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Microbial Ecology for Environmental Biotechnology
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Microbial Ecology for Environmental Biotechnology

A special issue of International Journal of Environmental Research and Public Health (ISSN 1660-4601). This special issue belongs to the section "Environmental Science and Engineering".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 12347

Special Issue Editors

Dr. Ben Ozer Oyserman

E-Mail Website
Leading Guest Editor
Netherlands Institute of Ecology, Wageningen, Netherlands
Interests: environmental engineering; ecology and evolutionary biology; agriculture; microbiome engineering; microbiome-associated phenotypes
Dr. Christopher E. Lawson

E-Mail Website
Guest Editor
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Interests: environmental biotechnology; systems biology; synthetic biology; microbiome engineering
Dr. Matthew J. Scarborough

E-Mail Website
Guest Editor
Department of Civil and Environmental Engineering, The University of Vermont, Burlington, Vermont, USA
Interests: biological wastewater treatment; anaerobic digestion; microbial ecology

Special Issue Information

Dear Colleagues,

Microbial ecology is at the base of many environmental biotechnologies. By altering operational parameters or otherwise modifying system inputs, the taxonomic and functional diversity of microbial communities can be steered to produce desired emergent ecosystem functions. Thus, to optimize a bioprocess for a local environment and desired output, an understanding of microbial ecology is paramount. As societal demand shifts towards increased sustainability and circularity, understanding and exploiting the underlying microbial ecology and how it relates to emergent ecosystem functions is increasingly relevant. For example, activated sludge processes for wastewater treatment are under multiple and contrasting pressures to increase nutrient removal efficiency and decrease greenhouse gas emissions. These contrasting and multifaceted pressures mirror those in many biotechnologies, which are turning to microbial ecology to leverage complex emergent ecosystem properties, such as disease suppression in agricultural systems. Across sectors, engineered microbial ecosystems will play a key role in shaping a sustainable future. This Special Issue of International Journal of Environmental Research and Public Health (IJERPH) focuses on the current state of microbial ecology research related to all engineered ecosystems.

Potential topics include, but are not limited to, the following:

  • Microbial ecology of engineered ecosystems, including activated sludge, anaerobic digestion, biofiltration, bioenergy, aquaculture, and other agricultural systems;
  • Microbial interactions and population dynamics in engineered ecosystems;
  • Application of molecular biology approaches to environmental biotechnologies;
  • The development or application of techniques to steer microbial community structure or function.
  • Development and analysis of novel environmental biotechnologies for resource recovery, sustainable water and waste treatment, and renewable energy production;
  • Fate and removal of emerging contaminants and microplastics in the environment;
  • Molecular tools for microbial source tracking and pathogen detection.

Dr. Christopher E. Lawson
Dr. Ben Ozer Oyserman
Dr. Matthew J. Scarborough
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. International Journal of Environmental Research and Public Health is an international peer-reviewed open access monthly 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 2500 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

  • Microbial ecology
  • Community assembly
  • Engineered ecosystems
  • Biotechnology
  • Ecosystem function
  • Sustainability
  • Microbiome engineering

Published Papers (4 papers)

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Research

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18 pages, 4781 KiB  
Article
Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System
by Aracely Zambrano-Romero, Dario X. Ramirez-Villacis, Gabriel Trueba, Reyes Sierra-Alvarez, Antonio Leon-Reyes, Paul Cardenas and Valeria Ochoa-Herrera
Int. J. Environ. Res. Public Health 2022, 19(3), 1484; https://doi.org/10.3390/ijerph19031484 - 28 Jan 2022
Cited by 1 | Viewed by 2637
Abstract
Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 [...] Read more.
Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD. Full article
(This article belongs to the Special Issue Microbial Ecology for Environmental Biotechnology)
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14 pages, 4284 KiB  
Article
Bioremediation of Petroleum Hydrocarbons Using Acinetobacter sp. SCYY-5 Isolated from Contaminated Oil Sludge: Strategy and Effectiveness Study
by Yiyun Cai, Runkai Wang, Pinhua Rao, Baichun Wu, Lili Yan, Lijiang Hu, Sangsook Park, Moonhee Ryu and Xiaoya Zhou
Int. J. Environ. Res. Public Health 2021, 18(2), 819; https://doi.org/10.3390/ijerph18020819 - 19 Jan 2021
Cited by 31 | Viewed by 3589
Abstract
Biodegradation has been considered as an ideal technique for total petroleum hydrocarbon (TPH) contamination, but its efficiency is limited by its application in the field. Herein, an original TPH-degrading strain, SCYY-5, was isolated from contaminated oil sludge and identified as Acinetobacter sp. by [...] Read more.
Biodegradation has been considered as an ideal technique for total petroleum hydrocarbon (TPH) contamination, but its efficiency is limited by its application in the field. Herein, an original TPH-degrading strain, SCYY-5, was isolated from contaminated oil sludge and identified as Acinetobacter sp. by 16S rDNA sequence analysis. The biological function of the isolate was investigated by heavy metal tolerance, carbon, and nitrogen source and degradation tests. To enhance its biodegradation efficiency, the response surface methodology (RSM) based on a function model was adopted to investigate and optimize the strategy of microbial and environmental variables for TPH removal. Furthermore, the performance of the system increased to 79.94% with the further addition of extra nutrients, suggesting that the RSM and added nutrients increased the activity of bacteria to meet the needs of the co-metabolism matrix during growth or degradation. These results verified that it is feasible to adopt the optimal strategy of combining bioremediation with RSM to improve the biodegradation efficiency, for contaminated oil sludge. Full article
(This article belongs to the Special Issue Microbial Ecology for Environmental Biotechnology)
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9 pages, 623 KiB  
Perspective
The Soil Microbiota Recovery in the Agroecosystem: Minimal Information and a New Framework for Sustainable Agriculture
by Alessandro Bergna, Stephen J. Maund and Claudio Screpanti
Int. J. Environ. Res. Public Health 2022, 19(9), 5423; https://doi.org/10.3390/ijerph19095423 - 29 Apr 2022
Cited by 1 | Viewed by 1993
Abstract
The efficient management of soil represents a mission of vital importance for meeting the continuously increasing agricultural demand in a sustainable way. Decades of research identified in the biotechnological potential of soil microorganisms an always more practicable channel for achieving these goals. Due [...] Read more.
The efficient management of soil represents a mission of vital importance for meeting the continuously increasing agricultural demand in a sustainable way. Decades of research identified in the biotechnological potential of soil microorganisms an always more practicable channel for achieving these goals. Due to the complexity of soil microbial communities and their tight connection to soil characteristics, it is still difficult to define universal strategies for an efficient and sustainable agroecosystem management. We here propose a new framework for the assessment of the impact of agricultural practices in the agroecosystem that revolves around the concept of microbial community recovery. This assessment is based on the selection of (i) a representative temporal interval, (ii) a representative agricultural system and (iii) monitoring tools able to assess the expression levels of microbial functionality in soil. This approach can be especially valuable for evaluating the effects of agrochemicals and other agronomical amendments (of different nature: biological, physical, chemical) on the soil microbiota. In the same way precision-medicine tries to tailor drugs on an always smaller subset of patients’ characteristics, a new generation of agrochemicals can be developed and tested considering soil characteristics in order to minimize their off-target effects. What remains central in this paradigm is the promotion of Soil Health maintenance practices. As for healthy humans, a healthy soil is more resilient and tolerates treatments and stresses better while recovering more quickly. Full article
(This article belongs to the Special Issue Microbial Ecology for Environmental Biotechnology)
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19 pages, 765 KiB  
Perspective
Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods
by Anna Y. Alekseeva, Anneloes E. Groenenboom, Eddy J. Smid and Sijmen E. Schoustra
Int. J. Environ. Res. Public Health 2021, 18(19), 10093; https://doi.org/10.3390/ijerph181910093 - 26 Sep 2021
Cited by 8 | Viewed by 2692
Abstract
Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems [...] Read more.
Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used. Full article
(This article belongs to the Special Issue Microbial Ecology for Environmental Biotechnology)
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