Hermawan Et Al., 2024
Hermawan Et Al., 2024
Abstract. Hermawan MA, Pangastuti A, Setyaningsih R. 2024. Imidacloprid degradation by potential ⠀soil bacteria isolated⠀from rice
fields in⠀Grobogan, Central Java, Indonesia. Nusantara Bioscience 16: 284-291. Imidacloprid a widely used pesticide is known for its
polar nature, resistance to evaporation, and persistence in soil. When concentrations exceed environmental thresholds, imidacloprid can
act as a pollutant, disrupting ecosystems, altering soil pH, and decreasing soil fertility. This study aimed to isolate and i dentify soil
bacteria from rice fields capable of degrading imidacloprid and to highlight their potential role in bioremediation. Isolated bacteria are
identified based on morphological characteristics, their ability to degrade imidacloprid and through molecular tests using 16S rRNA.
Four bacterial colonies were obtained from the isolation results with different morphological variations. The degradation test results
showed that the isolates were able to grow in media containing imidacloprid and were able to reduce imidacloprid by 26.66-31.75%.
Based on 16S rRNA gene analysis, isolate IT1 was identified as Enterobacterales, IT2 was identified as the Enterobacteriaceae, IT3 as
Pectobacterium aroidearum strain CCRMPA670, and IT4 was identified as Bacillus thuringiensis strain FDAARGOS_791.
Keywords: Bacillus thuringiensis, Bacteria, biodegradation, imidacloprid, Pectobacterium aroidearum, rice field
a high ability to grow in rice fields that are applied by Isolation and purification of potential pesticide
imidacloprid and the ability to degrade the residue of the imidacloprid degrading bacterial isolates
imidacloprid pesticide and know the level of efficiency of The soil was dried and ground with a mortar and then
the isolates selected to re-feminist the imidacloprid residue sieved through a 0.2 mM mesh to remove physical
in the soil. impurities. Each soil sample was weighed and 5 grams
were taken using an analytical balance. Vortex was used to
homogenize the soil samples after they were put in bottles
MATERIALS AND METHODS with 45 mL of distilled water. Subsequently, centrifugation
was carried out at 10,000 x g for 20 minutes (Irfan et al.
Study area 2021), referred to as a 10-1 dilution. One millilitre of the
The sampling was conducted in the Godong, Wirosari, liquid was pipetted from the 10-1 dilution and added to a
and Ngaringan Sub-districts of Grobogan, Central Java, reaction tube holding nine millilitres of distilled water to
Indonesia (Figure 1). Grobogan is located at an altitude of make a 10-2 dilution. This process was repeated
100-500 meters above sea level with coordinates 7° 1' sequentially up to a 10-7 dilution using the serial dilution
18.188" S 110° 57' 45.306" E. The land in Grobogan is technique. Serial dilution was performed to reduce the
mostly used for the agricultural sector, such as rice fields density of microorganisms in the soil samples, facilitating
and plantations. the isolation of purer bacterial colonies on culture media
(Bhattacherjee et al. 2020).
Sample collection All the dilutions (10-1 to 10-7) were spread using the
The samples used were collected from the Grobogan pour plate method on 15 mL of MSM agar media
region, consisting of soil exposed to imidacloprid supplemented with 2 ppm of imidacloprid as the sole
pesticides based on a long history of using the pest- carbon source in petri dishes. The minimal salts medium
repellent pesticide for brown planthopper, namely Avidor (MSM, g/L) consisted of K2HPO4 2.27 g, KH2PO4 0.95 g,
25 WP brand (imidacloprid 25%). The sampling locations and (NH4)2SO4 0.67 g per 1 L of deionized water, adjusted
were at three points in the Sub-districts of Godong, to pH 7.0 (Coleman 2002). The inoculated plates were then
Wirosari, and Ngaringan, with soil samples taken from the incubated for 48 hours at 28°C (Yadav et al. 2021).
central area due to the likelihood of containing a significant Bacteria obtained from the mixed culture were purified
amount of pesticide residues and being the main rice using the quadrant streaking method with four streaks until
cultivation area. Using a scoop, 500 grams of soil samples no other bacterial mixtures were present. Pure isolates were
were taken from the top layer of soil (depth of 0–15 cm) also inoculated into glycerol stocks and stored in the
(Gautam and Dubey 2022). The collected soil was then freezer.
placed in an ice box (filled with ice bags to maintain a
temperature of ±4°C) to preserve the soil conditions (Alwi
et al. 2023).
Figure 1. Locations of soil sampling sites: Wirosari, Godong, and Ngaringan Sub-districts of Grobogan, Central Java, Indonesia (7° 1'
18.188" S 110° 57' 45.306" E)
286 N U SA NTA RA B I OSC IE NC E 16 (2): 284-291, November 2024
Growth of bacterial isolates to measure Optical Density (OD) at 600 nm. The bacterial
Bacterial isolates were cultured in erlenmeyer flasks growth curve was generated based on the OD values
containing 250 mL of Minimal Salts Medium (MSM) obtained over time. Following the construction of the
supplemented with two ppm imidacloprid. Subsequently, bacterial growth curve, a test for bacterial resistance to
the cultures were placed on a shaker incubator at 28°C and imidacloprid was conducted by observing the OD values at
150 rpm for 24 hours, allowing them to reach the 600 nm under various concentrations of imidacloprid.
exponential growth phase. A 10 mL sample was extracted Subsequently, a test of imidacloprid pesticide degradation
and centrifuged at 8000 x g for 15 minutes, the supernatant by bacteria was performed using High-Performance Liquid
was then discarded and replaced with 10 mL of sterile Chromatography (HPLC). The data obtained consisted of
distilled water, followed by vortex. The Optical Density residual imidacloprid concentrations after incubation with
(OD) values were measured using a UV-Vis bacteria. The acquired data were then analyzed
spectrophotometer at a wavelength of 600 nm (Mishra et al. descriptively and qualitatively. The sequences obtained
2014). Absorbance values were recorded every three hours from the sequencing process underwent a similarity test
until the bacterial culture entered the stationary phase. using BLASTn features on NCBI, utilizing the 'nr/nt' or
'Bacteria' database.
Imidacloprid pesticide degradation test
The isolates cultured were transferred in a volume of 10
mL into a reaction tube containing 250 mL of liquid MSM RESULTS AND DISCUSSION
with two ppm imidacloprid. The reaction tube was
incubated at 170 rpm and 28°C. Samples were detected and Imidacloprid residue
measured on days 0, 3, 5, 7, 10, 12, 14, 17, 19, and 21. The soil sample from Wirosari exhibited the highest
Pesticide imidacloprid degradation was assessed using residue levels compared to the soil samples from Godong
High-Performance Liquid Chromatography (HPLC) (Hu et and Ngaringan (Table 1). According to the Indonesian
al. 2013). Minister of Health and Minister of Agriculture Decree No.
881/MENKES/SKB/VIII/1996 and No.
Identification of selected bacterial isolates 711/Kpts/TP.270/8/1996 Regarding the Maximum Residue
The bacterial DNA genome from the isolate was Limits of Pesticides in Agricultural Products, the maximum
extracted using the Quick-DNATM Kit from Zymo residue limit for imidacloprid in soil should be 0.5 ppm.
Research, following the manufacturer's protocol. DNA The soil in Ngaringan and Godong has imidacloprid
obtained was then used as a template for the Amplification residues approaching the maximum allowable limit, while
of DNA 16S rRNA. Amplification using a pair of 67F (5′- the Wirosari soil exceeds the imidacloprid residue limit
CCTACGGGNGGCWGCAG-3′) and Primer 1387R (5′- permitted by the Department of Agriculture.
ACTACHV GGGTATCTAATCC-3′) and for sequencing
using a primary 785F (5′-GGATTAGATACCCTGGTA-3′) Isolation of indigenous bacteria
and 907R (5′-CCGTCAATTCMTTTRAGTTT-3′) to target The isolates capable of growing on MSM +
the partial region of the 16S rRNA gene. PCR reactions imidacloprid media were coded as IT1, IT2, IT3, and IT4.
were performed in a thermocycler with 7.5 μL My Taq Red Color dissimilarity was the most noticeable aspect of
Mix buffer (2x), 0.5 μL forward primer, 0.5 μL reverse isolates characterization. According to Table 2 and Figure
primer, 0.5 µL DNA template, and 19.8 μL ddH2O. The 2, The color of isolates IT1, IT2, IT3, and IT4 were light
denaturation, amplification, and annealing processes each pink color, brick-red color, whitish-yellow color, and white
had 30 cycles. The cycle parameters were as follows: initial color, respectively.
primer denaturation at 95°C for 5 minutes, 30 cycles of
denaturation at 95°C for 45 seconds, annealing at 62°C for Bacterial growth
45 seconds, extension at 72°C for 2 minutes, and a final All bacterial isolates experienced an exponential growth
extension at 72 °C for 72 minutes (McCabe et al. 1999). phase from hour 3 to 51, except for isolate IT1, which that it
The PCR products were then kept at 4°C for subsequent ended its exponential phase at hour 54 (Figure 3). The
analysis by electrophoresis. The amplified products were bacterial growth results from the unique capabilities of each
electrophoresed on a 1% agarose gel. Electrophoresis was bacterial isolate in utilizing nutrients present in the media,
carried out for 45 minutes at an electric voltage of 84 V in ultimately leading to variations in metabolic efficiency.
1x TAE buffer. The DNA amplicons in the agarose gel
were stained with gel red dye. DNA visualization was
performed using a UV transilluminator (Gao et al. 2021).
The amplified DNA was then subjected to DNA Table 1. The content of imidacloprid residue Grobogan, Central
sequencing. The 16S rDNA amplicon was subsequently Java, Indonesia, soil sample
sent to a third party for sequencing processing.
Soil samples Residue (ppm)
Data analysis Ngaringan 0.47
The growth curve of imidacloprid degrading bacteria Godong 0.45
was constructed, and the findings were obtained by Wirosari 0.50
incubating the bacteria with a UV-Vis spectrophotometer
HERMAWAN et al. – Imidacloprid degradation by potential soil bacteria isolated 287
A B
C D
Table 2. The characteristics of bacterial isolates from the rice fields in Grobogan, Central Java, Indonesia
Isolates code Elevation Margin Colony color Shape of colony Shape of cell
IT 1 Convex Entire Light pink Circular Bacilli
IT 2 Convex Entire Brick red Circular Bacilli
IT 3 Convex Entire Whitish yellow Circular Bacilli
IT 4 Convex Entire White Circular Bacilli
Table 3. Similarity of 16S rRNA gene sequences of bacterial isolates using the BLAST-n program
Isolates code Related species Query cover (%) Similarity (%) ACC Numbers
IT 1 Serratia nevei strain 2017-45-174 76 86.83 CP109739.1
IT 2 Serratia marcescens strain JW-CZ2 100 89.51 CP055161.1
IT 3 Pectobacterium aroidearum strain CCRMPA670 90 99.83 MN883868.1
IT 4 Bacillus thuringiensis strain FDAARGOS_791 100 98.57 CP054568.1
A C
B D
Figure 4. Growth of bacterial isolates on MSM + imidacloprid media: A. IT1, B. IT2, C. IT3, D. IT4
nutrients in the growth medium, temperature conditions, control and a plant growth promoter. In another study,
and media pH. Then, enter the stationary phase until 72 Tepidibacillus decaturensis strain ST1 was able to degrade
hours. The stationary phase occurs if the number of bacterial imidacloprid effectively in liquid media, slurry, and soil
cells stops increases (Jõers et al. 2020). Although there is no microcosms (Tiwari et al. 2023).
growth in the stationary phase, cells can still grow and The results of molecular analysis revealed that IT1 was
divide themselves. In this phase, the number of growing identified at the level of the order Enterobacterales and IT2
bacteria is balanced with the number of dead bacteria (Risna isolates identified at the level of the Enterobacteriaceae
et al. 2022). Bacterial isolates demonstrate the ability to family. Isolates IT3 and IT4 were identified as
thrive in MSM+imidaclopridmedia due to their utilization Pectobacterium proidearum strain CCRMPA670 and B.
of carbon and nitrogen sources in the media. This aligns thuringiensis strain FDAARGOS_791. The similarity of
with the findings of Zamule et al. (2021), who reported that the 16S rRNA gene is one of the characteristics of a close-
various bacterial strains, including Pseudomonas related bacterium. The 16S rRNA gene is very
fluorescens, Pseudomonas putida, Pseudomonas conservative, so changes that occur in this gene usually
aeruginosa, Alcaligenes faecalis, Escherichia coli and occur slowly and gradually. This causes closely related
Streptococcus lactis can flourish in imidacloprid-containing bacteria to have a similar similarity to the 16S rRNA gene
media. (Sharma et al. 2014). Determination of potential bacterial
The highest percentage of decreased imidacloprid in identity is based on the criteria for the percentage of
test was 31.75%, in IT1 isolates, while the percentage of similarities ≥99% shows the similarity of species, the
reduction in IT3 isolates was lower than in the other three percentage of similarity ≥95%-<99% shows the similarity
isolates. The percentage of decreased imidacloprid was of the genus, and the percentage of similarity <95% shows
increased from day 0 to 21st day, this shows the potential the similarity of the family (Collins et al. 1994). Church et
for degradation or reduction of imidacloprid by the isolates. al. (2020) reported that comparing sequences of the 16S
Bacteria that can grow in MSM+imidacloprid media are rRNA gene can help distinguish organisms at the genus
bacteria that have enzymes that can break the chemical level across key bacterial phyla and classify strains at
structure of imidacloprid into simpler molecules, which various levels. Pectobacterium is included in the gram-
bacteria can then use as a source of carbon and nitrogen. negative bacteria Enterobacteriaceae found in rice fields'
Other bacteria that are unable to grow in soil (Rossmann et al. 2018). Bacillus is generally used as a
MSM+imidacloprid media do not have the enzymes needed plant growth booster agent found in plantations and rice
to utilize the carbon imidacloprid content. These bacteria fields (Akinrinlola et al. 2018). Pang et al. (2020) state that
have enzymes that can break imidacloprid, but these Pectobacterium can grow and survive under high levels of
enzymes are not efficient enough to produce enough energy imidacloprid. According to Vu et al. (2022),
for bacterial growth. Cycoń and Seget (2015) reported that Pectobacterium can resist imidacloprid pesticides, and the
the activity of the enzyme dehydrogenase, bacteria have developed mechanisms to protect themselves.
hexaphosphatase, and urease in soil bacteria given Ferreira et al. (2016) research states that B. thuringiensis is
imidacloprid has decreased performance. Every pesticide able to degradate imidacloprid. Other members of the
application that affects the microbial community and its genus Bacillus who also showed the ability to degrade
biochemical activity in the soil can be estimated to produce imidacloprid compounds such as Bacillus cereus (Talpur et
changes in the level of soil enzyme activity. Akoijam and al. 2023), and Bacillus wehenstephanensis (Shetti et al.
Singh (2015) observed that Bacillus aerophilus and B. 2021). Bacillus striatum, which contains CYP353D1v2
alkalinitrilicus are capable of degrading over 90% of genes exhibits strong resistance to imidacloprid (Pang et al.
imidacloprid in clay loam within 56 days. The degradation 2020). Soil-dwelling bacteria from the genus Bacillus have
produces metabolites, such as 6-chloronicotinic acid, the ability to break down pesticides into simpler residues.
nitrosimine, and imidacloprid-NTG, which remain B. cereus was identified as an efficient catalyst for
unaffected by sterilization. In another study, B. cepacia degrading imidacloprid, metabolizing 92% of it within 11
strain CH 9 was able to degrade 69% of the 50 ppm days at a neutral pH. Through optimization using the Box-
imidacloprid in 20 days after inoculation in MSM media Behnken design, the bacteria transformed imidacloprid into
(Bhattacherjee et al. 2020). Ochrobacterium sp. strain 6-CNA via the intermediate’s guanidine and 5-hydroxy
BCL-1 can degrade 67.67% from 50 ppm imidacloprid in imidacloprid (Talpur et al. 2023). The B. cereus is
48 hours after the application as mentioned in the literature considered a promising tool for removing imidacloprid
(Hu et al. 2013). Akoijam and Singh (2015) have observed from contaminated water and soil (Gangola et al. 2021).
that the loss of imidacloprid follows the first pseudo-order Isolating the enzyme responsible for this degradation could
kinetics when applied at levels of 50, 100, and 150 ppm in provide a pathway for commercial use of purified enzymes.
sandy clay enriched with B. aerophilus with a part-time In conclusion, 4 colonies obtained with different
value of 14.33, 15, 15, 05, and 18.81 days. A strain of B. morphological variations namely IT1, IT2, IT3, and IT4.
thuringiensis isolated from polluted marine sediments has Analysis of degradation activity using the HPLC method
been shown to degrade 71% of imidacloprid within 11 days showed that all isolates have the ability to grow in MSM,
(Obayori et al. 2024). Trichoderma, one of the most which contains imidacloprid and succeed in reducing the
promising biological control agents, is found across various imidacloprid content by 26.66-31.75%. Based on 16S
agricultural climates and is prevalent in soil and root rRNA gene analysis, isolate IT1 was identified as
ecosystems, it has the ability to serve as both a biological Enterobacterales, IT2 was identified into the
290 N U SA NTA RA B I OSC IE NC E 16 (2): 284-291, November 2024
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ACKNOWLEDGEMENTS 10.3390/microorganisms11071641.
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