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Water
Volume 14
Issue 2
10.3390/w14020142
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Article

Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity

by
Ilaria Chicca
1,
Simone Becarelli
1,2,
Giacomo Bernabei
1,
Giovanna Siracusa
1 and
Simona Di Gregorio
1,*
1
Department of Biology, University of Pisa, Via Luca Ghini, 13, 56126 Pisa, Italy
2
BD Biodigressioni srl, Lungarno Mediceo 40, 56126 Pisa, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Xuwang Zhang
Water 2022, 14(2), 142; https://doi.org/10.3390/w14020142
Received: 4 December 2021 / Revised: 25 December 2021 / Accepted: 1 January 2022 / Published: 6 January 2022
(This article belongs to the Special Issue Biotechnologies for the Environment: Strategies for Containment and Depletion of Pollution in Wastewaters, Air, Soils and Sediments)
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Abstract

Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources. Bacterial isolates belonging to Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps. were isolated for their capacity to utilise diesel oil, bitumen, pyrene, anthracene, dibenzothiphene, and their mixture as sole carbon sources. Pseudomonas, Arthrobacter, Achromobacter and Microbacterium sps. showed plant growth promoting activity, producing indole-3-acetic acid and expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. In parallel to the culturomic approach, in the microbial community of interest, bacterial community metabarcoding and predictive functional metagenomic analysis were adopted to confirm the potentiality of the isolates in terms of their functional representativeness. The combination of isolation and molecular approaches for the characterisation of a TPH contaminated soil microbial community is proposed as an instrument for the construction of an artificial hydrocarbonoclastic microbiota for environmental restoration. View Full-Text
Keywords: culturomic; microbiota; predictive functional metagenomic analysis; Pseudomonas; Arthrobacter; Achromobacter; Bacillus; Lysinibacillus; Microbacterium; 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase; indole-3-acetic acid culturomic; microbiota; predictive functional metagenomic analysis; Pseudomonas; Arthrobacter; Achromobacter; Bacillus; Lysinibacillus; Microbacterium; 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase; indole-3-acetic acid
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MDPI and ACS Style

Chicca, I.; Becarelli, S.; Bernabei, G.; Siracusa, G.; Di Gregorio, S. Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity. Water 2022, 14, 142. https://doi.org/10.3390/w14020142

AMA Style

Chicca I, Becarelli S, Bernabei G, Siracusa G, Di Gregorio S. Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity. Water. 2022; 14(2):142. https://doi.org/10.3390/w14020142

Chicago/Turabian Style

Chicca, Ilaria, Simone Becarelli, Giacomo Bernabei, Giovanna Siracusa, and Simona Di Gregorio. 2022. "Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity" Water 14, no. 2: 142. https://doi.org/10.3390/w14020142

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