1
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Salam LB. Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment. World J Microbiol Biotechnol 2024; 40:172. [PMID: 38630153 DOI: 10.1007/s11274-024-03972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.
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Affiliation(s)
- Lateef B Salam
- Microbiology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Ondo State, Nigeria.
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2
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Peng H, Darlington APS, South EJ, Chen HH, Jiang W, Ledesma-Amaro R. A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities. Nat Microbiol 2024; 9:848-863. [PMID: 38326570 PMCID: PMC10914607 DOI: 10.1038/s41564-023-01596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model and key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic and overexpression yeast strains that can be used to create co-cultures through exchange of essential metabolites. Using these strains as modules, we engineered two- and three-member consortia using different cross-feeding architectures. Through a combination of ensemble modelling and experimentation, we explored how cellular (for example, metabolite production strength) and environmental (for example, initial population ratio, population density and extracellular supplementation) factors govern population dynamics in these systems. We tested the use of the toolkit in a division of labour biomanufacturing case study and show that it enables enhanced and tuneable antioxidant resveratrol production. We expect this toolkit to become a useful resource for a variety of applications in synthetic ecology and biomanufacturing.
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Affiliation(s)
- Huadong Peng
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexander P S Darlington
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, UK
| | - Eric J South
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Hao-Hong Chen
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Wei Jiang
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College London, London, UK.
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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3
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Chen X, He C, Zhang Q, Bayakmetov S, Wang X. Modularized Design and Construction of Tunable Microbial Consortia with Flexible Topologies. ACS Synth Biol 2024; 13:183-194. [PMID: 38166159 PMCID: PMC10805104 DOI: 10.1021/acssynbio.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/04/2024]
Abstract
Complex and fluid bacterial community compositions are critical to diversity, stability, and function. However, quantitative and mechanistic descriptions of the dynamics of such compositions are still lacking. Here, we develop a modularized design framework that allows for bottom-up construction and the study of synthetic bacterial consortia with different topologies. We showcase the microbial consortia design and building process by constructing amensalism and competition consortia using only genetic circuit modules to engineer different strains to form the community. Functions of modules and hosting strains are validated and quantified to calibrate dynamic parameters, which are then directly fed into a full mechanistic model to accurately predict consortia composition dynamics for both amensalism and competition without further fitting. More importantly, such quantitative understanding successfully identifies the experimental conditions to achieve coexistence composition dynamics. These results illustrate the process of both computationally and experimentally building up bacteria consortia complexity and hence achieve robust control of such fluid systems.
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Affiliation(s)
- Xingwen Chen
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Changhan He
- Department
of Mathematics, University of California
Irvine, Irvine, California 92697, United States
| | - Qi Zhang
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Samat Bayakmetov
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiao Wang
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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4
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Kannan P, Verma I, Banerjee B, Saleena LM. Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach. Arch Microbiol 2023; 206:27. [PMID: 38112856 DOI: 10.1007/s00203-023-03765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.
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Affiliation(s)
- Priya Kannan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Ishita Verma
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Bhargabi Banerjee
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India.
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5
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Zong DM, Sadeghpour M, Molinari S, Alnahhas RN, Hirning AJ, Giannitsis C, Ott W, Josić K, Bennett MR. Tunable Dynamics in a Multistrain Transcriptional Pulse Generator. ACS Synth Biol 2023; 12:3531-3543. [PMID: 38016068 DOI: 10.1021/acssynbio.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
One challenge in synthetic biology is the tuning of regulatory components within gene circuits to elicit a specific behavior. This challenge becomes more difficult in synthetic microbial consortia since each strain's circuit must function at the intracellular level and their combination must operate at the population level. Here we demonstrate that circuit dynamics can be tuned in synthetic consortia through the manipulation of strain fractions within the community. To do this, we construct a microbial consortium comprised of three strains of engineered Escherichia coli that, when cocultured, use homoserine lactone-mediated intercellular signaling to create a multistrain incoherent type-1 feedforward loop (I1-FFL). Like naturally occurring I1-FFL motifs in gene networks, this engineered microbial consortium acts as a pulse generator of gene expression. We demonstrate that the amplitude of the pulse can be easily tuned by adjusting the relative population fractions of the strains. We also develop a mathematical model for the temporal dynamics of the microbial consortium. This model allows us to identify population fractions that produced desired pulse characteristics, predictions that were confirmed for all but extreme fractions. Our work demonstrates that intercellular gene circuits can be effectively tuned simply by adjusting the starting fractions of each strain in the consortium.
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Affiliation(s)
- David M Zong
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Mehdi Sadeghpour
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
| | - Sara Molinari
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Andrew J Hirning
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Charilaos Giannitsis
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas 77004, United States
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, United States
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6
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Singha NA, Neihsial R, Kipgen L, Lyngdoh WJ, Nongdhar J, Chettri B, Singh P, Singh AK. Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures. Curr Microbiol 2023; 81:22. [PMID: 38017305 DOI: 10.1007/s00284-023-03529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023]
Abstract
Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.
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Affiliation(s)
- Ningombam A Singha
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Roselin Neihsial
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Lhinglamkim Kipgen
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Waniabha J Lyngdoh
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Jopthiaw Nongdhar
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Bobby Chettri
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Prabhakar Singh
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
| | - Arvind K Singh
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
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7
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Alghamdi MA, Ayed L, Aljarad MR, Altayeb HN, Abbes S, Chaieb K. Whole genome sequencing analysis and Box-Behnken design for the optimization of the decolourization of mixture textile dyes by halotolerant microbial consortium. Microbiol Res 2023; 276:127481. [PMID: 37651966 DOI: 10.1016/j.micres.2023.127481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
The use of dyes in textile industries has resulted in substantially contaminated soil, water and ecosystem including fauna and flora. So, the application of eco-friendly approach for dyes removal is in great demand. The goal of this research was to develop and test a bacterial consortium for biodegrading dyes in artificial textile effluent (ATE) derived from mixture of Indigo carmine (40 mg/l); Malachite green (20 mg/l); Cotton bleu (40 mg/l); Bromocresol green (20 mg/l) and CI Reactive Red 66 (40 mg/l) dissolved in artificial seawater. The Box-Behnken design (BBD) which combine six variables with three levels each was used to determine the potential removal of dyes in ATE, by the selected microbial consortium (M31 and M69b). The experimental process indicated that decolourization of ATE reached 77.36 % under these conditions values: salinity (30 g/l), pH (9), peptone (5 g/l), inoculum size (1.5 108 CFU/ml), agitation (150 rpm) and contact time (72 h). The decolourization was confirmed by FTIR spectrum analysis of ATE before and after bacterial treatment. Bacterial strains used in this study were identified as Halomonas pacifica M31 and Shewanella algae M69b using 16 rDNA sequences. Moreover, the total genome analysis of M31 and M69b validated the implication of bacterial genes in mixture dyes removal. Therefore, the effect of the selected bacterial consortium on ATE removal was confirmed and it may be used in industrial wastewater treatment to issuing environmental safety.
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Affiliation(s)
| | - Lamia Ayed
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Mohamed Rajeh Aljarad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hisham N Altayeb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Samir Abbes
- Laboratory of Genetic, Biodiversity and Bio-resources Valorisation, University of Monastir, Monastir, Tunisia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Tunisia
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8
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Lin Q, Li L, De Vrieze J, Li C, Fang X, Li X. Functional conservation of microbial communities determines composition predictability in anaerobic digestion. ISME J 2023; 17:1920-1930. [PMID: 37666974 PMCID: PMC10579369 DOI: 10.1038/s41396-023-01505-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Lingjuan Li
- Department of Biology, University of Antwerp, 2610, Wilrijk, Belgium
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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9
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Janusz G, Mazur A, Pawlik A, Kołodyńska D, Jaroszewicz B, Marzec-Grządziel A, Koper P. Metagenomic Analysis of the Composition of Microbial Consortia Involved in Spruce Degradation over Time in Białowieża Natural Forest. Biomolecules 2023; 13:1466. [PMID: 37892148 PMCID: PMC10604581 DOI: 10.3390/biom13101466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Andrzej Mazur
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (A.M.); (P.K.)
| | - Anna Pawlik
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Dorota Kołodyńska
- Faculty of Chemistry, Maria Curie Skłodowska University, M. Curie Skłodowska Sq. 2, 20-031 Lublin, Poland;
| | - Bogdan Jaroszewicz
- Białowieża Geobotanical Station, Faculty of Biology, University of Warsaw, Sportowa 19, 17-230 Białowieża, Poland;
| | - Anna Marzec-Grządziel
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation, Czartoryskich 8 Str., 24-100 Puławy, Poland;
| | - Piotr Koper
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (A.M.); (P.K.)
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10
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Kieft B, Finke N, McLaughlin RJ, Nallan AN, Krzywinski M, Crowe SA, Hallam SJ. Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nat Commun 2023; 14:5380. [PMID: 37666802 PMCID: PMC10477309 DOI: 10.1038/s41467-023-40907-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Niko Finke
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ryan J McLaughlin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Aditi N Nallan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.
- Bradshaw Research Institute for Minerals and Mining (BRIMM), University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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11
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Scott WT, Benito-Vaquerizo S, Zimmermann J, Bajić D, Heinken A, Suarez-Diez M, Schaap PJ. A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. PLoS Comput Biol 2023; 19:e1011363. [PMID: 37578975 PMCID: PMC10449394 DOI: 10.1371/journal.pcbi.1011363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
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Affiliation(s)
- William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
| | - Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany
| | - Djordje Bajić
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Almut Heinken
- Inserm U1256 Laboratoire nGERE, Université de Lorraine, Nancy, France
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
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12
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Zhang H, Shi J, Chen C, Yang M, Lu J, Zhang B. Heterotrophic Bioleaching of Vanadium from Low-Grade Stone Coal by Aerobic Microbial Consortium. Int J Environ Res Public Health 2022; 19:13375. [PMID: 36293959 PMCID: PMC9603648 DOI: 10.3390/ijerph192013375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Bioleaching is a viable method that assists in increasing the vanadium output in an economical and environmentally friendly manner. Most bioleaching is conducted by pure cultures under autotrophic conditions, which frequently require strong acidity and produce acid wastewater. However, little is known about heterotrophic bioleaching of vanadium by mixed culture. This study investigated the bioleaching of vanadium from low-grade stone coal by heterotrophic microbial consortium. According to the results, vanadium was efficiently extracted by the employed culture, with the vanadium recovery percentage in the biosystem being 7.24 times greater than that in the control group without inoculum. The average vanadium leaching concentration reached 680.7 μg/L in the first three cycles. The kinetic equation indicated that the main leaching process of vanadium was modulated by a diffusion process. Scanning electron microscopy revealed traces of bacterial erosion with fluffy structures on the surface of the treated stone coal. X-ray photoelectron spectroscopy confirmed the reduction of the vanadium content in the stone coal after leaching. Analysis of high-throughput 16S rRNA gene sequencing revealed that the metal-oxidizing bacteria, Acidovorax and Delftia, and the heterotrophic-metal-resistant Pseudomonas, were significantly enriched in the bioleaching system. Our findings advance the understanding of bioleaching by aerobic heterotrophic microbial consortium and offer a promising technique for vanadium extraction from low-grade stone coals.
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13
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McLeish AG, Gong S, Greenfield P, Midgley DJ, Paulsen IT. Microbial Community Shifts on Organic Rocks of Different Maturities Reveal potential Catabolisers of Organic Matter in Coal. Microb Ecol 2022; 84:780-793. [PMID: 34686899 DOI: 10.1007/s00248-021-01857-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/13/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
The global trend of transiting to more renewable energy sources requires transition fuels, such as coal seam gas, to supplement and secure energy needs. In order to optimise strategies and technologies for enhancing gas production, an understanding of the fundamental microbial processes and interactions would be advantageous. Models have recently begun mapping the microbial roles and interactions in coal seam environments, from direct coal degradation to methanogenesis. This study seeks to expand those models by observing community compositional shifts in the presence of differing organic matter by conducting 16S rRNA microbial surveys using formation water from the Surat and Sydney Basins grown on varying types of organic matter (black and brown coal, oil shale, humic acid, and lignin). A total of 135 microbes were observed to become enriched in the presence of added organic matter in comparison to carbon-free treatments. These surveys allowed detailed analysis of microbial compositions in order to extrapolate which taxa favour growth in the presence of differing organic matter. This study has experimentally demonstrated shifts in the microbial community composition due to differing carbon sources and, for the first time, generated a conceptual model to map putative degradation pathways regarding subsurface microbial consortia.
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Affiliation(s)
- Andrew G McLeish
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia.
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia.
| | - Se Gong
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia
| | - Paul Greenfield
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, Australia
| | - David J Midgley
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia
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14
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Sarma S, Patel N, Patel A, Desai C, Sharma S, Dedania S, Rudakiya DM, Vishwakarma AS, Vahora S, Narra M. Rapid decomposition of rice straw by application of a novel microbial consortium and study its microbial community dynamics. World J Microbiol Biotechnol 2022; 38:212. [PMID: 36053338 DOI: 10.1007/s11274-022-03399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022]
Abstract
Rice straw decomposition is an attractive solution to open-field burning but the traditional method has slow kinetics and takes 60-90 days to obtain mature compost. In this study, we propose to boost up the decomposition process by addition of a novel microbial consortium rich in lignocellulolytic microbes. C: N ratio of the compost reached 11.69% and degradation efficiency of cellulose and hemicellulose was found to be 64 and 87% respectively within 25 days. Lignocellulolytic activity of the microbial consortium was confirmed by plate and activity assay. These parameters clearly indicated that a mature compost was obtained in 25 days. The 16S rRNA gene amplicon sequencing and functional analysis of predicted genes indicated amino acid and carbohydrate metabolism as the major metabolic pathway during composting. The tertiary level of functional analysis revealed the major metabolic pathways in the bacterial communities as pentose phosphate pathway, glycolysis and tricarboxylic acid cycle.
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Affiliation(s)
- Shyamali Sarma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Nidhi Patel
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Aesha Patel
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Chirayu Desai
- Gujarat Biotechnology University, Near Gujarat International Finance Tec-City, Gandhinagar, Gujarat, 382355, India
| | - Shaishav Sharma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Samir Dedania
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Darshan M Rudakiya
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Alok S Vishwakarma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Samir Vahora
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India
| | - Madhuri Narra
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, P. Box No. 2, Vallabh Vidyanagar, Gujarat, 388120, India.
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15
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Gutiérrez Mena J, Kumar S, Khammash M. Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback. Nat Commun 2022; 13:4808. [PMID: 35973993 PMCID: PMC9381578 DOI: 10.1038/s41467-022-32392-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 06/20/2022] [Accepted: 07/29/2022] [Indexed: 12/19/2022] Open
Abstract
Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strain E. coli community. In addition, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context of E. coli and use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.
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Affiliation(s)
- Joaquín Gutiérrez Mena
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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16
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Dai C, Wu H, Wang X, Zhao K, Lu Z. Network and meta-omics reveal the cooperation patterns and mechanisms in an efficient 1,4-dioxane-degrading microbial consortium. Chemosphere 2022; 301:134723. [PMID: 35489450 DOI: 10.1016/j.chemosphere.2022.134723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/18/2022] [Revised: 04/09/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
1,4-Dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mixed cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial consortium CH1. A 1,4-dioxane-degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and had a potential of being one of the important degraders due to its high relative abundance, highly expressed monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium could be involved in the intermediates metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) differentially high-expressed. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators cooperated with ZM13 in the way of providing amino acids or fatty acids, as well as relieving environmental stresses to promote biodegradation. These results provide new insights into our understandings of the microbial interactions during 1,4-dioxane degradation, and have important implications for predicting microbial cooperation and constructing efficient and stable synthetic 1,4-dioxane-degrading consortia for practical remediation.
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Affiliation(s)
- Chuhan Dai
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
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17
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Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol 2022; 7:34-47. [PMID: 34873292 PMCID: PMC9261505 DOI: 10.1038/s41564-021-01014-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022]
Abstract
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.
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Affiliation(s)
- Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Yue Clare Lou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Michael Xu
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zeyi Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sara J Smith
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Kimberly Tang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Trenton K Owens
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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18
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Roszak M, Jabłońska J, Stachurska X, Dubrowska K, Kajdanowicz J, Gołębiewska M, Kiepas-Kokot A, Osińska B, Augustyniak A, Karakulska J. Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil. Int J Mol Sci 2021; 22:13469. [PMID: 34948267 PMCID: PMC8708151 DOI: 10.3390/ijms222413469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 11/26/2022] Open
Abstract
The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process.
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Affiliation(s)
- Marta Roszak
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, Al. Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
| | - Joanna Jabłońska
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology in Szczecin, Al. Piastów 42, 71-065 Szczecin, Poland
| | - Xymena Stachurska
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
| | - Kamila Dubrowska
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology in Szczecin, Al. Piastów 42, 71-065 Szczecin, Poland
| | - Justyna Kajdanowicz
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
| | - Marta Gołębiewska
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
| | - Anna Kiepas-Kokot
- Department of Environmental Management, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, ul. Słowackiego 17, 71-434 Szczecin, Poland;
| | - Beata Osińska
- Research Institute of Animal Production PIB Kołbacz Sp. z o.o., Warcisława Street 1, 74-106 Kołbacz, Poland;
| | - Adrian Augustyniak
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology in Szczecin, Al. Piastów 42, 71-065 Szczecin, Poland
- Chair of Building Materials and Construction Chemistry, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Jolanta Karakulska
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Al. Piastów 45, 70-311 Szczecin, Poland; (M.R.); (J.J.); (X.S.); (K.D.); (J.K.); (M.G.); (J.K.)
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19
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Quince C, Nurk S, Raguideau S, James R, Soyer OS, Summers JK, Limasset A, Eren AM, Chikhi R, Darling AE. STRONG: metagenomics strain resolution on assembly graphs. Genome Biol 2021; 22:214. [PMID: 34311761 PMCID: PMC8311964 DOI: 10.1186/s13059-021-02419-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 08/22/2020] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
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Affiliation(s)
- Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, MD, USA.
| | - Sebastien Raguideau
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Robert James
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | | | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Rayan Chikhi
- Department of Computational Biology, Institut Pasteur, C3BI USR 3756 IP CNRS, Paris, France
| | - Aaron E Darling
- The iThree institute, University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia
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Zhang W, Ren X, Lei Q, Wang L. Screening and Comparison of Lignin Degradation Microbial Consortia from Wooden Antiques. Molecules 2021; 26:molecules26102862. [PMID: 34066118 PMCID: PMC8151908 DOI: 10.3390/molecules26102862] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 11/16/2022] Open
Abstract
Lignin, which is a component of wood, is difficult to degrade in nature. However, serious decay caused by microbial consortia can happen to wooden antiques during the preservation process. This study successfully screened four microbial consortia with lignin degradation capabilities (J-1, J-6, J-8 and J-15) from decayed wooden antiques. Their compositions were identified by genomic sequencing, while the degradation products were analyzed by GC-MS. The lignin degradation efficiency of J-6 reached 54% after 48 h with an initial lignin concentration of 0.5 g/L at pH 4 and rotation speed of 200 rpm. The fungal consortium of J-6 contained Saccharomycetales (98.92%) and Ascomycota (0.56%), which accounted for 31% of the total biomass. The main bacteria in J-6 were Shinella sp. (47.38%), Cupriavidus sp. (29.84%), and Bosea sp. (7.96%). The strongest degradation performance of J-6 corresponded to its composition, where Saccharomycetales likely adapted to the system and improved lignin degradation enzymes activities, and the abundant bacterial consortium accelerated lignin decomposition. Our work demonstrated the potential utilization of microbial consortia via the synergy of microbial consortia, which may overcome the shortcomings of traditional lignin biodegradation when using a single strain, and the potential use of J-6 for lignin degradation/removal applications.
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Affiliation(s)
- Wen Zhang
- School of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
- Correspondence: (W.Z.); (L.W.); Tel./Fax: +86-0571-88297098 (W.Z.); +86-0571-85278909 (L.W.)
| | - Xueyan Ren
- School of Engineering, Westlake University, Hangzhou 310024, China;
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Qiong Lei
- Jingzhou Conservation Center of Hubei Province, Wood Lacquer Protection Research Department, Jingzhou 434020, China;
| | - Lei Wang
- School of Engineering, Westlake University, Hangzhou 310024, China;
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Correspondence: (W.Z.); (L.W.); Tel./Fax: +86-0571-88297098 (W.Z.); +86-0571-85278909 (L.W.)
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21
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Niederdorfer R, Hausherr D, Palomo A, Wei J, Magyar P, Smets BF, Joss A, Bürgmann H. Temperature modulates stress response in mainstream anammox reactors. Commun Biol 2021; 4:23. [PMID: 33398049 PMCID: PMC7782526 DOI: 10.1038/s42003-020-01534-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/17/2020] [Indexed: 01/29/2023] Open
Abstract
Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (DO) and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to DO shocks under 20 °C and 14 °C. While pulse disturbances of 0.3 mg L-1 DO prompted only moderate declines in the NH4+ removal rates, 1.0 mg L-1 DO led to complete but reversible inhibition of the NH4+ removal activity in all reactors. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of DO perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Community-wide gene expression differed significantly depending on the temperature regime in all reactors, and we found a noticeable impact of DO disturbances on genes involved in transcription, translation, replication and posttranslational modification at 20 °C but not 14 °C. Genome-centric analysis revealed that different anammox species and other key biofilm taxa differed in their transcriptional responses to distinct temperature regimes and DO disturbances.
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Affiliation(s)
- Robert Niederdorfer
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Surface Waters-Research and Management, 6047, Kastanienbaum, Switzerland.
| | - Damian Hausherr
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Process Engineering, 8600, Duebendorf, Switzerland
| | - Alejandro Palomo
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jing Wei
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Air Pollution & Environmental Technology, 8600, Duebendorf, Switzerland
| | - Paul Magyar
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Adriano Joss
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Process Engineering, 8600, Duebendorf, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Surface Waters-Research and Management, 6047, Kastanienbaum, Switzerland
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22
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Martínez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat Microbiol 2021; 6:123-135. [PMID: 33139880 PMCID: PMC7752763 DOI: 10.1038/s41564-020-00794-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 12/08/2019] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid-host and phage-host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant 'Candidatus Microthrix parvicella' population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Megeno S.A., Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Sujun Li
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Tony J Lam
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Benoît J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathan D Hicks
- TGen North, Flagstaff, AZ, USA
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Cindy M Liu
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Lance B Price
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | - Paul S Keim
- TGen North, Flagstaff, AZ, USA
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karoline Faust
- Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Haixu Tang
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Neuroscience, University of California, La Jolla, CA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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23
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Cui L, Zhu B, Zhang X, Chan Z, Zhao C, Zeng R, Yang S, Chen S. Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems. Genes (Basel) 2020; 12:genes12010040. [PMID: 33396721 PMCID: PMC7823961 DOI: 10.3390/genes12010040] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 01/22/2023] Open
Abstract
The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.
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Affiliation(s)
- Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Xiaobo Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Zhuhua Chan
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, No. 178 Daxue Road, Xiamen 361005, China; (Z.C.); (R.Z.)
| | - Chungui Zhao
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, No. 178 Daxue Road, Xiamen 361005, China; (Z.C.); (R.Z.)
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
- Correspondence: (S.Y.); (S.C.)
| | - Shicheng Chen
- Department of Biomedical Diagnostic and Therapeutic Sciences, School of Health Sciences, Oakland University, Rochester, MI 48309, USA
- Correspondence: (S.Y.); (S.C.)
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24
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Gong G, Zhou S, Luo R, Gesang Z, Suolang S. Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community. BMC Microbiol 2020; 20:302. [PMID: 33036549 PMCID: PMC7547465 DOI: 10.1186/s12866-020-01993-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 04/23/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. RESULTS Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. CONCLUSIONS Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.
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Affiliation(s)
- Ga Gong
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Saisai Zhou
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Runbo Luo
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Zhuoma Gesang
- Animal Epidemic Prevention and Control Center of Tibet Autonomous Region, Lasa, Tibet, China
| | - Sizhu Suolang
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China.
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25
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Park HJ, Kwon JH, Yun J, Cho KS. Characterization of nitrous oxide reduction by Azospira sp. HJ23 isolated from advanced wastewater treatment sludge. J Environ Sci Health A Tox Hazard Subst Environ Eng 2020; 55:1459-1467. [PMID: 32960129 DOI: 10.1080/10934529.2020.1812321] [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: 05/13/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
A new nitrous oxide (N2O)-reducing bacterium was isolated from a consortium that was enriched using advanced wastewater treatment sludge as an inoculum and N2O as the sole nitrogen source. The isolated facultative anaerobe was identified as Azospira sp. HJ23. Azospira sp. HJ23 exhibited optimum N2O-reducing activity with a C/N ratio of 62 at pH 6 in the temperature range of 37 °C to 40 °C. The optimum carbon source for N2O reduction was a mixture of glucose and acetate. The maximum rate of N2O reduction by Azospira sp. HJ23 was 4.8 mmol·g-dry cell-1·h-1, and its N2O-reducing activity was higher than other known N2O reducers. Azospira sp. HJ23 possessed several functional genes for denitrification. These included narG (NO3- reductase), nirK (NO2- reductase), norB (NO reductase), and nosZ (N2O reductase) genes. These results suggest that Azospira sp. HJ23 can be applied in the denitrification process to minimalize N2O emission.
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Affiliation(s)
| | | | | | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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26
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Yan C, Duan G, Wu FX, Pan Y, Wang J. BRWMDA:Predicting Microbe-Disease Associations Based on Similarities and Bi-Random Walk on Disease and Microbe Networks. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:1595-1604. [PMID: 30932846 DOI: 10.1109/tcbb.2019.2907626] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Many current studies have evidenced that microbes play important roles in human diseases. Therefore, discovering the associations between microbes and diseases is beneficial to systematically understanding the mechanisms of diseases, diagnosing, and treating complex diseases. It is well known that finding new potential microbe-disease associations via biological experiments is a time-consuming and expensive process. However, the computation methods can provide an opportunity to effectively predict microbe-disease associations. In recent years, efforts toward predicting microbe-disease associations are not in proportional to the importance of microbes to human diseases. In this study, we develop a method (called BRWMDA) to predict new microbe-disease associations based on similarity and improving bi-random walk on the disease and microbe networks. BRWMDA integrates microbe network, disease network, and known microbe-disease associations into a single network. After calculating the Gaussian Interaction Profile (GIP) kernel similarity of microbes based on known microbe-disease associations, the microbe network is obtained by adjusting the similarity with the logistics function. In addition, the disease network is computed by the similarity network fusion (SNF) method with the symptom-based similarity and the GIP kernel similarity based on known microbe-disease associations. Then, these two networks of microbe and disease are connected by known microbe-disease associations. Based on the assumption that similar microbes are normally associated with similar diseases and vice versa, BRWMDA is employed to predict new potential microbe-disease associations via random walk with different steps on microbe and disease networks, which reasonably uses the similarity of microbe network and disease network. The 5-fold cross validation and Leave One Out Cross Validation (LOOCV) are adopted to assess the prediction performance of our BRWMDA algorithm, as well as other competing methods for comparison. 5-fold cross validation experiments show that BRWMDA obtained the maximum AUC value of 0.9087, which is again superior to other methods of 0.9025(NGRHMDA), 0.8797 (LRLSHMDA), 0.8571 (KATZHMDA), 0.7782 (HGBI), and 0.5629 (NBI). In addition, BRWMDA also outperforms other methods in terms of LOOCV, whose AUC value is 0.9397, which is superior to other methods of 0.9111(NGRHMDA), 0.8909 (LRLSHMDA), 0.8644 (KATZHMDA), 0.7866 (HGBI), and 0.5553 (NBI). Case studies also illustrate that BRWMDA is an effective method to predict microbe-disease associations.
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27
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Abstract
As synthetic biocircuits become more complex, distributing computations within multi-strain microbial consortia becomes increasingly beneficial. However, designing distributed circuits that respond predictably to variation in consortium composition remains a challenge. Here we develop a two-strain gene circuit that senses and responds to which strain is in the majority. This involves a co-repressive system in which each strain produces a signaling molecule that signals the other strain to down-regulate production of its own, orthogonal signaling molecule. This co-repressive consortium links gene expression to ratio of the strains rather than population size. Further, we control the cross-over point for majority via external induction. We elucidate the mechanisms driving these dynamics by developing a mathematical model that captures consortia response as strain fractions and external induction are varied. These results show that simple gene circuits can be used within multicellular synthetic systems to sense and respond to the state of the population.
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Affiliation(s)
| | - Mehdi Sadeghpour
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Mathematics, University of Houston, Houston, TX, USA
| | - Ye Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Alexis A Frey
- Department of Biosciences, Rice University, Houston, TX, USA
| | - William Ott
- Department of Mathematics, University of Houston, Houston, TX, USA
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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28
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Lu M, Jiang W, Gao Q, Zhang M, Hong Q. Degradation of dibutyl phthalate (DBP) by a bacterial consortium and characterization of two novel esterases capable of hydrolyzing PAEs sequentially. Ecotoxicol Environ Saf 2020; 195:110517. [PMID: 32220793 DOI: 10.1016/j.ecoenv.2020.110517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 12/17/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Phthalate esters (PAEs), a class of toxic anthropogenic compounds, have been predominantly used as additives or plasticizers, and great concern and interests have been raised regarding its environmental behavior and degradation mechanism. In the present study, a bacterial consortium consisting of Microbacterium sp. PAE-1 and Pandoraea sp. PAE-2 was isolated by the enrichment method, which could degrade dibutyl phthalate (DBP) completely by biochemical cooperation. DBP was converted to phthalic acid (PA) via monobutyl phthalate (MBP) by two sequential hydrolysis steps in strain PAE-1, and then PA was further degraded by strain PAE-2. Strain PAE-1 could hydrolyze many dialkyl Phthalate esters (PAEs) including dimethyl, diethyl, dibutyl, dipentyl, benzyl butyl, dihexyl, di-(2-ethyhexyl) and their corresponding monoalkyl PAEs. Two esterase genes named dpeH and mpeH, located in the same transcription unit, were cloned from strain PAE-1 by the shotgun method and heterologously expressed in Escherichia. coli (DE3). The Km and kcat values of DpeH for DBP were 9.60 ± 0.97 μM and (2.72 ± 0.06) × 106 s-1, while those of MpeH for MBP were 18.61 ± 2.00 μM and (5.83 ± 1.00) × 105 s-1, respectively. DpeH could only hydrolyze dialkyl PAEs to the corresponding monoalkyl PAEs, which were then hydrolyzed to PA by MpeH. DpeH shares the highest similarity (53%) with an alpha/beta hydrolase from Microbacterium sp. MED-G48 and MpeH shows only 25% identity with a secreted lipase from Trichophyton benhamiae CBS 112371, indicating that DpeH and MpeH are two novel hydrolases against PAEs.
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Affiliation(s)
- Meiyu Lu
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Wankui Jiang
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Qinqin Gao
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Mingliang Zhang
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Qing Hong
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China.
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29
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Sharma M, Nandy A, Taylor N, Venkatesan SV, Ozhukil Kollath V, Karan K, Thangadurai V, Tsesmetzis N, Gieg LM. Bioelectrochemical remediation of phenanthrene in a microbial fuel cell using an anaerobic consortium enriched from a hydrocarbon-contaminated site. J Hazard Mater 2020; 389:121845. [PMID: 31862354 DOI: 10.1016/j.jhazmat.2019.121845] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 09/15/2019] [Revised: 11/15/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAH) are organic pollutants that require remediation due to their detrimental impact on human and environmental health. In this study, we used a novel approach of sequestering a model PAH, phenanthrene, onto a solid carbon matrix bioanode in a microbial fuel cell (MFC) to assess its biodegradation coupled with power generation. Here, the bioanode serves as a site for enrichment of electroactive and hydrocarbon-degrading microorganisms, which can simultaneously act to biodegrade a pollutant and generate power. Carbon cloth electrodes loaded with two rates of phenanthrene (2 and 20 mg cm-2) were compared using dual chamber MFCs that were operated for 50 days. The lower loading rate of 2 mg cm-2 was most efficient in the degradation of phenanthrene and had higher power production capacities (37 mW m-2) as compared to the higher loading rate of 20 mg cm-2 (power production of 19.2 mW m-2). FTIR (Fourier-Transform Infrared Spectroscopy) analyses showed a depletion in absorbance peak signals associated with phenanthrene. Microbes known to have electroactive properties or phenanthrene biodegradation abilities like Pseudomonas, Rhodococcus, Thauera and Ralstonia were enriched over time in the MFCs, substantiating the electrochemical and FTIR analyses. The MFC approach taken here thus offers great promise towards PAH bioelectroremediation.
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Affiliation(s)
- Mohita Sharma
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Arpita Nandy
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Nicole Taylor
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Senthil Velan Venkatesan
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Vinayaraj Ozhukil Kollath
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Kunal Karan
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Venkataraman Thangadurai
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, Texas, 77251-7171, USA
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. Chemosphere 2020; 243:125242. [PMID: 31995861 DOI: 10.1016/j.chemosphere.2019.125242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 08/15/2019] [Revised: 10/13/2019] [Accepted: 10/26/2019] [Indexed: 05/18/2023]
Abstract
Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
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Affiliation(s)
- Eglantina Lopez-Echartea
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Shinjini Mukherjee
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belgium
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kim Yrjälä
- University of Helsinki, Department of Forest Sciences, Helsinki, Finland; Zhejiang A&F University, State Key Laboratory of Subtropical Silviculture, Zhejiang, China.
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Gupta A, Sar P. Characterization and application of an anaerobic, iron and sulfate reducing bacterial culture in enhanced bioremediation of acid mine drainage impacted soil. J Environ Sci Health A Tox Hazard Subst Environ Eng 2020; 55:464-482. [PMID: 31971065 DOI: 10.1080/10934529.2019.1709362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/29/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Development of an appropriate bioremediation strategy for acid mine drainage (AMD) impacted environment is imperative for sustainable mining but remained critically challenged due to the paucity of knowledge on desired microbiological factors and their nutrient requirements. The present study was conducted to utilize the potential of an anaerobic, acid-tolerant, Fe3+ and SO42- reducing microbial consortium for in situ remediation of highly acidic (pH 3.21), SO42- rich (6285 mg/L) mine drainage impacted soil (AIS). A microbial consortium enriched from AMD system and composed of Clostridiales and Bacillales members was characterized and tested for in situ application through microcosms. A combination of bioaugmentation (enriched consortium) and biostimulation (cellulose) allowed 97% reduction in dissolved sulfate and rise in pH up to 7.5. 16S rRNA gene-based amplicon sequencing confirmed that although the bioaugmented community could survive in AIS, availability of carbon source was necessary for superior iron- and sulfate- reduction. Quantitative PCR of dsrB gene confirmed the role of carbon source in boosting the SO42- reduction activities of sulfate reducers. This study demonstrated that native AIS harbored limited catabolic activities required for the remediation but addition of catabolically active microbial populations along with necessary carbon and energy source facilitate the bioremediation of AIS.
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Affiliation(s)
- Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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Antonelli F, Esposito A, Calvo L, Licursi V, Tisseyre P, Ricci S, Romagnoli M, Piazza S, Guerrieri F. Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing. PLoS One 2020; 15:e0227639. [PMID: 31917800 PMCID: PMC6952188 DOI: 10.1371/journal.pone.0227639] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/23/2019] [Indexed: 11/19/2022] Open
Abstract
Black patinas are very common biological deterioration phenomena on lapideous artworks in outdoor environments. These substrates, exposed to sunlight, and atmospheric and environmental agents (i.e. wind and temperature changes), represent extreme environments that can only be colonized by highly versatile and adaptable microorganisms. Black patinas comprise a wide variety of microorganisms, but the morphological plasticity of most of these microorganisms hinders their identification by optical microscopy. This study used Next-Generation Sequencing (NGS) (including shotgun and amplicon sequencing) to characterize the black patina of the travertine embankments (muraglioni) of the Tiber River in Rome (Italy). Overall, the sequencing highlighted the rich diversity of bacterial and fungal communities and allowed the identification of more than one hundred taxa. NGS confirmed the relevance of coccoid and filamentous cyanobacteria observed by optical microscopy and revealed an informative landscape of the fungal community underlining the presence of microcolonial fungi and phylloplane yeasts. For the first time high-throughput sequencing allowed the exploration of the expansive diversity of bacteria in black patina, which has so far been overlooked in routine analyses. Furthermore, the identification of euendolithic microorganisms and weathering agents underlines the biodegradative role of black patina, which has often been underestimated. Therefore, the use of NGS to characterize black patinas could be useful in choosing appropriate conservation treatments and in the monitoring of stone colonization after the restoration interventions.
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Affiliation(s)
- Federica Antonelli
- Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology–CIBIO, University of Trento, Trento, Italy
| | - Ludovica Calvo
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Valerio Licursi
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | | | - Sandra Ricci
- Biology Laboratory, Istituto Superiore per la Conservazione e per il Restauro (ISCR), Rome, Italy
| | - Manuela Romagnoli
- Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy
| | - Silvano Piazza
- Department of Cellular, Computational and Integrative Biology–CIBIO, University of Trento, Trento, Italy
| | - Francesca Guerrieri
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Epigenetics and epigenomic of hepatocellular carcinoma, U1052, Cancer Research Center of Lyon (CRCL), Lyon, France
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Wang D, Cai X, Lv X, Wang Y, Gao X, Zhu Y, Zhang T, Mao Y. Phylogenetic characterization of bromate-reducing microbial community enriched anaerobically from activated sludge. Ecotoxicol Environ Saf 2019; 184:109630. [PMID: 31520951 DOI: 10.1016/j.ecoenv.2019.109630] [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: 07/04/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 06/10/2023]
Abstract
Bromate is a weakly carcinogenic disinfection by-product generated from naturally existing bromide during ozonation. In order to uncover the phylogenetic diversity of bromate-reducing aquatic bacteria, the microbial mixed cultures were enriched anaerobically from various activated sludge samples with a high concentration of 3.6 mmol/L bromate which served as the electron acceptor in batch-fed reactors. Then the phylogenetic diversity was characterized by employing 16S rRNA gene-based clone libraries and high-throughput sequencing. Results showed that as highest as 48.65 mg/L [BrO3--Br] (0.61 mmol/L) could be reduced to Br- within an operational cycle of 48 h, indicating the presence of bromate-reducing bacteria. The microbial analysis based on 16S rRNA gene clone libraries indicated that the dominant bacteria in the enriched consortium were affiliated to the genera of Aeromonas, which had been reported and implied its functional application to reduce bromate. In addition, some other subdivisions of bromate-reducing bacteria were enriched at different operational cycles. The abundance of the genus Rivibacter belonging to Comamonadaceae were increased after 10 cycles enrichment, which might represent another type of novel bromate bio-reducers. The study provided new insights for the phylogenetic diversity of the bromate-reducing microorganisms while further researches are required to verify the bromate bio-reduction mechanism.
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Affiliation(s)
- Dan Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Xunchao Cai
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Xinyue Lv
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Yicheng Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Xue Gao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yunlong Zhu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China.
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Gómez G, Salinas M, Ruiz-Tagle N, Sossa K, Vidal G. Molecular weight distribution of the recalcitrant organic matter contained in kraft mill effluents and the identification of microbial consortia responsible for an anaerobic biodegradable fraction. J Environ Sci Health A Tox Hazard Subst Environ Eng 2019; 55:281-291. [PMID: 31698987 DOI: 10.1080/10934529.2019.1688019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/05/2019] [Revised: 10/19/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
The objective of this research was to evaluate the distribution of the molecular weights of the recalcitrant organic matter contained in kraft mill effluents and identify microbial consortia responsible for an anaerobic biodegradable fraction. As a result, the average removal efficiencies of chemical organic demand (COD) and biological oxygen demand (BOD5) during the entire period of operation were 28% and 53%, respectively. The non-biodegradable organic matter was detected at molecular weights less than 1000 Da. However, most of the organic matter was in the molecular weight fraction higher than 10000 Da with 32 ± 11.6% COD as well as color (42.3 ± 8.7%), total phenolic compounds (35.9 ± 7.9%) and adsorbable organic compounds (AOX) (13.0 ± 2.7%). Methanogenic acetoclastic archaea of the genera Methanomethylovorans and Methanosarcina were found in the surface and middle zones of the reactor. Moreover, Methanosaeta and Methanolinea were identified in the low zone of the reactor. In all zones of the reactor, Desulfomicrobium and Desulfovibrio were found to be the most dominant genera of sulfate-reducing bacteria (SRB).
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Affiliation(s)
- Gloria Gómez
- Engineering and Biotechnology Environmental Group, Environmental Science Faculty & Center EULA-Chile, University of Concepción, Concepción, Chile
| | - Miguel Salinas
- Area Servicios Nueva Aldea, Wood Pulp & Energy, Celulosa Arauco y Constitución S.A, Nueva Aldea, Chile
| | - Nathaly Ruiz-Tagle
- Biofilm Laboratory and Environmental Microbiology, Biotechnology Center, University of Concepción, Concepción, Chile
| | - Katherine Sossa
- Biofilm Laboratory and Environmental Microbiology, Biotechnology Center, University of Concepción, Concepción, Chile
| | - Gladys Vidal
- Engineering and Biotechnology Environmental Group, Environmental Science Faculty & Center EULA-Chile, University of Concepción, Concepción, Chile
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Su H, Hu X, Wang L, Xu W, Xu Y, Wen G, Li Z, Cao Y. Contamination of antibiotic resistance genes (ARGs) in a typical marine aquaculture farm: source tracking of ARGs in reared aquatic organisms. J Environ Sci Health B 2019; 55:220-229. [PMID: 31680622 DOI: 10.1080/03601234.2019.1684747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the prevalence and concentrations of antibiotic resistance genes (ARGs) in aquaculture is receiving increasing scientific interest, there is little understanding of the direct sources and dissemination pathways of ARGs in marine aquaculture-reared organisms. This study investigated the dynamics of ARGs and the bacterial community throughout the rearing period in a typical marine aquaculture farm in South China. The results demonstrated that sul1 and qnrD were predominant in the sediment, and qnrD and qnrA were predominant in the intestinal tracts of shrimps. Network analysis showed that the chemical oxygen demand, total organic carbon, dissolved organic carbon, suspended solids, and total phosphorus were positively correlated with the predominant ARGs. The results of the network and source tracking analyses indicate that environmental factors and the bacterial community may drive the dissemination of ARGs dissemination in the environment and in shrimp reared by marine aquaculture, and sediment is the most direct and important medium in this dissemination. These results aid in improving our understanding of the sources, level, and dissemination of ARGs in marine aquaculture.
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Affiliation(s)
- Haochang Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Xiaojuan Hu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Linglong Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Wujie Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Yu Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Guoliang Wen
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Zhuojia Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yucheng Cao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Shenzhen Base South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
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Yin T, Tran NH, Huiting C, He Y, Gin KYH. Biotransformation of polyfluoroalkyl substances by microbial consortia from constructed wetlands under aerobic and anoxic conditions. Chemosphere 2019; 233:101-109. [PMID: 31170581 DOI: 10.1016/j.chemosphere.2019.05.227] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 04/21/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
The wide application of 6:2 fluorotelomer sulfonate (6:2 FTS) and its precursors results in their ubiquitous occurrence in the environment. This study investigated the biotransformation of 6:2 FTS using fresh slurries collected from constructed wetland under aerobic and anoxic conditions. Biotransformation rates of 6:2 FTS was extremely slow under both aerobic and anoxic conditions. The analysis of transformation products showed that less than 0.7 mol% of initial concentration of 6:2 FTS was biotransformed under anoxic conditions. Effects of 6:2 FTS on the shifts in microbial community in wetland slurry during aerobic and anoxic transformation were evaluated using 16S rRNA gene amplicon sequencing. Under aerobic conditions, 6:2 FTS altered the microbial community structure, in which Methylocaldum (Gamma-proteobacteria) became the predominant genus after being exposed to 6:2 FTS. This means that Methylocaldum appears to have higher tolerance to 6:2 FTS and seems to be potential 6:2 FTS-degrading bacteria. Under anoxic transformation, only the genus Methanomethylovorans (Euryarchaeota) was increased remarkably in wetland slurry exposed to 6:2 FTS.
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Affiliation(s)
- Tingru Yin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore, 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore, 117411, Singapore
| | - Ngoc Han Tran
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Viet Nam; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore, 117411, Singapore
| | - Chen Huiting
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore, 117411, Singapore
| | - Yiliang He
- School of Environmental Science and Technology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore, 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore, 117411, Singapore.
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Dong QY, Wang Z, Shi LD, Lai CY, Zhao HP. Anaerobic methane oxidation coupled to chromate reduction in a methane-based membrane biofilm batch reactor. Environ Sci Pollut Res Int 2019; 26:26286-26292. [PMID: 31286367 DOI: 10.1007/s11356-019-05709-7] [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: 12/14/2018] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Chromate can be reduced by methanotrophs in a membrane biofilm reactor (MBfR). In this study, we cultivated a Cr(VI)-reducing biofilm in a methane (CH4)-based membrane biofilm batch reactor (MBBR) under anaerobic conditions. The Cr(VI) reduction rate increased to 0.28 mg/L day when the chromate concentration was ≤ 2.2 mg/L but declined sharply to 0.01 mg/L day when the Cr(VI) concentration increased to 6 mg/L. Isotope tracing experiments showed that part of the 13C-labeled CH4 was transformed to 13CO2, suggesting that the biofilm may reduce Cr(VI) by anaerobic methane oxidation (AnMO). Microbial community analysis showed that a methanogen, i.e., Methanobacterium, dominated in the biofilm, suggesting that this genus is probably capable of carrying out AnMO. The abundance of Methylomonas, an aerobic methanotroph, decreased significantly, while Meiothermus, a potential chromate-reducing bacterium, was enriched in the biofilm. Overall, the results showed that the anaerobic environment inhibited the activity of aerobic methanotrophs while promoting AnMO bacterial enrichment, and high Cr(VI) loading reduced Cr(VI) flux by inhibiting the methane oxidation process.
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Affiliation(s)
- Qiu-Yi Dong
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Wang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun-Yu Lai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
- Advanced Water Management Centre, The University of Queensland, St. Lucia, 4072, Queensland, Australia.
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China.
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Ganesh Kumar A, Nivedha Rajan N, Kirubagaran R, Dharani G. Biodegradation of crude oil using self-immobilized hydrocarbonoclastic deep sea bacterial consortium. Mar Pollut Bull 2019; 146:741-750. [PMID: 31426216 DOI: 10.1016/j.marpolbul.2019.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 10/10/2018] [Revised: 05/14/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
Hydrocarbonoclastic bacterial consortium that utilizes crude oil as carbon and energy source was isolated from marine sediment collected at a depth of 2100 m. Molecular characterization by 16S rRNA gene sequences confirmed that these isolates as Oceanobacillus sp., Nesiotobacter sp., Ruegeria sp., Photobacterium sp., Enterobacter sp., Haererehalobacter sp., Exiguobacterium sp., Acinetobacter sp. and Pseudoalteromonas sp. Self-immobilized consortium degraded more than 85% of total hydrocarbons after 10 days of incubation with 1% (v/v) of crude oil and 0.05% (v/v) of Tween 80 (non-ionic surfactant) at 28 ± 2 °C. The addition of nitrogen and phosphorus sources separately i.e. 0.1% (v/v) of CO (NH2)2 or K2HPO4 enhanced the hydrocarbon utilization percentage. The pathways of microbial degradation of hydrocarbons were confirmed by FTIR, GC-MS, 1H and 13C NMR spectroscopy analyses. These results demonstrated a novel approach using hydrocarbonoclastic self-immobilized deep sea bacterial consortium for eco-friendly bioremediation.
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Affiliation(s)
- A Ganesh Kumar
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - N Nivedha Rajan
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - R Kirubagaran
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - G Dharani
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India.
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Pendegraft AH, Guo B, Yi N. Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data. PLoS One 2019; 14:e0220961. [PMID: 31437194 PMCID: PMC6706006 DOI: 10.1371/journal.pone.0220961] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 07/26/2019] [Indexed: 01/12/2023] Open
Abstract
The analyses of large volumes of metagenomic data extracted from aggregate populations of microscopic organisms residing on and in the human body are advancing contemporary understandings of the integrated participation of microbes in human health and disease. Next generation sequencing technology facilitates said analyses in terms of diversity, community composition, and differential abundance by filtering and binning microbial 16S rRNA genes extracted from human tissues into operational taxonomic units. However, current statistical tools restrict study designs to investigations of limited numbers of host characteristics mediated by limited numbers of samples potentially yielding a loss of relevant information. This paper presents a Bayesian hierarchical negative binomial model as an efficient technique capable of compensating for multivariable sets including tens or hundreds of host characteristics as covariates further expanding analyses of human microbiome count data. Simulation studies reveal that the Bayesian hierarchical negative binomial model provides a desirable strategy by often outperforming three competing negative binomial model in terms of type I error while simultaneously maintaining consistent power. An application of the Bayesian hierarchical negative binomial model using subsets of the open data published by the American Gut Project demonstrates an ability to identify operational taxonomic units significantly differentiable among persons diagnosed by a medical professional with either inflammatory bowel disease or irritable bowel syndrome that are consistent with contemporary gastrointestinal literature.
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Affiliation(s)
- Amanda H. Pendegraft
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Boyi Guo
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nengjun Yi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Lou L, Huang Q, Lou Y, Lu J, Hu B, Lin Q. Adsorption and degradation in the removal of nonylphenol from water by cells immobilized on biochar. Chemosphere 2019; 228:676-684. [PMID: 31063914 PMCID: PMC6771920 DOI: 10.1016/j.chemosphere.2019.04.151] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 03/28/2019] [Accepted: 04/20/2019] [Indexed: 05/23/2023]
Abstract
To investigate the role of adsorption by biochar and biodegradation by bacteria in the wastewater treatment system of microorganisms immobilized on biochar, Nonylphenol (NP) removal (adsorption + degradation) rates and degradation rates from water by NP degrading bacteria immobilized on bamboo charcoal (BC) and wood charcoal (WC) were examined in a short-term and long-term. Results showed that cells immobilized on different biochar had different NP removal effects, and cells immobilized on bamboo charcoal (I-BC) was better. After eight rounds of long-term reuse, the cumulative removal rate and the degradation rate of NP in water by I-BC were 93.95% and 41.86%, respectively, significantly higher than those of cells immobilized on wood charcoal (69.60%, 22.78%) and free cells (64.79%, 19.49%) (P < 0.01). The rise in the ratio of the degradation rate to the removal rate indicated that the long-term NP removal effect is more dependent on biodegradation. The amount of residual NP in I-BC still accounted for about 50%, indicating that the secondary pollution in the disposal of carrier could not be ignored. In addition, promotion effect of biochar on microorganisms were observed by SEM, quantitative PCR and 16S rRNA. Pseudomonas, Achromobacter, Ochrobactrum and Stenotrophomonas were predominant bacteria for NP degradation. The addition of biochar (especially bamboo charcoal) also effectively delayed the transformation of their community structure.
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MESH Headings
- Adsorption
- Bacteria/genetics
- Bacteria/metabolism
- Biodegradation, Environmental
- Bioreactors/microbiology
- Cells, Immobilized
- Charcoal/chemistry
- Microbial Consortia/genetics
- Microscopy, Electron, Scanning
- Phenols/chemistry
- Phenols/isolation & purification
- RNA, Ribosomal, 16S
- Sasa/chemistry
- Waste Disposal, Fluid/instrumentation
- Waste Disposal, Fluid/methods
- Wastewater/chemistry
- Water Pollutants, Chemical/chemistry
- Water Pollutants, Chemical/isolation & purification
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Affiliation(s)
- Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou, 310020, People's Republic of China.
| | - Qian Huang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310029, People's Republic of China; Academy of Environmental Planning & Design, Co., Ltd., Nanjing University, Nanjing, 210093, People's Republic of China
| | - Yiling Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310029, People's Republic of China
| | - Jingrang Lu
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310029, People's Republic of China
| | - Qi Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou, 310020, People's Republic of China.
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Liu J, Yao J, Sunahara G, Wang F, Li Z, Duran R. Nonferrous metal (loid) s mediate bacterial diversity in an abandoned mine tailing impoundment. Environ Sci Pollut Res Int 2019; 26:24806-24818. [PMID: 31240654 DOI: 10.1007/s11356-019-05092-3] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
Migration and transformation of toxic metal (loid) s in tailing sites inevitably lead to ecological disturbances and serious threats to the surroundings. However, the horizontal and vertical distribution of bacterial diversity has not been determined in nonferrous metal (loid) tailing ponds, especially in Guangxi China, where the world's largest and potentially most toxic sources of metal (loid) s are located. Distribution of bacterial communities was stable at horizontal levels. At the surface (0-10 cm), the stability was most attributed to Bacillus and Enterococcus, while bacterial communities at the subsurface (50 cm) were mainly contributed by Nitrospira and Sulfuricella. Variable vertical distribution of bacterial communities has led to the occurrence of specific genera and specific predicted functions (such as transcription regulation factors). Sulfurifustis (a S-oxidizing and inorganic carbon fixing bacteria) genera were specific at the surface, whereas Streptococcus-related genera were found at the surface and subsurface, but were more abundant in the latter depth. Physical-chemical parameters, such as pH, TN, and metal (loid) (As, Cd, Pb, Cu, and Zn) concentrations were the main drivers of bacterial community abundance, diversity, composition, and metabolic functions. These results increase our understanding of the physical-chemical effects on the spatial distribution of bacterial communities and provide useful insight for the bioremediation and site management of nonferrous metal (loid) tailings.
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Affiliation(s)
- Jianli Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Department of Natural Resource Sciences, McGill University, Montreal, H9X3V9, Quebec, Canada
| | - Fei Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Zifu Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Robert Duran
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
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Yang L, Wen Q, Zhao Y, Chen Z, Wang Q, Bürgmann H. New insight into effect of antibiotics concentration and process configuration on the removal of antibiotics and relevant antibiotic resistance genes. J Hazard Mater 2019; 373:60-66. [PMID: 30903957 DOI: 10.1016/j.jhazmat.2019.03.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/11/2018] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
To compare the performance and antibiotic-resistance character in different process configurations under different levels of antibiotics, anoxic/oxic-membrane bioreactors (MBR) 1#, MBR2# and a sequencing batch reactor (SBR) were operated with identical operating parameters. MBR1# and SBR were operated under high and increasing levels of antibiotics, MBR2# received constant and low concentration of antibiotics. Microbiological community and antibiotic resistance genes (ARGs) were investigated using 16S rDNA gene high-throughput sequencing and qPCR. More than 90% of penicillin and chlortetracycline were removed due to strong hydrolysis, followed by sulfamethoxazole (69.27%-86.25%) through biodegradation and norfloxacin (28.66%-53.86%) through adsorption. Process configuration affected total nitrogen removal more, while antibiotics concentration affected total phosphorus removal more. MBR1# outperformed SBR in reducing sulfamethoxazole, norfloxacin and ARGs due to the retention effect of the membrane module. Retention efficiency of ARGs in MBRs increased along the operation. Compared to the operational taxonomic unit (OTU) number before antibiotics addition, the OTU number in MBR1# and SBR decreased by 23.7% and 28.7%, while that in MBR2# kept relatively stable. Process configuration contributed to higher dissimilarity of microbial community than antibiotics concentration. The research provides an insight into the influence factors of antibiotics-containing wastewater treatment.
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Affiliation(s)
- Lian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Yaqi Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China; School of Civil Engineering, Lanzhou University of Technology, Lanzhou, 730070, PR China.
| | - Qiong Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China
| | - Helmut Bürgmann
- Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Eawag, CH-6047, Switzerland
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Feng R, Zhao G, Yang Y, Xu M, Huang S, Sun G, Guo J, Li J. Enhanced biological removal of intermittent VOCs and deciphering the roles of sodium alginate and polyvinyl alcohol in biofilm formation. PLoS One 2019; 14:e0217401. [PMID: 31116790 PMCID: PMC6530866 DOI: 10.1371/journal.pone.0217401] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/12/2019] [Indexed: 01/09/2023] Open
Abstract
Developing a robust biofilm is a prerequisite for a biotrickling filter to obtain the good performance in removing volatile organic compounds (VOCs). But the biofilm formation can be seriously disturbed under intermittent loading condition due to carbon starvation stress in idle time. In this study, a biotrickling filter, with its packing materials being modified by 3% sodium alginate and 5% polyvinyl alcohol (v/v = 1:3), was employed to treat intermittent VOCs. Results showed that the removal efficiencies of toluene, ethylbenzene, p-xylene, m-xylene, and o-xylene was significantly enhanced in the BTF compared to the control one. Under relatively lower inlet loading, nearly complete removal of the five pollutants was achieved. A quantitative analysis showed that the concentration of total organic compound (TOC) in the leachate maintained at a high level, and had a strongly positive correlation with the divergence of microbial communities. The capacity of biofilm formation in the BTF was approximately four-fold higher than the control BTF, while the quantity of EPS secreted was more than ten-fold. EPS comprised largely of protein, and to less extent, polysaccharide. The biofilm formed on the modified packing materials maintained higher levels of microbial diversity and stability, even when modifiers were complete depleted or the VOCs inlet loading was increased. This study highlights the importance of packing materials for reducing the gap in performance between laboratory and industrial applications of BTFs.
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Affiliation(s)
- Rongfang Feng
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
| | - Gang Zhao
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
| | - Yonggang Yang
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
| | - Meiying Xu
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
| | - Shaobin Huang
- School of Environment and Energy, South China University of Technology, Guangzhou, PR China
| | - Guoping Sun
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
| | - Jun Guo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
| | - Jianjun Li
- Guangdong Institute of Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, PR China
- * E-mail:
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45
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Gobbi A, Santini RG, Filippi E, Ellegaard-Jensen L, Jacobsen CS, Hansen LH. Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR. PLoS One 2019; 14:e0200979. [PMID: 30973938 PMCID: PMC6459482 DOI: 10.1371/journal.pone.0200979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/03/2019] [Indexed: 01/18/2023] Open
Abstract
Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition. To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers from 1.00 to 2.20 m. Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition. Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier. These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.
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Affiliation(s)
- Alex Gobbi
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Rui G. Santini
- Natural History Museum of Denmark, Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Elisa Filippi
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | | | - Lars H. Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- * E-mail:
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Horton DJ, Theis KR, Uzarski DG, Learman DR. Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes. FEMS Microbiol Ecol 2019; 95:fiz033. [PMID: 30855669 PMCID: PMC6447756 DOI: 10.1093/femsec/fiz033] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/10/2019] [Indexed: 12/16/2022] Open
Abstract
Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystem services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships among nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa that may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.
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Affiliation(s)
- Dean J Horton
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
| | - Kevin R Theis
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, USA
| | - Donald G Uzarski
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
| | - Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
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Fan L, Wang Z, Chen M, Qu Y, Li J, Zhou A, Xie S, Zeng F, Zou J. Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment. Sci Total Environ 2019; 657:1194-1204. [PMID: 30677886 DOI: 10.1016/j.scitotenv.2018.12.069] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [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: 11/01/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Environmental microbiota plays important roles in the intestinal microbiota of aquatic animals. The Pacific white shrimp with high commercial value and euryhaline property has become the most important commercial species of shrimp in the world. However, the association between shrimp intestine and sediment at freshwater and marine cultured environment should be investigated to reveal the microbiota differences. In the present study, Miseq sequencing technology and bioinformatics were used to comprehensively compare the bacterial communities and all samples' V3-V4 regions of 16S rRNA gene were sequenced. Results showed that 55 phyla and 789 genera were identified due to the classifiable sequence. Sequencing data demonstrated statistically significant diverse microbiota compositions in the shrimp intestine and sediment at freshwater and marine cultured environment at the phylum and genus level. At the phylum level, the dominant phyla in all groups were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, Cyanobacteria, Bacteroidetes, Acidobacteria, Verrucomicrobia, Saccharibacteria. Proteobacteria were the most abundant and largest phylum except in the intestine of marine cultured shrimp and Actinobacteria may be enriched in the shrimp intestine from sediment. At the genus level, nine out of the twelve dominant genera exhibited statistically significant differences among all groups. Moreover, Lactobacillus tend to be enriched in the freshwater cultured shrimp intestine, while Synechococcus and Vibrio extremely abundance in the marine cultured shrimp intestine. These results showed that the bacterial compositions are mostly the same in shrimp intestine and sediment, while with different relative abundances of the bacterial communities. In conclusion, this study may greatly enhance our understanding of the microbiota characteristics between shrimp and sediment. Moreover, it provided guidance for the healthy aquaculture at freshwater and marine cultured environment.
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Affiliation(s)
- Lanfen Fan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China; Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou 510642, PR China.
| | - Zhenlu Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Miaoshan Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Yuexin Qu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Junyi Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Aiguo Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Shaolin Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Fang Zeng
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Jixing Zou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China.
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Feng F, Liu ZG, Song YX, Jiang CK, Chai XL, Tang CJ, Chai LY. The application of aged refuse in nitrification biofilter: Process performance and characterization. Sci Total Environ 2019; 657:1227-1236. [PMID: 30677889 DOI: 10.1016/j.scitotenv.2018.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 06/20/2018] [Revised: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
High adsorption capacity, good biocompatibility and low cost are highly demanded for biofilter used in ammonium-rich wastewater treatment. In this study, we used SEM, BET, XRD and 16S rRNA to document the evidence for good performance in adsorption and biodegradation in aged refuse. Parallel experiment between raw and inert refuse showed ammonium adsorption occurred at the initial week, with the highest ammonium removal efficiency of 90.36%, but saturated during the subsequent long-term operation. Meanwhile, over 6months' operation of an aged refuse biofilter was conducted to confirm that nitrification was the main pathway of ammonium conversion. The maximum nitrogen loading rate could reach up to as high as 1.28kg/m3/d, with ammonium removal efficiency at 99%. Further, high nitrifier biodiversity were detected with 'Nitrosomonas' and 'Nitrospira' in domination in the refuse. However, Nitrospira would outcompete Nitrosomonas under the oxygen limiting condition and resulted in the failure of partial nitrification. The physicochemical and biological analysis show that biodegradation is the main ammonium conversion pathway, which is the critical finding of this work. This investigation would help to accelerate the application of the aged refuse process in ammonium-rich wastewater treatment.
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Affiliation(s)
- Fan Feng
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Zhi-Gong Liu
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Yu-Xia Song
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Chu-Kuan Jiang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Xi-Lin Chai
- The Jiangxi Provincial Collaborative Research Institute for Environmental Protection Industry, Wannian 335500, China
| | - Chong-Jian Tang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China.
| | - Li-Yuan Chai
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
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Lee J, Cho J, Cho YJ, Cho A, Woo J, Lee J, Hong SG, Sul WJ, Kim OS. The latitudinal gradient in rock-inhabiting bacterial community compositions in Victoria Land, Antarctica. Sci Total Environ 2019; 657:731-738. [PMID: 30677938 DOI: 10.1016/j.scitotenv.2018.12.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 10/11/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
The harsh conditions in Victoria Land, Antarctica have formed a simple ecosystem dominated by microbes that use rocks as shelters to avoid environmental stressors. The area is composed of basement rocks that illustrate the history of complex deformation, thus it is highly valuable not only in perspectives of geology but also in biological aspects. Because this region is inhospitable to higher-level organisms and receives least external influences, it can be an ideal environment to investigate the relationship between rock-inhabiting bacterial communities and environmental factors. In such conditions, inorganics dissolved from minerals can be considered as key factors influencing rock-inhabiting bacterial communities. Thus, the present study attempted to explore rock-inhabiting bacterial communities throughout Victoria Land, to identify environmental parameters that are more influential on bacterial community compositions, and to investigate latitudinal gradients in environmental parameters and rock-inhabiting bacterial communities. The results suggested that (i) rock-inhabiting bacterial communities in Victoria Land predominately consisted of either Actinobacteria or Proteobacteria; (ii) latitudinal gradients in rock-inhabiting bacterial community compositions and some environmental parameters were observed; (iii) latitude, pH, nitrate, and sulfate significantly correlated with the dominant phyla; and (iv) the Classification and Regression Tree (CART) analysis demonstrated that latitude, pH, and sulfate concentrations could explain the dominant phylum with 89% accuracy. These findings can provide important insight into the link between environmental factors and rock-inhabiting bacterial community compositions in conditions with extremely cold temperatures and high levels of radiation, which could also be of interest in astrobiology.
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Affiliation(s)
- Jaejin Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Agricultural & Biosystems Engineering, Iowa State University, Ames, IA 50011, United States of America
| | - Junho Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Yong-Joon Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Ahnna Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jusun Woo
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jongik Lee
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ok-Sun Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea.
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Young JM, Skvortsov T, Kelleher BP, Mahaney WC, Somelar P, Allen CCR. Effect of soil horizon stratigraphy on the microbial ecology of alpine paleosols. Sci Total Environ 2019; 657:1183-1193. [PMID: 30677885 DOI: 10.1016/j.scitotenv.2018.11.442] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
There is remarkable potential for research at the interface between the earth sciences and environmental microbiology that may lead to advances in our understanding of the role of bacterial communities in the surface or subsurface environment of our planet. One mainstay of sedimentary classification is the concept of differential soil and/or paleosol horizons being the result of primarily physical and chemical weathering, with relatively little understanding of how microbial communities between these stratified horizons differ, if at all. In this study we evaluate the differences in microbial community taxonomy and biogeochemical functional potential between stratified soil horizons in an alpine paleosol environment using next-generation sequencing (NGS) shotgun sequencing. Paleosols represent a unique environment to study the effect of differences soil horizon environments on the microbial community due to their relative isolation, and the fact that three distinct stratified soil horizons can be identified within the top 30 cm of the soil. This enables us to assess variation in microbial community composition that will be relatively distinct from variation due to distance alone. We test the hypothesis that variation in soil community composition is linked to variation in the physical and chemical parameters that define stratigraphy. Multivariate statistical analysis of sequencing reads from soil horizons across five sampling sites revealed that 1223 microbial genera vary significantly and consistently in abundance across stratified soil horizons at class level. Specifically Ktedonobacter, Bacilli and Betaproteobacteria responded most strongly to soil depth. Alpha diversity showed a positive correlation with soil depth. Beta diversity, however, did not differ significantly between horizons. Genes involved in carbohydrate and nitrogen metabolism were found to be more abundant in Ah horizon samples. Closer inspection of carbohydrate metabolism genes revealed that genes involved in CO2 fixation, fermentation and saccharide metabolism decreased in abundance with depth while one‑carbon metabolism increased down profile.
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