1
|
Ruiz-Haddad L, Ali M, Pronk M, van Loosdrecht MC, Saikaly PE. Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100387. [PMID: 38322240 PMCID: PMC10845257 DOI: 10.1016/j.ese.2024.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 02/08/2024]
Abstract
Currently, the most cost-effective and efficient method for phosphorus (P) removal from wastewater is enhanced biological P removal (EPBR) via polyphosphate-accumulating organisms (PAOs). This study integrates a literature review with genomic analysis to uncover the phylogenetic and metabolic diversity of the relevant PAOs for wastewater treatment. The findings highlight significant differences in the metabolic capabilities of PAOs relevant to wastewater treatment. Notably, Candidatus Dechloromonas and Candidatus Accumulibacter can synthesize polyhydroxyalkanoates, possess specific enzymes for ATP production from polyphosphate, and have electrochemical transporters for acetate and C4-dicarboxylates. In contrast, Tetrasphaera, Candidatus Phosphoribacter, Knoellia, and Phycicoccus possess PolyP-glucokinase and electrochemical transporters for sugars/amino acids. Additionally, this review explores various detection methods for polyphosphate and PAOs in activated sludge wastewater treatment plants. Notably, FISH-Raman spectroscopy emerges as one of the most advanced detection techniques. Overall, this review provides critical insights into PAO research, underscoring the need for enhanced strategies in biological phosphorus removal.
Collapse
Affiliation(s)
- Lucia Ruiz-Haddad
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Ali
- Department of Civil, Structural & Environmental Engineering, Trinity College Dublin, The University of Dublin, Dublin, 2, Ireland
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Delft, 2629 HZ, the Netherlands
| | | | - Pascal E. Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| |
Collapse
|
2
|
Lee H, Chaudhary DK, Kim DU. Enterovirga aerilata sp. nov. and Knoellia koreensis sp. nov., isolated from an automobile air conditioning system. Int J Syst Evol Microbiol 2024; 74. [PMID: 38743058 DOI: 10.1099/ijsem.0.006383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Two strictly aerobic and rod-shaped bacteria, labelled as DB1703T and DB2414ST, were obtained from an automobile air conditioning system. Strain DB1703T was Gram-stain-negative, while strain DB2414ST was Gram-stain-positive. Both strains were catalase-positive and oxidase-negative. Strains DB1703T and DB2414ST were able to grow at 18-42 °C. Strain DB1703T grew within a NaCl range of 0-3 % and a pH range of 6.0-8.0; while strain DB2414ST grew at 0-1 % and pH 6.5-8.5. The phylogenetic and 16S rRNA gene sequence analysis indicated that strains DB1703T and DB2414ST belonged to the genera Enterovirga and Knoellia, respectively. Strain DB1703T showed the closest phylogenetic similarity to Enterovirga rhinocerotis YIM 100770T (94.8 %), whereas strain DB2414ST was most closely related to Knoellia remsis ATCC BAA-1496T (97.7 %). The genome sizes of strains DB1703T and DB2414ST were 4 652 148 and 4 282 418 bp, respectively, with DNA G+C contents of 68.8 and 70.5 mol%, respectively. Chemotaxonomic data showed Q-10 as the sole ubiquinone in DB1703T and ML-8 (H4) in DB2414ST. The predominant cellular fatty acid in DB1703T was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), whereas iso-C16 : 0, C17 : 1 ω8c, and iso-C15 : 0 were dominant in DB2414ST. Overall, the polyphasic taxonomic comparisons showed that strains DB1703T and DB2414ST were distinct from their closest taxa and represent novel species within the genera Enterovirga and Knoellia, respectively. Accordingly, we propose the names Enterovirga aerilata sp. nov., with the type strain DB1703T (=KCTC 72724T=NBRC 114759T), and Knoellia koreensis sp. nov., with the type strain DB2414ST (=KCTC 49355T=NBRC 114620T).
Collapse
Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| |
Collapse
|
3
|
Singleton CM, Petriglieri F, Wasmund K, Nierychlo M, Kondrotaite Z, Petersen JF, Peces M, Dueholm MS, Wagner M, Nielsen PH. The novel genus, 'Candidatus Phosphoribacter', previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide. THE ISME JOURNAL 2022; 16:1605-1616. [PMID: 35217776 PMCID: PMC9123174 DOI: 10.1038/s41396-022-01212-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 01/19/2023]
Abstract
The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally.
Collapse
Affiliation(s)
- C M Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - F Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - K Wasmund
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - M Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Z Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - J F Petersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - M Peces
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - M S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - M Wagner
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - P H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| |
Collapse
|
4
|
Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 414] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
Collapse
Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
5
|
Beeby M, Gumbart JC, Roux B, Jensen GJ. Architecture and assembly of the Gram-positive cell wall. Mol Microbiol 2013; 88:664-72. [PMID: 23600697 PMCID: PMC3663049 DOI: 10.1111/mmi.12203] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2013] [Indexed: 12/30/2022]
Abstract
The bacterial cell wall is a mesh polymer of peptidoglycan--linear glycan strands cross-linked by flexible peptides--that determines cell shape and provides physical protection. While the glycan strands in thin 'Gram-negative' peptidoglycan are known to run circumferentially around the cell, the architecture of the thicker 'Gram-positive' form remains unclear. Using electron cryotomography, here we show that Bacillus subtilis peptidoglycan is a uniformly dense layer with a textured surface. We further show it rips circumferentially, curls and thickens at free edges, and extends longitudinally when denatured. Molecular dynamics simulations show that only atomic models based on the circumferential topology recapitulate the observed curling and thickening, in support of an 'inside-to-outside' assembly process. We conclude that instead of being perpendicular to the cell surface or wrapped in coiled cables (two alternative models), the glycan strands in Gram-positive cell walls run circumferentially around the cell just as they do in Gram-negative cells. Together with providing insights into the architecture of the ultimate determinant of cell shape, this study is important because Gram-positive peptidoglycan is an antibiotic target crucial to the viability of several important rod-shaped pathogens including Bacillus anthracis, Listeria monocytogenes, and Clostridium difficile.
Collapse
Affiliation(s)
- Morgan Beeby
- California Institute of Technology and Howard Hughes Medical Institute, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - James C. Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Benoît Roux
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- Department of Biochemistry and Molecular Biology and Gordon Center for Integrative Science, The University of Chicago, Chicago, Illinois 60637
| | - Grant J. Jensen
- California Institute of Technology and Howard Hughes Medical Institute, 1200 E. California Blvd, Pasadena, CA 91125, USA
| |
Collapse
|
6
|
Falk S, Liu B, Braker G. Isolation, genetic and functional characterization of novel soil nirK-type denitrifiers. Syst Appl Microbiol 2010; 33:337-47. [DOI: 10.1016/j.syapm.2010.06.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 06/03/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022]
|
7
|
Ghosh S, Osman S, Vaishampayan P, Venkateswaran K. Recurrent isolation of extremotolerant bacteria from the clean room where Phoenix spacecraft components were assembled. ASTROBIOLOGY 2010; 10:325-35. [PMID: 20446872 DOI: 10.1089/ast.2009.0396] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The microbial burden of the Phoenix spacecraft assembly environment was assessed in a systematic manner via several cultivation-based techniques and a suite of NASA-certified, cultivation-independent biomolecule-based detection assays. Extremotolerant bacteria that could potentially survive conditions experienced en route to Mars or on the planet's surface were isolated with a series of cultivation-based assays that promoted the growth of a variety of organisms, including spore formers, mesophilic heterotrophs, anaerobes, thermophiles, psychrophiles, alkaliphiles, and bacteria resistant to UVC radiation and hydrogen peroxide exposure. Samples were collected from the clean room where Phoenix was housed at three different time points, before (1P), during (2P), and after (3P) Phoenix's presence at the facility. There was a reduction in microbial burden of most bacterial groups, including spore formers, in samples 2P and 3P. Analysis of 262 isolates from the facility demonstrated that there was also a shift in predominant cultivable bacterial populations accompanied by a reduction in diversity during 2P and 3P. It is suggested that this shift was a result of increased cleaning when Phoenix was present in the assembly facility and that certain species, such as Acinetobacter johnsonii and Brevundimonas diminuta, may be better adapted to environmental conditions found during 2P and 3P. In addition, problematic bacteria resistant to multiple extreme conditions, such as Bacillus pumilus, were able to survive these periods of increased cleaning.
Collapse
Affiliation(s)
- Sudeshna Ghosh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | | | | |
Collapse
|
8
|
Vaishampayan P, Probst A, Krishnamurthi S, Ghosh S, Osman S, McDowall A, Ruckmani A, Mayilraj S, Venkateswaran K. Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room. Int J Syst Evol Microbiol 2009; 60:1031-1037. [PMID: 19666815 DOI: 10.1099/ijs.0.008979-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five Gram-stain-positive, motile, aerobic strains were isolated from a clean room of the Kennedy Space Center where the Phoenix spacecraft was assembled. All strains are rod-shaped, spore-forming bacteria, whose spores were resistant to UV radiation up to 1000 J m(-2). The spores were subterminally positioned and produced an external layer. A polyphasic taxonomic study including traditional biochemical tests, fatty acid analysis, cell-wall typing, lipid analyses, 16S rRNA gene sequencing and DNA-DNA hybridization studies was performed to characterize these novel strains. 16S rRNA gene sequencing and lipid analyses convincingly grouped these novel strains within the genus Bacillus as a cluster separate from already described species. The similarity of 16S rRNA gene sequences among the novel strains was >99 %, but the similarity was only about 97 % with their nearest neighbours Bacillus pocheonensis, Bacillus firmus and Bacillus bataviensis. DNA-DNA hybridization dissociation values were <24 % to the closest related type strains. The novel strains had a G+C content 35.6+/-0.5 mol% and could liquefy gelatin but did not utilize or produce acids from any of the carbon substrates tested. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) and the cell-wall diamino acid was meso-diaminopimelic acid. Based on phylogenetic and phenotypic results, it is concluded that these strains represent a novel species of the genus Bacillus, for which the name Bacillus horneckiae sp. nov. is proposed. The type strain is 1P01SC(T) (=NRRL B-59162(T) =MTCC 9535(T)).
Collapse
Affiliation(s)
- Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Alexander Probst
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Sudeshna Ghosh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Shariff Osman
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Alasdair McDowall
- Broad and Beckman Research Centers, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arunachalam Ruckmani
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| |
Collapse
|
9
|
Li Z, Jensen GJ. Electron cryotomography: a new view into microbial ultrastructure. Curr Opin Microbiol 2009; 12:333-40. [PMID: 19427259 PMCID: PMC2747746 DOI: 10.1016/j.mib.2009.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/20/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
Electron cryotomography (ECT) is an emerging technology that allows thin samples such as small bacterial cells to be imaged in 3D in a nearly native state to 'molecular' (approximately 4nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. Here we briefly explain ECT, review its recent contributions to microbiology, and conclude with a discussion of future prospects.
Collapse
Affiliation(s)
- Zhuo Li
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | | |
Collapse
|