Microorganisms for Environmental and Industrial Applications

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

Deadline for manuscript submissions: closed (20 September 2017) | Viewed by 51627

Special Issue Editor


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Guest Editor
School of Biomedical Sciences, University of Western Australia, Crawley 6009, Australia
Interests: biocorrosion; bioelectrochemistry; bioflotation; biogeochemistry; bioleaching; biomining; biooxidation; bioprecipitation; bioreduction; bioremediation; circular economy; resource recovery; waste management; wastewater treatment
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Special Issue Information

Dear Colleagues,

Microorganisms play a key role in the biogeochemical cycling of various elements, and can therefore be used for various environmental and industrial applications. Examples of microbially catalysed processes are biodegradation, bioleaching, bioprecipitation, biooxidation, bioreduction, bioaccumulation and bioflotation. These can be used for degrading and removing contaminants from water, soil and air, extracting value from low grade resources and waste streams, and generating value added products, such as energy, nanomaterials and chemicals. Microorganisms utilised in environmental and industrial applications include a range of bacteria, archaea and eukaryotes such as fungi and microalgae. For this Special Issue of Microorganisms, we invite you to send contributions concerning any aspects relating to microorganisms utilised in environmental and industrial applications, including but not limited to ecology, diversity, physiology, detection methods and processes.

Anna H. Kaksonen
Guest Editor

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Keywords

  • bioflotation
  • biodegradation
  • bioenergy
  • bioleaching
  • biomining
  • biooxidation
  • bioprecipitation
  • bioreduction
  • bioremediation
  • biotechnical treatment
  • environmental microbiology
  • industrial microbiology
  • resource recovery

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Published Papers (8 papers)

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Editorial

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2 pages, 150 KiB  
Editorial
Editorial for Special Issue “Microorganisms for Environmental and Industrial Applications”
by Anna H. Kaksonen
Microorganisms 2018, 6(3), 62; https://doi.org/10.3390/microorganisms6030062 - 2 Jul 2018
Viewed by 2527
Abstract
Microorganisms play an essential role in the biogeochemical cycling of elements, and therefore
they hold potential for various environmental and industrial applications[...] Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)

Research

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17 pages, 1187 KiB  
Article
Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
by Maryam Rezadehbashi and Susan A. Baldwin
Microorganisms 2018, 6(1), 16; https://doi.org/10.3390/microorganisms6010016 - 23 Feb 2018
Cited by 31 | Viewed by 5078
Abstract
Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM [...] Read more.
Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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15 pages, 2273 KiB  
Article
Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM
by Gretchen L. W. Heavner, Cresten B. Mansfeldt, Garrett E. Debs, Sage T. Hellerstedt, Annette R. Rowe and Ruth E. Richardson
Microorganisms 2018, 6(1), 13; https://doi.org/10.3390/microorganisms6010013 - 8 Feb 2018
Cited by 16 | Viewed by 4973
Abstract
Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent [...] Read more.
Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10−12 to 5.9 × 10−10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R2 = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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1364 KiB  
Article
Relationship among Phosphorus Circulation Activity, Bacterial Biomass, pH, and Mineral Concentration in Agricultural Soil
by Dinesh Adhikari, Tianyi Jiang, Taiki Kawagoe, Takamitsu Kai, Kenzo Kubota, Kiwako S. Araki and Motoki Kubo
Microorganisms 2017, 5(4), 79; https://doi.org/10.3390/microorganisms5040079 - 4 Dec 2017
Cited by 23 | Viewed by 5751
Abstract
Improvement of phosphorus circulation in the soil is necessary to enhance phosphorus availability to plants. Phosphorus circulation activity is an index of soil’s ability to supply soluble phosphorus from organic phosphorus in the soil solution. To understand the relationship among phosphorus circulation activity; [...] Read more.
Improvement of phosphorus circulation in the soil is necessary to enhance phosphorus availability to plants. Phosphorus circulation activity is an index of soil’s ability to supply soluble phosphorus from organic phosphorus in the soil solution. To understand the relationship among phosphorus circulation activity; bacterial biomass; pH; and Fe, Al, and Ca concentrations (described as mineral concentration in this paper) in agricultural soil, 232 soil samples from various agricultural fields were collected and analyzed. A weak relationship between phosphorus circulation activity and bacterial biomass was observed in all soil samples (R2 = 0.25), and this relationship became significantly stronger at near-neutral pH (6.0–7.3; R2 = 0.67). No relationship between phosphorus circulation activity and bacterial biomass was observed at acidic (pH < 6.0) or alkaline (pH > 7.3) pH. A negative correlation between Fe and Al concentrations and phosphorus circulation activity was observed at acidic pH (R2 = 0.72 and 0.73, respectively), as well as for Ca at alkaline pH (R2 = 0.64). Therefore, bacterial biomass, pH, and mineral concentration should be considered together for activation of phosphorus circulation activity in the soil. A relationship model was proposed based on the effects of bacterial biomass and mineral concentration on phosphorus circulation activity. The suitable conditions of bacterial biomass, pH, and mineral concentration for phosphorus circulation activity could be estimated from the relationship model. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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6430 KiB  
Article
Microbial Community Structure and Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine Water
by Malin Bomberg, Jarno Mäkinen, Marja Salo and Mona Arnold
Microorganisms 2017, 5(3), 61; https://doi.org/10.3390/microorganisms5030061 - 20 Sep 2017
Cited by 15 | Viewed by 5584
Abstract
Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L−1 sulfate, using granular sludge from an industrial [...] Read more.
Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L−1 sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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1609 KiB  
Article
MALDI-TOF MS for the Identification of Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near Unconventional Natural Gas Extraction Sites
by Inês C. Santos, Misty S. Martin, Doug D. Carlton, Catarina L. Amorim, Paula M. L. Castro, Zacariah L. Hildenbrand and Kevin A. Schug
Microorganisms 2017, 5(3), 47; https://doi.org/10.3390/microorganisms5030047 - 10 Aug 2017
Cited by 20 | Viewed by 12616
Abstract
Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have [...] Read more.
Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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727 KiB  
Article
Tellurite and Tellurate Reduction by the Aerobic Anoxygenic Phototroph Erythromonas ursincola, Strain KR99 Is Carried out by a Novel Membrane Associated Enzyme
by Chris Maltman, Lynda J. Donald and Vladimir Yurkov
Microorganisms 2017, 5(2), 20; https://doi.org/10.3390/microorganisms5020020 - 19 Apr 2017
Cited by 20 | Viewed by 4708
Abstract
Erythromonas ursincola, strain KR99 isolated from a freshwater thermal spring of Kamchatka Island in Russia, resists and reduces very high levels of toxic tellurite under aerobic conditions. Reduction is carried out by a constitutively expressed membrane associated enzyme, which was purified and [...] Read more.
Erythromonas ursincola, strain KR99 isolated from a freshwater thermal spring of Kamchatka Island in Russia, resists and reduces very high levels of toxic tellurite under aerobic conditions. Reduction is carried out by a constitutively expressed membrane associated enzyme, which was purified and characterized. The tellurite reductase has a molecular weight of 117 kDa, and is comprised of two subunits (62 and 55 kDa) in a 1:1 ratio. Optimal activity occurs at pH 7.0 and 28 °C. Tellurite reduction has a Vmax of 5.15 µmol/min/mg protein and a Km of 3.36 mM. The enzyme can also reduce tellurate with a Vmax and Km of 1.08 µmol/min/mg protein and 1.44 mM, respectively. This is the first purified membrane associated Te oxyanion reductase. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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Review

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2211 KiB  
Review
Biotechnological Applications of Microbial (Per)chlorate Reduction
by Ouwei Wang and John D. Coates
Microorganisms 2017, 5(4), 76; https://doi.org/10.3390/microorganisms5040076 - 24 Nov 2017
Cited by 29 | Viewed by 7732
Abstract
While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation [...] Read more.
While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration. This ability, along with other novel aspects of the metabolism, have resulted in a wide and disparate range of potential biotechnological applications being proposed, including enzymatic perchlorate detection; gas gangrene therapy; enhanced xenobiotic bioremediation; oil reservoir bio-souring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and, biogenic oxygen production for planetary exploration. While previous reviews focus on the fundamental science of microbial (per)chlorate reduction (for example see Youngblut et al., 2016), here, we provide an overview of the emerging biotechnological applications of (per)chlorate respiration and the underlying organisms and enzymes to environmental and biotechnological industries. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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