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Camargo FP, Sakamoto IK, Delforno TP, Midoux C, Duarte ICS, Silva EL, Bize A, Varesche MBA. Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment. Environ Technol 2023; 44:3141-3160. [PMID: 35298346 DOI: 10.1080/09593330.2022.2052361] [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: 12/05/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.
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Affiliation(s)
- Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | | | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), Antony, France
| | | | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos (UFSCar) São Carlos, Brazil
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), Antony, France
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Guérin-Rechdaoui S, Bize A, Levesque-Ninio C, Janvier A, Lacroix C, Le Brizoual F, Barbier J, Amsaleg CR, Azimi S, Rocher V. Fate of SARS-CoV-2 coronavirus in wastewater treatment sludge during storage and thermophilic anaerobic digestion. Environ Res 2022; 214:114057. [PMID: 35995225 PMCID: PMC9391084 DOI: 10.1016/j.envres.2022.114057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/01/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Since the COVID-19 outbreak has started in late 2019, SARS-CoV-2 has been widely detected in human stools and in urban wastewater. No infectious SARS-CoV-2 particles have been detected in raw wastewater until now, but it has been reported occasionally in human stools. This has raised questions on the fate of SARS-CoV-2 during wastewater treatment and notably in its end-product, wastewater treatment sludge, which is classically valorized by land spreading for agricultural amendment. In the present work, we focused on SARS-CoV-2 stability in wastewater treatment sludge, either during storage (4 °C, room temperature) or thermophilic anaerobic digestion (50 °C). Anaerobic digestion is one of the possible processes for sludge valorization. Experiments were conducted in laboratory pilots; SARS-CoV-2 detection was based on RT-quantitative PCR or RT-digital droplet PCR. In addition to SARS-CoV-2, Bovine Coronavirus (BCoV) particles were used as surrogate virus. The RNA from SARS-CoV-2 particles, inactivated or not, was close to the detection limit but stable in wastewater treatment sludge, over the whole duration of the assays at 4 °C (55 days) and at ambient temperature (∼20 °C, 25 days). By contrast, the RNA levels of BCoV and inactivated SARS-CoV-2 particles decreased rapidly during the thermophilic anaerobic digestion of wastewater treatment sludge lasting for 5 days, with final levels that were close to the detection limit. Although the particles' infectivity was not assessed, these results suggest that thermophilic anaerobic digestion is a suitable process for sludge sanitation, consistent with previous knowledge on other coronaviruses.
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Affiliation(s)
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PROSE, Antony, 92160, France
| | - Camille Levesque-Ninio
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Alice Janvier
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Carlyne Lacroix
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Florence Le Brizoual
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Jérôme Barbier
- ID Solutions, Development Department, Grabels, 34790, France
| | | | - Sam Azimi
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Vincent Rocher
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
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Ngo VQH, Enault F, Midoux C, Mariadassou M, Chapleur O, Mazéas L, Loux V, Bouchez T, Krupovic M, Bize A. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ Microbiol 2022; 24:4853-4868. [PMID: 35848130 PMCID: PMC9796341 DOI: 10.1111/1462-2920.16120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/29/2022] [Indexed: 01/01/2023]
Abstract
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
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Affiliation(s)
- Vuong Quoc Hoang Ngo
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGEClermont‐FerrandFrance
| | - Cédric Midoux
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance,Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Mahendra Mariadassou
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Olivier Chapleur
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Laurent Mazéas
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Valentin Loux
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Théodore Bouchez
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, CNRS UMR6047, Archaeal Virology UnitParisFrance
| | - Ariane Bize
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
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Viveros ML, Azimi S, Pichon E, Roose-Amsaleg C, Bize A, Durandet F, Rocher V. Wild type and variants of SARS-COV-2 in Parisian sewage: presence in raw water and through processes in wastewater treatment plants. Environ Sci Pollut Res Int 2022; 29:67442-67449. [PMID: 36029443 PMCID: PMC9418656 DOI: 10.1007/s11356-022-22665-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 08/18/2022] [Indexed: 05/30/2023]
Abstract
The presence of SARS-CoV-2 RNA has been extensively reported at the influent of wastewater treatment plants (WWTPs) worldwide, and its monitoring has been proposed as a potential surveillance tool to early alert of epidemic outbreaks. However, the fate of the SARS-CoV-2 RNA in the treatment process of WWTP has not been widely studied yet; therefore, in this study, we aimed to evaluate the efficiency of treatment processes in reducing SARS-CoV-2 RNA levels in wastewater. The treatment process of three WWTPs of the Parisian area in France was monitored on six different weeks over a period of 2 months (from April 14 to June 9, 2021). SARS-CoV-2 RNA copies were detected using digital polymerase chain reaction (dPCR). Investigation on the presence of variants of concern (Del69-70, E484K, and L452R) was also performed. Additionally, SARS-CoV-2 RNA loads in the WWTPs influents were expressed as the viral concentration in per population equivalent (PE) and showed a good correlation with French public health indicators (incidence rate). SARS-CoV-2 RNA loads were notably reduced along the water treatment lines of the three WWTPs studied (2.5-3.4 log reduction). Finally, very low SARS-CoV-2 RNA loads were detected in effluents (non-detected in over half of the samples) which indicated that the potential risk of the release of wastewater effluents to the environment is probably insignificant, in the case of WWTPs enabling an efficient biological removal of nitrogen.
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Affiliation(s)
| | - Sam Azimi
- SIAAP - Direction Innovation, 82 avenue Kléber, 92700, Colombes, France
| | - Elodie Pichon
- GEOBIOMICS, 335 rue Louis Lépine, 34000, Montpellier, France
| | | | - Ariane Bize
- PRocédés biOtechnologiques Au Service de L'Environnement, INRAE Université Paris-Saclay, INRAE, 92761, Antony, France
| | | | - Vincent Rocher
- SIAAP - Direction Innovation, 82 avenue Kléber, 92700, Colombes, France
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Hao L, Fan L, Chapleur O, Guenne A, Bize A, Bureau C, Lü F, He P, Bouchez T, Mazéas L. Gradual development of ammonia-induced syntrophic acetate-oxidizing activities under mesophilic and thermophilic conditions quantitatively tracked using multiple isotopic approaches. Water Res 2021; 204:117586. [PMID: 34474248 DOI: 10.1016/j.watres.2021.117586] [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: 05/07/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Insights into microbiota adaptation to increased ammonia stress, and identification of indicator microorganisms can help to optimize the operation of anaerobic digesters. To identify microbial indicators and investigate their metabolic contribution to acetoclastic methanogenesis (AM), syntrophic acetate oxidation (SAO) or hydrogenotrophic methanogenesis (HM), 40 anaerobic batch reactors fed with acetate of 110 mmol/L were set up at NH4+-N concentrations of 0.14 g/L, 5.00 g/L or 7.00 g/L, inoculated with thermophilic or mesophilic microbiota with or without pre-exposure to ammonia stress. Four stable carbon isotope probing approaches were applied in parallel, with [1,2-13C]-CH3COOH, [2-13C]-CH3COOH, [13C]NaHCO3 or non-labeled CH3COOH used individually. The last three approaches were used to quantify the methanogenic pathways by tracking labeled 13C or natural 13C signatures in the resulting CH4 and CO2, and consistently detected the dynamic transition of dominant pathways from AM to SAO-HM under ammonia stress. Results of quantitative PCR and fluorescence in-situ hybridization illustrated the procedure, acetotrophic methanogens being outcompeted by acetate-oxidizing syntrophs. The first and last isotope-labeling approaches were designed to probe the active acetate-mineralizing microbes with DNA-SIP. Known acetate-oxidizing bacteria like Syntrophaceticus and Tepidanaerobacter, as well as novel members of Pseudomonas, Bacillus and Symbiobacteraceae were detected, with Methanoculleus as the predominant H2/CO2-utilizing partner. Using NanoSIMS, some bacterial cells were observed to be fixing CO2 from [13C]NaHCO3. In this study, Methanosaeta was only active with ammonia < 200 mg-N/L; the syntrophs catalyzing SAO-HM started to compete with AM-conducting Methanosarcina at intermediate concentrations of ammonia, i.e. 200-500 mg-N/L, and outcompeted the acetotrophic methanogens with ammonia > 500 mg-N/L. Under ammonia stress, diverse known and novel microbial taxa were involved in acetate mineralization, comparable with those identified in previous studies.
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Affiliation(s)
- Liping Hao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Lu Fan
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Angéline Guenne
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Chrystelle Bureau
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France
| | - Fan Lü
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China.
| | - Théodore Bouchez
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France.
| | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, Antony 92761, France.
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Godon JJ, Bize A, Ngo H, Cauquil L, Almeida M, Petit MA, Zemb O. Bacterial Consumption of T4 Phages. Microorganisms 2021; 9:microorganisms9091852. [PMID: 34576747 PMCID: PMC8472381 DOI: 10.3390/microorganisms9091852] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022] Open
Abstract
The bacterial consumption of viruses not been reported on as of yet even though bacteria feed on almost anything. Viruses are widely distributed but have no acknowledged active biocontrol. Viral biomass undoubtedly reintegrates trophic cycles; however, the mechanisms of this phase still remain unknown. 13C-labelled T4 phages monitor the increase of the density of the bacterial DNA concomitant with the decrease of plaque forming units. We used 12C T4 phages as a control. T4 phage disappearance in wastewater sludge was found to occur mainly through predation by Aeromonadacea. Phage consumption also favours significant in situ bacterial growth. Furthermore, an isolated strain of Aeromonas was observed to grow on T4 phages as sole the source of carbon, nitrogen, and phosphorus. Bacterial species are capable of consuming bacteriophages in situ, which is likely a widespread and underestimated type of biocontrol. This assay is anticipated as a starting point for harnessing the bacterial potential in limiting the diffusion of harmful viruses within environments such as in the gut or in water.
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Affiliation(s)
- Jean-Jacques Godon
- INRAE, Univ Montpellier, LBE, 11100 Narbonne, France
- Correspondence: (J.-J.G.); (O.Z.); Tel.: +33-4-68-42-51-54 (J.-J.G.); +33-5-61-28-50-99 (O.Z.)
| | - Ariane Bize
- PRocédés biOtechnologiques au Service de l’Environnement, INRAE, Université Paris-Saclay, 92761 Antony, France; (A.B.); (H.N.)
| | - Hoang Ngo
- PRocédés biOtechnologiques au Service de l’Environnement, INRAE, Université Paris-Saclay, 92761 Antony, France; (A.B.); (H.N.)
| | - Laurent Cauquil
- GenPhySE, INRAE, Université de Toulouse, 31320 Castanet-Tolosan, France;
| | - Mathieu Almeida
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Marie-Agnès Petit
- AgroParisTech, Micalis Institute, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Olivier Zemb
- GenPhySE, INRAE, Université de Toulouse, 31320 Castanet-Tolosan, France;
- Correspondence: (J.-J.G.); (O.Z.); Tel.: +33-4-68-42-51-54 (J.-J.G.); +33-5-61-28-50-99 (O.Z.)
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Camargo FP, Sakamoto IK, Delforno TP, Mariadassou M, Loux V, Midoux C, Duarte ICS, Silva EL, Bize A, Varesche MBA. Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions. J Environ Manage 2021; 291:112631. [PMID: 33932835 DOI: 10.1016/j.jenvman.2021.112631] [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: 11/23/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Energy recovery from lignocellulosic waste has been studied as an alternative to the problem of inappropriate waste disposal. The present study aimed at characterizing the microbial community and the functional activity of reactors applied to H2 production through lignocellulosic waste fermentation in optimized conditions. The latter were identified by means of Rotational Central Composite Design (RCCD), applied to optimize allochthonous inoculum concentration (2.32-5.68 gTVS/L of granular anaerobic sludge), pH (4.32-7.68) and Citrus Peel Waste (CPW) concentration (1.55-28.45 g/L). After validation, the conditions identified for optimal H2 production were 4 gSTV/L of allochthonous inoculum, 29.8 g/L of CPW (substrate) and initial pH of 8.98. In these conditions, 48.47 mmol/L of H2 was obtained, which is 3.64 times higher than the concentration in unoptimized conditions (13.31 mmol H2/L using 15 g/L of CPW, 2 gTVS/L of allochthonous inoculum, pH 7.0). Acetogenesis was the predominant pathway, and maximal concentrations of 3,731 mg/L of butyric acid and 3,516 mg/L of acetic acid were observed. Regarding the metataxonomic profile, Clostridium genus was dramatically favored in the optimized condition (79.78%) when compared to the allochthonous inoculum (0.43%). It was possible to identify several genes related to H2 (i.e dehydrogenases) and volatile fatty acids (VFA) production and with cellulose degradation, especially some CAZymes from the classes Auxiliary Activities, Glycoside Hydrolases and Glycosyl Transferase. By means of differential gene expression it was observed that cellulose degradation and acetic acid production pathways were overabundant in samples from the optimized reactors, highlighting endo-β-1,4-glucanase/cellulose, endo-β-1,4-xylanase, β-glucosidase, β-mannosidase, cellulose β-1,4-cellobiosidase, cellobiohydrolase, and others, as main the functions.
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Affiliation(s)
- Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - Tiago Palladino Delforno
- Department of Biology, Federal University of São Carlos (UFSCar), João Leme dos Santos Highway, Km 101, zipcode 18052-780, Sorocaba, São Paulo, Brazil
| | - Mahendra Mariadassou
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350, Jouy-en-Josas, France; Université Paris Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Valentin Loux
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350, Jouy-en-Josas, France; Université Paris Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350, Jouy-en-Josas, France; Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), 92761, Antony, France; Université Paris Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Iolanda Cristina Silveira Duarte
- Department of Biology, Federal University of São Carlos (UFSCar), João Leme dos Santos Highway, Km 101, zipcode 18052-780, Sorocaba, São Paulo, Brazil
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos (UFSCar), Rod Washington Luiz, Km 235, SP 310, 13565-905, São Carlos, SP, Brazil
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), 92761, Antony, France
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil.
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Bize A, Midoux C, Mariadassou M, Schbath S, Forterre P, Da Cunha V. Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history. BMC Genomics 2021; 22:186. [PMID: 33726663 PMCID: PMC7962313 DOI: 10.1186/s12864-021-07471-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors. RESULTS For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile. CONCLUSION This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.
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Affiliation(s)
- Ariane Bize
- Université Paris-Saclay, INRAE, PROSE, F-92761, Antony, France.
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, PROSE, F-92761, Antony, France.,Université Paris-Saclay, INRAE, MaIAGE, F-78350, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, F-78350, Jouy-en-Josas, France
| | - Mahendra Mariadassou
- Université Paris-Saclay, INRAE, MaIAGE, F-78350, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, F-78350, Jouy-en-Josas, France
| | - Sophie Schbath
- Université Paris-Saclay, INRAE, MaIAGE, F-78350, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, F-78350, Jouy-en-Josas, France
| | - Patrick Forterre
- Institut Pasteur, Unité de Virologie des Archées, Département de Microbiologie, 25 Rue du Docteur Roux, 75015, Paris, France. .,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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9
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Delforno TP, Macedo TZ, Midoux C, Lacerda GV, Rué O, Mariadassou M, Loux V, Varesche MBA, Bouchez T, Bize A, Oliveira VM. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. Sci Total Environ 2019; 649:482-494. [PMID: 30176460 DOI: 10.1016/j.scitotenv.2018.08.328] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 07/10/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathway. A homemade bioinformatics pipeline combined with an R workflow was developed to perform the RNAseq data analysis. UASB_SL and UASB_LW showed similar values of LAS biological degradation (~47%) and removal (53-55%). Rarefaction analysis revealed that 1-2 million reads were sufficient to access the whole functional capacity. In the first step of LAS biodegradation pathway, fumarate reductase subunit C was detected and taxonomically assigned to the genus Syntrophobacter (0.002% - UASB_SL; 0.0015% - UASB_LW; not detected - UASB_Control). In the second step, many enzymes related to beta-oxidation were observed and most of them with low relative abundance in UASB Control and taxonomically related with Smithella, Acinetobacter and Syntrophorhabdus. For the ring cleavage step, the abundance of 6 OCH CoA hydrolase putative gene was ten times higher in UASB_SL and UASB_LW when compared to UASB_Control, and assigned to Desulfomonile and Syntrophorhabdus. Finally, the adenylylsulfate reductase, taxonomically related with Desulfovibrio and Desulfomonile, was observed in the desulfonation step with the highest relative abundance in UASB_LW.
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Affiliation(s)
- Tiago P Delforno
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil.
| | - Thais Z Macedo
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil
| | - Cédric Midoux
- Irstea, UR HBAN, F-92761 Antony, France; Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Gileno V Lacerda
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil
| | - Olivier Rué
- Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Mahendra Mariadassou
- Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Valentin Loux
- Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Maria B A Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil
| | | | | | - Valéria M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil
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10
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Tian JH, Pourcher AM, Bize A, Wazeri A, Peu P. Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw. Bioresour Technol 2017; 237:31-38. [PMID: 28411050 DOI: 10.1016/j.biortech.2017.03.142] [Citation(s) in RCA: 3] [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: 01/27/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
A new pretreatment method of lignocellulosic biomass was explored by using a wet aerobic process with an alkaline lignin and a mineral salt solution. This treatment significantly improved structural modification of rape straw used as substrate model in this study. Change in cellulose accessibility to cellulase of rape straw rose up to six fold within the first days of this pretreatment without generated significant modification of van Soest lignocellulose fractionation. The biological pretreatment apply to rape straw induced a high microbial activity revealed by quantitative PCR and sequencing techniques, suggesting that bacteria including Xanthomonadales and Sphingobacteriales may be involved in this lignocellulosic biomass transformation. Moreover, results of this work demonstrate that the endogenous microbial community associated with rape straw plays a key role in its alteration.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Anne-Marie Pourcher
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Ariane Bize
- IRSTEA, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, CS 10030, F-92761 Antony, France
| | - Alaa Wazeri
- Egypt-Japan University of Science and Technology (E-JUST), Environmental Engineering Department, P.O. Box 179, New Borg El-Arab City 21934, Alexandria, Egypt
| | - Pascal Peu
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France.
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11
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Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A. Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties. PLoS One 2017; 12:e0170524. [PMID: 28114419 PMCID: PMC5256962 DOI: 10.1371/journal.pone.0170524] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 10/14/2016] [Accepted: 01/05/2017] [Indexed: 11/25/2022] Open
Abstract
Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the “xyl-doc” cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.
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Affiliation(s)
| | - Alain Guillot
- UMR 1319 MICALIS, PAPPSO, INRA, Jouy-en-Josas, France
| | | | | | | | | | | | | | | | - Diana Z. Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | | | | | - Gérard Mortha
- LGP2, UMR CNRS 5518, Grenoble INP-Pagora, Saint Martin d'Hères, France
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12
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Hao L, Bize A, Conteau D, Chapleur O, Courtois S, Kroff P, Desmond-Le Quéméner E, Bouchez T, Mazéas L. New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions. Water Res 2016; 102:158-169. [PMID: 27340817 DOI: 10.1016/j.watres.2016.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 03/02/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 05/07/2023]
Abstract
Analyses on bacterial, archaeal communities at family level and methane-production metabolism were conducted in thirteen full-scale and pilot-scale anaerobic sludge digesters. These digesters were operated at different conditions regarding solids concentration, sludge retention time, organic loading rate and feedstock composition, seeking to optimize digester capacity. Correlations between process parameters and identified microbial phylotypes were evaluated based on relative abundance of these phylotypes determined by Quantitative PCR and 16S rDNA amplicon sequencing. Results showed that, Total Solids concentration (TS), among the evaluated operational parameters, demonstrated the most positive correlation with chemical parameters (including NH3 and VFAs) and significant impact on the abundance of key microbial phylotypes regardless of other factors. Digesters were grouped into 'Higher-TS' with higher stress (TS > 44 g/L, NH3 > 90 mg/L, VFAs > 300 mg/L) and 'Lower-TS' under easier status (TS ≤ 44 g/L, NH3 < 120 mg/L, VFAs < 525 mg/L) in this study. We identified the key microbial phylotypes, i.e. the most abundant and discriminating populations, in 'Higher-TS' digesters with high biogas production rate, which were the class Clostridia, the family Methanosarcinaceae and the order Methanobacteriales. Thermoanaerobacteraceae and Syntrophomonadaceae were identified as key families of Clostridia. Methane was produced both from acetoclastic and hydrogenotrophic methanogenesis. By contrast, in 'Higher-TS' digesters with low biogas production rate, the classes Alpha-, Beta- and Gamma-proteobacteria were detected in higher percentages, of which Rhodobacteraceae, Comamonadaceae and Xanthomonadaceae were the most abundant families respectively, and Methanomicrobiales was the prevailing methanogen order. Consistently, hydrogenotrophic pathway was predominant for methanogenesis, indicating existence of syntrophic acetate oxidation in such 'high-stress', low biogas production rate digesters. These microbial phylotypes were therefore considered to be associated to 'Higher-TS' operation. In 'Lower-TS' digesters, the abundance of the class Delta-proteobacteria, the families Anaerolineaceae, Rikenellaceae, Candidatus Cloacamonas and Methanosaetaceae was obviously higher compared with those in 'Higher-TS' digesters, which were thus considered to be marker phylotypes of easy status. The influence of TS and NH3 on the microbiome should be considered when a 'TS-increasing' strategy is applied to increase digester capacity.
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Affiliation(s)
- Liping Hao
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Ariane Bize
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Delphine Conteau
- Suez - CIRSEE, 38 rue du Président Wilson, 78230, Le Pecq, France
| | - Olivier Chapleur
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Sophie Courtois
- Suez - CIRSEE, 38 rue du Président Wilson, 78230, Le Pecq, France
| | - Pablo Kroff
- Suez - CIRSEE, 38 rue du Président Wilson, 78230, Le Pecq, France
| | | | - Théodore Bouchez
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Laurent Mazéas
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France.
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13
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Poirier S, Bize A, Bureau C, Bouchez T, Chapleur O. Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators? Water Res 2016; 100:296-305. [PMID: 27208731 DOI: 10.1016/j.watres.2016.05.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [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: 02/25/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 06/05/2023]
Abstract
Performance stability is a key operational issue for anaerobic digestion (AD) and phenolic compounds are regularly mentioned as a major cause of digester failures. To get more insights into AD microbiota response to a wide range of inhibition levels, anaerobic batch toxicity assays were conducted with ten phenol concentrations up to 5.00 g/L. Final AD performance was not impaired up to 1.00 g/L. However, progressive shifts in microbial community structure were detected from 0.50 g/L. The methanogenic function was maintained along with increasing initial phenol concentrations up to 2.00 g/L thanks to the emergence of genus Methanoculleus at the expense of Methanosarcina. Within syntrophic populations, family Syntrophomonadaceae proportion was gradually reduced by phenol while Synergistaceae gained in importance in the microbiome. Moreover, at 2.00 g/L, the relative abundance of families belonging to order Clostridiales dropped, leading to the predominance of populations assigned to order Bacteroidales even though it did not prevent final AD performance deterioration. It illustrates the high level of adaptability of archaeal and bacterial communities and suggests the possibility of determining early warning microbial indicators associated with phenol inhibition.
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Affiliation(s)
- Simon Poirier
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Ariane Bize
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Chrystelle Bureau
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Théodore Bouchez
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Olivier Chapleur
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
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14
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Bize A, Cardona L, Desmond-Le Quéméner E, Battimelli A, Badalato N, Bureau C, Madigou C, Chevret D, Guillot A, Monnet V, Godon JJ, Bouchez T. Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge. Proteomics 2015; 15:3532-43. [PMID: 26260998 DOI: 10.1002/pmic.201500041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/02/2015] [Accepted: 08/05/2015] [Indexed: 01/05/2023]
Abstract
Two parallel anaerobic digestion lines were designed to match a "bovid-like" digestive structure. Each of the lines consisted of two continuous stirred tank reactors placed in series and separated by an acidic treatment step. The first line was inoculated with industrial inocula whereas the second was seeded with cow digestive tract contents. After 3 months of continuous sewage sludge feeding, samples were recovered for shotgun metaproteomic and DNA-based analysis. Strikingly, protein-inferred and 16S ribosomal DNA tags based taxonomic community profiles were not consistent. PCA however revealed a similar clustering pattern of the samples, suggesting that reproducible methodological and/or biological factors underlie this observation. The performances of the two digestion lines did not differ significantly and the cow-derived inocula did not establish in the reactors. A low throughput metagenomic dataset (3.4 × 10(6) reads, 1.1 Gb) was also generated for one of the samples. It allowed a substantial increase of the analysis depth (11 vs. 4% of spectral identification rate for the combined samples). Surprisingly, a high proportion of proteins from members of the "Candidatus Competibacter" group, a key microbial player usually found in activated sludge plants, was retrieved in our anaerobic digester samples. Data are available via ProteomeXchange with identifier PXD002420 (http://proteomecentral.proteomexchange.org/dataset/PXD002420).
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Affiliation(s)
| | | | | | - Audrey Battimelli
- INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
| | | | | | | | | | - Alain Guillot
- INRA, UMR1319 MICALIS, PAPPSO, Jouy-en-Josas, France
| | | | - Jean-Jacques Godon
- INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
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15
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Bize A, Sezonov G, Prangishvili D. [Enigmatic archaeal viruses]. Biol Aujourdhui 2013; 207:169-79. [PMID: 24330970 DOI: 10.1051/jbio/2013015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 11/14/2022]
Abstract
Viruses infecting microorganisms of the third domain of life, Archaea, are still poorly characterized: to date, only about fifty of these viruses have been isolated. Their hosts are hyperthermophilic, acidothermophilic, and extreme halophilic or methanogenic archaea. Their morphotypes are highly diverse and their gene content is very specific. Some of these viruses have developed extraordinary mechanisms to open the cell wall thanks to the formation of exceptional pyramidal nanostructures. The still limited knowledge about the biology of archaeoviruses should develop rapidly in the coming years.
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Affiliation(s)
| | - Guennadi Sezonov
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France - UMR 7138 Systématique, Adaptation, Évolution, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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16
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Chapleur O, Bize A, Serain T, Mazéas L, Bouchez T. Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of13C-cellulose in batch digesters. FEMS Microbiol Ecol 2013; 87:616-29. [DOI: 10.1111/1574-6941.12249] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/25/2013] [Accepted: 11/08/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Olivier Chapleur
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Ariane Bize
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Thibaut Serain
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Laurent Mazéas
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
| | - Théodore Bouchez
- Hydrosystems and Bioprocesses Research Unit; Irstea; Antony Cedex France
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17
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Jaubert C, Danioux C, Oberto J, Cortez D, Bize A, Krupovic M, She Q, Forterre P, Prangishvili D, Sezonov G. Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol 2013; 3:130010. [PMID: 23594878 PMCID: PMC3718332 DOI: 10.1098/rsob.130010] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus-host interactions and the CRISPR/Cas defence mechanism in Archaea.
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Affiliation(s)
- Carole Jaubert
- Département de Microbiologie, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
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18
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Abstract
Since their discovery in the early 1980s, viruses that infect the third domain of life, the Archaea, have captivated our attention because of their virions' unusual morphologies and proteins, which lack homologues in extant databases. Moreover, the life cycles of these viruses have unusual features, as revealed by the recent discovery of a novel virus egress mechanism that involves the formation of specific pyramidal structures on the host cell surface. The available data elucidate the particular nature of the archaeal virosphere and shed light on questions concerning the origin and evolution of viruses and cells. In this review, we summarize the current knowledge of archeoviruses, their interaction with hosts and plasmids and their role in the evolution of life.
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Affiliation(s)
- Mery Pina
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Paris, France
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19
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Chenoune M, Tissier R, Lidouren F, Couvreur N, Bize A, Ghaleh B, Berdeaux A. F010 L’hypothermie induite par ventilation liquide totale permet d’induire une cardioprotection persistante après une ischémie myocardique prolongée chez le lapin. Arch Cardiovasc Dis 2009. [DOI: 10.1016/s1875-2136(09)72263-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Bize A, Peng X, Prokofeva M, Maclellan K, Lucas S, Forterre P, Garrett RA, Bonch-Osmolovskaya EA, Prangishvili D. Viruses in acidic geothermal environments of the Kamchatka Peninsula. Res Microbiol 2008; 159:358-66. [PMID: 18565736 DOI: 10.1016/j.resmic.2008.04.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 04/16/2008] [Accepted: 04/16/2008] [Indexed: 10/22/2022]
Abstract
Screening for viruses in samples taken from acidic hot springs of Kamchatka (Russia) revealed a collection of morphotypes, including linear, spherical and complex fusiform shapes, which show partial similarity to those found in acidic geothermal environments in other geographical locations. One of the viruses, Acidianus filamentous virus 9, AFV9, was isolated and its structure and genome were studied in detail.
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Affiliation(s)
- Ariane Bize
- Molecular Biology of the Gene in Extremophiles Unit, Institut Pasteur, rue du Dr. Roux 25, 75724 Paris Cedex 15, France
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