Microbial Communities in Stressed and Polluted Soils Related to Plant Phylogeny

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 28834

Special Issue Editors

Botany & Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
Interests: environmental catalysts, bioremediation, nanoparticles, wastewater treatment, microbial ecology
Special Issues, Collections and Topics in MDPI journals
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
Special Issues, Collections and Topics in MDPI journals
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

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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  
Article
Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties
Plants 2021, 10(10), 1987; https://doi.org/10.3390/plants10101987 - 23 Sep 2021
Cited by 4 | Viewed by 2072
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. [...] Read more.
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
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22 pages, 5451 KiB  
Article
Evaluate the Toxicity of Pyrethroid Insecticide Cypermethrin before and after Biodegradation by Lysinibacillus cresolivuorans Strain HIS7
Plants 2021, 10(9), 1903; https://doi.org/10.3390/plants10091903 - 14 Sep 2021
Cited by 15 | Viewed by 2623
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 [...] Read more.
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
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26 pages, 14640 KiB  
Article
Green Synthesized ZnO Nanoparticles Mediated by Streptomyces plicatus: Characterizations, Antimicrobial and Nematicidal Activities and Cytogenetic Effects
Plants 2021, 10(9), 1760; https://doi.org/10.3390/plants10091760 - 25 Aug 2021
Cited by 24 | Viewed by 3144
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 [...] Read more.
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
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12 pages, 1019 KiB  
Article
Fresh Compost Tea Application Does Not Change Rhizosphere Soil Bacterial Community Structure, and Has No Effects on Soybean Growth or Yield
Plants 2021, 10(8), 1638; https://doi.org/10.3390/plants10081638 - 10 Aug 2021
Cited by 8 | Viewed by 2815
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 [...] Read more.
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
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28 pages, 874 KiB  
Article
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
Plants 2021, 10(3), 520; https://doi.org/10.3390/plants10030520 - 10 Mar 2021
Cited by 9 | Viewed by 2804
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 [...] Read more.
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
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22 pages, 2965 KiB  
Article
Plant Growth-Promoting Endophytic Bacterial Community Inhabiting the Leaves of Pulicaria incisa (Lam.) DC Inherent to Arid Regions
Plants 2021, 10(1), 76; https://doi.org/10.3390/plants10010076 - 01 Jan 2021
Cited by 76 | Viewed by 5522
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. [...] Read more.
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
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Review

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33 pages, 3944 KiB  
Review
Harnessing Bacterial Endophytes for Promotion of Plant Growth and Biotechnological Applications: An Overview
Plants 2021, 10(5), 935; https://doi.org/10.3390/plants10050935 - 07 May 2021
Cited by 95 | Viewed by 8698
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 [...] Read more.
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
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