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Microorganisms in Biomass Conversion and Biofuel Production

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

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 14844

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Special Issue Editors

Dr. Zaixing Huang

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Guest Editor

Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY 82072, USA
Interests: biogenic natural gas; carbon capture and storage; bioremediation; anaerobic digestion

Dr. Huan He

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Guest Editor

School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou 221116, China
Interests: microbial community around coal mine; coal biotransformation; biogenic coal bed methane; coal-based solid waste recycling; ecological restoration of coal mine
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Special Issue Information

Dear Colleagues,

The topic of biomass conversion and biofuel production is one of the most important aspects directly related to several of the seventeen Sustainable Development Goals defined by the United Nations. Biomass conversion and biofuel production could provide feedstock and viable renewable energy resources, particularly in the context of deteriorating supplies of fossil fuels, accelerated global warming attributed to anthropogenic emissions, and unstable geopolitical situations. Biomass conversion and bioenergy production have a broad scope that covers a wide spectrum of topics ranging from the conversion of biomass to ethanol via fermentation to biogas production via anaerobic digestion. These technologies are deemed sustainable and cost-effective. Microorganisms, individually or synergistically, have played an essential and pivotal role, in that numerous intermediates and end products are produced through processes at cellular or enzymatic levels. This Special Issue aims to provide a platform for scientists working in the field of biomass conversion and biofuel production to exchange their recent research, with a focus on the production of fuels and chemicals including but not limited to biogas (biomethane), hydrogen, ethanol, butanol, acetone, and a wide range of organic acids through microbial processes. All work related to this topic is welcomed.

Dr. Zaixing Huang
Dr. Huan He
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. 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.

Keywords

biomass conversion
biofuel
microorganisms
sustainability
anaerobic digestion
fermentation
bioenergy
biohydrogen
biodegradation
biogas

Published Papers (10 papers)

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Research

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15 pages, 1183 KiB

Open AccessArticle

Remediation Approaches to Reduce Hydrocarbon Contamination in Petroleum-Polluted Soil

by Abdelkareem Elgazali, Hakima Althalb, Izzeddin Elmusrati, Hasna M. Ahmed and Ibrahim M. Banat

Microorganisms 2023, 11(10), 2577; https://doi.org/10.3390/microorganisms11102577 - 17 Oct 2023

Cited by 1 | Viewed by 1711

Abstract

Heavy metals pollution associated with oil spills has become a major concern worldwide. It is essential to break down these contaminants in the environment. In the environment, microbes have been used to detoxify and transform hazardous components. The process can function naturally or can be enhanced by adding nutrients, electron acceptors, or other factors. This study investigates some factors affecting hydrocarbon remediation technologies/approaches. Combinations of biological, chemical, and eco-toxicological techniques are used for this process while monitoring the efficacy of bacterial products and nutrient amendments to stimulate the biotransformation of contaminated soil. Different hydrocarbon removal levels were observed with bacterial augmentation (Beta proteobacterium and Rhodococcus ruber), exhibiting a total petroleum hydrocarbon (TPH) reduction of 61%, which was further improved to a 73% reduction using bacterial augmentation combined with nutrient amendment (nitrogen, potassium, and phosphorus). A heavy metal analysis of the polluted soils showed that the combination of nutrient and bacterial augmentation resulted in a significant reduction (p-value < 0.05) in lead, zinc, and barium. Toxicity testing also showed that a reduction of up to 50% was achieved using these remediation approaches. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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15 pages, 2898 KiB

Open AccessArticle

Comparison of Various Reducing Agents for Methane Production by Methanothermobacter marburgensis

by Maximilian Peter Mock, Rayen Ochi, Maria Bieringer, Tim Bieringer, Raimund Brotsack and Stephan Leyer

Microorganisms 2023, 11(10), 2533; https://doi.org/10.3390/microorganisms11102533 - 10 Oct 2023

Cited by 1 | Viewed by 1152

Abstract

Biological methanation is driven by anaerobic methanogenic archaea, cultivated in different media, which consist of multiple macro and micro nutrients. In addition, a reducing agent is needed to lower the oxidation–reduction potential (ORP) and enable the growth of oxygen-sensitive organisms. Until now, sodium sulfide (Na₂S) has been used mainly for this purpose based on earlier published articles at the beginning of anaerobic microbiology research. In a continuation of earlier investigations, in this study, the usage of alternative reducing agents like sodium dithionite (Na₂S₂O₄) and L-Cysteine-HCl shows that similar results can be obtained with fewer environmental and hazardous impacts. Therefore, a newly developed comparison method was used for the cultivation of Methanothermobacter marburgensis. The median methane evolution rate (MER) for the alternatives was similar compared to Na₂S at different concentrations (0.5, 0.25 and 0.1 g/L). However, the use of 0.25 g/L Na₂S₂O₄ or 0.1 g/L L-Cys-HCl led to stable MER values over consecutive batches compared to Na₂S. It was also shown that a lower concentration of reducing agent leads to a higher MER. In conclusion, Na₂S₂O₄ or L-Cys-HCl can be used as a non-corrosive and non-toxic reducing agent for ex situ biological methanation. Economically, Na₂S₂O₄ is cheaper, which is particularly interesting for scale-up purposes. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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34 pages, 9658 KiB

Open AccessArticle

Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics

by Julia Hassa, Tom Jonas Tubbesing, Irena Maus, Robert Heyer, Dirk Benndorf, Mathias Effenberger, Christian Henke, Benedikt Osterholz, Michael Beckstette, Alfred Pühler, Alexander Sczyrba and Andreas Schlüter

Microorganisms 2023, 11(10), 2412; https://doi.org/10.3390/microorganisms11102412 - 27 Sep 2023

Viewed by 1209

Abstract

The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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20 pages, 1660 KiB

Open AccessArticle

Microbiome Diversity of Anaerobic Digesters Is Enhanced by Microaeration and Low Frequency Sound

by John H. Loughrin, Rohan R. Parekh, Getahun E. Agga, Philip J. Silva and Karamat R. Sistani

Microorganisms 2023, 11(9), 2349; https://doi.org/10.3390/microorganisms11092349 - 20 Sep 2023

Cited by 1 | Viewed by 1290

Abstract

Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at week seven, the digesters underwent four treatments: control, microaeration with 6 mL air L⁻¹ digestate per day, treatment with a 1000 Hz sine wave, or treatment with the sound wave and microaeration. Both microaeration and sound enhanced biogas production relative to the control, while their combination was not as effective as microaeration alone. At week six, over 80% of the microbiome of the four digesters was composed of the three phyla Actinobacteria, Proteobacteria, and Firmicutes, with less than 10% Euryarchaeota and Bacteroidetes. At week 23, the digester microbiomes were more diverse with the phyla Spirochaetes, Synergistetes, and Verrucomicrobia increasing in proportion and the abundance of Actinobacteria decreasing. At week 42, Firmicutes, Bacteroidetes, Euryarchaeota, and Actinobacteria were the most dominant phyla, comprising 27.8%, 21.4%, 17.6%, and 12.3% of the microbiome. Other than the relative proportions of Firmicutes being increased and proportions of Bacteroidetes being decreased by the treatments, no systematic shifts in the microbiomes were observed due to treatment. Rather, microbial diversity was enhanced relative to the control. Given that both air and sound treatment increased biogas production, it is likely that they improved poultry litter breakdown to promote microbial growth. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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26 pages, 4150 KiB

Open AccessArticle

Salinity-Induced Physiochemical Alterations to Enhance Lipid Content in Oleaginous Microalgae Scenedesmus sp. BHU1 via Two-Stage Cultivation for Biodiesel Feedstock

by Rahul Prasad Singh, Priya Yadav, Ajay Kumar, Abeer Hashem, Graciela Dolores Avila-Quezada, Elsayed Fathi Abd_Allah and Rajan Kumar Gupta

Microorganisms 2023, 11(8), 2064; https://doi.org/10.3390/microorganisms11082064 - 11 Aug 2023

Cited by 3 | Viewed by 1130

Abstract

In the recent past, various microalgae have been considered a renewable energy source for biofuel production, and their amount and extent can be enhanced by applying certain types of stress including salinity. Although microalgae growing under salinity stress result in a higher lipid content, they simultaneously reduce in growth and biomass output. To resolve this issue, the physiochemical changes in microalgae Scenedesmus sp. BHU1 have been assessed through two-stage cultivation. In stage-I, the maximum carbohydrate and lipid contents (39.55 and 34.10%) were found at a 0.4 M NaCl concentration, while in stage-II, the maximum carbohydrate and lipid contents (42.16 and 38.10%) were obtained in the 8-day-old culture. However, under increased salinity, Scenedesmus sp. BHU1 exhibited a decrease in photosynthetic attributes, including Chl-a, Chl-b, Fv/Fm, Y(II), Y(NPQ), NPQ, qP, qL, qN, and ETRmax but increased Y(NO) and carotenoids content. Apart from physiological attributes, osmoprotectants, stress biomarkers, and nonenzymatic antioxidants were also studied to elucidate the role of reactive oxygen species (ROS) facilitated lipid synthesis. Furthermore, elemental and mineral ion analysis of microalgal biomass was performed to evaluate the biomass quality for biofuel and cell homeostasis. Based on fluorometry analysis, we found the maximum neutral lipids in the 8-day-old grown culture at stage-II in Scenedesmus sp. BHU1. Furthermore, the use of Fourier-transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectroscopy analyses confirmed the presence of higher levels of hydrocarbons and triacylglycerides (TAGs) composed of saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) in the 8-day-old culture. Therefore, Scenedesmus sp. BHU1 can be a promising microalga for potential biodiesel feedstock. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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8 pages, 1139 KiB

Open AccessCommunication

Storage and Algal Association of Bacteria That Protect Microchloropsis salina from Grazing by Brachionus plicatilis

by Carolyn L. Fisher, Michelle V. Fong, Pamela D. Lane, Skylar Carlson and Todd W. Lane

Microorganisms 2023, 11(3), 786; https://doi.org/10.3390/microorganisms11030786 - 18 Mar 2023

Viewed by 1235

Abstract

Loss of algal production from the crashes of algal mass cultivation systems represents a significant barrier to the economic production of microalgal-based biofuels. Current strategies for crash prevention can be too costly to apply broadly as prophylaxis. Bacteria are ubiquitous in microalgal mass production cultures, however few studies investigate their role and possible significance in this particular environment. Previously, we demonstrated the success of selected protective bacterial communities to save Microchloropsis salina cultures from grazing by the rotifer Brachionus plicatilis. In the current study, these protective bacterial communities were further characterized by fractionation into rotifer-associated, algal-associated, and free-floating bacterial fractions. Small subunit ribosomal RNA amplicon sequencing was used to identify the bacterial genera present in each of the fractions. Here, we show that Marinobacter, Ruegeria, and Boseongicola in algae and rotifer fractions from rotifer-infected cultures likely play key roles in protecting algae from rotifers. Several other identified taxa likely play lesser roles in protective capability. The identification of bacterial community members demonstrating protective qualities will allow for the rational design of microbial communities grown in stable co-cultures with algal production strains in mass cultivation systems. Such a system would reduce the frequency of culture crashes and represent an essentially zero-cost form of algal crop protection. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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10 pages, 2875 KiB

Open AccessCommunication

Multi-Temperatures Pyrolysis Gas Chromatography: A Rapid Method to Differentiate Microorganisms

by Yun Yang Wan, Ying Jia Zhu, Liang Jiang and Na Luo

Microorganisms 2022, 10(12), 2333; https://doi.org/10.3390/microorganisms10122333 - 25 Nov 2022

Cited by 1 | Viewed by 1514

Abstract

The identification of microorganisms using single-temperatures pyrolysis gas chromatography (ST-PyGC) has limitations, for example, the risk of missing characteristic peaks that are essential to the chemotaxonomic interpretation. In this paper, we proposed a new multi-temperature PyGC (MT-PyGC) method as an alternative to ST-PyGC, without sacrificing its speed and quality. Six bacteria (three Gram-positive and three Gram-negative), one micro-fungus and one archaeon, representing microorganisms from different domains, were analyzed by MT-PyGC. It is found that MT pyrograms cover a more complete range of characteristic peaks than ST. Coupling with thermogravimetric analysis, chemotaxonomic information extracted from pyrograms by MT-PyGC have the potential for the differentiation of microorganisms from environments including deep subterranean reservoirs and biomass conversion/biofuel production. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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17 pages, 7283 KiB

Open AccessArticle

Anaerobic Digestion of Chicken Manure in the Presence of Magnetite, Granular Activated Carbon, and Biochar: Operation of Anaerobic Reactors and Microbial Community Structure

by Elvira E. Ziganshina and Ayrat M. Ziganshin

Microorganisms 2022, 10(7), 1422; https://doi.org/10.3390/microorganisms10071422 - 14 Jul 2022

Cited by 10 | Viewed by 1911

Abstract

The influence of magnetite nanoparticles, granular activated carbon (GAC), and biochar, as well as their combinations on the anaerobic digestion of chicken manure and the structure of microbial communities was studied. The addition of magnetite, GAC, and biochar increased the rate of methane production and the total methane yield. It has been observed that these additives stimulated anaerobic microorganisms to reduce the concentration of accumulated volatile organic acids. Various bacterial species within the classes Bacteroidia and Clostridia were found at higher levels in the anaerobic reactors but in different proportions depending on the experiment. Members of the genera Methanosarcina, Methanobacterium, Methanothrix, and Methanoculleus were mainly detected within the archaeal communities in the anaerobic reactors. Compared to the 16S rRNA gene-based study, the mcrA gene approach allowed a higher level of Methanosarcina in the system with GAC + magnetite to be detected. Based on our findings, the combined use of granular activated carbon and magnetite at appropriate dosages will improve biomethane production. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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Review

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11 pages, 616 KiB

Open AccessReview

Thermophilic Fungi as the Microbial Agents of Choice for the Industrial Co-Fermentation of Wood Wastes and Nitrogen-Rich Organic Wastes to Bio-Methane

by John G. Ingersoll

Microorganisms 2023, 11(10), 2600; https://doi.org/10.3390/microorganisms11102600 - 21 Oct 2023

Viewed by 940

Abstract

The novel industrial approach of co-fermenting wood wastes with agricultural wastes that are rich in nitrogen such as animal manures to produce bio-methane (renewable natural gas) fuel via thermophilic anaerobic digestion mimics an analogous process occurring in lower termites, but it relies instead on thermophilic fungi along with other thermophilic microorganisms comprising suitable bacteria and archaea. Wood microbial hydrolysis under thermophilic temperatures (range of 55 °C to 70 °C) and aerobic or micro-aerobic conditions constitutes the first step of the two-step (hydrolysis and fermentation) dry thermophilic anaerobic digestion industrial process, designated as “W2M3+2”, that relies on thermophilic fungi species, most of which grow naturally in wood piles. Eleven thermophilic fungi have been identified as likely agents of the industrial process, and their known growth habitats and conditions have been reviewed. Future research is proposed such that the optimal growth temperature of these thermophilic fungi could be increased to the higher thermophilic range approaching 70 °C, and a tolerance to partial anaerobic conditions can be obtained by modifying the fungal microbiome via a symbiotic existence with bacteria and/or viruses. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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14 pages, 970 KiB

Open AccessReview

Elucidating the Role of Biofilm-Forming Microbial Communities in Fermentative Biohydrogen Process: An Overview

by Patrick T. Sekoai, Viren Chunilall, Bruce Sithole, Olivier Habimana, Sizwe Ndlovu, Obinna T. Ezeokoli, Pooja Sharma and Kelvin O. Yoro

Microorganisms 2022, 10(10), 1924; https://doi.org/10.3390/microorganisms10101924 - 28 Sep 2022

Cited by 3 | Viewed by 1730

Abstract

Amongst the biofuels described in the literature, biohydrogen has gained heightened attention over the past decade due to its remarkable properties. Biohydrogen is a renewable form of H₂ that can be produced under ambient conditions and at a low cost from biomass residues. Innovative approaches are continuously being applied to overcome the low process yields and pave the way for its scalability. Since the process primarily depends on the biohydrogen-producing bacteria, there is a need to acquire in-depth knowledge about the ecology of the various assemblages participating in the process, establishing effective bioaugmentation methods. This work provides an overview of the biofilm-forming communities during H₂ production by mixed cultures and the synergistic associations established by certain species during H₂ production. The strategies that enhance the growth of biofilms within the H₂ reactors are also discussed. A short section is also included, explaining techniques used for examining and studying these biofilm structures. The work concludes with some suggestions that could lead to breakthroughs in this area of research. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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