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Harthern-Flint SL, Dolfing J, Mrozik W, Meynet P, Eland LE, Sim M, Davenport RJ. Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557. Front Microbiol 2021; 12:670928. [PMID: 34276604 PMCID: PMC8281962 DOI: 10.3389/fmicb.2021.670928] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.
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Affiliation(s)
| | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.,Faculty Engineering and Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wojciech Mrozik
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Paola Meynet
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Sim
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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Wu LJ, Lee S, Park S, Eland LE, Wipat A, Holden S, Errington J. Geometric principles underlying the proliferation of a model cell system. Nat Commun 2020; 11:4149. [PMID: 32811832 PMCID: PMC7434903 DOI: 10.1038/s41467-020-17988-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria can form wall-deficient variants, or L-forms, that divide by a simple mechanism that does not require the FtsZ-based cell division machinery. Here, we use microfluidic systems to probe the growth, chromosome cycle and division mechanism of Bacillus subtilis L-forms. We find that forcing cells into a narrow linear configuration greatly improves the efficiency of cell growth and chromosome segregation. This reinforces the view that L-form division is driven by an excess accumulation of surface area over volume. Cell geometry also plays a dominant role in controlling the relative positions and movement of segregating chromosomes. Furthermore, the presence of the nucleoid appears to influence division both via a cell volume effect and by nucleoid occlusion, even in the absence of FtsZ. Our results emphasise the importance of geometric effects for a range of crucial cell functions, and are of relevance for efforts to develop artificial or minimal cell systems.
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Affiliation(s)
- Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| | - Seoungjun Lee
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.13097.3c0000 0001 2322 6764Present Address: Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX UK
| | - Sungshic Park
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.1006.70000 0001 0462 7212Interdisciplinary Computing and Complex BioSystems research group, School of Computing, Newcastle University, Newcastle upon Tyne, NE4 5TG UK
| | - Lucy E. Eland
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.1006.70000 0001 0462 7212Interdisciplinary Computing and Complex BioSystems research group, School of Computing, Newcastle University, Newcastle upon Tyne, NE4 5TG UK
| | - Anil Wipat
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.1006.70000 0001 0462 7212Interdisciplinary Computing and Complex BioSystems research group, School of Computing, Newcastle University, Newcastle upon Tyne, NE4 5TG UK
| | - Séamus Holden
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
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Jana S, Charlton SGV, Eland LE, Burgess JG, Wipat A, Curtis TP, Chen J. Nonlinear rheological characteristics of single species bacterial biofilms. NPJ Biofilms Microbiomes 2020; 6:19. [PMID: 32286319 PMCID: PMC7156450 DOI: 10.1038/s41522-020-0126-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 05/19/2019] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions and exhibit resistance to physical as well as chemical perturbations. In dynamic environments, where periodic or aperiodic flows over surfaces are involved, biofilms can be subjected to large shear forces. The ability to withstand these forces, which is often attributed to the resilience of the extracellular matrix. This attribute of the extracellular matrix is referred to as viscoelasticity and is a result of self-assembly and cross-linking of multiple polymeric components that are secreted by the microbes. We aim to understand the viscoelastic characteristic of biofilms subjected to large shear forces by performing Large Amplitude Oscillatory Shear (LAOS) experiments on four species of bacterial biofilms: Bacillus subtilis, Comamonas denitrificans, Pseudomonas fluorescens and Pseudomonas aeruginosa. We find that nonlinear viscoelastic measures such as intracycle strain stiffening and intracycle shear thickening for each of the tested species, exhibit subtle or distinct differences in the plot of strain amplitude versus frequency (Pipkin diagram). The biofilms also exhibit variability in the onset of nonlinear behaviour and energy dissipation characteristics, which could be a result of heterogeneity of the extracellular matrix constituents of the different biofilms. The results provide insight into the nonlinear rheological behaviour of biofilms as they are subjected to large strains or strain rates; a situation that is commonly encountered in nature, but rarely investigated.
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Affiliation(s)
- Saikat Jana
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK.
| | | | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK.
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Lahme S, Callbeck CM, Eland LE, Wipat A, Enning D, Head IM, Hubert CR. Comparison of sulfide‐oxidizing
Sulfurimonas
strains reveals a new mode of thiosulfate formation in subsurface environments. Environ Microbiol 2020; 22:1784-1800. [DOI: 10.1111/1462-2920.14894] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Sven Lahme
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
| | | | - Lucy E. Eland
- School of ComputingNewcastle University Newcastle upon Tyne UK
| | - Anil Wipat
- School of ComputingNewcastle University Newcastle upon Tyne UK
| | - Dennis Enning
- ExxonMobil Upstream Research Company Spring Texas USA
| | - Ian M. Head
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
| | - Casey R.J. Hubert
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
- Department of Biological SciencesUniversity of Calgary Calgary Canada
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Charlton SGV, White MA, Jana S, Eland LE, Jayathilake PG, Burgess JG, Chen J, Wipat A, Curtis TP. Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms. J Bacteriol 2019; 201:e00101-19. [PMID: 31182499 PMCID: PMC6707926 DOI: 10.1128/jb.00101-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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] [Indexed: 12/13/2022] Open
Abstract
Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover.
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Affiliation(s)
- Samuel G V Charlton
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A White
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Saikat Jana
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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Eland LE, Davenport RJ, Santos ABD, Mota Filho CR. Molecular evaluation of microalgal communities in full-scale waste stabilisation ponds. Environ Technol 2019; 40:1969-1976. [PMID: 29400147 DOI: 10.1080/09593330.2018.1435730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 09/14/2017] [Accepted: 01/25/2018] [Indexed: 06/07/2023]
Abstract
Waste stabilisation ponds (WSPs) are widely used across the world as a passive wastewater treatment for domestic wastewaters, but little is known about their ecology, especially their phototrophic communities. This study uses molecular methods and flow cytometry to assess the cyanobacterial and eukaryotic communities longitudinally throughout two systems, one treating domestic wastewater and the other mixed industrial/domestic wastewaters. More variation was seen between the systems than between different stages in the treatment processes for both eukaryotic and cyanobacterial communities. Chlorella species and Planktophrix cyanobacteria dominated both treatment systems. Arthrospira cyanobacteria were detected only in the industrial/domestic system. The balance between non-photosynthetic and photosynthetic organisms is rarely considered, though both play vital roles in WSP functioning. Flow cytometry showed that the facultative and first maturation pond in the industrial system contained a lower proportion of photosynthetic organisms compared to the domestic system. This is reflected in the species richness data and low dissolved oxygen levels detected. All data indicated that both systems are significantly different from one another and that variation longitudinally throughout the systems is lower. A more systematic study is needed to determine if it is the wastewater source rather than the initial inoculum that drives community composition.
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Affiliation(s)
- Lucy E Eland
- a School of Civil Engineering and Geosciences, Newcastle University , Newcastle-upon-Tyne , UK
| | - Russell J Davenport
- a School of Civil Engineering and Geosciences, Newcastle University , Newcastle-upon-Tyne , UK
| | - Andre Bezerra Dos Santos
- b Departamento de Engenharia Hidráulica e Ambiental , Universidade Federal do Ceará , Fortaleza , Brazil
| | - Cesar R Mota Filho
- a School of Civil Engineering and Geosciences, Newcastle University , Newcastle-upon-Tyne , UK
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Eland LE, Davenport R, Mota CR. Evaluation of DNA extraction methods for freshwater eukaryotic microalgae. Water Res 2012; 46:5355-5364. [PMID: 22853974 DOI: 10.1016/j.watres.2012.07.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 06/01/2023]
Abstract
The use of molecular methods to investigate microalgal communities of natural and engineered freshwater resources is in its infancy, with the majority of previous studies carried out by microscopy. Inefficient or differential DNA extraction of microalgal community members can lead to bias in downstream community analysis. Three commercially available DNA extraction kits have been tested on a range of pure culture freshwater algal species with diverse cell walls and mixed algal cultures taken from eutrophic waste stabilization ponds (WSP). DNA yield and quality were evaluated, along with DNA suitability for amplification of 18S rRNA gene fragments by polymerase chain reaction (PCR). QiagenDNeasy(®) Blood and Tissue kit (QBT), was found to give the highest DNA yields and quality. Denaturant Gradient Gel Electrophoresis (DGGE) was used to assess the diversity of communities from which DNA was extracted. No significant differences were found among kits when assessing diversity. QBT is recommended for use with WSP samples, a conclusion confirmed by further testing on communities from two tropical WSP systems. The fixation of microalgal samples with ethanol prior to DNA extraction was found to reduce yields as well as diversity and is not recommended.
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Affiliation(s)
- Lucy E Eland
- Newcastle University, School of Civil Engineering of Geosciences, Newcastle upon Tyne NE1 7RU, United Kingdom.
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