1
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Jiang C, McIlroy SJ, Qi R, Petriglieri F, Yashiro E, Kondrotaite Z, Nielsen PH. Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge. Water Res 2021; 191:116779. [PMID: 33401166 DOI: 10.1016/j.watres.2020.116779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/06/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.
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Affiliation(s)
- Chenjing Jiang
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark; Key Laboratory of Engineering Oceanography, Second Institute of Oceanography, SOA, Hangzhou, 310012, China
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Rong Qi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 10085, China
| | - Francesca Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Erika Yashiro
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Zivile Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
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2
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Dueholm MS, Andersen KS, McIlroy SJ, Kristensen JM, Yashiro E, Karst SM, Albertsen M, Nielsen PH. Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax). mBio 2020; 11:e01557-20. [PMID: 32963001 PMCID: PMC7512547 DOI: 10.1128/mbio.01557-20] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/18/2020] [Indexed: 02/08/2023] Open
Abstract
High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.
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Affiliation(s)
- Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jannie Munk Kristensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Erika Yashiro
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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3
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Herbst FA, Gonçalves SCL, Behr T, McIlroy SJ, Nielsen PH. Proteogenomic Refinement of the Neomegalonema perideroedes T Genome Annotation. Proteomics 2019; 19:e1800330. [PMID: 30865376 DOI: 10.1002/pmic.201800330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 02/10/2019] [Indexed: 12/14/2022]
Abstract
Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema) which belongs to the Alphaproteobacteria. N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species-being the only sequenced member of its proposed family-the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. Here, a proteomic dataset for the refinement of the N. perideroedes genome annotations is generated which clearly indicates the shortcomings of high-throughput in silico genome annotation.
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Affiliation(s)
- Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Aalborg East, Denmark
| | - Sandra Cristina Lopes Gonçalves
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Aalborg East, Denmark
| | - Tobias Behr
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Aalborg East, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Aalborg East, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Aalborg East, Denmark
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4
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Nierychlo M, Miłobędzka A, Petriglieri F, McIlroy B, Nielsen PH, McIlroy SJ. The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants. FEMS Microbiol Ecol 2018; 95:5199189. [DOI: 10.1093/femsec/fiy228] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/20/2018] [Indexed: 01/07/2023] Open
Affiliation(s)
- Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Aleksandra Miłobędzka
- Microbial Ecology and Environmental Biotechnology Department, Faculty of Biology, Institute of Botany, Biological and Chemical Research Centre, University of Warsaw; Żwirki i Wigury 101, Warsaw 02–089, Poland
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, Warsaw 00–653, Poland
| | - Francesca Petriglieri
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Bianca McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
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5
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Petriglieri F, Nierychlo M, Nielsen PH, McIlroy SJ. In situ visualisation of the abundant Chloroflexi populations in full-scale anaerobic digesters and the fate of immigrating species. PLoS One 2018; 13:e0206255. [PMID: 30383873 PMCID: PMC6211663 DOI: 10.1371/journal.pone.0206255] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/09/2018] [Indexed: 11/18/2022] Open
Abstract
Anaerobic digestion is a key process for the conversion of waste organics to biogas for energy and is reliant on the synergistic activities of complex microbial communities. Members of the phylum Chloroflexi are often found to be abundant in these systems, yet little is known of their role, with most members yet to be cultured or identified. The aim of this study was to characterize the Chloroflexi communities present in full-scale anaerobic digesters receiving excess sludge from wastewater treatment plants. The core genus-level-phylotypes were identified from extensive 16S rRNA gene amplicon sequencing surveys of 19 full-scale systems over a 6 year period. The T78 and Leptolinea, and the RB349 and SJA-170, were found to be the most abundant genera of mesophilic and thermophilic digesters, respectively. With the exception of Leptolinea, these phylotypes are known only by their 16S rRNA gene sequence, and their morphology and metabolic potentials are not known. Fluorescence in situ hybridisation (FISH) probes were designed for these phylotypes, with their application revealing a similar thin filamentous morphology, indicating a possible role for these organisms in maintaining floc structure. The new FISH probes provide a useful tool for future efforts to characterize these organisms in situ. FISH also suggests that immigrating Chloroflexi species die off in the anaerobic digester environment and their high abundance in anaerobic digesters, observed with DNA based sequencing surveys, was quite possibly due to the persistence of their DNA after their death. This observation is important for the interpretation of popular DNA-based sequencing methods applied for the characterisation of communities with substantial immigration rates, such as anaerobic digesters.
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Affiliation(s)
- Francesca Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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6
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Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY, Aslan H, Meyer RL, Albertsen M, Nielsen PH, Dueholm MS. Novel prosthecate bacteria from the candidate phylum Acetothermia. ISME J 2018; 12:2225-2237. [PMID: 29884828 PMCID: PMC6092417 DOI: 10.1038/s41396-018-0187-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 03/20/2018] [Indexed: 02/05/2023]
Abstract
Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an operational taxonomic unit belonging to Acetothermia was detected at high abundance in four full-scale anaerobic digesters by 16S rRNA gene amplicon sequencing. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with long nanopore reads. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtains energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy, and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.
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Affiliation(s)
- Liping Hao
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Hüsnü Aslan
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
| | - Morten Simonsen Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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7
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Jiang C, Qi R, Hao L, McIlroy SJ, Nielsen PH. Monitoring foaming potential in anaerobic digesters. Waste Manag 2018; 75:280-288. [PMID: 29478959 DOI: 10.1016/j.wasman.2018.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Foaming in anaerobic digestion (AD) systems for biogas generation can give serious operational problems. The cause of such foaming events is often unclear, and it is therefore not an easy task to predict and subsequently apply preventative measures. Methods for the measurement of the foaming potential of digester sludge are often implemented, but no standardized method is available. In this study, we investigated parameters influencing the foam formation during experimental aeration tests of full-scale digester sludge, including air flow, time, and total solids concentration, and proposed an optimized method for standard use. In a survey of 16 full-scale AD systems located at wastewater treatment plants in Denmark, all sludge samples were classified into three groups (non-foaming, pre-foaming, and actually foaming) according to their foam height/propensity and stability. Extensive surveillance of plants with the proposed classification system will enable the determination of cut-off values to help to identify foaming or pre-foaming sludge, and to associate these with operational conditions leading to foaming episodes.
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Affiliation(s)
- Chenjing Jiang
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark; Key Laboratory of Engineering Oceanography, Second Institute of Oceanography, SOA, Hangzhou 310012, China
| | - Rong Qi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Liping Hao
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
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8
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McIlroy SJ, Kirkegaard RH, McIlroy B, Nierychlo M, Kristensen JM, Karst SM, Albertsen M, Nielsen PH. MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. Database (Oxford) 2017; 2017:3074787. [PMID: 28365734 PMCID: PMC5467571 DOI: 10.1093/database/bax016] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022]
Abstract
Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL http://www.midasfieldguide.org.
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Affiliation(s)
- Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Bianca McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Jannie Munk Kristensen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
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9
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Kirkegaard RH, Dueholm MS, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. ISME J 2016; 10:2352-64. [PMID: 27058503 PMCID: PMC5030696 DOI: 10.1038/ismej.2016.43] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life.
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Affiliation(s)
- Rasmus Hansen Kirkegaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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10
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McIlroy SJ, Karst SM, Nierychlo M, Dueholm MS, Albertsen M, Kirkegaard RH, Seviour RJ, Nielsen PH. Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. ISME J 2016; 10:2223-34. [PMID: 26905629 DOI: 10.1038/ismej.2016.14] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/17/2015] [Accepted: 01/04/2016] [Indexed: 11/09/2022]
Abstract
Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. Filaments with the Eikelboom 0092 morphotype are commonly associated with such bulking episodes. Members of the uncultured B45 phylotype, which is embraced within the phylum Chloroflexi, were recently shown to exhibit this morphology. Although these organisms are among the most abundant populations recorded in activated sludge processes, nothing is known about their metabolic characteristics. In this study, a genome sequence, representing the B45 phylotype, was retrieved from a metagenome generated from an activated sludge WWTP. The genome consisted of two chromosomes and one plasmid, which were 4.0, 1.0 and 0.04 Mbps in size, respectively. A metabolic model was constructed for this organism, based on annotation of its genome, showing its ability to generate energy by respiration, utilizing oxygen, nitrite or nitrous oxide as electron acceptors, or by fermentation of sugars. The ability of B45 members to ferment sugars under anaerobic conditions was validated in situ with microautoradiography-fluorescence in situ hybridization. The provisional name of 'Candidatus Promineofilum breve' is proposed for this species. This study represents the first detailed information on an uncultured genus of filamentous organisms from activated sludge.
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Affiliation(s)
- Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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11
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McIlroy SJ, Awata T, Nierychlo M, Albertsen M, Kindaichi T, Nielsen PH. Characterization of the In Situ Ecophysiology of Novel Phylotypes in Nutrient Removal Activated Sludge Treatment Plants. PLoS One 2015; 10:e0136424. [PMID: 26340564 PMCID: PMC4560404 DOI: 10.1371/journal.pone.0136424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/03/2015] [Indexed: 02/01/2023] Open
Abstract
An in depth understanding of the ecology of activated sludge nutrient removal wastewater treatment systems requires detailed knowledge of the community composition and metabolic activities of individual members. Recent 16S rRNA gene amplicon surveys of activated sludge wastewater treatment plants with nutrient removal indicate the presence of a core set of bacterial genera. These organisms are likely responsible for the bulk of nutrient transformations underpinning the functions of these plants. While the basic activities of some of these genera in situ are known, there is little to no information for the majority. This study applied microautoradiography coupled with fluorescence in situ hybridization (MAR-FISH) for the in situ characterization of selected genus-level-phylotypes for which limited physiological information is available. These included Sulfuritalea and A21b, both within the class Betaproteobacteria, as well as Kaga01, within sub-group 10 of the phylum Acidobacteria. While the Sulfuritalea spp. were observed to be metabolically versatile, the A21b and Kaga01 phylotypes appeared to be highly specialized.
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Affiliation(s)
- Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Takanori Awata
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464–8603, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1–4–1 Kagamiyama, Higashihiroshima, 739–8527, Japan
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1–4–1 Kagamiyama, Higashihiroshima, 739–8527, Japan
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- * E-mail:
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McIlroy SJ, Saunders AM, Albertsen M, Nierychlo M, McIlroy B, Hansen AA, Karst SM, Nielsen JL, Nielsen PH. MiDAS: the field guide to the microbes of activated sludge. Database (Oxford) 2015; 2015:bav062. [PMID: 26120139 PMCID: PMC4483311 DOI: 10.1093/database/bav062] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/27/2015] [Indexed: 01/10/2023]
Abstract
The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes—knowledge that will be an invaluable resource for the optimal design and operation of these systems. Database URL:http://www.midasfieldguide.org
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Affiliation(s)
- Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Aaron Marc Saunders
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Bianca McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Aviaja Anna Hansen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg East DK-9220, Denmark
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McIlroy SJ, Starnawska A, Starnawski P, Saunders AM, Nierychlo M, Nielsen PH, Nielsen JL. Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems. Environ Microbiol 2014; 18:50-64. [DOI: 10.1111/1462-2920.12614] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Jon McIlroy
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Anna Starnawska
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Piotr Starnawski
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Aaron Marc Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Marta Nierychlo
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Jeppe Lund Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
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McIlroy SJ, Kristiansen R, Albertsen M, Karst SM, Rossetti S, Nielsen JL, Tandoi V, Seviour RJ, Nielsen PH. Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. ISME J 2013; 7:1161-72. [PMID: 23446830 DOI: 10.1038/ismej.2013.6] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
'Candidatus Microthrix parvicella' is a lipid-accumulating, filamentous bacterium so far found only in activated sludge wastewater treatment plants, where it is a common causative agent of sludge separation problems. Despite attracting considerable interest, its detailed physiology is still unclear. In this study, the genome of the RN1 strain was sequenced and annotated, which facilitated the construction of a theoretical metabolic model based on available in situ and axenic experimental data. This model proposes that under anaerobic conditions, this organism accumulates preferentially long-chain fatty acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment plants with enhanced biological phosphorus removal reveals high similarity, with few metabolic differences between the axenic and the dominant community 'Ca. M. parvicella' strains. Hence, the metabolic model presented in this paper could be considered generally applicable to strains in full-scale treatment systems. The genomic information obtained here will provide the basis for future research into in situ gene expression and regulation. Such information will give substantial insight into the ecophysiology of this unusual and biotechnologically important filamentous bacterium.
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Affiliation(s)
- Simon Jon McIlroy
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
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Kristiansen R, Nguyen HTT, Saunders AM, Nielsen JL, Wimmer R, Le VQ, McIlroy SJ, Petrovski S, Seviour RJ, Calteau A, Nielsen KL, Nielsen PH. A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal. ISME J 2012. [PMID: 23178666 DOI: 10.1038/ismej.2012.136] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Members of the genus Tetrasphaera are considered to be putative polyphosphate accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) from wastewater. Although abundant in Danish full-scale wastewater EBPR plants, how similar their ecophysiology is to 'Candidatus Accumulibacter phosphatis' is unclear, although they may occupy different ecological niches in EBPR communities. The genomes of four Tetrasphaera isolates (T. australiensis, T. japonica, T. elongata and T. jenkinsii) were sequenced and annotated, and the data used to construct metabolic models. These models incorporate central aspects of carbon and phosphorus metabolism critical to understanding their behavior under the alternating anaerobic/aerobic conditions encountered in EBPR systems. Key features of these metabolic pathways were investigated in pure cultures, although poor growth limited their analyses to T. japonica and T. elongata. Based on the models, we propose that under anaerobic conditions the Tetrasphaera-related PAOs take up glucose and ferment this to succinate and other components. They also synthesize glycogen as a storage polymer, using energy generated from the degradation of stored polyphosphate and substrate fermentation. During the aerobic phase, the stored glycogen is catabolized to provide energy for growth and to replenish the intracellular polyphosphate reserves needed for subsequent anaerobic metabolism. They are also able to denitrify. This physiology is markedly different to that displayed by 'Candidatus Accumulibacter phosphatis', and reveals Tetrasphaera populations to be unusual and physiologically versatile PAOs carrying out denitrification, fermentation and polyphosphate accumulation.
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Affiliation(s)
- Rikke Kristiansen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
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