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Zou Z, Yang H, Zhang S, Chi W, Wang X, Liu Z. Nitrogen removal performance and microbial community analysis of immobilized biological fillers in rare earth mine wastewater. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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2
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Robles-Aguilar AA, Grunert O, Hernandez-Sanabria E, Mysara M, Meers E, Boon N, Jablonowski ND. Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine ( Lupinus angustifolius). FRONTIERS IN PLANT SCIENCE 2020; 11:572741. [PMID: 33329631 PMCID: PMC7717983 DOI: 10.3389/fpls.2020.572741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/19/2020] [Indexed: 05/11/2023]
Abstract
Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.
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Affiliation(s)
- Ana A. Robles-Aguilar
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
| | - Oliver Grunert
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- Greenyard Horticulture, Ghent, Belgium
| | - Emma Hernandez-Sanabria
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Bacteriology, VIB – KU Leuven Center for Microbiology, Rega Institute, Leuven, Belgium
| | - Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Center, StudieCentrum voor Kernenergie⋅Centre d’étude de l’Energie Nucléaire (SCK⋅CEN), Mol, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Erik Meers
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- *Correspondence: Nico Boon,
| | - Nicolai D. Jablonowski
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
- Nicolai D. Jablonowski,
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3
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Piwosz K, Shabarova T, Tomasch J, Šimek K, Kopejtka K, Kahl S, Pieper DH, Koblížek M. Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS). THE ISME JOURNAL 2018; 12:2640-2654. [PMID: 29980795 PMCID: PMC6194029 DOI: 10.1038/s41396-018-0213-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/01/2018] [Accepted: 06/09/2018] [Indexed: 01/07/2023]
Abstract
The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.
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Affiliation(s)
- Kasia Piwosz
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic
| | - Tanja Shabarova
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 37005, Česke Budějovice, Czech Republic
| | - Jürgen Tomasch
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 37005, Česke Budějovice, Czech Republic
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, CZ-37005, České Budějovice, Czech Republic
| | - Silke Kahl
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Dietmar H Pieper
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic.
- Faculty of Science, University of South Bohemia in České Budějovice, CZ-37005, České Budějovice, Czech Republic.
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4
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Meng J, Li J, Li J, Antwi P, Deng K, Nan J, Xu P. Enhanced nitrogen removal from piggery wastewater with high NH 4+ and low COD/TN ratio in a novel upflow microaerobic biofilm reactor. BIORESOURCE TECHNOLOGY 2018; 249:935-942. [PMID: 29145120 DOI: 10.1016/j.biortech.2017.10.108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
To enhance nutrient removal more cost-efficiently in microaerobic process treating piggery wastewater characterized by high ammonium (NH4+-N) and low chemical oxygen demand (COD) to total nitrogen (TN) ratio, a novel upflow microaerobic biofilm reactor (UMBR) was constructed and the efficiency in nutrient removal was evaluated with various influent COD/TN ratios and reflux ratios. The results showed that the biofilm on the carriers had increased the biomass in the UMBR and enhanced the enrichment of slow-growth-rate bacteria such as nitrifiers, denitrifiers and anammox bacteria. The packed bed allowed the microaerobic biofilm process perform well at a low reflux ratio of 35 with a NH4+-N and TN removal as high as 93.1% and 89.9%, respectively. Compared with the previously developed upflow microaerobic sludge reactor, the UMBR had not changed the dominant anammox approach to nitrogen removal, but was more cost-efficiently in treating organic wastewater with high NH4+-N and low COD/TN ratio.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Philip Antwi
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Pianpian Xu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
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Bacterial Tubulins A and B Exhibit Polarized Growth, Mixed-Polarity Bundling, and Destabilization by GTP Hydrolysis. J Bacteriol 2017; 199:JB.00211-17. [PMID: 28716960 DOI: 10.1128/jb.00211-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria of the genus Prosthecobacter express homologs of eukaryotic α- and β-tubulin, called BtubA and BtubB (BtubA/B), that have been observed to assemble into filaments in the presence of GTP. BtubA/B polymers are proposed to be composed in vitro by two to six protofilaments in contrast to that in vivo, where they have been reported to form 5-protofilament tubes named bacterial microtubules (bMTs). The btubAB genes likely entered the Prosthecobacter lineage via horizontal gene transfer and may be derived from an early ancestor of the modern eukaryotic microtubule (MT). Previous biochemical studies revealed that BtubA/B polymerization is reversible and that BtubA/B folding does not require chaperones. To better understand BtubA/B filament behavior and gain insight into the evolution of microtubule dynamics, we characterized in vitro BtubA/B assembly using a combination of polymerization kinetics assays and microscopy. Like eukaryotic microtubules, BtubA/B filaments exhibit polarized growth with different assembly rates at each end. GTP hydrolysis stimulated by BtubA/B polymerization drives a stochastic mechanism of filament disassembly that occurs via polymer breakage and/or fast continuous depolymerization. We also observed treadmilling (continuous addition and loss of subunits at opposite ends) of BtubA/B filament fragments. Unlike MTs, polymerization of BtubA/B requires KCl, which reduces the critical concentration for BtubA/B assembly and induces it to form stable mixed-orientation bundles in the absence of any additional BtubA/B-binding proteins. The complex dynamics that we observe in stabilized and unstabilized BtubA/B filaments may reflect common properties of an ancestral eukaryotic tubulin polymer.IMPORTANCE Microtubules are polymers within all eukaryotic cells that perform critical functions; they segregate chromosomes, organize intracellular transport, and support the flagella. These functions rely on the remarkable range of tunable dynamic behaviors of microtubules. Bacterial tubulin A and B (BtubA/B) are evolutionarily related proteins that form polymers. They are proposed to be evolved from the ancestral eukaryotic tubulin, a missing link in microtubule evolution. Using microscopy and biochemical approaches to characterize BtubA/B assembly in vitro, we observed that they exhibit complex and structurally polarized dynamic behavior like eukaryotic microtubules but differ in how they self-associate into bundles and how this bundling affects their stability. Our results demonstrate the diversity of mechanisms through which tubulin homologs promote filament dynamics and monomer turnover.
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6
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Pu J, Feng C, Liu Y, Li R, Kong Z, Chen N, Tong S, Hao C, Liu Y. Pyrite-based autotrophic denitrification for remediation of nitrate contaminated groundwater. BIORESOURCE TECHNOLOGY 2014; 173:117-123. [PMID: 25299487 DOI: 10.1016/j.biortech.2014.09.092] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/12/2014] [Accepted: 09/17/2014] [Indexed: 06/04/2023]
Abstract
In this study, pyrite-based denitrification using untreated pyrite (UP) and acid-pretreated pyrite (AP) was evaluated as an alternative to elemental sulfur based denitrification. Pyrite-based denitrification resulted in a favorable nitrate removal rate constant (0.95 d(-1)), sulfate production of 388.00 mg/L, and a stable pH. The pretreatment of pyrite with acid led to a further increase in the nitrate removal rate constant (1.03 d(-1)) and reduction in initial sulfate concentration (224.25±7.50 mg/L). By analyzing the microbial community structure using Denaturing Gradient Gel Electrophoresis, it was confirmed that Sulfurimonas denitrificans (S. denitrificans) could utilize pyrite as an electron donor. A stable pH was observed over the entire experimental period, indicating that the use of a pH buffer reagent would not be necessary for pyrite-based denitrification. Therefore, pyrite could effectively replace elemental sulfur as an electron donor in autotrophic denitrification for nitrate-contaminated groundwater remediation.
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Affiliation(s)
- Jiaoyang Pu
- Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences, Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chuanping Feng
- Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences, Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Ying Liu
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Rui Li
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhe Kong
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Nan Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shuang Tong
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chunbo Hao
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Ye Liu
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
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7
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Lee J, Park B, Woo SG, Lee J, Park J. Prosthecobacter algae sp. nov., isolated from activated sludge using algal metabolites. Int J Syst Evol Microbiol 2013; 64:663-667. [PMID: 24170774 DOI: 10.1099/ijs.0.052787-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, fusiform-shaped, facultatively anaerobic bacterial strain, designated EBTL04(T), was isolated from activated sludge using algal metabolites and taxonomically characterized through polyphasic investigation. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EBTL04(T) belongs to the family Verrucomicrobiaceae, class Verrucomicrobiae, and is closely related to Prosthecobacter dejongeii DSM 12251(T) (98.6 % sequence similarity), Prosthecobacter fusiformis ATCC 25309(T) (97.9 %), Prosthecobacter debontii DSM 14044(T) (97.5%), Prosthecobacter vanneervenii DSM 12252(T) (94.7%) and Prosthecobacter fluviatilis KCTC 22182(T) (93.7%). The G+C content of the genomic DNA of strain EBTL04(T) was 62.7 mol%. The menaquinone MK-6 was detected as the predominant quinone. Strain EBTL04(T) contained phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine as major polar lipids. A fatty acid profile with C(16 : 1)ω5c, iso-C(14 : 0), C(16 : 0), anteiso-C(15 : 0) and C(14 : 0) as the major components supported the classification of strain EBTL04(T) in the genus Prosthecobacter. Based on several phenotypic, genotypic and chemotaxonomic features, strain EBTL04(T) was clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL04(T) should be considered to represent a novel species of the genus Prosthecobacter, for which the name Prosthecobacter algae sp. nov. is proposed. The type strain is EBTL04(T) ( = KCTC 23681(T) = JCM 18053(T)).
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Affiliation(s)
- Jangho Lee
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Banghyo Park
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Sung-Geun Woo
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Juyoun Lee
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Joonhong Park
- School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
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Otsuka S, Suenaga T, Vu HT, Ueda H, Yokota A, Senoo K. Brevifollis gellanilyticus gen. nov., sp. nov., a gellan-gum-degrading bacterium of the phylum
Verrucomicrobia. Int J Syst Evol Microbiol 2013; 63:3075-3078. [DOI: 10.1099/ijs.0.048793-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic properties of strain DC2c-G4T, a Gram-staining-negative, ovoid, gellan-gum-degrading bacterial isolate, were examined. Phylogenetic analysis based on 16S rRNA gene sequences identified this isolate as a member of the phylum
Verrucomicrobia
and closest to the genus
Prosthecobacter
. The 16S rRNA gene sequence similarities between this isolate and any of the type strains of species of the genus
Prosthecobacter
were less than 95 %. In addition, the absence of a single prostheca and the predominant menaquinone MK-7(H2) supported the differentiation of this isolate from the genus
Prosthecobacter
. Here, we propose Brevifollis gellanilyticus gen. nov., sp. nov. to accommodate the isolate. The type strain of the type species is DC2c-G4T ( = NBRC 108608T = CIP 110457T).
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Affiliation(s)
- Shigeto Otsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taku Suenaga
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hoan Thi Vu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Ueda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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9
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Otsuka S, Ueda H, Suenaga T, Uchino Y, Hamada M, Yokota A, Senoo K. Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class
Verrucomicrobiae. Int J Syst Evol Microbiol 2013; 63:1982-1986. [DOI: 10.1099/ijs.0.041848-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic properties of strain DC2a-G7T, a Gram-negative, ovoid to rod-shaped, gellan gum-lysing bacterium, were examined. The 16S rRNA gene sequence similarity showed that DC2a-G7T is a member of the phylum
Verrucomicrobia
and the closest type strain of a species with a validly published name is
Verrucomicrobium spinosum
DSM 4136T, with a sequence similarity of 91.2 %. In addition to this similarity value lower than 95 %, the absence of prostheca, the orangey-red colony colour and the compositions of the major menaquinones and polar lipids also supported the differentiation of this bacterium from the genus
Verrucomicrobium
. Here, we propose the name Roseimicrobium gellanilyticum gen. nov., sp. nov. for the isolate. The type strain of Roseimicrobium gellanilyticum is DC2a-G7T ( = NBRC 108606T = DSM 25532T).
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Affiliation(s)
- Shigeto Otsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Ueda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taku Suenaga
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshihito Uchino
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusa-Kamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusa-Kamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol 2012; 78:7042-7. [PMID: 22843531 DOI: 10.1128/aem.01617-12] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To determine if there is a core microbial community in the microbial populations of different wastewater treatment plants (WWTPs) and to investigate the effects of wastewater characteristics, operational parameters, and geographic locations on microbial communities, activated sludge samples were collected from 14 wastewater treatment systems located in 4 cities in China. High-throughput pyrosequencing was used to examine the 16S rRNA genes of bacteria in the wastewater treatment systems. Our results showed that there were 60 genera of bacterial populations commonly shared by all 14 samples, including Ferruginibacter, Prosthecobacter, Zoogloea, Subdivision 3 genera incertae sedis, Gp4, Gp6, etc., indicating that there is a core microbial community in the microbial populations of WWTPs at different geographic locations. The canonical correspondence analysis (CCA) results showed that the bacterial community variance correlated most strongly with water temperature, conductivity, pH, and dissolved oxygen (DO) content. Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 25.7% of the variance of bacterial communities independently, followed by operational parameters (23.9%) and geographic location (14.7%). Results of this study provided insights into the bacterial community structure and diversity in geographically distributed WWTPs and discerned the relationships between bacterial community and environmental variables in WWTPs.
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11
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Pilhofer M, Ladinsky MS, McDowall AW, Petroni G, Jensen GJ. Microtubules in bacteria: Ancient tubulins build a five-protofilament homolog of the eukaryotic cytoskeleton. PLoS Biol 2011; 9:e1001213. [PMID: 22162949 PMCID: PMC3232192 DOI: 10.1371/journal.pbio.1001213] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 10/25/2011] [Indexed: 01/21/2023] Open
Abstract
Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as "bacterial microtubules" (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening.
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Affiliation(s)
- Martin Pilhofer
- California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Division of Biology, Pasadena, California, United States of America
- * E-mail: (GJJ); (MP)
| | - Mark S. Ladinsky
- California Institute of Technology, Pasadena, California, United States of America
| | - Alasdair W. McDowall
- California Institute of Technology, Pasadena, California, United States of America
| | - Giulio Petroni
- Dipartimento di Biologia, University of Pisa, Pisa, Italy
| | - Grant J. Jensen
- California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Division of Biology, Pasadena, California, United States of America
- * E-mail: (GJJ); (MP)
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12
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Martin-Galiano AJ, Oliva MA, Sanz L, Bhattacharyya A, Serna M, Yebenes H, Valpuesta JM, Andreu JM. Bacterial tubulin distinct loop sequences and primitive assembly properties support its origin from a eukaryotic tubulin ancestor. J Biol Chem 2011; 286:19789-803. [PMID: 21467045 DOI: 10.1074/jbc.m111.230094] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of the unique bacterial tubulin BtubA/B from Prosthecobacter is very similar to eukaryotic αβ-tubulin but, strikingly, BtubA/B fold without eukaryotic chaperones. Our sequence comparisons indicate that BtubA and BtubB do not really correspond to either α- or β-tubulin but have mosaic sequences with intertwining features from both. Their nucleotide-binding loops are more conserved, and their more divergent sequences correspond to discrete surface zones of tubulin involved in microtubule assembly and binding to eukaryotic cytosolic chaperonin, which is absent from the Prosthecobacter dejongeii draft genome. BtubA/B cooperatively assembles over a wider range of conditions than αβ-tubulin, forming pairs of protofilaments that coalesce into bundles instead of microtubules, and it lacks the ability to differentially interact with divalent cations and bind typical tubulin drugs. Assembled BtubA/B contain close to one bound GTP and GDP. Both BtubA and BtubB subunits hydrolyze GTP, leading to disassembly. The mutant BtubA/B-S144G in the tubulin signature motif GGG(T/S)G(S/T)G has strongly inhibited GTPase, but BtubA-T147G/B does not, suggesting that BtubB is a more active GTPase, like β-tubulin. BtubA/B chimera bearing the β-tubulin loops M, H1-S2, and S9-S10 in BtubB fold, assemble, and have reduced GTPase activity. However, introduction of the α-tubulin loop S9-S10 with its unique eight-residue insertion impaired folding. From the sequence analyses, its primitive assembly features, and the properties of the chimeras, we propose that BtubA/B were acquired shortly after duplication of a spontaneously folding α- and β-tubulin ancestor, possibly by horizontal gene transfer from a primitive eukaryotic cell, followed by divergent evolution.
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Affiliation(s)
- Antonio J Martin-Galiano
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Mercury and other heavy metals influence bacterial community structure in contaminated Tennessee streams. Appl Environ Microbiol 2010; 77:302-11. [PMID: 21057024 DOI: 10.1128/aem.01715-10] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, including Proteobacteria (ranging from 22.9 to 58.5% per sample), Cyanobacteria (0.2 to 32.0%), Acidobacteria (1.6 to 30.6%), Verrucomicrobia (3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within the Proteobacteria group that includes sulfate-reducing bacteria and within the Verrucomicrobia group appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on the in situ microbial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.
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Arnds J, Knittel K, Buck U, Winkel M, Amann R. Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. Syst Appl Microbiol 2010; 33:139-48. [PMID: 20226613 DOI: 10.1016/j.syapm.2009.12.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 12/21/2009] [Accepted: 12/23/2009] [Indexed: 12/21/2022]
Abstract
Members of the highly diverse bacterial phylum Verrucomicrobia are globally distributed in various terrestrial and aquatic habitats. They are key players in soils, but little is known about their role in aquatic systems. Here, we report on the design and evaluation of a 16S rRNA-targeted probe set for the identification of Verrucomicrobia and of clades within this phylum. Subsequently, the probe set was applied to a study concerning the seasonal abundance of Verrucomicrobia in waters of the humic lake Grosse Fuchskuhle (Germany) by catalyzed reporter deposition fluorescence in situ hybridization. The lake hosted diverse Verrucomicrobia clades in all seasons. Either Spartobacteria (up to 19%) or Opitutus spp. (up to 7%) dominated the communities, whereas Prosthecobacter spp. were omnipresent in low numbers (<1%). Verrucomicrobial abundance and community composition varied between the seasons, and between more and less humic basins, but were rather stable in oxic and seasonally anoxic waters.
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Affiliation(s)
- Julia Arnds
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Celsiusstrasse 1, 28359 Bremen, Germany
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