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Microorganisms
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Microbial Remediation of Soils: Bioaugmentation and Biostimulation towards Improved Soil...
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Microbial Remediation of Soils: Bioaugmentation and Biostimulation towards Improved Soil and Human Health

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 12965

Special Issue Editor

Dr. Tarah S. Sullivan

E-Mail Website
Guest Editor
Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
Interests: soil biogeochemistry; siderophore processes; metals and micronutrients; bioremediation; soil microbiome

Special Issue Information

Dear Colleagues,

The dramatically increasing global human populations face challenges of sustainable food production, micronutrient malnutrition, and waste accumulation and disposal. Within the arena of metals in our environment, the classical conundrums of feast and famine face scientists and consumers alike, and the soil microbiome ultimately brings all these issues to bear. The biogeochemical processes microorganisms undergo to transform and eliminate toxic and trace metals in soil can be harnessed to address these eminent global challenges, both with regard to the detoxification of contaminated soils and environments, and to the rehabilitation of overworked or degraded soils. This fundamental metal biogeochemistry can be used toward the greater good, through either natural or synthetic microbial communities, to the ultimate improvement of soil health and, consequently, human health as well. In this Special Issue, we invite research articles and reviews to move beyond simple surveys of the soil microbiome and seek a better understanding of the processes and mechanisms that underlie the movement of trace metals, micronutrients, and toxic substances controlling the microbial capacity to remediate. Through bioaugmentation and biostimulation in soils, we direct and manage the microbial remediation of metals in such a way as to limit human and environmental exposure to toxins, while simultaneously increasing sustainable fuel and nutritious food production strategies.

Dr. Tarah S. Sullivan
Guest Editor

Manuscript Submission Information

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Keywords

  • metal biogeochemistry
  • bioremediation
  • biostimulation
  • bioaugmentation
  • synthetic microbiome
  • micronutrient malnutrition
  • soil health
  • phytoremediation
  • plant growth promoting microorganisms
  • microbial siderophores

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Published Papers (3 papers)

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Research

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14 pages, 3230 KiB  
Article
Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes
by Wenjing Liu, Kai Xue, Runpeng Hu, Jizhong Zhou, Joy D. Van Nostrand, Jannis Dimitrou, Laura Giagnoni and Giancarlo Renella
Microorganisms 2022, 10(1), 140; https://doi.org/10.3390/microorganisms10010140 - 11 Jan 2022
Cited by 1 | Viewed by 2102
Abstract
Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees [...] Read more.
Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3−-N and P concentrations. The microbial taxa–area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m2, which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term. Full article
(This article belongs to the Special Issue Microbial Remediation of Soils: Bioaugmentation and Biostimulation towards Improved Soil and Human Health)
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16 pages, 1297 KiB  
Article
Microbial Response to Phytostabilization in Mining Impacted Soils Using Maize in Conjunction with Biochar and Compost
by Thomas F. Ducey, Gilbert C. Sigua, Jeffrey M. Novak, James A. Ippolito, Kurt A. Spokas and Mark G. Johnson
Microorganisms 2021, 9(12), 2545; https://doi.org/10.3390/microorganisms9122545 - 9 Dec 2021
Cited by 5 | Viewed by 2480
Abstract
Even after remediation, mining impacted soils can leave behind a landscape inhospitable to plant growth and containing residual heavy metals. While phytostabilization can be used to restore such sites by limiting heavy metal spread, it is reliant on soil capable of supporting plant [...] Read more.
Even after remediation, mining impacted soils can leave behind a landscape inhospitable to plant growth and containing residual heavy metals. While phytostabilization can be used to restore such sites by limiting heavy metal spread, it is reliant on soil capable of supporting plant growth. Manure-based biochars, coupled with compost, have demonstrated the ability to improve soil growth conditions in mine impacted soils, however there is a paucity of information regarding their influence on resident microbial populations. The objective of this study was to elucidate the impact of these soil amendments on microbial community structure and function in mine impacted soils placed under phytostabilization management with maize. To this aim, a combination of phospholipid fatty acid (PLFA) and enzymatic analyses were performed. Results indicate that microbial biomass is significantly increased upon addition of biochar and compost, with maximal microbial biomass achieved with 5% poultry litter biochar and compost (62.82 nmol g−1 dry soil). Microbial community structure was impacted by biochar type, rate of application, and compost addition, and influenced by pH (r2 = 0.778), EC (r2 = 0.467), and Mg soil concentrations (r2 = 0.453). In three of the four enzymes analyzed, poultry litter biochar treatments were observed with increased activity rates that were often significantly greater than the unamended control. Overall, enzyme activities rates were influenced by biochar type and rate, and addition of compost. These results suggest that using a combination of biochar and compost can be utilized as a management tool to support phytostabilization strategies in mining impacted soils. Full article
(This article belongs to the Special Issue Microbial Remediation of Soils: Bioaugmentation and Biostimulation towards Improved Soil and Human Health)
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Review

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21 pages, 1317 KiB  
Review
Glyphosate Pollution Treatment and Microbial Degradation Alternatives, a Review
by María Luisa Castrejón-Godínez, Efraín Tovar-Sánchez, Leticia Valencia-Cuevas, Marcos Eduardo Rosas-Ramírez, Alexis Rodríguez and Patricia Mussali-Galante
Microorganisms 2021, 9(11), 2322; https://doi.org/10.3390/microorganisms9112322 - 10 Nov 2021
Cited by 24 | Viewed by 7360
Abstract
Glyphosate is a broad-spectrum herbicide extensively used worldwide to eliminate weeds in agricultural areas. Since its market introduction in the 70’s, the levels of glyphosate agricultural use have increased, mainly due to the introduction of glyphosate-resistant transgenic crops in the 90’s. Glyphosate presence [...] Read more.
Glyphosate is a broad-spectrum herbicide extensively used worldwide to eliminate weeds in agricultural areas. Since its market introduction in the 70’s, the levels of glyphosate agricultural use have increased, mainly due to the introduction of glyphosate-resistant transgenic crops in the 90’s. Glyphosate presence in the environment causes pollution, and recent findings have proposed that glyphosate exposure causes adverse effects in different organisms, including humans. In 2015, glyphosate was classified as a probable carcinogen chemical, and several other human health effects have been documented since. Environmental pollution and human health threats derived from glyphosate intensive use require the development of alternatives for its elimination and proper treatment. Bioremediation has been proposed as a suitable alternative for the treatment of glyphosate-related pollution, and several microorganisms have great potential for the biodegradation of this herbicide. The present review highlights the environmental and human health impacts related to glyphosate pollution, the proposed alternatives for its elimination through physicochemical and biological approaches, and recent studies related to glyphosate biodegradation by bacteria and fungi are also reviewed. Microbial remediation strategies have great potential for glyphosate elimination, however, additional studies are needed to characterize the mechanisms employed by the microorganisms to counteract the adverse effects generated by the glyphosate exposure. Full article
(This article belongs to the Special Issue Microbial Remediation of Soils: Bioaugmentation and Biostimulation towards Improved Soil and Human Health)
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