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Microorganisms
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Metabolic Diversity of Anaerobic Microbial Communities
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Metabolic Diversity of Anaerobic Microbial Communities

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

Deadline for manuscript submissions: closed (20 October 2018) | Viewed by 35557

Special Issue Editor

Dr. Sabine Kleinsteuber

E-Mail Website
Guest Editor
Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
Interests: environmental microbiology; microbial ecology; biotechnology; anaerobic microbes; microbial communities; molecular methods; anaerobic digestion; fermentation pathways; metagenomics; biodegradation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Anaerobic microorganisms, among them the oldest life-forms on Earth, display the most manifold metabolic pathways and lifestyles, which have been ever invented by evolution, such as various mechanisms for energy conservation, carbon fixation, elemental cycling, fermentative conversion of organic matter and syntrophic interactions, enabling life on the thermodynamic edge. Anaerobic microbial communities play essential roles in biogeochemical cycles, natural attenuation of contaminated sites and various biotechnological processes, such as wastewater treatment, anaerobic digestion of organic waste and fermentative formation of valuable products. Interest in the ecology of anaerobic environments has grown due to the recent development of advanced techniques to explore so far not cultivated microbes and candidate phyla, such as single cell genomics and advanced bioinformatics for the reconstruction of population genomes from complex metagenomes. In this Special Issue of Microorganisms, we invite you to submit contributions concerning any aspects related to anaerobic microbes and their metabolic functions, from the microbial ecology of diverse anoxic habitats to the physiology of novel isolates and candidate species, and from fundamental to applied aspects of anaerobic microorganisms in natural and engineered environments.

Dr. Sabine Kleinsteuber
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.

Keywords

  • anaerobic microbes
  • anaerobic environments
  • anaerobic bioreactors
  • anaerobic digestion
  • anaerobic conversions
  • anaerobic biodegradation
  • (meta)genomics of anaerobes
  • syntrophy
  • energy conservation in anaerobes
  • metabolic pathways in anaerobes

Published Papers (7 papers)

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Research

13 pages, 1420 KiB  
Article
Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds
by Luka Šafarič, Sepehr Shakeri Yekta, Tong Liu, Bo H. Svensson, Anna Schnürer, David Bastviken and Annika Björn
Microorganisms 2018, 6(4), 105; https://doi.org/10.3390/microorganisms6040105 - 11 Oct 2018
Cited by 10 | Viewed by 3825
Abstract
Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a [...] Read more.
Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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18 pages, 1884 KiB  
Article
Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities
by Susanne Günther, Daniela Becker, Thomas Hübschmann, Susann Reinert, Sabine Kleinsteuber, Susann Müller and Christian Wilhelm
Microorganisms 2018, 6(4), 103; https://doi.org/10.3390/microorganisms6040103 - 04 Oct 2018
Cited by 11 | Viewed by 4098
Abstract
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived [...] Read more.
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived from engineered algae. The microbial community structure was measured on the single cell level using flow cytometry. Abiotic and operational reactor parameters were analyzed in parallel. The R-based tool flowCyBar facilitated visualization of community dynamics and indicated sub-communities involved in glycolate fermentation and methanogenesis. Cell sorting and amplicon sequencing of 16S rRNA and mcrA genes were used to identify the key organisms involved in the anaerobic conversion process. The microbial community allowed a constant fermentation, although it was sensitive to high glycolate concentrations in the feed. A linear correlation between glycolate loading rate and biogas amount was observed (R2 = 0.99) for glycolate loading rates up to 1.81 g L−1 day−1 with a maximum in biogas amount of 3635 mL day−1 encompassing 45% methane. The cytometric diversity remained high during the whole cultivation period. The dominating bacterial genera were Syntrophobotulus, Clostridia genus B55_F, Aminobacterium, and Petrimonas. Methanogenesis was almost exclusively performed by the hydrogenotrophic genus Methanobacterium. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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19 pages, 3021 KiB  
Article
Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source
by Tong Liu, Li Sun, Åke Nordberg and Anna Schnürer
Microorganisms 2018, 6(3), 80; https://doi.org/10.3390/microorganisms6030080 - 05 Aug 2018
Cited by 22 | Viewed by 4257
Abstract
This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started [...] Read more.
This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started with two different inocula were used. These reactors initially showed great differences depending on inoculum source, but eventually showed similar performance and overall microbial community structure. At the start of the present experiment, the substrate was complemented with milled feed wheat, added all at once or divided into two portions. The starting hypothesis was that process performance depends on initial inoculum source and microbial diversity, and thus that reactor performance is influenced by the feeding regime. In response to the substrate change, all reactors showed increases and decreases in volumetric and specific methane production, respectively. However, specific methane yield and development of the microbial community showed differences related to the initial inoculum source, confirming the hypothesis. However, the different feeding regimes had only minor effects on process performance and overall community structure, but still induced differences in the cellulose-degrading community and in cellulose degradation. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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17 pages, 1861 KiB  
Article
Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture
by Courtney R. A. Toth, Carolina Berdugo-Clavijo, Corynne M. O’Farrell, Gareth M. Jones, Andriy Sheremet, Peter F. Dunfield and Lisa M. Gieg
Microorganisms 2018, 6(3), 65; https://doi.org/10.3390/microorganisms6030065 - 10 Jul 2018
Cited by 18 | Viewed by 5101
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due [...] Read more.
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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12 pages, 3008 KiB  
Article
Sulfate-Reducing Naphthalene Degraders Are Picky Eaters
by Sarah J. Wolfson, Abigail W. Porter, Lee J. Kerkhof, Lora M. McGuinness, Roger C. Prince and Lily Y. Young
Microorganisms 2018, 6(3), 59; https://doi.org/10.3390/microorganisms6030059 - 25 Jun 2018
Cited by 4 | Viewed by 3524
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common organic contaminants found in anoxic environments. The capacity for PAH biodegradation in unimpacted environments, however, has been understudied. Here we investigate the enrichment, selection, and sustainability of a microbial community from a pristine environment on naphthalene as [...] Read more.
Polycyclic aromatic hydrocarbons (PAHs) are common organic contaminants found in anoxic environments. The capacity for PAH biodegradation in unimpacted environments, however, has been understudied. Here we investigate the enrichment, selection, and sustainability of a microbial community from a pristine environment on naphthalene as the only amended carbon source. Pristine coastal sediments were obtained from the Jacques Cousteau National Estuarine Research Reserve in Tuckerton, New Jersey, an ecological reserve which has no direct input or source of hydrocarbons. After an initial exposure to naphthalene, primary anaerobic transfer cultures completely degraded 500 µM naphthalene within 139 days. Subsequent transfer cultures mineralized naphthalene within 21 days with stoichiometric sulfate loss. Enriched cultures efficiently utilized only naphthalene and 2-methylnaphthalene from the hydrocarbon mixtures in crude oil. To determine the microorganisms responsible for naphthalene degradation, stable isotope probing was utilized on cultures amended with fully labeled 13C-naphthalene as substrate. Three organisms were found to unambiguously synthesize 13C-DNA from 13C-naphthalene within 7 days. Phylogenetic analysis revealed that 16S rRNA genes from two of these organisms are closely related to the known naphthalene degrading isolates NaphS2 and NaphS3 from PAH-contaminated sites. A third 16S rRNA gene was only distantly related to its closest relative and may represent a novel naphthalene degrading microbe from this environment. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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13 pages, 950 KiB  
Article
Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows
by Lee James Opdahl, Michael G. Gonda and Benoit St-Pierre
Microorganisms 2018, 6(1), 17; https://doi.org/10.3390/microorganisms6010017 - 24 Feb 2018
Cited by 47 | Viewed by 6442
Abstract
The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate [...] Read more.
The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6–50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcus flavefaciens and Fibrobacter succinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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10 pages, 1907 KiB  
Communication
Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters
by Emine Gozde Ozbayram, Orhan Ince, Bahar Ince, Hauke Harms and Sabine Kleinsteuber
Microorganisms 2018, 6(1), 15; https://doi.org/10.3390/microorganisms6010015 - 14 Feb 2018
Cited by 67 | Viewed by 7438
Abstract
Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do [...] Read more.
Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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