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Microorganisms
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Microbial Resource Management
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Microbial Resource Management

A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (31 October 2015) | Viewed by 77205

Special Issue Editor

Prof. Willy Verstraete

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Guest Editor
Faculty Bio-Engineering Sciences, Laboratory Microbial Ecology and Technology; LabMET, 9000 Ghent, Belgium
Interests: biotech to upgrade; the cyclic economy; microbial resource management
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

For a long time, microbiologists struggled with the concept of “mixed cultures”. Scientific data had to be reliable and reproducible and descriptions of mixed cultures, consortia, microcosms, etc, were to be considered with care because their validity could be questionable. Yet, at the same time, the mixed cultures in and around us, and in the overall ecosystems in which we live, are responsible for a plethora of crucial actions, sometimes detrimental, but most often very positive for the quality of our lives and for life in general on the planet.

The concept of “microbial resource management” is analogous to that of “human resource management”. We all are aware that in a dynamic open environment, be it human or microbial, there is a need for complementing talents, traits, and capacities by bringing various actuators together in a proper setting. Once the proper team is established, there is a need to maintain it by constant exchange of information and distribution of mutual gains. Clearly, be it the science of scouting for top performers, the knowledge of maintaining such top performers either as “pure” cultures or as “microbiomes” in culture collections, the engineering capacity to guarantee the functionality of industrially important microbiomes in various agro and environmental industries—all these aspects are currently very much in the front line of fundamental science and also of industrial microbiology and environmental technology.

Prof. Willy Verstraete
Guest Editor

Manuscript Submission Information

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Keywords

  • microbiomes
  • synthetic biology
  • environmental processes
  • mixed culture fermentations
  • microbial interactions
  • patented strains and consortia
  • evolutionary microbiology
  • microbial process engineering and technology

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Published Papers (9 papers)

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Research

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1357 KiB  
Article
Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester—A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?
by Marietta Liebrich, Anne Kleyböcker, Monika Kasina, Rona Miethling-Graff, Andrea Kassahun and Hilke Würdemann
Microorganisms 2016, 4(1), 17; https://doi.org/10.3390/microorganisms4010017 - 17 Mar 2016
Cited by 2 | Viewed by 7056
Abstract
The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the [...] Read more.
The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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788 KiB  
Article
Aspergillus oryzae–Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates
by Justin P. Jahnke, Thomas Hoyt, Hannah M. LeFors, James J. Sumner and David M. Mackie
Microorganisms 2016, 4(1), 10; https://doi.org/10.3390/microorganisms4010010 - 4 Feb 2016
Cited by 3 | Viewed by 6237
Abstract
Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, [...] Read more.
Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This “bio-hybrid FC” continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol—water mixtures, using the same FC. The A. oryzae–S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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2146 KiB  
Article
Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities
by Lisa Oberding and Lisa M. Gieg
Microorganisms 2016, 4(1), 5; https://doi.org/10.3390/microorganisms4010005 - 5 Jan 2016
Cited by 8 | Viewed by 7180
Abstract
Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly [...] Read more.
Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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1321 KiB  
Article
Influence of pH Regulation Mode in Glucose Fermentation on Product Selection and Process Stability
by Zuhaida Mohd-Zaki, Juan R. Bastidas-Oyanedel, Yang Lu, Robert Hoelzle, Steven Pratt, Fran R. Slater and Damien J. Batstone
Microorganisms 2016, 4(1), 2; https://doi.org/10.3390/microorganisms4010002 - 4 Jan 2016
Cited by 40 | Viewed by 8579
Abstract
Mixed culture anaerobic fermentation generates a wide range of products from simple sugars, and is potentially an effective process for producing renewable commodity chemicals. However it is difficult to predict product spectrum, and to control the process. One of the key control handles [...] Read more.
Mixed culture anaerobic fermentation generates a wide range of products from simple sugars, and is potentially an effective process for producing renewable commodity chemicals. However it is difficult to predict product spectrum, and to control the process. One of the key control handles is pH, but the response is commonly dependent on culture history. In this work, we assess the impact of pH regulation mode on the product spectrum. Two regulation modes were applied: in the first, pH was adjusted from 4.5 to 8.5 in progressive steps of 0.5 and in the second, covered the same pH range, but the pH was reset to 5.5 before each change. Acetate, butyrate, and ethanol were produced throughout all pH ranges, but there was a shift from butyrate at pH < 6.5 to ethanol at pH > 6.5, as well as a strong and consistent shift from hydrogen to formate as pH increased. Microbial analysis indicated that progressive pH resulted in dominance by Klebsiella, while reset pH resulted in a bias towards Clostridium spp., particularly at low pH, with higher variance in community between different pH levels. Reset pH was more responsive to changes in pH, and analysis of Gibbs free energy indicated that the reset pH experiments operated closer to thermodynamic equilibrium, particularly with respect to the formate/hydrogen balance. This may indicate that periodically resetting pH conforms better to thermodynamic expectations. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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890 KiB  
Article
Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals
by Jennifer M. Lang, Racheal Erb, Jennifer L. Pechal, John R. Wallace, Ryan W. McEwan and Mark Eric Benbow
Microorganisms 2016, 4(1), 1; https://doi.org/10.3390/microorganisms4010001 - 4 Jan 2016
Cited by 27 | Viewed by 7292
Abstract
Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as [...] Read more.
Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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Review

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993 KiB  
Review
The Opportunity for High-Performance Biomaterials from Methane
by Peter James Strong, Bronwyn Laycock, Syarifah Nuraqmar Syed Mahamud, Paul Douglas Jensen, Paul Andrew Lant, Gene Tyson and Steven Pratt
Microorganisms 2016, 4(1), 11; https://doi.org/10.3390/microorganisms4010011 - 3 Feb 2016
Cited by 99 | Viewed by 15661
Abstract
Polyhydroxyalkanoate (PHA) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. Their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. Further, they are [...] Read more.
Polyhydroxyalkanoate (PHA) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. Their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. Further, they are the only commodity polymer that can be synthesised intracellularly, ensuring stereoregularity and high molecular weight. However, despite offering enormous potential for many years, they are still not making a significant impact. This is broadly because commercial uptake has been limited by variable performance (inconsistent polymer properties) and high production costs of the raw polymer. Additionally, the main type of PHA produced naturally is poly-3-hydroxybutyrate (PHB), which has limited scope due to its brittle nature and low thermal stability, as well as its tendency to embrittle over time. Production cost is strongly impacted by the type of the feedstock used. In this article we consider: the production of PHAs from methanotrophs using methane as a cost-effective substrate; the use of mixed cultures, as opposed to pure strains; and strategies to generate a poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer (PHBV), which has more desirable qualities such as toughness and elasticity. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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Other

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1252 KiB  
Essay
Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection
by Marta F. Simões, Nicolina Dias, Cledir Santos and Nelson Lima
Microorganisms 2016, 4(2), 21; https://doi.org/10.3390/microorganisms4020021 - 22 Jun 2016
Cited by 8 | Viewed by 7584
Abstract
Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in [...] Read more.
Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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1998 KiB  
Opinion
Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems
by Tom H. J. A. Sleutels, Sam D. Molenaar, Annemiek Ter Heijne and Cees J. N. Buisman
Microorganisms 2016, 4(1), 7; https://doi.org/10.3390/microorganisms4010007 - 5 Jan 2016
Cited by 58 | Viewed by 7523
Abstract
A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a [...] Read more.
A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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354 KiB  
Essay
The Microbial Resource Research Infrastructure MIRRI: Strength through Coordination
by Erko Stackebrandt, Manuela Schüngel, Dunja Martin and David Smith
Microorganisms 2015, 3(4), 890-902; https://doi.org/10.3390/microorganisms3040890 - 18 Nov 2015
Cited by 11 | Viewed by 8499
Abstract
Microbial resources have been recognized as essential raw materials for the advancement of health and later for biotechnology, agriculture, food technology and for research in the life sciences, as their enormous abundance and diversity offer an unparalleled source of unexplored solutions. Microbial domain [...] Read more.
Microbial resources have been recognized as essential raw materials for the advancement of health and later for biotechnology, agriculture, food technology and for research in the life sciences, as their enormous abundance and diversity offer an unparalleled source of unexplored solutions. Microbial domain biological resource centres (mBRC) provide live cultures and associated data to foster and support the development of basic and applied science in countries worldwide and especially in Europe, where the density of highly advanced mBRCs is high. The not-for-profit and distributed project MIRRI (Microbial Resource Research Infrastructure) aims to coordinate access to hitherto individually managed resources by developing a pan-European platform which takes the interoperability and accessibility of resources and data to a higher level. Providing a wealth of additional information and linking to datasets such as literature, environmental data, sequences and chemistry will enable researchers to select organisms suitable for their research and enable innovative solutions to be developed. The current independent policies and managed processes will be adapted by partner mBRCs to harmonize holdings, services, training, and accession policy and to share expertise. The infrastructure will improve access to enhanced quality microorganisms in an appropriate legal framework and to resource-associated data in a more interoperable way. Full article
(This article belongs to the Special Issue Microbial Resource Management)
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