Microbial Communities in Anaerobic Digesters

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 4882

Special Issue Editor

Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
Interests: aquatic microbiology; microbial ecology; biofilms; biofouling; anaerobic digestion; oral microbiology

Special Issue Information

Dear Colleagues,

Anaerobic digestion is a method for the breakdown of organic compounds by an interconnected microbial community into a renewable energy source, biogas, containing methane. The anaerobic digester is a human-made ecosystem that carries out the treatment of organic wastes at lower energy requirements and generates lower amounts of biomass than aerobic digestion. One of the concerns about anaerobic digestion technology is the stability of the process.

Like natural ecosystems, the anaerobic digester faces perturbations and disturbances that affect the quality and quantity of resources as well as change the environmental conditions. These changes affect the microbial community abundance, diversity, and activity. However, the species and functional diversity of the community also help to determine how resistant and resilient the digester is to a disturbance. Thus, understanding the complex nature of the microbial community in anaerobic digesters is important to maintaining digester stability. The cutting-edge tools of metagenomics, transcriptomics, proteomics, and metabolomics can be used to elucidate the interactions involved and provide the basis for future research.

This Special Issue is seeking contributions including comprehensive reviews and experimental research about the microbial communities from all varieties of anaerobic digesters. The journal and I hope to hear from you soon.

Prof. Dr. James Maki
Guest Editor

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Keywords

  • Anaerobic Digestion
  • Microbial Communities
  • Hydrolysis
  • Acidogenesis
  • Syntrophic Acetogenesis
  • Methanogenesiss

Published Papers (2 papers)

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Research

20 pages, 3387 KiB  
Article
Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources
by Daniela Becker, Denny Popp, Fabian Bonk, Sabine Kleinsteuber, Hauke Harms and Florian Centler
Microorganisms 2023, 11(2), 420; https://doi.org/10.3390/microorganisms11020420 - 07 Feb 2023
Cited by 4 | Viewed by 1737
Abstract
Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To [...] Read more.
Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species—15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes. Full article
(This article belongs to the Special Issue Microbial Communities in Anaerobic Digesters)
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15 pages, 4372 KiB  
Article
Microbial Community Successional Changes in a Full-Scale Mesophilic Anaerobic Digester from the Start-Up to the Steady-State Conditions
by Barbara Tonanzi, Simona Crognale, Andrea Gianico, Stefano Della Sala, Paola Miana, Maria Chiara Zaccone and Simona Rossetti
Microorganisms 2021, 9(12), 2581; https://doi.org/10.3390/microorganisms9122581 - 13 Dec 2021
Cited by 11 | Viewed by 2289
Abstract
Anaerobic digestion is a widely used technology for sewage sludge stabilization and biogas production. Although the structure and composition of the microbial communities responsible for the process in full-scale anaerobic digesters have been investigated, little is known about the microbial successional dynamics during [...] Read more.
Anaerobic digestion is a widely used technology for sewage sludge stabilization and biogas production. Although the structure and composition of the microbial communities responsible for the process in full-scale anaerobic digesters have been investigated, little is known about the microbial successional dynamics during the start-up phase and the response to variations occurring in such systems under real operating conditions. In this study, bacterial and archaeal population dynamics of a full-scale mesophilic digester treating activated sludge were investigated for the first time from the start-up, performed without adding external inoculum, to steady-state operation. High-throughput 16S rRNA gene sequencing was used to describe the microbiome evolution. The large majority of the reads were affiliated to fermentative bacteria. Bacteroidetes increased over time, reaching 22% of the total sequences. Furthermore, Methanosaeta represented the most abundant methanogenic component. The specific quantitative data generated by real-time PCR indicated an enrichment of bacteria and methanogens once the steady state was reached. The analysis allowed evaluation of the microbial components more susceptible to the shift from aerobic to anaerobic conditions and estimation of the microbial components growing or declining in the system. Additionally, activated sludge was investigated to evaluate the microbial core selected by the WWTP operative conditions. Full article
(This article belongs to the Special Issue Microbial Communities in Anaerobic Digesters)
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