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Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant–Soil Interactions".

Deadline for manuscript submissions: closed (24 December 2021) | Viewed by 31004

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Special Issue Editors

Dr. Saad El-Din Hassan

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Botany & Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
Interests: environmental catalysts, bioremediation, nanoparticles, wastewater treatment, microbial ecology
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Prof. Dr. Mohamed Hijri

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Guest Editor

Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
Interests: environmental microbiology; plant-microbe interaction; mycorrhizal symbiosis; fungal biology; microbial genomics
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Dr. Arnab Bhowmik

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Guest Editor

Department of Natural Resources and Environmental Design, North Carolina A&T State University, Greensboro, NC 27411, USA
Interests: carbon and nitrogen cycling in agroecosystems; soil health and sustainable agriculture; soil management and greenhouse gas emission; CBD hemp best management practices
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Aims and Scope

The journal Plants is planning to publish a Special Issue entitled “Microbial Diversity in Stressed and Polluted Soils Related to Plant Phylogeny.” A relevant understanding of how microbial communities respond to natural and stressed environments that contain a broad variety of toxic organic and inorganic compounds will substantially expand our knowledge of microbial ecology, evolution, behaviour and conservation. Variation of the microbial community structure in natural or polluted soils is directly related to plant phylogeny. This has implications for plant selection in phytoremediation, as microbial associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between microorganisms and plants will enable the design of treatments that specifically promote effective bioremediating communities.

Research areas of interest to this issue include:

Microbial interactions and plant phylogeny
Molecular, genomic, and metagenomic analysis of microbial biodiversity
Other culture-dependent methods will be considered, if covers significant aspects of plant-microbe interactions
Microbial and plant ecology in stressed environments
Phytoremediation

Dr. Saad El-Din Hassan
Prof. Dr. Mohamed Hijri
Dr. Arnab Bhowmik
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

biotechnology of microbial ecology
plant ecology
biodiversity
plant-microbe interactions
high throughout sequencing
phytoremediation
microbial endophytes
nanotechnology
polluted soil

Published Papers (7 papers)

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Research

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21 pages, 2004 KiB

Open AccessFeature PaperArticle

Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties

by Fahad Alotaibi, Soon-Jae Lee, Marc St-Arnaud and Mohamed Hijri

Plants 2021, 10(10), 1987; https://doi.org/10.3390/plants10101987 - 23 Sep 2021

Cited by 4 | Viewed by 2269

Abstract

Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salixpurpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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22 pages, 5451 KiB

Open AccessFeature PaperArticle

Evaluate the Toxicity of Pyrethroid Insecticide Cypermethrin before and after Biodegradation by Lysinibacillus cresolivuorans Strain HIS7

by Ebrahim Saied, Amr Fouda, Ahmed M. Alemam, Mahmoud H. Sultan, Mohammed G. Barghoth, Ahmed A. Radwan, Salha G. Desouky, Islam H. El Azab, Nihal El Nahhas and Saad El-Din Hassan

Plants 2021, 10(9), 1903; https://doi.org/10.3390/plants10091903 - 14 Sep 2021

Cited by 17 | Viewed by 2829

Abstract

Herein, bacterial isolate HIS7 was obtained from contaminated soil and exhibited high efficacy to degrade pyrethroid insecticide cypermethrin. The HIS7 isolate was identified as Lysinibacillus cresolivuorans based on its morphology and physiology characteristics as well as sequencing of 16S rRNA. The biodegradation percentages of 2500 ppm cypermethrin increased from 57.7% to 86.9% after optimizing the environmental factors at incubation condition (static), incubation period (8-days), temperature (35 °C), pH (7), inoculum volume (3%), and the addition of extra-carbon (glucose) and nitrogen source (NH₄Cl₂). In soil, L. cresolivuorans HIS7 exhibited a high potential to degrade cypermethrin, where the degradation percentage increased from 54.7 to 93.1% after 7 to 42 days, respectively. The qualitative analysis showed that the bacterial degradation of cypermethrin in the soil was time-dependent. The High-Performance Liquid Chromatography (HPLC) analysis of the soil extract showed one peak for control at retention time (R.T.) of 3.460 min and appeared three peaks after bacterial degradation at retention time (R.T.) of 2.510, 2.878, and 3.230 min. The Gas chromatography–mass spectrometry (GC–MS) analysis confirmed the successful degradation of cypermethrin by L. cresolivuorans in the soil. The toxicity of biodegraded products was assessed on the growth performance of Zea mays using seed germination and greenhouse experiment and in vitro cytotoxic effect against normal Vero cells. Data showed the toxicity of biodegraded products was noticeably decreased as compared with that of cypermethrin before degradation. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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26 pages, 14640 KiB

Open AccessArticle

Green Synthesized ZnO Nanoparticles Mediated by Streptomyces plicatus: Characterizations, Antimicrobial and Nematicidal Activities and Cytogenetic Effects

by Mohamed H. Kalaba, Saad A. Moghannem, Ahmad S. El-Hawary, Ahmed A. Radwan, Mohamed H. Sharaf and Abdelghany S. Shaban

Plants 2021, 10(9), 1760; https://doi.org/10.3390/plants10091760 - 25 Aug 2021

Cited by 25 | Viewed by 3350

Abstract

Zinc oxide nanoparticles (ZnO-NPs) are regarded as one of the most promising kinds of materials in a variety of fields, including agriculture. Therefore, this study aimed to biosynthesize and characterize ZnO-NPs and evaluate their different biological activities. Seven isolates of actinomycetes were obtained and screened for ZnO-NPs synthesis. The isolate MK-104 was chosen and identified as the Streptomyces plicatus MK-104 strain. The biosynthesized ZnO-NPs exhibited an absorbance peak at 350 nm and were spherical in shape with an average size of 21.72 ± 4.27 nm under TEM. XRD and DLS methods confirmed these results. The biosynthesized ZnO-NPs demonstrated activity against plant pathogenic microbes such as Erwinia amylovora, Aspergillus flavus, Aspergillus niger, Fusarium oxysporum, Fusarium moniliform and Alternaria alternata, with MIC values ranging from 15.6 to 500 µg/mL. Furthermore, ZnO-NPs had a significant effect on Meloidogyne incognita, with death percentages of 88.2, 93.4 and 96.72% after 24, 48 and 72 h of exposure, respectively. Vicia faba seeds were treated with five concentrations of ZnO-NPs (12.5, 25, 50, 100 and 200 µg/mL). Low-moderate ZnO-NP concentrations (12.5–50 µg/mL) were shown to promote seed germination and seedling development, while the mitotic index (MI) decreased as the dosage of ZnO-NPs increased. Micronuclei (MNs) and the chromosomal abnormality index increased as well. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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12 pages, 1019 KiB

Open AccessArticle

Fresh Compost Tea Application Does Not Change Rhizosphere Soil Bacterial Community Structure, and Has No Effects on Soybean Growth or Yield

by Rana Bali, Jonathan Pineault, Pierre-Luc Chagnon and Mohamed Hijri

Plants 2021, 10(8), 1638; https://doi.org/10.3390/plants10081638 - 10 Aug 2021

Cited by 9 | Viewed by 2973

Abstract

Soil bacteria drive key ecosystem functions, including nutrient mobilization, soil aggregation and crop bioprotection against pathogens. Bacterial diversity is thus considered a key component of soil health. Conventional agriculture reduces bacterial diversity in many ways. Compost tea has been suggested as a bioinoculant that may restore bacterial community diversity and promote crop performance under conventional agriculture. Here, we conducted a field experiment to test this hypothesis in a soybean-maize rotation. Compost tea application had no influence on bacterial diversity or community structure. Plant growth and yield were also unresponsive to compost tea application. Combined, our results suggest that our compost tea bacteria did not thrive in the soil, and that the positive impacts of compost tea applications reported elsewhere may be caused by different microbial groups (e.g., fungi, protists and nematodes) or by abiotic effects on soil (e.g., contribution of nutrients and dissolved organic matter). Further investigations are needed to elucidate the mechanisms through which compost tea influences crop performance. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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28 pages, 874 KiB

Open AccessArticle

Short Rotation Intensive Culture of Willow, Spent Mushroom Substrate and Ramial Chipped Wood for Bioremediation of a Contaminated Site Used for Land Farming Activities of a Former Petrochemical Plant

by Maxime Fortin Faubert, Mohamed Hijri and Michel Labrecque

Plants 2021, 10(3), 520; https://doi.org/10.3390/plants10030520 - 10 Mar 2021

Cited by 9 | Viewed by 2958

Abstract

The aim of this study was to investigate the bioremediation impacts of willows grown in short rotation intensive culture (SRIC) and supplemented or not with spent mushroom substrate (SMS) and ramial chipped wood (RCW). Results did not show that SMS significantly improved either biomass production or phytoremediation efficiency. After the three growing seasons, RCW-amended S. miyabeana accumulated significantly more Zn in the shoots, and greater increases of some PAHs were found in the soil of RCW-amended plots than in the soil of the two other ground cover treatments’ plots. Significantly higher Cd concentrations were found in the shoots of cultivar ‘SX61’. The results suggest that ‘SX61’ have reduced the natural attenuation of C10-C50 that occurred in the unvegetated control plots. The presence of willows also tended to increase the total soil concentrations of PCBs. Furthermore, we found that many contaminant concentrations were subject to seasonal oscillations, showing average increases throughout the whole experimental site after a growing period, while showing significantly different variations, such as lesser increases or even decreases, after a dormant period. These observations suggest that contaminants may have leached or degraded faster in untreated conditions, and conversely to have mobilized towards trees through water flow driven by plant transpiration during growing seasons. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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22 pages, 2965 KiB

Open AccessArticle

Plant Growth-Promoting Endophytic Bacterial Community Inhabiting the Leaves of Pulicaria incisa (Lam.) DC Inherent to Arid Regions

by Amr Fouda, Ahmed M. Eid, Albaraa Elsaied, Ehab F. El-Belely, Mohammed G. Barghoth, Ehab Azab, Adil A. Gobouri and Saad El-Din Hassan

Plants 2021, 10(1), 76; https://doi.org/10.3390/plants10010076 - 01 Jan 2021

Cited by 81 | Viewed by 5816

Abstract

In this study, 15 bacterial endophytes linked with the leaves of the native medicinal plant Pulicaria incisa were isolated and identified as Agrobacterium fabrum, Acinetobacter radioresistant, Brevibacillus brevis, Bacillus cereus, Bacillus subtilis, Paenibacillus barengoltzii, and Burkholderia cepacia. These isolates exhibited variant tolerances to salt stress and showed high efficacy in indole-3-acetic acid (IAA) production in the absence/presence of tryptophan. The maximum productivity of IAA was recorded for B. cereus BI-8 and B. subtilis BI-10 with values of 117 ± 6 and 108 ± 4.6 μg mL⁻¹, respectively, in the presence of 5 mg mL⁻¹ tryptophan after 10 days. These two isolates had a high potential in phosphate solubilization and ammonia production, and they showed enzymatic activities for amylase, protease, xylanase, cellulase, chitinase, and catalase. In vitro antagonistic investigation showed their high efficacy against the three phytopathogens Fusarium oxysporum, Alternaria alternata, and Pythium ultimum, with inhibition percentages ranging from 20% ± 0.2% to 52.6% ± 0.2% (p ≤ 0.05). Therefore, these two endophytic bacteria were used as bio-inoculants for maize seeds, and the results showed that bacterial inoculations significantly increased the root length as well as the fresh and dry weights of the roots compared to the control plants. The Zea mays plant inoculated with the two endophytic strains BI-8 and BI-10 significantly improved (p ≤ 0.05) the growth performance as well as the nutrient uptake compared with an un-inoculated plant. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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Review

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33 pages, 3944 KiB

Open AccessReview

Harnessing Bacterial Endophytes for Promotion of Plant Growth and Biotechnological Applications: An Overview

by Ahmed M. Eid, Amr Fouda, Mohamed Ali Abdel-Rahman, Salem S. Salem, Albaraa Elsaied, Ralf Oelmüller, Mohamed Hijri, Arnab Bhowmik, Amr Elkelish and Saad El-Din Hassan

Plants 2021, 10(5), 935; https://doi.org/10.3390/plants10050935 - 07 May 2021

Cited by 100 | Viewed by 9608

Abstract

Endophytic bacteria colonize plants and live inside them for part of or throughout their life without causing any harm or disease to their hosts. The symbiotic relationship improves the physiology, fitness, and metabolite profile of the plants, while the plants provide food and shelter for the bacteria. The bacteria-induced alterations of the plants offer many possibilities for biotechnological, medicinal, and agricultural applications. The endophytes promote plant growth and fitness through the production of phytohormones or biofertilizers, or by alleviating abiotic and biotic stress tolerance. Strengthening of the plant immune system and suppression of disease are associated with the production of novel antibiotics, secondary metabolites, siderophores, and fertilizers such as nitrogenous or other industrially interesting chemical compounds. Endophytic bacteria can be used for phytoremediation of environmental pollutants or the control of fungal diseases by the production of lytic enzymes such as chitinases and cellulases, and their huge host range allows a broad spectrum of applications to agriculturally and pharmaceutically interesting plant species. More recently, endophytic bacteria have also been used to produce nanoparticles for medical and industrial applications. This review highlights the biotechnological possibilities for bacterial endophyte applications and proposes future goals for their application. Full article

(This article belongs to the Special Issue Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny)

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