1
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Li Z, Cun S, Han G, Guo X, Liu B, Huang T, Hou D, Liu R, Liu X. New insight into soluble extracellular metabolites during sludge bulking process based on excitation-emission matrix spectroscopy and ultrahigh-performance liquid chromatography-mass spectrometry. ENVIRONMENTAL RESEARCH 2023; 219:115161. [PMID: 36580981 DOI: 10.1016/j.envres.2022.115161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Soluble extracellular metabolites (SEM) produced by microorganisms might significantly change during sludge bulking, which is a major operational problem caused by the excessive growth of filamentous bacteria. However, knowledge remains limited about the dynamics and potential role of SEM in the bulking of sludge. In this study, filamentous bulking was simulated in a laboratory-scale reactor and changes to SEM characteristics during the bulking process were investigated using excitation-emission matrix spectroscopy and ultrahigh-performance liquid chromatography-mass spectrometry. SEM components changed significantly at different phases of sludge bulking. Changes in SEM were closely correlated with the structure of the bacterial community. Based on the EEM profiles, significant increases in fulvic acid-like and humic acid-like substances in SEM were observed with the development of filamentous bulking. The degree of humification in SEM showed a clear increasing trend. Untargeted extracellular metabolomic analysis showed that the intensity of berberine and isorhamnetin in SEM increased significantly during the bulking phase, which might synergistically facilitate the development of filamentous bulking.
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Affiliation(s)
- Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Cun
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Ganghua Han
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Ting Huang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Deyin Hou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China.
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, University of Chinese Academy of Sciences, Beijing, China.
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2
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Mohd Din ARJ, Suzuki K, Honjo M, Amano K, Nishimura T, Moriuchi R, Dohra H, Ishizawa H, Kimura M, Tashiro Y, Futamata H. Imbalance in Carbon and Nitrogen Metabolism in Comamonas testosteroni R2 Is Caused by Negative Feedback and Rescued by L-arginine. Microbes Environ 2021; 36. [PMID: 34645730 PMCID: PMC8674442 DOI: 10.1264/jsme2.me21050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The collapse of Comamonas testosteroni R2 under chemostat conditions and the aerobic growth of strain R2 under batch conditions with phenol as the sole carbon source were investigated using physiological and transcriptomic techniques. Phenol-/catechol-degrading activities under chemostat conditions gradually decreased, suggesting that metabolites produced from strain R2 accumulated in the culture, which caused negative feedback. The competitive inhibition of phenol hydroxylase and catechol dioxygenase was observed in a crude extract of the supernatant collected from the collapsed culture. Transcriptomic analyses showed that genes related to nitrogen transport were up-regulated; the ammonium transporter amtB was up-regulated approximately 190-fold in the collapsed status, suggesting an increase in the concentration of ammonium in cells. The transcriptional levels of most of the genes related to gluconeogenesis, glycolysis, the pentose phosphate pathway, and the TCA and urea cycles decreased by ~0.7-fold in the stable status, whereas the activities of glutamate synthase and glutamine synthetase increased by ~2-fold. These results suggest that ammonium was assimilated into glutamate and glutamine via 2-oxoglutarate under the limited supply of carbon skeletons, whereas the synthesis of other amino acids and nucleotides was repressed by 0.6-fold. Furthermore, negative feedback appeared to cause an imbalance between carbon and nitrogen metabolism, resulting in collapse. The effects of amino acids on negative feedback were investigated. L-arginine allowed strain R2 to grow normally, even under growth-inhibiting conditions, suggesting that the imbalance was corrected by the stimulation of the urea cycle, resulting in the rescue of strain R2.
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Affiliation(s)
- Abd Rahman Jabir Mohd Din
- Graduate School of Science and Technology, Shizuoka University.,Innovation Centre in Agritechnology for Advanced Bioprocess, UTM Pagoh Research Center
| | - Kenshi Suzuki
- Microbial Ecotechnology (Social Cooperation Laboratory), Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University
| | - Koki Amano
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Tomoka Nishimura
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Ryota Moriuchi
- Research Institution of Green Science and Technology, Shizuoka University
| | - Hideo Dohra
- Research Institution of Green Science and Technology, Shizuoka University
| | - Hidehiro Ishizawa
- Research Institution of Green Science and Technology, Shizuoka University
| | - Motohiko Kimura
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Yosuke Tashiro
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University.,Research Institution of Green Science and Technology, Shizuoka University
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3
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Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. MICROBIAL ECOLOGY 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
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4
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Abdul Aziz FA, Suzuki K, Honjo M, Amano K, Mohd Din ARJB, Tashiro Y, Futamata H. Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture. J Biosci Bioeng 2020; 131:77-83. [PMID: 33268319 DOI: 10.1016/j.jbiosc.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/24/2022]
Abstract
The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp. P-10, under chemostat conditions supplied with phenol as a sole carbon and energy source. Population densities of all strains were monitored by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase. Although the supply of phenol was stopped to allow perturbation in the SBC, all of the strains coexisted and the degradation of phenol was maintained for more than 800 days. The qPCR analyses showed that strains LAB-08 and R2 became dominant simultaneously, whereas strain P-10 was a minor population. This phenomenon was observed before and after the phenol-supply stoppage. The kinetic parameters for phenol of the SBC changed before and after the phenol-supply stoppage, which suggests a change in functional roles of strains in the SBC. Transcriptional levels of phenol hydroxylase and catechol dioxygenases of three strains were monitored by reverse-transcription qPCR (RT-qPCR). The RT-qPCR analyses revealed that all strains shared phenol and survived independently before the phenol-supply stoppage. After the stoppage, strain P-10 would incur the cost for degradation of phenol and catechol, whereas strains LAB-08 and R2 seemed to be cheaters using metabolites, indicating the development of the metabolic network. These results indicated that it is important for the management and redesign of microbial communities to understand the metabolism of bacterial communities.
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Affiliation(s)
- Fatma Azwani Abdul Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Kenshi Suzuki
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Koki Amano
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | | | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan; Research Institution of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan.
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5
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Chen J, Wade MJ, Dolfing J, Soyer OS. Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer. J R Soc Interface 2020; 16:20190129. [PMID: 31064258 PMCID: PMC6544901 DOI: 10.1098/rsif.2019.0129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.
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Affiliation(s)
- Jing Chen
- 1 School of Life Sciences, University of Warwick , Coventry CV4 7AL , UK
| | - Matthew J Wade
- 3 School of Engineering, Newcastle University , Newcastle NE1 7RU , UK.,4 School of Mathematics and Statistics, McMaster University , Hamilton, Ontario , Canada L8S 4K1
| | - Jan Dolfing
- 3 School of Engineering, Newcastle University , Newcastle NE1 7RU , UK
| | - Orkun S Soyer
- 1 School of Life Sciences, University of Warwick , Coventry CV4 7AL , UK.,2 Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick , Coventry CV4 7AL , UK
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6
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Dang H, Klotz MG, Lovell CR, Sievert SM. Editorial: The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients. Front Microbiol 2019; 10:115. [PMID: 30800101 PMCID: PMC6375845 DOI: 10.3389/fmicb.2019.00115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Martin G Klotz
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,School of Molecular Biosciences, Washington State University, Richland, WA, United States
| | - Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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7
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Pousti M, Zarabadi MP, Abbaszadeh Amirdehi M, Paquet-Mercier F, Greener J. Microfluidic bioanalytical flow cells for biofilm studies: a review. Analyst 2019; 144:68-86. [PMID: 30394455 DOI: 10.1039/c8an01526k] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive experimental results include time-varying biofilm properties, structural and chemical heterogeneity, and especially their strong sensitivity to environmental cues. Therefore, in addition to judicious choice of measurement tools, a well-designed biofilm study requires strict control over experimental conditions, more so than most chemical studies. Due to excellent control over a host of physiochemical parameters, microfluidic flow cells have become indispensable in microbiological studies. Not surprisingly, the number of lab-on-chip studies focusing on biofilms and other microbiological systems with expanded analytical capabilities has expanded rapidly in the past decade. In this paper, we comprehensively review the current state of microfluidic bioanalytical research applied to bacterial biofilms and offer a perspective on new approaches that are expected to drive continued advances in this field.
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Affiliation(s)
- Mohammad Pousti
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec City, Québec G1 V 0A6, Canada
| | - Mir Pouyan Zarabadi
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec City, Québec G1 V 0A6, Canada
| | - Mehran Abbaszadeh Amirdehi
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec City, Québec G1 V 0A6, Canada
| | - François Paquet-Mercier
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec City, Québec G1 V 0A6, Canada
| | - Jesse Greener
- Département de chimie, Faculté des sciences et de génie, Université Laval, Québec City, Québec G1 V 0A6, Canada and CHU de Quebec Research Centre, Laval University, 10 rue de l'Espinay, Quebec City, (QC) G1L 3L5, Canada
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8
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Haruta S, Saito Y, Futamata H. Editorial: Development of Microbial Ecological Theory: Stability, Plasticity, and Evolution of Microbial Ecosystems. Front Microbiol 2017; 7:2069. [PMID: 28066386 PMCID: PMC5174121 DOI: 10.3389/fmicb.2016.02069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/07/2016] [Indexed: 12/02/2022] Open
Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University Hachioji, Japan
| | - Yasuhisa Saito
- Department of Mathematics, Shimane University Matsue, Japan
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka UniversityShizuoka, Japan; Department of Applied Chemistry and Biochemical Engineering, Shizuoka UniversityHamamatsu, Japan
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9
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Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00948-16. [PMID: 27660772 PMCID: PMC5034123 DOI: 10.1128/genomea.00948-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas sp. LAB-08 was isolated from a phenol-fed bioreactor constructed with contaminated aquifer soil as the inoculum. Strain LAB-08 utilized phenol as a sole carbon and energy source. Here, we report the genome sequence and annotation of Pseudomonas sp. LAB-08.
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10
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Aziz FAA, Suzuki K, Ohtaki A, Sagegami K, Hirai H, Seno J, Mizuno N, Inuzuka Y, Saito Y, Tashiro Y, Hiraishi A, Futamata H. Interspecies interactions are an integral determinant of microbial community dynamics. Front Microbiol 2015; 6:1148. [PMID: 26539177 PMCID: PMC4611161 DOI: 10.3389/fmicb.2015.01148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/05/2015] [Indexed: 11/26/2022] Open
Abstract
This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.
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Affiliation(s)
- Fatma A A Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia Serdang, Malaysia ; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Kenshi Suzuki
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Akihiro Ohtaki
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Keita Sagegami
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Hidetaka Hirai
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Jun Seno
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Naoko Mizuno
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Yuma Inuzuka
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Yasuhisa Saito
- Department of Mathematics, Shimane University Matsue, Japan
| | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Akira Hiraishi
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Hiroyuki Futamata
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
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11
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Paquet-Mercier F, Karas A, Safdar M, Aznaveh NB, Zarabadi M, Greener J. Development and calibration of a microfluidic biofilm growth cell with flow-templating and multi-modal characterization. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:1557-62. [PMID: 25570268 DOI: 10.1109/embc.2014.6943900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the development of a microfluidic flow-templating platform with multi-modal characterization for studies of biofilms and their precursor materials. A key feature is a special three inlet flow-template compartment, which confines and controls the location of biofilm growth against a template wall. Characterization compartments include Raman imaging to study the localization of the nutrient solutions, optical microscopy to quantify biofilm biomass and localization, and cyclic voltammetry for flow velocity measurements. Each compartment is tested and then utilized to make preliminary measurements.
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12
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Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y. The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. Front Microbiol 2014; 5:575. [PMID: 25400628 PMCID: PMC4214200 DOI: 10.3389/fmicb.2014.00575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 11/13/2022] Open
Abstract
Investigation of microbial interspecies interactions is essential for elucidating the function and stability of microbial ecosystems. However, community-based analyses including molecular-fingerprinting methods have limitations for precise understanding of interspecies interactions. Construction of model microbial consortia consisting of defined mixed cultures of isolated microorganisms is an excellent method for research on interspecies interactions. In this study, a model microbial consortium consisting of microorganisms that convert acetate into methane directly (Methanosaeta thermophila) and syntrophically (Thermacetogenium phaeum and Methanothermobacter thermautotrophicus) was constructed and the effects of elevated CO2 concentrations on intermicrobial competition were investigated. Analyses on the community dynamics by quantitative RT-PCR and fluorescent in situ hybridization targeting their 16S rRNAs revealed that high concentrations of CO2 have suppressive effects on the syntrophic microorganisms, but not on the aceticlastic methanogen. The pathways were further characterized by determining the Gibbs free energy changes (ΔG) of the metabolic reactions conducted by each microorganism under different CO2 concentrations. The ΔG value of the acetate oxidation reaction (T. phaeum) under high CO2 conditions became significantly higher than -20 kJ per mol of acetate, which is the borderline level for sustaining microbial growth. These results suggest that high concentrations of CO2 undermine energy acquisition of T. phaeum, resulting in dominance of the aceticlastic methanogen. This study demonstrates that investigation on model microbial consortia is useful for untangling microbial interspecies interactions, including competition among microorganisms occupying the same trophic niche in complex microbial ecosystems.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
- Research Center for Advanced Science and Technology, The University of TokyoTokyo, Japan
| | - Rina Yoshida
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Tomoyuki Sato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
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13
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Mathematical Modeling of Microbial Community Dynamics: A Methodological Review. Processes (Basel) 2014. [DOI: 10.3390/pr2040711] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Aznaveh NB, Safdar M, Wolfaardt G, Greener J. Micropatterned biofilm formations by laminar flow-templating. LAB ON A CHIP 2014; 14:2666-72. [PMID: 24722812 DOI: 10.1039/c4lc00084f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a microfluidic device capable of patterning linear biofilm formations using a flow templating approach. We describe the design considerations and fabrication methodology of a two level flow-templating micro-bioreactor (FT-μBR), which generates a biofilm growth stream surrounded on 3 sides by a growth inhibiting confinement stream. Through a combination of experiments and simulations we comprehensively evaluate and exploit control parameters to manipulate the biofilm growth template stream dimensions. The FT-μBR is then used to grow biofilm patterns with controllable dimensions. A proof-of-principle study using the device demonstrates its utility in conducting biofilm growth rate measurements under different shear stress environments. This opens the way for quantitative studies into the effects of the local shear environment on biofilm properties and for the synthesis of a new generation of functional biomaterials with controllable properties.
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Affiliation(s)
- Nahid Babaei Aznaveh
- Département de Chimie, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.
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Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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