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Microorganisms
Special Issues
Mono- and Multi-Species Biofilms in Bioprocesses
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Mono- and Multi-Species Biofilms in Bioprocesses

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

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 16903

Special Issue Editor

Dr. Frank Delvigne

E-Mail Website
Guest Editor
Universite de Liege, Liege, Belgium
Interests: microbial population physiology; bistable systems in E. coli and B. amyloliquefaciens

Special Issue Information

Dear Colleagues，

Actual biotechnological processes rely mainly on the use of microbial cells in the planktonic state. However, it has been shown that biofilms could be an interesting alternative for improving bioprocessing techniques (i.e., increasing the robustness of the microbial population to environmental fluctuations, increasing the resistance to inhibitors and by-products, and facilitating the transition from batch to continuous bioprocessing). Biofilm applications have been limited in biotechnology due to the lack of dedicated cultivation/monitoring tools and the potential instability of the biofilm phase (biofilm disruption and release of the cells back to the liquid phase). New perspectives are now arising considering the technological developments made at the level of the process analytical technologies (PAT) and bioreactor design. Moreover, the progress made at the level of the understanding of biofilm physiology has led to the identification of new metabolic engineering targets allowing further improvements to the robustness of the biofilm phase.

Biofilms have also been proposed as a way to engineer the microbiome for specific functions. Indeed, the spatial structuration of environmental conditions within the biofilm matrix promotes the co-existence of several species and leads to the stabilization of microbial interactions. This technology thus opens an avenue for the development of new bioprocesses based on the utilization of microbial communities (either natural or engineered).

This Special Issue will be focused on the design and use of single- and multi-species biofilms in the field of industrial, environmental, and health biotechnology, with a special emphasis on the approaches (metabolic and reactor engineering, modeling, management of microbial interactions, etc.) enabling the rapid application of biofilms to real applications.

Dr. Frank Delvigne
Guest Editor

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. Microorganisms 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 2700 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.

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Published Papers (5 papers)

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Research

14 pages, 2360 KiB  
Article
Characterization of the Bacterial Biofilm Communities Present in Reverse-Osmosis Water Systems for Haemodialysis
by Juan-Pablo Cuevas, Ruben Moraga, Kimberly Sánchez-Alonzo, Cristian Valenzuela, Paulina Aguayo, Carlos T. Smith, Apolinaria García, Ítalo Fernandez and Víctor L Campos
Microorganisms 2020, 8(9), 1418; https://doi.org/10.3390/microorganisms8091418 - 15 Sep 2020
Cited by 9 | Viewed by 3144
Abstract
Biofilm in reverse osmosis (RO) membranes is a common problem in water treatment at haemodialysis facilities. Bacteria adhere and proliferate on RO membranes, forming biofilms, obstructing and damaging the membranes and allowing the transfer of bacteria and/or cellular components potentially harmful to the [...] Read more.
Biofilm in reverse osmosis (RO) membranes is a common problem in water treatment at haemodialysis facilities. Bacteria adhere and proliferate on RO membranes, forming biofilms, obstructing and damaging the membranes and allowing the transfer of bacteria and/or cellular components potentially harmful to the health of haemodialysis patients. Our aim was to characterize the bacterial community associated to biofilm of RO membranes and to identify potentially pathogenic bacteria present in the haemodialysis systems of two dialysis centres in Chile. The diversity of the bacterial communities present on RO membranes and potable and osmosed water samples was evaluated using Illumina sequencing. Additionally, bacteria from potable water, osmosed water and RO membrane samples were isolated, characterized and identified by Sanger’s sequencing. The molecular analyses of metagenomics showed that the phyla having a greater relative abundance in both dialysis centres were Proteobacteria and Planctomycetes. Pseudomonas, Stenotrophomonas, Agrobacterium, Pigmentiphaga, Ralstonia, Arthrobacter, Bacteroides and Staphylococcus were bacterial genera isolated from the different samples obtained at both haemodialysis centres. Pseudomonas spp. was a bacterial genus with greater frequency in all samples. Pseudomonas and Staphylococcus showed higher levels of resistance to the antibiotics tested. Results demonstrated the presence of potentially pathogenic bacteria, showing resistance to antimicrobials on RO membranes and in osmosed water in both dialysis centres studied. Full article
(This article belongs to the Special Issue Mono- and Multi-Species Biofilms in Bioprocesses)
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14 pages, 2890 KiB  
Article
A Novel System for Real-Time, In Situ Monitoring of CO2 Sequestration in Photoautotrophic Biofilms
by Patrick Ronan, Otini Kroukamp, Steven N. Liss and Gideon Wolfaardt
Microorganisms 2020, 8(8), 1163; https://doi.org/10.3390/microorganisms8081163 - 31 Jul 2020
Cited by 6 | Viewed by 2692
Abstract
Climate change brought about by anthropogenic CO2 emissions has created a critical need for effective CO2 management solutions. Microalgae are well suited to contribute to efforts aimed at addressing this challenge, given their ability to rapidly sequester CO2 coupled with [...] Read more.
Climate change brought about by anthropogenic CO2 emissions has created a critical need for effective CO2 management solutions. Microalgae are well suited to contribute to efforts aimed at addressing this challenge, given their ability to rapidly sequester CO2 coupled with the commercial value of their biomass. Recently, microalgal biofilms have garnered significant attention over the more conventional suspended algal growth systems, since they allow for easier and cheaper biomass harvesting, among other key benefits. However, the path to cost-effectiveness and scaling up is hindered by a need for new tools and methodologies which can help evaluate, and in turn optimize, algal biofilm growth. Presented here is a novel system which facilitates the real-time in situ monitoring of algal biofilm CO2 sequestration. Utilizing a CO2-permeable membrane and a tube-within-a-tube design, the CO2 sequestration monitoring system (CSMS) was able to reliably detect slight changes in algal biofilm CO2 uptake brought about by light–dark cycling, light intensity shifts, and varying amounts of phototrophic biomass. This work presents an approach to advance our understanding of carbon flux in algal biofilms, and a base for potentially useful innovations to optimize, and eventually realize, algae biofilm-based CO2 sequestration. Full article
(This article belongs to the Special Issue Mono- and Multi-Species Biofilms in Bioprocesses)
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14 pages, 1164 KiB  
Article
Biofilm Mode of Cultivation Leads to an Improvement of the Entomotoxic Patterns of Two Aspergillus Species
by Frédéric Francis, Florent Druart, José Diana Di Mavungu, Marthe De Boevre, Sarah De Saeger and Frank Delvigne
Microorganisms 2020, 8(5), 705; https://doi.org/10.3390/microorganisms8050705 - 11 May 2020
Cited by 2 | Viewed by 2228
Abstract
Two fungi, i.e., Aspergillus flavus Link and Aspergillus oryzae (Ahlb.) E. Cohn, were cultivated according to two methodologies, namely submerged and biofilm cultures with the primary aim to use their secondary metabolites the supernatant CL50, and CL90 varied between 1.3% [...] Read more.
Two fungi, i.e., Aspergillus flavus Link and Aspergillus oryzae (Ahlb.) E. Cohn, were cultivated according to two methodologies, namely submerged and biofilm cultures with the primary aim to use their secondary metabolites the supernatant CL50, and CL90 varied between 1.3% (v/v) to 12.7% (v/v) for incubation times from 24 to 72 h. While the A. flavus supernatant entomotoxicity was higher than this of A. oryzae, the biofilm culture application increased the efficiency of the former. Proteomic analysis of the supernatants revealed discrepancies among the two species and modes of cultivation. Furthermore, the secondary metabolite profiles of both Aspergillus cultures were verified. Aspergillic acid, beta-cyclopiazonic acid, cyclopiazonic acid, ferrineospergillin, flavacol, and spermadin A were most predominant. Generally, these secondary metabolites were present in higher concentrations in the supernatants of A. flavus and biofilm cultures. These molecular identifications correlated positively with entomotoxic activity. Noteworthy, the absence of carcinogenic aflatoxins was remarkable, and it will allow further valorization to produce A. flavus to develop potential biopesticides. Full article
(This article belongs to the Special Issue Mono- and Multi-Species Biofilms in Bioprocesses)
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19 pages, 2970 KiB  
Article
Growth Dynamics of Bacterial Populations in a Two-Compartment Biofilm Bioreactor Designed for Continuous Surfactin Biosynthesis
by Hannah Luise Brück, François Coutte, Pascal Dhulster, Sébastien Gofflot, Philippe Jacques and Frank Delvigne
Microorganisms 2020, 8(5), 679; https://doi.org/10.3390/microorganisms8050679 - 7 May 2020
Cited by 11 | Viewed by 4291
Abstract
Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment biofilm bioreactor was designed consisting of a stirred tank reactor and a trickle-bed reactor containing a structured [...] Read more.
Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment biofilm bioreactor was designed consisting of a stirred tank reactor and a trickle-bed reactor containing a structured metal packing for biofilm formation. A strong and poor biofilm forming B. subtilis 168 strain due to restored exopolysaccharides (EPS) production or not were cultivated in the system to study the growth behavior of the planktonic and biofilm population for the establishment of a growth model. A high dilution rate was used in order to promote biofilm formation on the packing and wash out unwanted planktonic cells. Biofilm development kinetics on the packing were assessed through a total organic carbon mass balance. The EPS+ strain showed a significantly improved performance in terms of adhesion capacity and surfactin production. The mean surfactin productivity of the EPS+ strain was about 37% higher during the continuous cultivation compared to the EPS- strain. The substrate consumption together with the planktonic cell and biofilm development were properly predicted by the model (α = 0.05). The results show the efficiency of the biofilm bioreactor for continuous surfactin production using an EPS producing strain. Full article
(This article belongs to the Special Issue Mono- and Multi-Species Biofilms in Bioprocesses)
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17 pages, 3043 KiB  
Article
Enhanced Adsorptive Bioremediation of Heavy Metals (Cd2+, Cr6+, Pb2+) by Methane-Oxidizing Epipelon
by Muhammad Faheem, Sadaf Shabbir, Jun Zhao, Philip G. Kerr, Nasrin Sultana and Zhongjun Jia
Microorganisms 2020, 8(4), 505; https://doi.org/10.3390/microorganisms8040505 - 1 Apr 2020
Cited by 13 | Viewed by 3951
Abstract
Cadmium (Cd), chromium (Cr) and lead (Pb) are heavy metals that have been classified as priority pollutants in aqueous environment while methane-oxidizing bacteria as a biofilter arguably consume up to 90% of the produced methane in the same aqueous environment before it escapes [...] Read more.
Cadmium (Cd), chromium (Cr) and lead (Pb) are heavy metals that have been classified as priority pollutants in aqueous environment while methane-oxidizing bacteria as a biofilter arguably consume up to 90% of the produced methane in the same aqueous environment before it escapes into the atmosphere. However, the underlying kinetics and active methane oxidizers are poorly understood for the hotspot of epipelon that provides a unique micro-ecosystem containing diversified guild of microorganisms including methane oxidizers for potential bioremediation of heavy metals. In the present study, the Pb2+, Cd2+and Cr6+ bioremediation potential of epipelon biofilm was assessed under both high (120,000 ppm) and near-atmospheric (6 ppm) methane concentrations. Epipelon biofilm demonstrated a high methane oxidation activity following microcosm incubation amended with a high concentration of methane, accompanied by the complete removal of 50 mg L−1 Pb2+ and 50 mg L−1 Cd2+ (14 days) and partial (20%) removal of 50 mg L−1 Cr6+ after 20 days. High methane dose stimulated a faster (144 h earlier) heavy metal removal rate compared to near-atmospheric methane concentrations. DNA-based stable isotope probing (DNA-SIP) following 13CH4 microcosm incubation revealed the growth and activity of different phylotypes of methanotrophs during the methane oxidation and heavy metal removal process. High throughput sequencing of 13C-labelled particulate methane monooxygenase gene pmoA and 16S rRNA genes revealed that the prevalent active methane oxidizers were type I affiliated methanotrophs, i.e., Methylobacter. Type II methanotrophs including Methylosinus and Methylocystis were also labeled only under high methane concentrations. These results suggest that epipelon biofilm can serve as an important micro-environment to alleviate both methane emission and the heavy metal contamination in aqueous ecosystems with constant high methane fluxes. Full article
(This article belongs to the Special Issue Mono- and Multi-Species Biofilms in Bioprocesses)
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