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Imachi H, Nobu MK, Miyazaki M, Tasumi E, Saito Y, Sakai S, Ogawara M, Ohashi A, Takai K. Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study. Nat Protoc 2022; 17:2784-2814. [DOI: 10.1038/s41596-022-00735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
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Abstract
The phylum "Candidatus Omnitrophica" (candidate division OP3) is ubiquitous in anaerobic habitats but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiotic cells. In this study, we enriched OP3 cells by double density gradient centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population by applying metagenomics and PCR for gap closure. Filaments of acetoclastic Methanosaeta, the largest morphotype in the culture community, contained empty cells, cells devoid of rRNA or of both rRNA and DNA, and dead cells according to transmission electron microscopy (TEM), thin-section TEM, scanning electron microscopy (SEM), catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), and LIVE/DEAD imaging. OP3 LiM cells were ultramicrobacteria (200 to 300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals of OP3 LiM cells attached to Bacteria and to Archaea indicated many rRNA molecules and an active metabolism, whereas free-living OP3 cells had weak signals. Metaproteomics revealed that OP3 LiM lives with highly expressed secreted proteins involved in depolymerization and uptake of macromolecules and an active glycolysis and energy conservation by the utilization of pyruvate via a pyruvate:ferredoxin oxidoreductase and an Rnf complex (ferredoxin:NAD oxidoreductase). Besides sugar fermentation, a nucleotidyl transferase may contribute to energy conservation by phosphorolysis, the phosphate-dependent depolymerization of nucleic acids. Thin-section TEM showed distinctive structures of predation. Our study demonstrated a predatory metabolism for OP3 LiM cells, and therefore, we propose the name "Candidatus Velamenicoccus archaeovorus" gen. nov., sp. nov., for OP3 LiM. IMPORTANCE Epibiotic bacteria are known to live on and off bacterial cells. Here, we describe the ultramicrobacterial anaerobic epibiont OP3 LiM living on Archaea and Bacteria. We detected sick and dead cells of the filamentous archaeon Methanosaeta in slowly growing methanogenic cultures. OP3 LiM lives as a sugar fermenter, likely on polysaccharides from outer membranes, and has the genomic potential to live as a syntroph. The predatory lifestyle of OP3 LiM was supported by its genome, the first closed genome for the phylum "Candidatus Omnitrophica," and by images of cell-to-cell contact with prey cells. We propose naming OP3 LiM "Candidatus Velamenicoccus archaeovorus." Its metabolic versatility explains the ubiquitous presence of "Candidatus Omnitrophica" 3 in anoxic habitats and gives ultramicrobacterial epibionts an important role in the recycling and remineralization of microbial biomass. The removal of polysaccharides from outer membranes by ultramicrobacteria may also influence biological interactions between pro- and eukaryotes.
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Harirchi S, Wainaina S, Sar T, Nojoumi SA, Parchami M, Parchami M, Varjani S, Khanal SK, Wong J, Awasthi MK, Taherzadeh MJ. Microbiological insights into anaerobic digestion for biogas, hydrogen or volatile fatty acids (VFAs): a review. Bioengineered 2022; 13:6521-6557. [PMID: 35212604 PMCID: PMC8973982 DOI: 10.1080/21655979.2022.2035986] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 11/02/2022] Open
Abstract
In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches for the deep and adequate understanding and manipulating it toward different products is process microbiology. Due to highly complexity of AD microbiome, it is critically important to study the involved microorganisms in AD. In recent years, in addition to traditional methods, novel molecular techniques and meta-omics approaches have been developed which provide accurate details about microbial communities involved AD. Better understanding of process microbiomes could guide us in identifying and controlling various factors in both improving the AD process and diverting metabolic pathway toward production of selective bio-products. This review covers various platforms of AD process that results in different final products from microbiological point of view. The review also highlights distinctive interactions occurring among microbial communities. Furthermore, assessment of these communities existing in the anaerobic digesters is discussed to provide more insights into their structure, dynamics, and metabolic pathways. Moreover, the important factors affecting microbial communities in each platform of AD are highlighted. Finally, the review provides some recent applications of AD for the production of novel bio-products and deals with challenges and future perspectives of AD.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190Borås, Sweden
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, 50190Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190Borås, Sweden
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Milad Parchami
- Swedish Centre for Resource Recovery, University of Borås, 50190Borås, Sweden
| | - Mohsen Parchami
- Swedish Centre for Resource Recovery, University of Borås, 50190Borås, Sweden
| | - Sunita Varjani
- Paryavaran Bhavan, Gujarat Pollution Control Board, Gandhinagar, Gujarat, India
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Jonathan Wong
- Department of Biology, Institute of Bioresource and Agriculture and, Hong Kong Baptist University, Hong Kong
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 712100, China
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Willenbücher K, Wibberg D, Huang L, Conrady M, Ramm P, Gätcke J, Busche T, Brandt C, Szewzyk U, Schlüter A, Barrero Canosa J, Maus I. Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing. Microorganisms 2022; 10:368. [PMID: 35208823 PMCID: PMC8879888 DOI: 10.3390/microorganisms10020368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.
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Affiliation(s)
- Katharina Willenbücher
- System Microbiology, Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany;
- Environmental Microbiology, Faculty of Process Sciences, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany; (U.S.); (J.B.C.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Marius Conrady
- Institute of Agricultural and Urban Ecological Projects, Berlin Humboldt University (IASP), Philippstr. 13, 10115 Berlin, Germany; (M.C.); (P.R.)
| | - Patrice Ramm
- Institute of Agricultural and Urban Ecological Projects, Berlin Humboldt University (IASP), Philippstr. 13, 10115 Berlin, Germany; (M.C.); (P.R.)
| | - Julia Gätcke
- Biophysics of Photosynthesis, Institute for Biology, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115 Berlin, Germany;
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
| | - Christian Brandt
- Institute for Infection Medicine and Hospital Hygiene, University Hospital Jena, Kastanienstraße 1, 07747 Jena, Germany;
| | - Ulrich Szewzyk
- Environmental Microbiology, Faculty of Process Sciences, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany; (U.S.); (J.B.C.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
| | - Jimena Barrero Canosa
- Environmental Microbiology, Faculty of Process Sciences, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany; (U.S.); (J.B.C.)
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (A.S.)
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Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. Viruses 2021; 13:v13101934. [PMID: 34696364 PMCID: PMC8540584 DOI: 10.3390/v13101934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 01/05/2023] Open
Abstract
Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.
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Hyman P, Trubl G, Abedon ST. Virus-Like Particle: Evolving Meanings in Different Disciplines. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:11-15. [PMID: 36148434 PMCID: PMC9041479 DOI: 10.1089/phage.2020.0026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Virus-like particle (VLP) is a term that has been in use for about 80 years. Usually, VLP has meant a particle that is like a virus, generally by appearance, but without either proven or actual virus functionality. Initially VLP referred to particles seen in electron microscope images of tissues. More recently, VLP has come to mean other things to other researchers. A key divergence has been use of VLP in association with vaccine and biotechnology applications versus use of VLP in enumeration of viruses in environmental samples. To these viral ecologists, a VLP is a particle that is virus sized, has nucleic acid, and could be a functional virus. But to vaccine developers and biotechnology researchers a VLP instead is a viral structure that intentionally lacks a viral genome. In this study, we look at the history of use of VLP, following changes in meaning as the technology to study VLPs changed.
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Affiliation(s)
- Paul Hyman
- Department of Biology and Toxicology, Ashland University, Ashland, Ohio, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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7
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Viruses in Extreme Environments, Current Overview, and Biotechnological Potential. Viruses 2021; 13:v13010081. [PMID: 33430116 PMCID: PMC7826561 DOI: 10.3390/v13010081] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/27/2022] Open
Abstract
Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.
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Sekoai PT, Engelbrecht N, du Preez SP, Bessarabov D. Thermophilic Biogas Upgrading via ex Situ Addition of H 2 and CO 2 Using Codigested Feedstocks of Cow Manure and the Organic Fraction of Solid Municipal Waste. ACS OMEGA 2020; 5:17367-17376. [PMID: 32715221 PMCID: PMC7377068 DOI: 10.1021/acsomega.0c01725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Bioconversion of renewable H2 and waste CO2 using methanogenic archaea is a promising technology for obtaining high-purity CH4, which can serve as an alternative for natural gas. This process is known as ex situ biogas upgrading. This work highlights the pathway toward the bioconversion of renewable H2 and CO2 into high-purity biomethane by exploiting highly accessible agro-municipal residues: cow manure (CM) and the organic fraction of solid municipal waste (OFSMW), which used to be called "waste materials". More specifically, an ex situ thermophilic (55 °C) biogas upgrading process was conducted by CM and OFSMW codigestion at different mass proportions: 100:0, 80:20, 70:30, 60:40, and 50:50. Maximum CH4 concentrations of 92-97 vol % and biogas volumetric production rates of 4954-6605 NmL/L.d were obtained from a batch reactor of 3 L working volume. Feedstock characterization, pH monitoring, and the carbon-to-nitrogen ratio were critical parameters to evaluate during biogas upgrading experiments. In this work, the usefulness of agro-municipal substrates is highlighted by producing high-purity biomethane-an energetic chemical to facilitate renewable energy conversion, which supports various end-use applications. This process therefore provides a solution to renewable energy storage challenges and future sustainable and green energy supply.
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9
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Altermann E, Schofield LR, Ronimus RS, Beatty AK, Reilly K. Inhibition of Rumen Methanogens by a Novel Archaeal Lytic Enzyme Displayed on Tailored Bionanoparticles. Front Microbiol 2018; 9:2378. [PMID: 30356700 PMCID: PMC6189367 DOI: 10.3389/fmicb.2018.02378] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Methane is a potent greenhouse gas, 25 times more efficient at trapping heat than carbon dioxide. Ruminant methane emissions contribute almost 30% to anthropogenic sources of global atmospheric methane levels and a reduction in methane emissions would significantly contribute to slowing global temperature rises. Here we demonstrate the use of a lytic enyzme, PeiR, from a methanogen virus that infects Methanobrevibacter ruminantium M1 as an effective agent inhibiting a range of rumen methanogen strains in pure culture. We determined the substrate specificity of soluble PeiR and demonstrated that the enzyme is capable of hydrolysing the pseudomurein cell walls of methanogens. Subsequently, peiR was fused to the polyhydroxyalkanoate (PHA) synthase gene phaC and displayed on the surface of PHA bionanoparticles (BNPs) expressed in Eschericia coli via one-step biosynthesis. These tailored BNPs were capable of lysing not only the original methanogen host strain, but a wide range of other rumen methanogen strains in vitro. Methane production was reduced by up to 97% for 5 days post-inoculation in the in vitro assay. We propose that tailored BNPs carrying anti-methanogen enzymes represent a new class of methane inhibitors. Tailored BNPs can be rapidly developed and may be able to modulate the methanogen community in vivo with the aim to lower ruminant methane emissions without impacting animal productivity.
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Affiliation(s)
- Eric Altermann
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Linley R Schofield
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand
| | - Ron S Ronimus
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand
| | - Amy K Beatty
- Soil Biology, Forage Science, AgResearch Ltd., Christchurch, New Zealand
| | - Kerri Reilly
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand
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10
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Methanosarcina Spherical Virus, a Novel Archaeal Lytic Virus Targeting Methanosarcina Strains. J Virol 2017; 91:JVI.00955-17. [PMID: 28878086 DOI: 10.1128/jvi.00955-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022] Open
Abstract
A novel archaeal lytic virus targeting species of the genus Methanosarcina was isolated using Methanosarcina mazei strain Gö1 as the host. Due to its spherical morphology, the virus was designated Methanosarcina spherical virus (MetSV). Molecular analysis demonstrated that MetSV contains double-stranded linear DNA with a genome size of 10,567 bp containing 22 open reading frames (ORFs), all oriented in the same direction. Functions were predicted for some of these ORFs, i.e., such as DNA polymerase, ATPase, and DNA-binding protein as well as envelope (structural) protein. MetSV-derived spacers in CRISPR loci were detected in several published Methanosarcina draft genomes using bioinformatic tools, revealing a potential protospacer-adjacent motif (PAM) motif (TTA/T). Transcription and expression of several predicted viral ORFs were validated by reverse transcription-PCR (RT-PCR), PAGE analysis, and liquid chromatography-mass spectrometry (LC-MS)-based proteomics. Analysis of core lipids by atmospheric pressure chemical ionization (APCI) mass spectrometry showed that MetSV and Methanosarcina mazei both contain archaeol and glycerol dialkyl glycerol tetraether without a cyclopentane moiety (GDGT-0). The MetSV host range is limited to Methanosarcina strains growing as single cells (M. mazei, Methanosarcina barkeri and Methanosarcina soligelidi). In contrast, strains growing as sarcina-like aggregates were apparently protected from infection. Heterogeneity related to morphology phases in M. mazei cultures allowed acquisition of resistance to MetSV after challenge by growing cultures as sarcina-like aggregates. CRISPR/Cas-mediated resistance was excluded since neither of the two CRISPR arrays showed MetSV-derived spacer acquisition. Based on these findings, we propose that changing the morphology from single cells to sarcina-like aggregates upon rearrangement of the envelope structure prevents infection and subsequent lysis by MetSV.IMPORTANCE Methanoarchaea are among the most abundant organisms on the planet since they are present in high numbers in major anaerobic environments. They convert various carbon sources, e.g., acetate, methylamines, or methanol, to methane and carbon dioxide; thus, they have a significant impact on the emission of major greenhouse gases. Today, very little is known about viruses specifically infecting methanoarchaea that most probably impact the abundance of methanoarchaea in microbial consortia. Here, we characterize the first identified Methanosarcina-infecting virus (MetSV) and show a mechanism for acquiring resistance against MetSV. Based on our results, we propose that growth as sarcina-like aggregates prevents infection and subsequent lysis. These findings allow new insights into the virus-host relationship in methanogenic community structures, their dynamics, and their phase heterogeneity. Moreover, the availability of a specific virus provides new possibilities to deepen our knowledge of the defense mechanisms of potential hosts and offers tools for genetic manipulation.
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Delforno TP, Lacerda Júnior GV, Noronha MF, Sakamoto IK, Varesche MBA, Oliveira VM. Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing. Microbiologyopen 2017; 6. [PMID: 28229558 PMCID: PMC5458456 DOI: 10.1002/mbo3.443] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin).
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Affiliation(s)
- Tiago Palladino Delforno
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda Júnior
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, São Paulo, Brazil
| | - Melline F Noronha
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, São Paulo, Brazil
| | - Isabel K Sakamoto
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos - University of São Paulo (EESC - USP) Campus II, São Carlos, São Paulo, Brazil
| | - Maria Bernadete A Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos - University of São Paulo (EESC - USP) Campus II, São Carlos, São Paulo, Brazil
| | - Valéria M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, São Paulo, Brazil
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12
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Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environ Microbiol 2016; 18:1162-75. [PMID: 26568175 PMCID: PMC7163765 DOI: 10.1111/1462-2920.13127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro‐food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant‐infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.
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Affiliation(s)
- Magdalena Calusinska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Martyna Marynowska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, ul. Kladki 24, 80-822, Gdansk, Poland
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Esther Lentzen
- Luxembourg Institute of Science and Technology, Materials Research and Technology (MRT), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
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13
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Müller B, Manzoor S, Niazi A, Bongcam-Rudloff E, Schnürer A. Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation. PLoS One 2015; 10:e0121237. [PMID: 25811859 PMCID: PMC4374699 DOI: 10.1371/journal.pone.0121237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/30/2015] [Indexed: 11/21/2022] Open
Abstract
This paper describes the genome-based analysis of Tepidanaerobacter acetatoxydans strain Re1, a syntrophic acetate-oxidising bacterium (SAOB). Principal issues such as environmental adaptations, metabolic capacities, and energy conserving systems have been investigated and the potential consequences for syntrophic acetate oxidation discussed. Briefly, in pure culture, T. acetatoxydans grows with different organic compounds and produces acetate as the main product. In a syntrophic consortium with a hydrogenotrophic methanogen, it can also reverse its metabolism and instead convert acetate to formate/H2 and CO2. It can only proceed if the product formed is continuously removed. This process generates a very small amount of energy that is scarcely enough for growth, which makes this particular syntrophy of special interest. As a crucial member of the biogas-producing community in ammonium-rich engineered AD processes, genomic features conferring ammonium resistance, bacterial defense, oxygen and temperature tolerance were found, as well as attributes related to biofilm formation and flocculation. It is likely that T. acetatoxydans can form an electrochemical gradient by putative electron-bifurcating Rnf complex and [Fe-Fe] hydrogenases, as observed in other acetogens. However, genomic deficiencies related to acetogenic metabolism and anaerobic respiration were discovered, such as the lack of formate dehydrogenase and F1F0 ATP synthase. This has potential consequences for the metabolic pathways used under SAO and non-SAO conditions. The two complete sets of bacteriophage genomes, which were found to be encoded in the genome, are also worthy of mention.
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Affiliation(s)
- Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, Sweden
- * E-mail:
| | - Shahid Manzoor
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
- University of the Punjab, Lahore, Pakistan
| | - Adnan Niazi
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, Sweden
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