Molecular and metabolic characterization of petroleum hydrocarbons degrading Bacillus cereus

Bacteria	References
Acinetobacter XS-4	Zou et al. 2023
Neorhizobium, Allorhizobium, Rhizobium, Pararhizobium, Pseudomonas, Nocardioides, Simplicispira	Eziuzor and Vogt 2023
Dehalococcoidia	Zehnle et al. 2023
Pinisolibacter aquiterrae	Bedics et al. 2022
Enterobacter	Hossain et al. 2022
Talaromyces sp.	Zhang et al. 2021
Pseudomonas pseudoalcaligenes, Rhodococcus	Feng et al. 2021; Chuah et al. 2022
Aquabacterium	Xu et al. 2019
Nesiotobacter exalbescens	Ganesh Kumar et al. 2019
Bradyrhizobium, Koribacter, Acidimicrobium	Jeffries et al. 2018
Sphingomonas	Zhou et al. 2016
Exiguobacterium aurantiacum	Mohanty and Mukherji 2008
Bacillus subtilis, Alcaligenes sp., Flavobacterium sp., Micrococcus roseus, Corynebacterium sp.	Adebusoye et al. 2007
Marinobacter, Alcanivorax, Sphingomonas, Gordonia, Micrococcus, Cellulomonas, Dietzia	Brito et al. 2006

Growth phases and petroleum hydrocarbons degradation potential analysis of *Bacillus cereus* strain sab41in present study. a) Growth curve showing lag, log, static, and death phases; b) graph showing degradation efficiency of petroleum by *B. cereus* strain sab41 estimated by measuring OD₆₀₀ of supernatant containing DCPIP.

Biochemical characterization of *Bacillus cereus* strain sab41 using Remel RapID^™ One panel.
a) Remel RapID^™ One panel showing the results; b) table illustrating the biochemical tests being analyzed in the present study.

Phylogenetic tree of *Bacillus cereus* strain sab41 constructed using MEGA 11 software.
A maximum composite likelihood neighbor-joining tree using a bootstrap value 100 was constructed.

GC chromatograms of *Bacillus cereus* strain sab41 showing the identified metabolites formed by degradation of petroleum hydrocarbons in the present study.
a) Peaks showing methylalcohol, methanoic acid, cyclohexene, cyclohexane, catechol, 4-methylcyclohexanone; b) peak showing benzoate; c) peak showing 3-methyl salicylic acid; d) peak showing acetaldehyde and o-cresol; e) peak showing 2-methylmuconate.

Pathways identified in *Bacillus cereus* strain sab41 associated with the degradation of alkanes and cycloalkanes.
a – alkane 1-monooxygenase; b – alcohol dehydrogenase; c – cyclohexanone monooxygenase; d – 6-hexanolactone hydrolase; a1 – benzoate 1,2-dioxygenase; a2 – dihydroxybenzoate dehydrogenase; a3 – catechol 1,2-dioxygenase; e – methane monooxygenase; f – methanol dehydrogenase; g – formaldehyde dehydrogenase; h – formate dehydrogenase

Pathways identified in *Bacillus cereus* strain sab41 involved in the degradation of aromatics.
a1, a2 – toluene 3-monooxygenase; b1, b2 – toluene 2-monooxygenase; c1 – toluene 4-monooxygenase; c2 – 4-hydroxymethyl hydroxylase; c3 – 4-hydroxybenzaldehyde dehydrogenase; d1 – xylene oxidase; d2 – alcohol dehydrogenase; d3 – aldehyde dehydrogenase

Benzene degradation pathways identified in *Bacillus cereus* strain sab41 in present study via GC-MS analysis.
a – benzylalcohol dehydrogenase; b – benzaldehyde dehydrogenase; c – benzoate CoA-ligase; d – 4-hydroxybenzoate CoA-ligase; e –4-hydroxybenoyl CoA reductase

Table II

Earlier reported pathways in petroleum degrading bacteria and the metabolites identified in Bacillus cereus strain sab41.

Petroleum hydrocarbon component	Pathway/bacterium reported in literature	Metabolites identified in present study	Reference
Methane	Methylomicrobium alcaliphilum 20Z	methylalcohol, methanone, methanoic acid	Kalyuzhnaya et al. 2013
Methylcyclohexane	Pseudophaeobacter, Gilvimarinus, Pseudomonas, Cycloclasticus, Roseovarius	cyclohexane carboxylic acid, benzoic acid, catechol, cis,cis-muconate	Li et al. 2023a
Toluene	Thauera sp. strain T1	benzoate, acetaldehyde, cyclohexene, pyruvate, cresol, 3-methyl catechol, 4-hydroxybenzoate	Heider et al. 1998; Muccee et al. 2019
	Toluene 4-monoxygenase pathway in Pseudomonas mendocina KR1	p-cresol, 4-hydroxybenzoate	Whited and Gibson 1991
	toluene 3-monooxygenase pathway in Pseudomonas pickettii	m-cresol, 3-methylcatechol	Olsen et al. 1994
Benzene	Acinetobacter calcoaceticus, Rhodopseudomonas palustris, Pseudomonas putida CSV86	benzoate, catechol, cis,cis-muconic acid, 4-hydroxybenzoate	Mackintosh and Fewson 1988; Egland et al. 1997; Basu et al. 2003
Xylene	m-xylene oxidation in Pseudomonas Pxy	m-tolualdehyde, 3-methylcatechol	Davey and Gibson 1974

Table III

Stoichiometric equations of reactions involved in formation of metabolic intermediates of petroleum hydrocarbons degradation identified in Bacillus cereus strain sab41

No. of reactions	Stoichiometric equations
Methane
1	$\begin{array}{l} \begin{matrix} C H_{3} O H & \to & C H_{2} O & + & 2 H^{+} \\ methylalcohol & methanone \end{matrix} \end{array}$
2	$\begin{matrix} C H_{2} O & + & \frac{1}{2} O_{2} & \to & C H_{2} O_{2} \\ methanone & methanoic acid \end{matrix}$
Methylcycleohexane
1	$\begin{matrix} C_{7} H_{12} O & + & \frac{1}{2} O_{2} & \to & C_{7} H_{12} O_{2} \\ methylcyclohexane & cyclohexane carboxylic acid \end{matrix}$
2	$\begin{matrix} C_{7} H_{12} O_{2} & \to & C_{6} H_{5} C O O H + 3 H_{2} \\ cyclohexane carboxylic acid & benzoic acid \end{matrix}$
3	$\begin{matrix} C_{7} H_{6} O_{5} & + & 2 H_{2} O \to C_{6} H_{6} O_{2} + C O_{2} + 2 H_{2} O \\ 2-hydro-1,2-dihydroxybenzoate & catechol \end{matrix}$
4	$\begin{matrix} C_{6} H_{6} O_{2} & + & O_{2} & \to & C_{6} H_{4} O_{4} & + & 2 H \\ c i s, c i s -muconate \end{matrix}$
Toluene
1 (Tbu, TMO, TOM)	$\begin{matrix} C_{6} H_{5} C H_{3} & + & O_{2} & \to & C_{7} H_{8} O \\ toluene & o -, m -, p -cresol \end{matrix}$
2 (Tbu, TMO)	$\begin{matrix} C_{7} H_{8} O & \to & C_{7} H_{8} O_{2} \\ 3 -methylcatechol \end{matrix}$
3 (TMO)	$\begin{matrix} C_{7} H_{6} O_{2} & + & \frac{1}{2} O_{2} & \to & C_{7} H_{6} \\ 4-hydroxybenzaldehyde & 4-hydroxybenzoate \end{matrix}$
Benzene
1 (pathway A)	$\begin{matrix} C_{7} H_{5} O_{2}^{_} & + & C_{21} H_{36} N_{7} O_{16} P_{3} S & \to & C_{28} H_{36} N_{7} O_{17} P_{3} S^{- 4} & + & \frac{1}{2} O_{2} \\ benzoate & CoA & benzoyl-CoA \end{matrix}$
2 (pathway B)	$\begin{matrix} C_{6} H_{5} O H & + & \frac{1}{2} O_{2} & \to & C_{6} H_{6} O_{2} \\ phenol & catechol \end{matrix}$
3	$\begin{matrix} C_{6} H_{6} O_{2} & + & O_{2} & \to & C_{6} H_{6} O_{4} \\ c i s, c i s -muconic acid \end{matrix}$
4 (pathway C)	$\begin{matrix} C_{6} H_{5} OH & + & C O_{2} & \to & C_{7} H_{6} O_{3} \\ phenol & 4 -hydroxybenzoate \end{matrix}$
Xylene
1	$\begin{matrix} C_{8} H_{10} O & \to & C_{8} H_{8} O & + & 2 H^{+} \\ m -methylbenzyl alcohol & m -tolualdehyde \end{matrix}$
2	$\begin{matrix} C_{7} H_{8} O_{4} & \to & C_{7} H_{8} O_{2} & + & O_{2} \\ 3 -methylcyclohexa-3,5-diene-1,2-diol-1-carboxylic acid & 3 -methylcatechol \end{matrix}$

Articles in this issue

DOI: https://doi.org/10.33073/pjm-2024-012 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331

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Language: English

Page range: 107 - 120

Submitted on: Sep 11, 2023

Accepted on: Feb 12, 2024

Published on: Mar 4, 2024

Published by: Polish Society of Microbiologists

In partnership with: Paradigm Publishing Services

Publication frequency: 4 issues per year

Keywords:

GC-MS,

Related subjects:

Microbiology and virology

© 2024 Nadia Hussain, Fatima Muccee, Muhammad Hammad, Farhan Mohiuddin, Saboor Muarij Bunny, Aansa Shahab, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Volume 73 (2024): Issue 1 (March 2024)

Molecular and metabolic characterization of petroleum hydrocarbons degrading Bacillus cereus

Figures & Tables

Table I

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

Fig. 6.

Fig. 7.

Table II

Table III

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