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Villemur R, Payette G, Geoffroy V, Mauffrey F, Martineau C. Dynamics of a methanol-fed marine denitrifying biofilm: 2-impact of environmental changes on the microbial community. PeerJ 2019; 7:e7467. [PMID: 31423359 PMCID: PMC6697039 DOI: 10.7717/peerj.7467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/12/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm. METHODS The original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59. RESULTS High proportions of M. nitratireducenticrescens occurred in the biofilm cultures. H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0-1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures. CONCLUSIONS These results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes of M. nitratireducenticrescens strain GP59 and H. nitrativorans strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm. Other denitrifying heterotrophic bacteria are present in low proportions, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments.
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Affiliation(s)
- Richard Villemur
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, Québec, Canada
| | - Geneviève Payette
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, Québec, Canada
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Chamberland J, Beaulieu-Carbonneau G, Lessard MH, Labrie S, Bazinet L, Doyen A, Pouliot Y. Effect of membrane material chemistry and properties on biofouling susceptibility during milk and cheese whey ultrafiltration. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2017.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Peck V, Quiza L, Buffet JP, Khdhiri M, Durand AA, Paquette A, Thiffault N, Messier C, Beaulieu N, Guertin C, Constant P. Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices. Microb Biotechnol 2016; 9:316-29. [PMID: 26853704 PMCID: PMC4835570 DOI: 10.1111/1751-7915.12348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/15/2015] [Indexed: 11/30/2022] Open
Abstract
The impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high‐throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment.
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Affiliation(s)
- Vincent Peck
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Liliana Quiza
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Jean-Philippe Buffet
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Mondher Khdhiri
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Audrey-Anne Durand
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Alain Paquette
- Centre d'étude de la forêt, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, Canada, H3C 3P8
| | - Nelson Thiffault
- Centre d'étude de la forêt, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, Canada, H3C 3P8.,Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs, 2700 Einstein, Québec, Québec, Canada, G1P 3W8
| | - Christian Messier
- Centre d'étude de la forêt, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, Canada, H3C 3P8.,Institut des Sciences de la Forêt Tempérée (ISFORT), Université du Québec en Outaouais (UQO), 58 rue Principale, Ripon, Québec, Canada, J0V 1V0
| | - Nadyre Beaulieu
- Produits Forestiers Résolu, 2419 Route 155 sud, La Tuque, Québec, Canada, G9X 3N8
| | - Claude Guertin
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Philippe Constant
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
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