future exploration as bioinoculants for stable ecosystems, biosafety, and sustainable agriculture. Similarly, Adeleke et al. [80] reported that Stenotrophomonas, an endophytic bacterium known as a human pathogen in the literature, exhibited plant growth-promoting traits and demonstrated bioinoculation efficacy in improving sunflower growth.

Although M. morganii BS3 remains underexplored in antifungal research, its observed antifungal activity highlights its potential as a novel source of antimicrobial secondary metabolites that warrant further investigation. This study thus broadens the current understanding of the genus′s ecological role and biological activities [78]. The demonstrated antifungal properties of these bacterial isolates emphasize their promise as biocontrol agents and suggest potential pharmaceutical applications [76]. However, further studies are necessary to characterize the active compounds, elucidate their modes of action, evaluate their antifungal spectrum, and assess biosafety concerns through field testing.

The plant inoculation response revealed the impact of each bacterial isolate on maize growth. The inoculated plants exhibited greater shoot length compared to the uninoculated, the control. An increase in the number of roots and the development of adventitious roots can significantly contribute to overall plant growth by facilitating nutrient uptake and water absorption from the soil [39,59]. Root development also provides anchorage, enhancing plant stability and improving survival under various environmental conditions [81].

Exploring soil- and plant-associated bacteria to promote maize seedling growth, particularly root elongation, is essential for understanding their role as plant growth promoters [3,4]. In this study, maize seedlings inoculated with each bacterial strain showed a significant increase in root length compared to the uninoculated control, confirming their potential as growth enhancers. These findings align with several recent studies highlighting the beneficial effects of rhizospheric and endophytic bacteria. For example, endophytic bacteria Bacillus MK2R2, Enterobacter B2L2, and Klebsiella E1S2, isolated from healthy leaves, stems, and roots of cultivated Triticum vulgare and wild Phragmites australis, have been reported to significantly enhance seminal, lateral, and primary root lengths [82]. This enhancement is largely attributed to the production of indole-3-acetic acid (IAA) and volatile organic compounds [83]. Similarly, a halotolerant Bacillus cereus strain isolated from the Saurashtra region was shown to improve root length, shoot length, fresh weight, and dry weight in groundnut plants [84]. Co-inoculation of the rhizobacterium B. cereus and the endophytic bacterium M. morganii has also been reported to enhance maize root length, likely due to their ability to produce IAA and solubilize soil nutrients [85].

The adaptability of endophytic and soil-dwelling Bacillus mycoides strains has been linked to their responsiveness to root exudates and the presence of specific genes that mediate plant–microbe interactions [86]. Bacterial consortia, such as nodulating Azospirillum and endophytic Bacillus species, have also been shown to facilitate nitrogen fixation and phosphate solubilization, thereby promoting maize root development [87]. Beyond root enhancement, plant growth-promoting (PGP) rhizobacteria and endophytic strains, including Bacillus, Pantoea, Burkholderia, Pseudomonas, and Stenotrophomonas, have demonstrated the ability to alleviate moderate water stress in maize. These bacteria stimulate root branching, enhancing both nutrient uptake and biomass production [24]. However, growth responses can vary depending on factors such as microbial strain, maize genotype, soil type, and environmental conditions like salinity or drought [30,59].

In the present study, the increase in stem diameter and leaf width in treated maize suggests that the rhizobacteria and endophytes not only promote root elongation but also support overall plant growth. Similar outcomes have been reported in maize plants inoculated with Bacillus endophyticus and Funneliformis mosseae, which showed increased stem diameter and leaf width linked to improved photosynthesis, nutrient uptake, and phytohormone production [88]. Moreover, the synergistic effects of groundnut root-associated endophytic bacteria, Rhizobium phaseoli S18, Rhizobium mayense S19, Pantoea dispersa YBB19B, and Kosakonia oryzae ESB1, suggest their potential as bioinoculants for plant growth promotion [89]. A study by Prassana et al. [90] reported groundnut-associated bacteria, including Azospirillum deltaense AMT1, Rhizobium spp., Caballeronia zhejiangensis BPT9, Burkholderia dolosa BPT8, and Bacillus safensis BPT6, with the potential to enhance groundnut growth under drought conditions. These benefits are likely due to improved water and nutrient absorption resulting from effective bacterial colonization [90]. Additionally, the significant increase in maize leaf weight following bacterial inoculation observed in this study can be attributed to enhanced nutrition via photosynthesis [83]. The increase in seedling fresh weight is also supported by findings from Zarei et al. [91], who reported enhanced fresh weight in maize seedlings treated with Pseudomonas fluorescens, confirming the growth-promoting potential of these bacterial strains.

5. Conclusions

This study highlights the potential of coastal microbial resources in promoting sustainable agriculture and food security. Five plant growth-promoting bacteria were identified. Among them, the endophytic bacterium W. chitiniclastica, isolated from groundnut roots, is reported for the first time in this context. While it shows promise as a bioinoculant, its use raises biosafety concerns, particularly regarding pathogenicity, environmental persistence, and potential transfer of antibiotic resistance genes. These risks necessitate strict adherence to biosafety protocols and regulatory approval before any field application.

Further research into W. chitiniclastica could uncover its role in enhancing plant growth, stress tolerance, and phytopathogen control. Genome sequencing and comparative genomics may reveal its metabolic pathways and adaptations to the groundnut rhizosphere. Additionally, strains such as E. cloacae BS1 and Bacillus cereus BS2 demonstrated phosphate-solubilizing and IAA-producing abilities, which are crucial for improving nutrient availability and crop productivity. However, practical application of these inoculants is challenged by field variability, formulation and storage issues, and regulatory hurdles.

To ensure effective use of microbial inoculants, future efforts should focus on optimizing formulations, conducting multi-location field trials, and developing tailored microbial consortia. Implementing strict microbiological safety standards and ensuring the use of well-characterized, non-pathogenic strains is critical. Emphasis on soil–plant–microbe interactions, coupled with supportive policy frameworks and farmer education, will facilitate the safe and sustainable integration of microbial-based biostimulants into modern agriculture while protecting environmental and public health.