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Han X, Wang J, Zhang J, Han B, Mei N, Fan R, Zhao J, Yao H, Yu X, Cai W. Digested extracellular DNA shortens the anodic startup of microbial electrolysis cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162642. [PMID: 36894072 DOI: 10.1016/j.scitotenv.2023.162642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
While the multiple functions of extracellular DNA (exDNA) in biofilm formation and electron transfer have been extensively studied in pure culture, its role in mixed anodic biofilm was still unknown. In this study, we employed DNase I enzyme to digest exDNA, thereby investigating its role in anodic biofilm formation based on the performance of four microbial electrolysis cells (MECs) groups with different DNase I enzyme concentration (0, 0.05, 0.1, 0.5 mg/mL). The responding time to reach 60 % maximum current of treatment group with DNase I enzyme has been significantly reduced to 83 %-86 % of the blank group (t-test, p < 0.01), indicating the exDNA digestion could promote the biofilm formation at the early stage. The anodic coulombic efficiency was enhanced by 10.74- 54.42 % in treatment group (t-test, p < 0.05), which could be ascribed to the higher absolute abundance of exoelectrogens. The lower relative abundance of exoelectrogens indicated the DNase I enzyme addition was beneficial for the enrichment of extensive species rather than exoelectrogens. As the DNase I enzyme augments the fluorescence signal of exDNA distribution in the small molecular weight region, implying the short chain exDNA could contribute to the biomass enhancement via boosting the most species enrichment. Furthermore, the exDNA alteration improved the complexity of microbial network. Our findings provide a new insight into the role of exDNA in the extracellular matrix of anodic biofilms.
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Affiliation(s)
- Xiangyu Han
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Jiaman Wang
- School of Engineering, Brown University, Providence, Rohde Island 02912, United States of America
| | - Jingjing Zhang
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Baohong Han
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Ning Mei
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Runchuan Fan
- School of Environment, Beijing Jiaotong University, Beijing 100044, China
| | - Jing Zhao
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Hong Yao
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Xiaohua Yu
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Weiwei Cai
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China.
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Nagler M, Podmirseg SM, Mayr M, Ascher-Jenull J, Insam H. The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool. Mol Ecol 2020; 30:438-450. [PMID: 33219564 PMCID: PMC7839673 DOI: 10.1111/mec.15740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023]
Abstract
Most commonly, next generation sequencing-based microbiome studies are performed on the total DNA (totDNA) pool; however, this consists of extracellular- (exDNA) and intracellular (iDNA) DNA fractions. By investigating the microbiomes of different anaerobic digesters over time, we found that totDNA suggested lower species richness considering all and/or only common species and yielded fewer unique reads as compared to iDNA. Additionally, exDNA-derived sequences were more similar to those from totDNA than from iDNA and, finally, iDNA showed the best performance in tracking temporal changes in microbial communities. We postulate that abundant sequences present within the exDNA fraction mask the overall results of totDNA and provide evidence that exDNA has the potential to qualitatively bias microbiome studies at least in the anaerobic digester environment as it contains information about cells that were lysed hours or days ago. iDNA, however, was found to be more appropriate in providing reliable genetic information about potentially alive as well as rare microbes within the target habitat.
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Affiliation(s)
- Magdalena Nagler
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Markus Mayr
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Heribert Insam
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
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3
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Grainha T, Magalhães AP, Melo LDR, Pereira MO. Pitfalls Associated with Discriminating Mixed-Species Biofilms by Flow Cytometry. Antibiotics (Basel) 2020; 9:antibiotics9110741. [PMID: 33121057 PMCID: PMC7694060 DOI: 10.3390/antibiotics9110741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/21/2022] Open
Abstract
Since biofilms are ubiquitous in different settings and act as sources of disease for humans, reliable methods to characterize and quantify these microbial communities are required. Numerous techniques have been employed, but most of them are unidirectional, labor intensive and time consuming. Although flow cytometry (FCM) can be a reliable choice to quickly provide a multiparametric analysis, there are still few applications on biofilms, and even less on the study of inter-kingdom communities. This work aimed to give insights into the application of FCM in order to more comprehensively analyze mixed-species biofilms, formed by different Pseudomonas aeruginosa and Candida albicans strains, before and after exposure to antimicrobials. For comparison purposes, biofilm culturability was also assessed determining colony-forming units. The results showed that some aspects, namely the microbial strain used, the morphological state of the cells and the biofilm matrix, make the accurate analysis of FCM data difficult. These aspects were even more challenging when double-species biofilms were being inspected, as they could engender data misinterpretations. The outcomes draw our attention towards the need to always take into consideration the characteristics of the biofilm samples to be analyzed through FCM, and undoubtedly link to the need for optimization of the processes tailored for each particular case study.
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Affiliation(s)
| | | | - Luís D. R. Melo
- Correspondence: (L.D.R.M.); (M.O.P.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-402 (M.O.P.)
| | - Maria O. Pereira
- Correspondence: (L.D.R.M.); (M.O.P.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-402 (M.O.P.)
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Asvapathanagul P, Garrido-Baserba M, Olson BH, Park HD, Chen D, Rosso D. Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol. J Mol Microbiol Biotechnol 2019; 28:293-304. [PMID: 31234170 DOI: 10.1159/000500875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. Escherichia coli, Gordonia amarae, and mixed liquor were used as controls. The fraction of total DNAbiofilm decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (>4 μgDNA/cm2), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for E. coli, and 0.39 and 0.40 log for G. amarae, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μgDNA/cm2). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.
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Affiliation(s)
- Pitiporn Asvapathanagul
- Department of Civil Engineering and Construction Engineering Management, California State University, Long Beach, California, USA,
| | - Manel Garrido-Baserba
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA.,Water-Energy Nexus Center, University of California, Irvine, California, USA
| | - Betty H Olson
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA.,Water-Energy Nexus Center, University of California, Irvine, California, USA
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
| | - Deqiang Chen
- College of Environment, Hohai University, Nanjing, China
| | - Diego Rosso
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA.,Water-Energy Nexus Center, University of California, Irvine, California, USA
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Lotti T, Carretti E, Berti D, Martina MR, Lubello C, Malpei F. Extraction, recovery and characterization of structural extracellular polymeric substances from anammox granular sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 236:649-656. [PMID: 30772722 DOI: 10.1016/j.jenvman.2019.01.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/28/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
The composition and colloidal properties of extracellular polymeric substances (EPS) from anammox granular sludge were investigated through a complete set of spectroscopic and scattering techniques. To fully characterize EPS, we developed a robust and reproducible extraction/recovery protocol specific for anammox biofilms, based on the change of water affinity under alternated alkaline and acidic conditions, each monitored with Z-potential and dynamic light scattering analysis. This method enabled both extraction as a colloidal suspension and recovery as a solid of large amounts of EPS (0.38 ± 0.04 and 0.21 ± 0.02 g/g, respectively), including for the first time its structural components. The dominance of the proteinaceous fraction was revealed by all methods tested, resulting in the highest protein/carbohydrates ratio reported for biofilms applied in the wastewater sector. The abundance of proteinaceous ordered structures and in particular of cross-β motifs was detected, indicating for the first time the presence of amyloid-like aggregates in anammox EPS, and suggesting the key role of the protein fraction in determining the mechanical properties of the parent biofilm. The robustness and reproducibility of the proposed method fill the current gap towards a reliable full-scale recovery as well as towards an accurate and meaningful investigation of anammox EPS and pave the way for further exploration of their applicative potential thus stimulating the desirable shift from the current wastewater treatment perspective towards biorefinery in a circular economy context.
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Affiliation(s)
- Tommaso Lotti
- Department of Civil and Environmental Engineering, Polytechnic University of Milan, Via Golgi 39, 20133 Milan, Italy; Civil and Environmental Engineering Department, University of Florence, Via di Santa Marta 3, 50139 Florence, Italy.
| | - Emiliano Carretti
- Department of Chemistry "Ugo Schiff" & CSGI Consortium, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino (FI), Florence, Italy.
| | - Debora Berti
- Department of Chemistry "Ugo Schiff" & CSGI Consortium, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino (FI), Florence, Italy.
| | - Maria Raffaella Martina
- Department of Chemistry "Ugo Schiff" & CSGI Consortium, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino (FI), Florence, Italy.
| | - Claudio Lubello
- Civil and Environmental Engineering Department, University of Florence, Via di Santa Marta 3, 50139 Florence, Italy.
| | - Francesca Malpei
- Department of Civil and Environmental Engineering, Polytechnic University of Milan, Via Golgi 39, 20133 Milan, Italy.
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Nagler M, Insam H, Pietramellara G, Ascher-Jenull J. Extracellular DNA in natural environments: features, relevance and applications. Appl Microbiol Biotechnol 2018; 102:6343-6356. [PMID: 29858957 PMCID: PMC6061472 DOI: 10.1007/s00253-018-9120-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/13/2023]
Abstract
Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
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Affiliation(s)
- Magdalena Nagler
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria.
| | - Heribert Insam
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
| | - Giacomo Pietramellara
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - Judith Ascher-Jenull
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
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Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL. Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environ Microbiol 2015; 18:273-87. [PMID: 26279094 DOI: 10.1111/1462-2920.13019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 11/30/2022]
Abstract
Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.
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Affiliation(s)
- Jeremy J Barr
- Department of Biology, San Diego State University, San Diego, CA, USA.,Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomedical Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Connor T Skennerton
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Toshikazu Fukushima
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Division of Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Marcus L Hastie
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Gene W Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Philip L Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
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