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So Y, Chhetri G, Kim I, Park S, Jung Y, Seo T. Roseateles caseinilyticus sp. nov. and Roseateles cellulosilyticus sp. nov., isolated from rice paddy field soil. Antonie Van Leeuwenhoek 2024; 117:87. [PMID: 38833203 DOI: 10.1007/s10482-024-01988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
Two novel Gram-stain-negative strains designated P7T and P8T, were isolated from the soil of a paddy field in Goyang, Republic of Korea, and identified as new species within the genus Roseateles through a polyphasic taxonomic approach. These aerobic, rod-shaped, non-sporulating strains demonstrated optimal growth at 30 °C, pH 7, and in the absence of NaCl (0% w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated close relationships with Roseateles saccharophilus DSM654T (98.7%) and Roseateles puraquae CCUG 52769T (98.96%), respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates with the most closely related strains with publicly available whole genomes were 82.0-85.5% and 25.0-30.2%, respectively. The predominant fatty acids identified were C16:0 and summed feature 3 (composed of C16:1 ω6c and/or C16:1 ω7c), with minor amounts of C12:0, C10:0 3-OH and summed feature 8 (composed of C18:1 ω7c and/or C18:1 ω6c; 26.4%). Ubiquinone 8 was the main quinone, and the polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, two unidentified phosphoaminolipids, one unidentified phosphoglycolipid, three unidentified phospholipids, and one unidentified aminolipid. The draft genome sequences revealed genomic DNA G + C contents of 70.1% for P7T and 68.2% for P8T. Comprehensive physiological, biochemical, and 16S rRNA sequence analyses confirm these isolates as novel species of the genus Roseateles, proposed to be named Roseateles caseinilyticus sp. nov for strain P7T (= KACC 22504T = TBRC 15694T) and Roseateles cellulosilyticus sp. nov. for strain P8T (= KACC 22505T = TBRC 15695T).
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Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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2
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Guliayeva D, Akhremchuk A, Sikolenko M, Evdokimova O, Valentovich L, Sidarenka A. Roseateles amylovorans sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917535 DOI: 10.1099/ijsem.0.006133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A Gram-stain-negative, rod-shaped, amylolytic bacterial strain, designated as bsSlp3-1T, was isolated from the Slepian water system, a freshwater reservoir. Strain bsSlp3-1T was found to be aerobic, oxidase-positive and catalase-negative, grew at 5-37 °C (optimum, 28 °C), pH 5.0-9.5 (optimum, pH 7.0) and low NaCl concentration (up to 1.0 %). Comparative analysis of 16S rRNA gene sequence similarity revealed that strain bsSlp3-1T clustered with Roseateles species and is closely related to Roseateles depolymerans KCTC 42856T (98.7 %) and Roseateles terrae CCUG 52222T (98.6 %). Whole-genome comparisons using average nucleotide identity and digital DNA-DNA hybridization values suggested that strain bsSlp3-1T represents a novel species within the genus Roseateles and is most closely related to Roseateles aquatilis CCUG 48205T (81.2 and 25.6 %, respectively). The genome of strain bsSlp3-1T consisted of a single circular chromosome with size 6 289 366 bp and DNA G+C content of 66.8 mol%. The predominant cellular fatty acids of bsSlp3-1T were cis-9-hexadecanoic and hexadecenoic acids. According to the data obtained in this work, strain bsSlp3-1T represents a novel Roseateles species for which the name Roseateles amylovorans sp. nov. is proposed. The type strain is bsSlp3-1T (=BIM B-1768T=NBIMCC 9098T=VKM B-3671T).
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Affiliation(s)
- Darya Guliayeva
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Artur Akhremchuk
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Maxim Sikolenko
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Olesya Evdokimova
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Leonid Valentovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Anastasiya Sidarenka
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
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3
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Wang S, Wang Y, Li P, Wang L, Su Q, Zuo J. Development and characterizations of hydrogenotrophic denitrification granular process: Nitrogen removal capacity and adaptability. BIORESOURCE TECHNOLOGY 2022; 363:127973. [PMID: 36122846 DOI: 10.1016/j.biortech.2022.127973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Hydrogenotrophic denitrification (HD) is a promising autotrophic biological process for advanced nitrogen removal, while sludge granulation was seldom reported. This study aimed to cultivate granular sludge to improve capacity and stability of HD process. The resulting HD granular sludge performed high nitrogen removal rate (NRR) of 0.42 ± 0.0.4 kgN/(m3·d) with low accumulation of nitrite and nitrous oxide emission. HD granular sludge reactor performed over 3 times higher NRR compared to that in HD fixed-bed biofilm reactor (0.13 ± 0.01 kgN/(m3·d). Besides, granular sludge reactor could treat groundwater well even at the low temperature of 15 °C. The dominant genera were Hydrogenophaga and Comamonas in granular sludge, and Dechloromonas in biofilm. Noticeably, sulfate in the groundwater stimulated the growth of sulfur converting microbes with increasing abundances of sulfite reductase gene and sulfate-reducing bacteria Desulfovibrio. This study highlights the potential implementation of HD process in granular sludge reactor for advance nitrogen removal from impaired groundwater.
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Affiliation(s)
- Sike Wang
- Department of Material and Environmental Engineering, Shenzhen Polytechnic, Shenzhen 518055, China; Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Yajiao Wang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73072, USA; State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li Wang
- Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Qingxian Su
- Department of Environmental Engineering, Technical University of Denmark, Kgs., Lyngby 2800, Denmark
| | - Jiane Zuo
- Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China; State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions. Syst Appl Microbiol 2022; 45:126352. [DOI: 10.1016/j.syapm.2022.126352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
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Hahn MW, Pitt A, Schmidt J, Koll U, Wolf J, Whitman WB, Bodelier PLE, Neumann-Schaal M. Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65T (=CCUG 56422T=DSM 107630T) and MWH-P2sevCIIIbT (=CCUG 56420T=DSM 107629T), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family
Alcaligenaceae
and revealed
Orrella amnicola
and
Orrella marina
(=
Algicoccus marinus
) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus
Orrella
represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65T and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIbT. Furthermore, we propose the reclassification of the species
Orrella amnicola
in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.
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Affiliation(s)
- Martin W. Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Meina Neumann-Schaal
- Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Makino A, Nakai R, Yoneda Y, Toyama T, Tanaka Y, Meng XY, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. Isolation of Aquatic Plant Growth-Promoting Bacteria for the Floating Plant Duckweed (Lemna minor). Microorganisms 2022; 10:microorganisms10081564. [PMID: 36013982 PMCID: PMC9416352 DOI: 10.3390/microorganisms10081564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) can exert beneficial growth effects on their host plants. Little is known about the phylogeny and growth-promoting mechanisms of PGPB associated with aquatic plants, although those of terrestrial PGPB have been well-studied. Here, we report four novel aquatic PGPB strains, MRB1–4 (NITE P-01645–P-01648), for duckweed Lemna minor from our rhizobacterial collection isolated from Lythrum anceps. The number of L. minor fronds during 14 days co-culture with the strains MRB1–4 increased by 2.1–3.8-fold, compared with an uninoculated control; the plant biomass and chlorophyll content in co-cultures also increased. Moreover, all strains possessed an indole-3-acetic acid production trait in common with a plant growth-promoting trait of terrestrial PGPB. Phylogenetic analysis showed that three strains, MRB-1, -3, and -4, were affiliated with known proteobacterial genera (Bradyrhizobium and Pelomonas); this report is the first to describe a plant-growth promoting activity of Pelomonas members. The gammaproteobacterial strain MRB2 was suggested to be phylogenetically novel at the genus level. Under microscopic observation, the Pelomonas strain MRB3 was epiphytic and adhered to both the root surfaces and fronds of duckweed. The duckweed PGPB obtained here could serve as a new model for understanding unforeseen mechanisms behind aquatic plant-microbe interactions.
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Affiliation(s)
- Ayaka Makino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Hokkaido, Japan; (A.M.); (R.N.)
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Hokkaido, Japan; (A.M.); (R.N.)
| | - Yasuko Yoneda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Tadashi Toyama
- Graduate School of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Yasuhiro Tanaka
- Graduate School of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Kazuhiro Mori
- Graduate School of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Michihiko Ike
- Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan;
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan;
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan
- Biotechnology Research Center, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Correspondence: ; Tel.: +81-29-861-6592
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Yang Y, Qiao S, Zheng M, Han Q, Wang R, Zhou J, Quan X. Polyaniline derived carbon membrane and its in-situ membrane fouling mitigation performance in MBR based on metal-free electro-Fenton. WATER RESEARCH 2022; 219:118564. [PMID: 35605394 DOI: 10.1016/j.watres.2022.118564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
An electro-enhanced membrane bioreactor (EMBR) was constructed with polyaniline-based carbon (PAC) separation membrane as the membrane-electrode, which could realize the in-situ electro-generation and activation of H2O2 to ·OH depending on the graphitic and pyridinic N as active sites without metal catalyst. After the continuous operation of the bioreactor for 74 days, approximately 77.41% irreversible membrane fouling occurred on the electrochemically enhanced membrane, which was less than that on the control membrane (85.96%). The ·OH oxidation combined with electrostatic barrier formed by -1.0 V enhanced PAC membrane suppressed the extracellular polymeric substances deposition on membrane. After operation, the strength of total cell, proteins, β-polysaccharides and α-polysaccharides on the membrane without bias were 5.17, 4.32, 9.65 and 16.31, respectively. In EMBR, the corresponding strength were 2.03, 3.35, 2.15 and 6.73. After calculation, the unblocked pores accounted for 35.3% and 78.5% of the total membrane surface in MBR and EMBR, respectively, indicating the fouling was alleviated obviously. Meanwhile, the EMBR owned a satisfactory wastewater treatment effect with average effluent chemical oxygen demand and NH4+-N around 18.98 mg/L and 0.68 mg/L. The successful implementation of this strategy achieved a green and metal-free method for ·OH production with electrochemical effect for membrane fouling control in MBR.
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Affiliation(s)
- Yue Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Sen Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Mingmei Zheng
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Qinqin Han
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Ruiyu Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
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Ikeda S, Okazaki K, Tsurumaru H, Suzuki T, Hirafuji M. Effects of Different Types of Additional Fertilizers on Root-associated Microbes of Napa Cabbage Grown in an Andosol Field in Japan. Microbes Environ 2022; 37. [PMID: 35650110 PMCID: PMC9530736 DOI: 10.1264/jsme2.me22013] [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 effects of different types of additional fertilizations (a compound fertilizer and Chiyoda-kasei) on the root-associated microbes of napa cabbage grown in an Andosol field were investigated by molecular community ana-lyses. Most of the closest known species of the bacterial sequences whose relative abundance significantly differed among fertilizers were sensitive to nitrogen fertilization and/or related to the geochemical cycles of nitrogen. The fungal community on the roots of napa cabbage was dominated by two genera, Bipolaris and Olpidium. The relative abundance of these two genera was affected by the types of fertilizers to some extent and showed a strong negative correlation.
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Affiliation(s)
- Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | - Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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Mogro EG, Cafiero JH, Lozano MJ, Draghi WO. The phylogeny of the genus Azohydromonas supports its transfer to the family Comamonadaceae. Int J Syst Evol Microbiol 2022; 72. [PMID: 35138242 DOI: 10.1099/ijsem.0.005234] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Azohydromonas encompasses five validly described species belonging to the betaproteobacterial class. Recognized for their potential biotechnological uses, they were first described as belonging to the genus Alcaligenes. The phylogeny of the 16S rRNA gene of the original strains as well as newly described species led to a description of these strains within a new bacterial genus, Azohydromonas. However, the phylogenetic position of this genus remains described as part of the family Alcaligenaceae, even those some authors have placed it within the order Burkholderiales. To unravel the precise position of the genus Azohydromonas, a wide phylogenomic analysis was performed. The results of 16S rRNA gene phylogeny, as well as those obtained by the multilocus analysis of homologous proteins and overall genome relatedness indices, support the reclassification of Azohydromonas in the Rubrivivax-Ideonella lineage of the family Comamonadaceae, so the transfer of this genus is proposed.
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Affiliation(s)
- Ezequiel Gerardo Mogro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET CCT La Plata, La Plata, Argentina
| | - Juan Hilario Cafiero
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET CCT La Plata, La Plata, Argentina
| | - Mauricio Javier Lozano
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET CCT La Plata, La Plata, Argentina
| | - Walter Omar Draghi
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET CCT La Plata, La Plata, Argentina
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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Dahal RH, Chaudhary DK, Kim DU, Kim J. Azohydromonas caseinilytica sp. nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method. Front Microbiol 2021; 12:647132. [PMID: 34093463 PMCID: PMC8175650 DOI: 10.3389/fmicb.2021.647132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
A bacterial strain, designated strain G-1-1-14T, was isolated from Kyonggi University forest soil during a study of previously uncultured bacterium. The cells of strain G-1-1-14T were motile by means of peritrichous flagella, Gram-stain-negative, rod-shaped, and able to grow autotrophically with hydrogen and fix nitrogen. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain G-1-1-14T belonged to the genus Azohydromonas. The closest species of strain G-1-1-14T were Azohydromonas ureilytica UCM-80T (98.4% sequence similarity), Azohydromonas lata IAM 12599T (97.5%), Azohydromonas riparia UCM-11T (97.1%), and Azohydromonas australica IAM 12664T (97.0%). The genome of strain G-1-1-14T was 6,654,139 bp long with 5,865 protein-coding genes. The genome consisted of N2-fixing genes (nifH) and various regulatory genes for CO2 fixation and H2 utilization. The principal respiratory quinone was ubiquinone-8, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The major fatty acids were summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), C16:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c), and cyclo-C17:0. The DNA G + C content was 69.9%. The average nucleotide identity (OrthoANI), in silico DNA–DNA hybridization (dDDH), and conventional DDH relatedness values were below the species demarcation values for novel species. Based on genomic, genetic, phylogenetic, phenotypic, and chemotaxonomic characterizations, strain G-1-1-14T represents a novel species within the genus Azohydromonas, for which the name Azohydromonas caseinilytica sp. nov. is proposed. The type strain is G-1-1-14T (= KACC 21615T = NBRC 114390T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea.,Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea.,Department of Environmental Engineering, Korea University Sejong Campus, Sejong City, South Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju-si, South Korea
| | - Jaisoo Kim
- Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea
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12
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Izaguirre JK, Barañano L, Castañón S, Santos JAL, Cesário MT, da Fonseca MMR, Alkorta I, Garbisu C. Economic and environmental assessment of bacterial poly(3-hydroxybutyrate) production from the organic fraction of municipal solid waste. BIORESOUR BIOPROCESS 2021; 8:39. [PMID: 38650259 PMCID: PMC10992733 DOI: 10.1186/s40643-021-00392-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
The management of municipal solid waste is a major logistic and environmental problem worldwide. Nonetheless, the organic fraction of municipal solid waste (OFMSW) is a valuable source of nutrients which can be used for a variety of purposes, according to the Circular Economy paradigm. Among the possible applications, the bioproduction of a biodegradable polyester, poly(3-hydroxybutyrate) [P(3HB)], using OFMSW as carbon platform is a promising strategy. Here, an economic and environmental assessment of bacterial P(3HB) production from OFMSW is presented based on previously published results. The SuperPro Designer® software was used to simulate P(3HB) production under our experimental parameters. Two scenarios were proposed depending on the fermentation medium: (1) enzymatic hydrolysate of OFMSW supplemented with glucose and plum waste juice; and (2) basal medium supplemented with glucose and plum waste juice. According to our results, both scenarios are not economically feasible under our experimental parameters. In Scenario 1, the low fermentation yield, the cost of the enzymes, the labour cost and the energy consumption are the factors that most contribute to that result. In Scenario 2, the cost of the extraction solvent and the low fermentation yield are the most limiting factors. The possibility of using process waste as raw material for the generation of other products must be investigated to enhance economic feasibility. From an environmental viewpoint, the photochemical oxidation potential (derived from the use of anisole as extraction solvent) and the generation of acid rain and global warming effect (caused by the burning of fuels for power generation) are the most relevant impacts associated to P(3HB) production under our experimental parameters.
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Affiliation(s)
- Jon Kepa Izaguirre
- NEIKER-Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Leire Barañano
- NEIKER-Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Sonia Castañón
- NEIKER-Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - José A L Santos
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - M Teresa Cesário
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - M Manuela R da Fonseca
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Carlos Garbisu
- NEIKER-Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain.
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13
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Wang H, Narsing Rao MP, Gao Y, Li X, Gao R, Xie Y, Li Q, Li W. Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca. BMC Microbiol 2021; 21:143. [PMID: 33980153 PMCID: PMC8114534 DOI: 10.1186/s12866-021-02206-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/19/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. RESULTS A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). CONCLUSION The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.
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Affiliation(s)
- Hongfei Wang
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanli Gao
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Xinyang Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong, 118000, China
| | - Yuanguo Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiuli Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China.
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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14
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Dai X, Wang Y, Luo L, Pfiffner SM, Li G, Dong Z, Xu Z, Dong H, Huang L. Detection of the deep biosphere in metamorphic rocks from the Chinese continental scientific drilling. GEOBIOLOGY 2021; 19:278-291. [PMID: 33559972 DOI: 10.1111/gbi.12430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
It is generally accepted that there is a vast, well-populated biosphere in the subsurface, but the depth limit of the terrestrial biosphere has yet to be determined, largely because of the lack of access to the subsurface. Here as part of the Chinese Continental Scientific Drilling (CCSD) project in eastern China, we acquired continuous rock cores and endeavored to probe the depth limit of the biosphere and the depth-dependent distribution of microorganisms at a geologically unique site, that is, a convergent plate boundary. Microbiological analyses of ultra-high-pressure metamorphic rock cores taken from the ground surface to 5,158-meter reveal that microbial distribution was continuous up to a depth of ~4,850 m, where temperature was estimated to be ~137°C. The metabolic state of these organisms at such great depth remains to be determined. Microbial abundance, ranging from 103 to 108 cells/g, was also related to porosity, but not to the depth and rock composition. In addition, microbial diversity systematically decreased with depth. Our results support the notion that temperature is a key factor in determining the lower limit of the biosphere in the continental subsurface.
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Affiliation(s)
- Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liqiang Luo
- National Research Center for Geoanalysis, Chinese Academy of Geological Sciences, Beijing, China
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - Guangyu Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiqin Xu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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15
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Asiri F, Chen CH, Hwangbo M, Shao Y, Chu KH. From Organic Wastes to Bioplastics: Feasibility of
Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella
denitrificans ZD1. ACS OMEGA 2020; 5:24158-24168. [PMID: 33015431 PMCID: PMC7528165 DOI: 10.1021/acsomega.9b04002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/03/2020] [Indexed: 05/04/2023]
Abstract
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Poly(3-hydroxybutyrate)
(PHB)—a renewable and biodegradable
polymer—is a promising alternative to nonbiodegradable synthetic
plastics that are derived from petrochemicals. The methods currently
employed for PHB production are costly, in part, due to the expensive
cultivation feedstocks and the need to sterilize the culture medium,
which is energy-intensive. This study investigates the feasibility
of nonsterile PHB production from several saline organic wastes using
a salt-tolerant strain, Zobellella denitrificans ZD1 (referred to as strain ZD1). Factors such as the pH, salinity,
carbon/nitrogen (C/N) ratio, nitrogen source, and electron acceptor
that might affect the growth of strain ZD1 and its PHB production
were determined. Our results showed successful nonsterile PHB production
by growing the strain ZD1 on nonsterile synthetic crude glycerol,
high-strength saline wastewater, and real municipal wastewater-activated
sludge under saline conditions. The PHB production was significantly
enhanced when the levels of salts and nitrate-nitrogen in the culture
medium were increased. This study suggested a promising low-cost nonsterile
PHB production strategy from organic wastes using strain ZD1.
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Affiliation(s)
- Fahad Asiri
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
| | - Chih-Hung Chen
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
- Department
of Environmental Engineering, National Cheng
Kung University, Tainan 70101, Taiwan
| | - Myung Hwangbo
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
| | - Yiru Shao
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
| | - Kung-Hui Chu
- Zachry
Department of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843-3136, United States
- . Tel: (979)-845-1403. Fax: (979)-862-1542
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16
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Xue H, Piao CG, Bian DR, Guo MW, Li Y. Azohydromonas aeria sp. nov., isolated from air. J Microbiol 2020; 58:543-549. [PMID: 32594456 DOI: 10.1007/s12275-020-9423-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 10/24/2022]
Abstract
A grey pink colored bacterium, strain t3-1-3T, was isolated from the air at the foot of the Xiangshan Mountain in Beijing, China. The cells are aerobic, Gram-stain-negative, non-spore-forming, motile and coccoid-rod shaped (0.9-1.2 × 1.9-2.1 μm). Strain t3-1-3T was catalase-positive and oxidase-negative and this strain grew at 4-42°C (optimum 28°C), a pH of 4.0-9.0 (optimum pH 7.0) and under 0-2% (w/v) NaCl (optimum 0-1% NaCl). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain t3-1-3T was closely related to Azohydromonas riparia UCM-11T (97.4% similarity), followed by Azohydromonas australica G1-2T (96.8%) and Azohydromonas ureilytica UCM-80T (96.7%). The genome of strain t3-1-3T contains 6,895 predicted protein-encoding genes, 8 rRNA genes, 62 tRNA genes and one sRNA gene, as well as five potential biosynthetic gene clusters, including clusters of genes coding for non-ribosomal peptide synthetase (NRPS), bacteriocin and arylpolyene and two clusters of genes for terpene. The predominant cellular fatty acids (> 10.0% of the total) in strain t3-1-3T were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 37.8%), summed feature 8 (C18:1ω7c and/or C18:1ω6c, 29.7%) and C16:0 (17.3%). Strain t3-1-3T contained ubiquinone-8 (Q-8) as the predominant respiratory quinone. The polar lipids of strain t3-1-3T comprised phosphatidyl ethanolamine (PE), phosphatidyl glycerol (PG), diphosphatidyl glycerol (DPG), an unidentified glycolipid (GL), an unidentified aminophospholipid (APL), two unidentified phospholipid (PL1-2) and five unidentified lipid (L1-5). The DNA G + C content of the type strain is 70.3%. The broader range of growth temperature, assimilation of malic acid and trisodium citrate, presence of C18:3ω6c and an unidentified glycolipid and absence of C12:0 2-OH and C16:0iso differentiate strain t3-1-3T from related species. Based on the taxonomic data presented in this study, we suggest that strain t3-1-3T represents a novel species within the genus Azohydromonas, for which the name Azohydromonas aeria sp. nov. is proposed. The type strain of Azohydromonas aeria is t3-1-3T (= CFCC 13393T = LMG 30135T).
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Affiliation(s)
- Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Chun-Gen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Dan-Ran Bian
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Min-Wei Guo
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, P. R. China.
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17
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Chatfield CH, Zaia J, Sauer C. Legionella pneumophila Attachment to Biofilms of an Acidovorax Isolate from a Drinking Water-Consortium Requires the Lcl-Adhesin Protein. Int Microbiol 2020; 23:597-605. [PMID: 32451737 DOI: 10.1007/s10123-020-00126-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/02/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022]
Abstract
Human infection by Legionella pneumophila (Lpn) only occurs via contaminated water from man-made sources, and eradication of these bacteria from man-made water systems is complicated by biofilm colonization. Using a continuously fed biofilm reactor model, we grew a biofilm consortium from potable water that was able to prolong recovery of Lpn CFU from biofilms. This effect was recreated using a subset of those species in a simplified consortium composed of eight bacterial isolates from the first biofilm reactor. In the reactor with the eight-species consortium, Lpn biofilm CFU was relatively stable over a 12-day trial. An isolate of Acidovorax from the consortium was, as a single species biofilm, able to promote Lpn surface attachment. Other isolates from the Pelomonas genus grew as equally robust biofilms alone, but did not promote surface attachment of Lpn. This attachment was disrupted by cationic polysaccharides and loss of the Lpn Lcl collagen-like adhesin protein. This work demonstrates that, while Lpn was fairly incompetent at attachment to surfaces to form a biofilm alone, pre-existing biofilms allowed attachment of Lpn as secondary colonizers. In addition, we demonstrate that initial attachment of Lpn to Acidovorax biofilms is likely via the Lcl-adhesin protein.
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Affiliation(s)
| | - Jenna Zaia
- Department of Biological Sciences, SUNY Cortland, Cortland, New York, USA
| | - Cassidy Sauer
- Department of Biological Sciences, SUNY Cortland, Cortland, New York, USA
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18
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Sisinthy S, Gundlapally SR. Mitsuaria chitinivorans sp. nov. a potential candidate for bioremediation: emended description of the genera Mitsuaria, Roseateles and Pelomonas. Arch Microbiol 2020; 202:1839-1848. [PMID: 32447433 DOI: 10.1007/s00203-020-01905-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 01/20/2023]
Abstract
As a part of studying the effect of deoxygenation, eutrophication and acidification on bacterial diversity, strain HWN-4T was isolated from tube well water and characterized. The draft genome sequencing of strain HWN-4T revealed a genome size of 5,774,764 bp and the annotation indicated 5102 coding sequences including 66 RNA genes. Strain HWN-4T is Gram negative, rod-shaped, motile in the log phase, catalase and oxidase positive, and the major fatty acids and respiratory quinone present are C10:0 3-OH, C14:0 3OH/C16:1 iso I, C16:1 ω7c/C16:1 ω6c, C16:0 and C17:0 cyclo and ubiquinone-8, respectively. The phylogenetic analyses, based on 16S rRNA gene sequence, indicated that strain HWN-4T is a member of the genus Mitsuaria. The average nucleotide identity (ANI) and genome-to-genome similarity between strain HWN-4T and all other species/strains of the genus Mitsuaria are less than (%) 95.0 and 70.0, respectively. This confirms the status of strain HWN-4T as a novel species. The species status is further confirmed by phenotypic differences exhibited by strain HWN-4T with other members of the same genus. Based on the collective differences exhibited by strain HWN-4T with other members of the genus Mitsuaria, the name Mitsuaria chitinivorans sp. nov. is proposed. Further, the diagnostic signature nucleotides were identified in the 16S rRNA gene sequences of members of the genera Mitsuaria, Pelomonas and Roseateles, that distinctly differentiate them and support an emendation of the genera. Besides, phylogenetic and structural characterization of chitinases from members of the genus Mitsuaria was performed. The type strain of Mitsuaria chitinivorans sp. nov. is HWN-4T = LMG 28685T = KTCC 42483T.
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Affiliation(s)
- Shivaji Sisinthy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
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19
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Theis KR, Romero R, Winters AD, Jobe AH, Gomez-Lopez N. Lack of Evidence for Microbiota in the Placental and Fetal Tissues of Rhesus Macaques. mSphere 2020; 5:e00210-20. [PMID: 32376701 PMCID: PMC7203455 DOI: 10.1128/msphere.00210-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
The prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine whether the fetal and placental tissues of rhesus macaques harbor bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profiles of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profiles of fetal and placental tissues did not exceed or differ from those of background technical controls. By contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCE Microbial invasion of the amniotic cavity (i.e., intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low-biomass microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g., microbial load and community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e., culture, quantitative real-time PCR [qPCR], and DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placental and fetal tissues of rhesus macaques.
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Affiliation(s)
- Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
- Detroit Medical Center, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, Florida, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA
| | - Alan H Jobe
- Cincinnati Children's Hospital, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
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20
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Tkacz A, Bestion E, Bo Z, Hortala M, Poole PS. Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison. mBio 2020; 11:e02785-19. [PMID: 32019791 PMCID: PMC7002342 DOI: 10.1128/mbio.02785-19] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 11/20/2022] Open
Abstract
Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Eloïne Bestion
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Zhiyan Bo
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marion Hortala
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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21
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Tang B, Yu Y, Liang J, Zhang Y, Bian X, Zhi X, Ding X. Reclassification of ' Polyangium brachysporum' DSM 7029 as Schlegelella brevitalea sp. nov. Int J Syst Evol Microbiol 2019; 69:2877-2883. [PMID: 31274403 DOI: 10.1099/ijsem.0.003571] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Strain DSM 7029, isolated from a soil sample in Greece, can produce antitumour glidobactins, and has been found, as a heterologous host, to produce useful nonribosomal peptide synthetase-polyketide synthase hybrid molecules known as epothilones. This strain was originally named 'Polyangium brachysporum' of the family Polyangiaceae and the order Myxococcales. However, phylogenetic analysis of the 16S rRNA gene sequence of strain DSM 7029 indicated that it was clustered with members of Schlegelella. Significant growth occurred at 25-42 °C, pH 5.0-10.0 and in the presence of 0-0.2 % (w/v) NaCl. The predominant ubiquinone was Q-8. The major fatty acids were C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1ω7c. The G+C content of genomic DNA was 67.51 mol%. The strain was clearly distinguishable from other neighbouring Schlegelella members and genera Caldimonas and Zhizhongheella, using phylogenetic analysis, fatty acid composition data and a range of physiological and biochemical characteristics and genome analysis. Therefore, strain DSM 7029 represents a novel species of the genus Schlegelella, for which the name Schlegelella brevitalea sp. nov. is proposed.
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Affiliation(s)
- Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China.,Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Yucong Yu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Junheng Liang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, PR China
| | - Xiaoying Bian
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, PR China
| | - Xiaoyang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
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22
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Papapostolou A, Karasavvas E, Chatzidoukas C. Oxygen mass transfer limitations set the performance boundaries of microbial PHA production processes – A model-based problem investigation supporting scale-up studies. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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23
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Grigore ME, Grigorescu RM, Iancu L, Ion RM, Zaharia C, Andrei ER. Methods of synthesis, properties and biomedical applications of polyhydroxyalkanoates: a review. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2019; 30:695-712. [DOI: 10.1080/09205063.2019.1605866] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mădălina Elena Grigore
- "Evaluation and Conservation of Cultural Heritage” Research Group, National Institute for Research and Development in Chemistry and Petrochemistry, ICECHIM, Bucharest, Romania
| | - Ramona Marina Grigorescu
- "Evaluation and Conservation of Cultural Heritage” Research Group, National Institute for Research and Development in Chemistry and Petrochemistry, ICECHIM, Bucharest, Romania
| | - Lorena Iancu
- "Evaluation and Conservation of Cultural Heritage” Research Group, National Institute for Research and Development in Chemistry and Petrochemistry, ICECHIM, Bucharest, Romania
| | - Rodica-Mariana Ion
- "Evaluation and Conservation of Cultural Heritage” Research Group, National Institute for Research and Development in Chemistry and Petrochemistry, ICECHIM, Bucharest, Romania
- Valahia University, Materials Engineering Department, 13th Aleey Sinaia, Targoviste, Romania
| | - Cătălin Zaharia
- Advanced Polymer Materials Group, University Politehnica of Bucharest, Bucharest, Romania
| | - Elena Ramona Andrei
- "Evaluation and Conservation of Cultural Heritage” Research Group, National Institute for Research and Development in Chemistry and Petrochemistry, ICECHIM, Bucharest, Romania
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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Özgören T, Pinar O, Bozdağ G, Denizci AA, Gündüz O, Çakır Hatır P, Kazan D. Assessment of poly(3-hydroxybutyrate) synthesis from a novel obligate alkaliphilic Bacillus marmarensis and generation of its composite scaffold via electrospinning. Int J Biol Macromol 2018; 119:982-991. [DOI: 10.1016/j.ijbiomac.2018.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 01/04/2023]
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27
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Moura RB, Santos CED, Okada DY, Martins TH, Ferraz Júnior ADN, Damianovic MHRZ, Foresti E. Carbon-nitrogen removal in a structured-bed reactor (SBRRIA) treating sewage: Operating conditions and metabolic perspectives. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:19-28. [PMID: 30025261 DOI: 10.1016/j.jenvman.2018.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/14/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
The present study evaluated the efficiency of a structured-bed reactor subjected to recirculation and intermittent aeration (SBRRIA) to promote nitrogen and carbon removal from domestic sewage. The intermittent aeration and the recycling rate of 3 keeps the desired mixing degree inside the SBRRIA. Four different operational conditions were tested by varying the hydraulic retention time (HRT) from 12 to 8 h and aerated and non-aerated periods (A/NA) from 2 h/1 h and 3 h/1 h. At the THD of 8 h and A/NA of 2 h/1 h there was a decrease in the nitrification process (77.5%) due to the increase of organic matter availability, affecting the total-N removal performance. However, by increasing the aerated period from 2 h to 3 h, the nitrification efficiency rose to 91.1%, reaching a total-N removal efficiency of 79%. The system reached a maximum total-N loading removed of 0.117 kgN.m-3.d-1 by applying an HRT of 8 h and an intermittent aeration cycle of 3 h, aerated and 1 h non-aerated. The simultaneous nitrification and denitrification (SND) process was related to a complex interplay among microorganisms affiliated mostly to Acidovorax sp., Comamonas sp., Dechloromonas sp., Hydrogenophaga sp., Mycobacterium sp., Rhodobacter sp., and Steroidobacter sp.
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Affiliation(s)
- Rafael B Moura
- Institute of Science and Technology, Federal University of Alfenas, Rod. José Aurélio Vilela, 11999, Cidade Universitária, 37715-400, Poços de Caldas, MG, Brazil; Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (EESC/USP), Av. João Dagnone 1100, 13563-120, São Carlos, SP, Brazil.
| | - Carla E D Santos
- Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (EESC/USP), Av. João Dagnone 1100, 13563-120, São Carlos, SP, Brazil
| | - Dagoberto Y Okada
- School of Technology, University of Campinas, Rua Paschoal Marmo, 1888, 13484-332, Limeira, SP, Brazil
| | - Tiago H Martins
- Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (EESC/USP), Av. João Dagnone 1100, 13563-120, São Carlos, SP, Brazil
| | - Antônio Djalma N Ferraz Júnior
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Rua Giuseppe Máximo Scolfaro 10000, 13083-970, Campinas, SP, Brazil
| | - Márcia H R Z Damianovic
- Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (EESC/USP), Av. João Dagnone 1100, 13563-120, São Carlos, SP, Brazil
| | - Eugenio Foresti
- Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (EESC/USP), Av. João Dagnone 1100, 13563-120, São Carlos, SP, Brazil
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28
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Ye J, Huang W, Wang D, Chen F, Yin J, Li T, Zhang H, Chen GQ. Pilot Scale-up of Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) Production by Halomonas bluephagenesis via Cell Growth Adapted Optimization Process. Biotechnol J 2018; 13:e1800074. [PMID: 29578651 DOI: 10.1002/biot.201800074] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/21/2018] [Indexed: 11/06/2022]
Abstract
Poly(3-hydroxybutyrate-co-4-hydroxybutyrate), P(3HB-co-4HB), is one of the most valuable biopolymers because of its flexible mechanical properties. In this study, the goal is to establish a scaled-up process of low cost P(3HB-co-4HB) from a 7.5-L fermentor to 1- and 5-m3 industrial bioreactors, respectively, using Halomonas bluephagenesis TD40 grown on glucose, γ-butyrolactone, and waste corn steep liquor (CSL) as substrates, under open non-sterile and fed-batch or continuous conditions. The non-sterile process enables the energy reduction for less steam consumption. Moreover, waste gluconate is successfully utilized to replace glucose as a carbon source for cell growth and PHA accumulation in 7.5-L fermentor, which opens the possibility of 60% of raw material cost reduction for recycling the waste resources. A mathematical model and rational calculation is established to help guide the feeding strategy and scale-up, respectively, leading to 100 g L-1 cell dry weight (CDW) containing 60.4% P(3HB-co-mol 13.5% 4HB) after 36 h of growth in the 5 m3 vessel. An even higher P(3HB-co-4HB) content of 74% is achieved by decreasing the use of waste CSL. A stable and continuous open process for efficient low-cost production of P(3HB-co-4HB) is successfully developed coupling fermentation with the downstream extraction processing.
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Affiliation(s)
- Jianwen Ye
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.,Tsinghua University, Center for Synthetic and Systems Biology, Beijing 100084, China.,Tsinghua University, Center for Nano and Micro-Mechanics, Beijing 100084, China
| | - Wuzhe Huang
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.,Bluepha Co., Ltd., Beijing 102206, China
| | | | | | - Jin Yin
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Teng Li
- Bluepha Co., Ltd., Beijing 102206, China
| | | | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.,Tsinghua University, Center for Synthetic and Systems Biology, Beijing 100084, China.,Tsinghua University, Center for Nano and Micro-Mechanics, Beijing 100084, China
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29
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Nam YH, Choi A, Hwang JM, Yim KJ, Kim JH, Choi GG, Chung EJ. Paucibacter aquatile sp. nov. isolated from freshwater of the Nakdong River, Republic of Korea. Arch Microbiol 2018; 200:877-882. [PMID: 29468317 DOI: 10.1007/s00203-018-1494-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/18/2018] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
Abstract
A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182T belongs to type strains of genus Paucibacter. Strain CR182T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain CR182T and P. oligotrophus CHU3T was 78.4% and the genome-to-genome distance was 22.2% on average. The genomic DNA G+C content calculated from the genome sequence was 66.3 mol%. Predominant cellular fatty acids of strain CR182T were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) (31.2%) and C16:0 (16.0%). Its major respiratory quinine was ubiquinone Q-8. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified phospholipids. Its genomic DNA G+C content was 66.3%. Based on data obtained from this polyphasic taxonomic study, strain CR182T represents a novel species belonging to genus Paucibacter, for which a name of P. aquatile sp. nov. is proposed. The type strain is CR182T (= KCCM 90284T = NBRC 113032T).
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Affiliation(s)
- Young Ho Nam
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Ahyoung Choi
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Jung Moon Hwang
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Kyung June Yim
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Jee-Hwan Kim
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Gang-Guk Choi
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Eu Jin Chung
- Freshwater Bioresources Culture Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea.
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Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS One 2017; 12:e0177488. [PMID: 28493994 PMCID: PMC5426677 DOI: 10.1371/journal.pone.0177488] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.
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Affiliation(s)
- Jessica M. Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Kristina D. Baker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Richard M. Zamor
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Steve Nikolai
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
- * E-mail:
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Nguyen TM, Kim J. Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in South Korea. J Microbiol 2017; 55:330-336. [PMID: 28124782 DOI: 10.1007/s12275-017-6519-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 11/26/2022]
Abstract
White and pale yellow coloured bacteria were isolated from the riverside soil, Daejeon, South Korea, and were designated UCM-11T, UCM-F25, and UCM-80T. We found that all strains were able to reduce nitrate, and the cells were aerobic and motile. The DNA G+C contents of UCM-11T, UCM-F25, and UCM-80T were between 68.9 to 71.2 mol% and the main ubiquinone was observed as Q-8. Based on16S rRNA gene sequences, strains UCM-11T and UCM-F25 were found to closely match with Azohydromonas australica IAM 12664T (98.48-98.55%), and the strain UCM-80T was the closest match with Azohydromonas lata IAM 12599T (98.34%). The presence of summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) as well as twokinds of hydroxyfatty acids consisting of C10:0 3-OH and C12:0 2-OH, and branched fatty acids containing C16:0 iso and C17:0 cyclo were detected in all the strains. Phosphatidylethanolamine was a major polar lipid. DNA-DNA relatedness confirmed UCM-11T, UCM-F25 and UCM-80T as novel members of the genus Azohydromonas. Based on the morphological, physiological, biochemical and genotypic characteristics, we suggest that strains UCM-11T, UCM-F25, and UCM-80T represent novel species within the genus Azohydromonas. The names Azohydromonas riparia sp. nov., and Azohydromonas ureilytica sp. nov. are proposed for the type strains UCM-11T (=KACC 18570T =NBRC 111646T) and UCM-80T (=KACC 18576T =NBRC 111658T), respectively.
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Affiliation(s)
- Tuan Manh Nguyen
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, 16227, Republic of Korea
- Thai Nguyen University of Agriculture and Forestry, Quyet Thang Commune, Thai Nguyen City, Vietnam
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, 16227, Republic of Korea.
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Zhao J, Wu J, Li X, Wang S, Hu B, Ding X. The Denitrification Characteristics and Microbial Community in the Cathode of an MFC with Aerobic Denitrification at High Temperatures. Front Microbiol 2017; 8:9. [PMID: 28154554 PMCID: PMC5243800 DOI: 10.3389/fmicb.2017.00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/03/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial fuel cells (MFCs) have attracted much attention due to their ability to generate electricity while treating wastewater. The performance of a double-chamber MFC with simultaneous nitrification and denitrification (SND) in the cathode for treating synthetic high concentration ammonia wastewater was investigated at different dissolved oxygen (DO) concentrations and high temperatures. The results showed that electrode denitrification and traditional heterotrophic denitrification co-existed in the cathode chamber. Electrode denitrification by aerobic denitrification bacterium (ADB) is beneficial for achieving a higher voltage of the MFC at high DO concentrations (3.0–4.2 mg/L), while traditional heterotrophic denitrification is conducive to higher total nitrogen (TN) removal at low DO (0.5–1.0 mg/L) concentrations. Under high DO conditions, the nitrous oxide production and TN removal efficiency were higher with a 50 Ω external resistance than with a 100 Ω resistance, which demonstrated that electrode denitrification by ADB occurred in the cathode of the MFC. Sufficient electrons were inferred to be provided by the electrode to allow ADB survival at low carbon:nitrogen ratios (≤0.3). Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) results showed that increasing the DO resulted in a change of the predominant species from thermophilic autotrophic nitrifiers and facultative heterotrophic denitrifiers at low DO concentrations to thermophilic ADB at high DO concentrations. The predominant phylum changed from Firmicutes to Proteobacteria, and the predominant class changed from Bacilli to Alpha, Beta, and Gamma Proteobacteria.
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Affiliation(s)
- Jianqiang Zhao
- School of Environmental Science and Engineering, Chang'an UniversityXi'an, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of EducationXi'an, China
| | - Jinna Wu
- School of Environmental Science and Engineering, Chang'an University Xi'an, China
| | - Xiaoling Li
- School of Civil Engineering, Chang'an University Xi'an, China
| | - Sha Wang
- School of Environmental Science and Engineering, Chang'an University Xi'an, China
| | - Bo Hu
- School of Civil Engineering, Chang'an University Xi'an, China
| | - Xiaoqian Ding
- School of Environmental Science and Engineering, Chang'an University Xi'an, China
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Rea MA, Zammit CM, Reith F. Bacterial biofilms on gold grains-implications for geomicrobial transformations of gold. FEMS Microbiol Ecol 2016; 92:fiw082. [PMID: 27098381 DOI: 10.1093/femsec/fiw082] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2016] [Indexed: 01/21/2023] Open
Abstract
The biogeochemical cycling of gold (Au), i.e. its solubilization, transport and re-precipitation, leading to the (trans)formation of Au grains and nuggets has been demonstrated under a range of environmental conditions. Biogenic (trans)formations of Au grains are driven by (geo)biochemical processes mediated by distinct biofilm consortia living on these grains. This review summarizes the current knowledge concerning the composition and functional capabilities of Au-grain communities, and identifies contributions of key-species involved in Au-cycling. To date, community data are available from grains collected at 10 sites in Australia, New Zealand and South America. The majority of detected operational taxonomic units detected belong to the α-, β- and γ-Proteobacteria and the Actinobacteria. A range of organisms appears to contribute predominantly to biofilm establishment and nutrient cycling, some affect the mobilization of Au via excretion of Au-complexing ligands, e.g. organic acids, thiosulfate and cyanide, while a range of resident Proteobacteria, especially Cupriavidus metallidurans and Delftia acidovorans, have developed Au-specific biochemical responses to deal with Au-toxicity and reductively precipitate mobile Au-complexes. This leads to the biomineralization of secondary Au and drives the environmental cycle of Au.
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Affiliation(s)
- Maria Angelica Rea
- School of Biological Sciences, The Sprigg Geobiology Centre, The University of Adelaide, Adelaide, South Australia 5005, Australia CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia
| | - Carla M Zammit
- School of Earth Sciences, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Frank Reith
- School of Biological Sciences, The Sprigg Geobiology Centre, The University of Adelaide, Adelaide, South Australia 5005, Australia CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia
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Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia. Sci Rep 2016; 6:18594. [PMID: 26729566 PMCID: PMC4700446 DOI: 10.1038/srep18594] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/23/2015] [Indexed: 12/17/2022] Open
Abstract
Inhabitants of Túquerres in the Colombian Andes have a 25-fold higher risk of gastric cancer than inhabitants of the coastal town Tumaco, despite similar H. pylori prevalences. The gastric microbiota was recently shown in animal models to accelerate the development of H. pylori-induced precancerous lesions. 20 individuals from each town, matched for age and sex, were selected, and gastric microbiota analyses were performed by deep sequencing of amplified 16S rDNA. In parallel, analyses of H. pylori status, carriage of the cag pathogenicity island and assignment of H. pylori to phylogeographic groups were performed to test for correlations between H. pylori strain properties and microbiota composition. The gastric microbiota composition was highly variable between individuals, but showed a significant correlation with the town of origin. Multiple OTUs were detected exclusively in either Tumaco or Túquerres. Two operational taxonomic units (OTUs), Leptotrichia wadei and a Veillonella sp., were significantly more abundant in Túquerres, and 16 OTUs, including a Staphylococcus sp. were significantly more abundant in Tumaco. There was no significant correlation of H. pylori phylogeographic population or carriage of the cagPAI with microbiota composition. From these data, testable hypotheses can be generated and examined in suitable animal models and prospective clinical trials.
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Mehmood A, Abdallah K, Khandekar S, Zhurina D, Srivastava A, Al-Karablieh N, Alfaro-Espinoza G, Pletzer D, Ullrich MS. Expression of extra-cellular levansucrase in Pseudomonas syringae is controlled by the in planta fitness-promoting metabolic repressor HexR. BMC Microbiol 2015; 15:48. [PMID: 25886911 PMCID: PMC4357207 DOI: 10.1186/s12866-015-0349-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/15/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Pseudomonas syringae pv. glycinea PG4180 causes bacterial blight on soybean plants and enters the leaf tissue through stomata or open wounds, where it encounters a sucrose-rich milieu. Sucrose is utilized by invading bacteria via the secreted enzyme, levansucrase (Lsc), liberating glucose and forming the polyfructan levan. P. syringae PG4180 possesses two functional lsc alleles transcribed at virulence-promoting low temperatures. RESULTS We hypothesized that transcription of lsc is controlled by the hexose metabolism repressor, HexR, since potential HexR binding sites were identified upstream of both lsc genes. A hexR mutant of PG4180 was significantly growth-impaired when incubated with sucrose or glucose as sole carbon source, but exhibited wild type growth when arabinose was provided. Analyses of lsc expression resulted in higher transcript and protein levels in the hexR mutant as compared to the wild type. The hexR mutant's ability to multiply in planta was reduced. HexR did not seem to impact hrp gene expression as evidenced by the hexR mutant's unaltered hypersensitive response in tobacco and its unmodified protein secretion pattern as compared to the wild type under hrp-inducing conditions. CONCLUSIONS Our data suggested a co-regulation of genes involved in extra-cellular sugar acquisition with those involved in intra-cellular energy-providing metabolic pathways in P. syringae.
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Affiliation(s)
- Amna Mehmood
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Khaled Abdallah
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Shaunak Khandekar
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Daria Zhurina
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Abhishek Srivastava
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Nehaya Al-Karablieh
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
- Hamdi Mango Center for Scientific Research, The University of Jordan, P.O. Box 13507, Amman, 11942, Jordan.
| | - Gabriela Alfaro-Espinoza
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Daniel Pletzer
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
| | - Matthias S Ullrich
- Molecular Life Science Research Center, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany.
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Andreessen B, Taylor N, Steinbüchel A. Poly(3-hydroxypropionate): a promising alternative to fossil fuel-based materials. Appl Environ Microbiol 2014; 80:6574-82. [PMID: 25149521 PMCID: PMC4249027 DOI: 10.1128/aem.02361-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are storage compounds synthesized by numerous microorganisms and have attracted the interest of industry since they are biobased and biodegradable alternatives to fossil fuel-derived plastics. Among PHAs, poly(3-hydroxypropionate) [poly(3HP)] has outstanding material characteristics and exhibits a large variety of applications. As it is not brittle like, e.g., the best-studied PHA, poly(3-hydroxybutyrate) [poly(3HB)], it can be used as a plasticizer in blends to improve their properties. Furthermore, 3-hydroxypropionic acid (3HP) is considered likely to become one of the new industrial building blocks, and it can be obtained from poly(3HP) by simple hydrolysis. Unfortunately, no natural organism is known to accumulate poly(3HP) so far. Thus, several efforts have been made to engineer genetically modified organisms capable of synthesizing the homopolymer or copolymers containing 3HP. In this review, the achievements made so far in efforts to obtain biomass which has accumulated poly(3HP) or 3HP-containing copolymers, as well as the properties of these polyesters and their applications, are compiled and evaluated.
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Affiliation(s)
- Björn Andreessen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Nicolas Taylor
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
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Limbri H, Gunawan C, Thomas T, Smith A, Scott J, Rosche B. Coal-packed methane biofilter for mitigation of green house gas emissions from coal mine ventilation air. PLoS One 2014; 9:e94641. [PMID: 24743729 PMCID: PMC3990720 DOI: 10.1371/journal.pone.0094641] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/17/2014] [Indexed: 11/18/2022] Open
Abstract
Methane emitted by coal mine ventilation air (MVA) is a significant greenhouse gas. A mitigation strategy is the oxidation of methane to carbon dioxide, which is approximately twenty-one times less effective at global warming than methane on a mass-basis. The low non-combustible methane concentrations at high MVA flow rates call for a catalytic strategy of oxidation. A laboratory-scale coal-packed biofilter was designed and partially removed methane from humidified air at flow rates between 0.2 and 2.4 L min-1 at 30°C with nutrient solution added every three days. Methane oxidation was catalysed by a complex community of naturally-occurring microorganisms, with the most abundant member being identified by 16S rRNA gene sequence as belonging to the methanotrophic genus Methylocystis. Additional inoculation with a laboratory-grown culture of Methylosinus sporium, as investigated in a parallel run, only enhanced methane consumption during the initial 12 weeks. The greatest level of methane removal of 27.2±0.66 g methane m-3 empty bed h-1 was attained for the non-inoculated system, which was equivalent to removing 19.7±2.9% methane from an inlet concentration of 1% v/v at an inlet gas flow rate of 1.6 L min-1 (2.4 min empty bed residence time). These results show that low-cost coal packing holds promising potential as a suitable growth surface and contains methanotrophic microorganisms for the catalytic oxidative removal of methane.
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Affiliation(s)
- Hendy Limbri
- School of Chemical Engineering, The University of New South Wales, Sydney, Australia
| | - Cindy Gunawan
- School of Chemical Engineering, The University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, Australia
| | - Andrew Smith
- School of Chemical Engineering, The University of New South Wales, Sydney, Australia
| | - Jason Scott
- School of Chemical Engineering, The University of New South Wales, Sydney, Australia
| | - Bettina Rosche
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- * E-mail:
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Vlahos N, Kormas KA, Pachiadaki MG, Meziti A, Hotos GN, Mente E. Changes of bacterioplankton apparent species richness in two ornamental fish aquaria. SPRINGERPLUS 2013; 2:66. [PMID: 23519098 PMCID: PMC3601261 DOI: 10.1186/2193-1801-2-66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/13/2013] [Indexed: 12/01/2022]
Abstract
We analysed the 16S rRNA gene diversity within the bacterioplankton community in the water column of the ornamental fish Pterophyllum scalare and Archocentrus nigrofasciatus aquaria during a 60-day growth experiment in order to detect any dominant bacterial species and their possible association with the rearing organisms. The basic physical and chemical parameters remained stable but the bacterial community at 0, 30 and 60 days showed marked differences in bacterial cell abundance and diversity. We found high species richness but no dominant phylotypes were detected. Only few of the phylotypes were found in more than one time point per treatment and always with low relative abundance. The majority of the common phylotypes belonged to the Proteobacteria phylum and were closely related to Acinetobacter junii, Pseudomonas sp., Nevskia ramosa, Vogesella perlucida, Chitinomonas taiwanensis, Acidovorax sp., Pelomonas saccharophila and the rest belonged to the α-Proteobacteria, Bacteroidetes, Actinobacteria, candidate division OP11 and one unaffiliated group. Several of these phylotypes were closely related to known taxa including Sphingopyxis chilensis, Flexibacter aurantiacus subsp. excathedrus and Mycobacterium sp. Despite the high phylogenetic diversity most of the inferred ecophysiological roles of the found phylotypes are related to nitrogen metabolism, a key process for fish aquaria.
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Affiliation(s)
- Nikolaos Vlahos
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, 384 46 Greece ; Department of Aquaculture & Fisheries Management, Technological Educational Institute of Mesolonghi, Mesolonghi, 30 200 Greece
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Abstract
This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3'-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations.
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Modeling and optimization of poly(3hydroxybutyrate-co-3hydroxyvalerate) production from cane molasses by Azohydromonas lata MTCC 2311 in a stirred-tank reactor: effect of agitation and aeration regimes. ACTA ACUST UNITED AC 2012; 39:987-1001. [DOI: 10.1007/s10295-012-1102-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 02/02/2012] [Indexed: 10/28/2022]
Abstract
Abstract
The effects of agitation and aeration rates on copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] production by Azohydromonas lata MTCC 2311 using cane molasses supplemented with propionic acid in a bioreactor were investigated. The experiments were conducted in a three-level factorial design by varying the impeller (150–500 rev min−1) and aeration (0.5–1.5 vvm) rates. Further, the data were fitted to mathematical models [quadratic polynomial equation and artificial neural network (ANN)] and process variables were optimized by genetic algorithm-coupled models. ANN and hybrid ANN-GA were found superior for modeling and optimization of process variables, respectively. The maximum copolymer concentration of 7.45 g l−1 with 21.50 mol% of 3HV was predicted at process variables: agitation speed, 287 rev min−1; and aeration rate, 0.85 vvm, which upon validation gave 7.20 g l−1 of P(3HB-co-3HV) with 21 mol% of 3HV with the prediction error (%) of 3.38 and 2.32, respectively. Agitation speed established a relative high importance of 72.19% than of aeration rate (27.80%) for copolymer accumulation. The volumetric gas–liquid mass transfer coefficient (k L a) was strongly affected by agitation and aeration rates. The highest P(3HB-co-3HV) productivity of 0.163 g l−1 h−1 was achieved at 0.17 s−1 of k L a value. During the early phase of copolymer production process, 3HB monomers were accumulated, which were shifted to 3HV units (9–21%) during the cultivation period of 24–42 h. The enhancement of 7.5 and 34% were reported for P(3HB-co-3HV) production and 3HV content, respectively, by hybrid ANN-GA paradigm, which revealed the significant utilization of cane molasses for improved copolymer production.
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Lima G, Parker B, Meyer J. Dechlorinating microorganisms in a sedimentary rock matrix contaminated with a mixture of VOCs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:5756-5763. [PMID: 22612587 DOI: 10.1021/es300214f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Microbiological characterizations of contaminant biodegradation in fractured sedimentary rock have primarily focused on the biomass suspended in groundwater samples and disregarded the biomass attached to fractures and in matrix pores. In fractured sedimentary rock, diffusion causes nearly all contaminant mass to reside in porous, low-permeability matrix. Microorganisms capable of contaminant degradation can grow in the matrix pores if the pores and pore throats are sufficiently large. In this study, the presence of dechlorinating microorganisms in rock matrices was investigated at a site where a fractured, flat-lying, sandstone-dolostone sequence has been contaminated with a mixture of chlorinated and aromatic hydrocarbons for over 40 years. The profile of organic contaminants as well as the distribution and characterization of the microbial community spatial variability was obtained through depth-discrete, high-frequency sampling along a 98-m continuous rock core. Dechlorinating microorganisms, such as Dehalococcoides and Dehalobacter, were detected in the rock matrices away from fracture surfaces, indicating that biodegradation within the rock matrix blocks should be considered as an important component of the system when evaluating the potential for natural attenuation or remediation at similar sedimentary rock sites.
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Affiliation(s)
- Gláucia Lima
- School of Engineering, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
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Yang C, Hamel C, Vujanovic V, Gan Y. Nontarget effects of foliar fungicide application on the rhizosphere: diversity of nifH gene and nodulation in chickpea field. J Appl Microbiol 2012; 112:966-74. [PMID: 22335393 PMCID: PMC3489047 DOI: 10.1111/j.1365-2672.2012.05262.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aims This study explores nontarget effects of fungicide application on field-grown chickpea. Methods and Results Molecular methods were used to test the effects of foliar application of fungicide on the diversity and distribution of nifH genes associated with two chickpea cultivars and their nodulation. Treatments were replicated four times in a split-plot design in the field, in 2008 and 2009. Chemical disease control did not change the richness of the nifH genes associated with chickpea, but selected different dominant nifH gene sequences in 2008, as revealed by correspondence analysis. Disease control strategies had no significant effect on disease severity or nifH gene distribution in 2009. Dry weather conditions rather than disease restricted plant growth that year, suggesting that reduced infection rather than the fungicide is the factor modifying the distribution of nifH gene in chickpea rhizosphere. Reduced nodule size and enhanced N2-fixation in protected plants indicate that disease control affects plant physiology, which may in turn influence rhizosphere bacteria. The genotypes of chickpea also affected the diversity of the nifH gene in the rhizosphere, illustrating the importance of plant selective effects on bacterial communities. Conclusions We conclude that the chemical disease control affects nodulation and the diversity of nifH gene in chickpea rhizosphere, by modifying host plant physiology. A direct effect of fungicide on the bacteria cannot be ruled out, however, as residual amounts of fungicide were found to accumulate in the rhizosphere soil of protected plants. Significance and Impact of the Study Systemic nontarget effect of phytoprotection on nifH gene diversity in chickpea rhizosphere is reported for the first time. This result suggests the possibility of manipulating associative biological nitrogen fixation in the field.
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Affiliation(s)
- C Yang
- Semiarid Prairie Agricultural Research Centre, AAFC, Swift Current, SK, Canada.
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Zafar M, Kumar S, Kumar S, Dhiman AK. Artificial intelligence based modeling and optimization of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) production process by using Azohydromonas lata MTCC 2311 from cane molasses supplemented with volatile fatty acids: a genetic algorithm paradigm. BIORESOURCE TECHNOLOGY 2012; 104:631-641. [PMID: 22074908 DOI: 10.1016/j.biortech.2011.10.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 10/07/2011] [Accepted: 10/08/2011] [Indexed: 05/31/2023]
Abstract
The present work describes the optimization of medium variables for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] by Azohydromonas lata MTCC 2311 using cane molasses supplemented with propionic acid. Genetic algorithm (GA) has been used for the optimization of P(3HB-co-3HV) production through the simulation of artificial neural network (ANN) and response surface methodology (RSM). The predictions by ANN are better than those of RSM and in good agreement with experimental findings. The highest P(3HB-co-3HV) concentration and 3HV content have been reported as 7.35 g/l and 16.84 mol%, respectively by hybrid ANN-GA. Upon validation, 7.20 g/l and 16.30 mol% of P(3HB-co-3HV) concentration and 3HV content have been found in the shake flask, whereas 6.70 g/l and 16.35 mol%, have been observed in a 3 l bioreactor, respectively. The specific growth rate and P(3HB-co-3HV) accumulation rate of 0.29 per h and 0.16 g/lh determined with cane molasses are comparable to those observed on pure substrates.
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Affiliation(s)
- Mohd Zafar
- Department of Chemical Engineering, Indian Institute of Technology Roorkee, Roorkee-247 667 (Uttarakhand), India
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Optimization of polyhydroxybutyrate (PHB) production by Azohydromonas lata MTCC 2311 by using genetic algorithm based on artificial neural network and response surface methodology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2011.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Li YH, Liu QF, Liu Y, Zhu JN, Zhang Q. Endophytic bacterial diversity in roots of Typha angustifolia L. in the constructed Beijing Cuihu Wetland (China). Res Microbiol 2010; 162:124-31. [PMID: 21111814 DOI: 10.1016/j.resmic.2010.09.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 09/29/2010] [Indexed: 11/27/2022]
Abstract
We investigated the community structure of endophytic bacteria in narrowleaf cattail (Typha angustifolia L.) roots growing in the Beijing Cuihu Wetland, China, using the 16S rDNA library technique. In total, 184 individual sequences were used to assess the diversity of endophytic bacteria. Phylogenetic analysis revealed that 161 clones (87.5%) were affiliated with Proteobacteria, other clones grouped into Cytophaga/Flexibacter/Bacteroids (3.3%), Fusobacteria (3.8%), and nearly 5% were uncultured bacteria. In Proteobacteria, the beta and gamma subgroups were the most abundant, accounting for approximately 46% and 36.6% of all Proteobacteria, respectively. The dominant genera included Rhodoferax, Pelomonas, Uliginosibacterium, Pseudomonas, Aeromonas, Rhizobium, Sulfurospirillum, Ilyobacter and Bacteroides. While some of these endophytic bacteria are capable of fixing nitrogen and can therefore improve plant growth, other endophytes may play important biological roles by removing nitrogen, phosphorus and/or organic matter from the water body and thus have the potential to enhance the phytoremediation of eutrophic water bodies. These bacteria have the potential to degrade xenobiota such as methane, methanol, methylated amines, catechol, oxochlorate, urea, cyanide, and 2,4-dichlorophenol. Hence, the use of certain endophytic bacteria in the process of phytoremediation could be a powerful approach for the restoration of eutrophic systems.
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Affiliation(s)
- Yan Hong Li
- College of Life Science, Capital Normal University, Xisanhuan North Road 105#, Haidian District, Beijing 100048, China.
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Ren Q, Ruth K, Thöny-Meyer L, Zinn M. Enatiomerically pure hydroxycarboxylic acids: current approaches and future perspectives. Appl Microbiol Biotechnol 2010; 87:41-52. [PMID: 20393709 PMCID: PMC2872024 DOI: 10.1007/s00253-010-2530-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/24/2010] [Accepted: 02/24/2010] [Indexed: 11/21/2022]
Abstract
The growing awareness of the importance of chirality in conjunction with biological activity has led to an increasing demand for efficient methods for the industrial synthesis of enantiomerically pure compounds. Polyhydroxyalkanotes (PHAs) are a family of polyesters consisting of over 140 chiral R-hydroxycarboxylic acids (R-HAs), representing a promising source for obtaining chiral chemicals from renewable carbon sources. Although some R-HAs have been produced for some time and certain knowledge of the production processes has been gained, large-scale production has not yet been possible. In this article, through analysis of the current advances in production of these acids, we present guidelines for future developments in biotechnological processes for R-HA production.
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Affiliation(s)
- Qun Ren
- Swiss Federal Laboratories for Materials Testing and Research (Empa), Laboratory for Biomaterials, 9014 St. Gallen, Switzerland.
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Witzig M, Boguhn J, Kleinsteuber S, Fetzer I, Rodehutscord M. Effect of the corn silage to grass silage ratio and feed particle size of diets for ruminants on the ruminal Bacteroides-Prevotella community in vitro. Anaerobe 2010; 16:412-9. [PMID: 20493960 DOI: 10.1016/j.anaerobe.2010.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 05/04/2010] [Accepted: 05/05/2010] [Indexed: 11/15/2022]
Abstract
This study examined whether different corn silage to grass silage ratios in ruminant rations and different grinding levels of the feed affect the composition of the ruminal Bacteroides-Prevotella community in vitro. Three diets, composed of 10% soybean meal as well as of different corn silage and grass silage proportions, were ground through 1mm or 4mm screened sieves and incubated in a semi-continuous rumen simulation system. On day 14 of the incubation microbes were harvested by centrifugation from the liquid effluent of fermenter vessels. Microbial DNA was extracted for single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes followed by sequencing of single SSCP bands. Fluorescence in situ hybridization (FISH) and real-time quantitative (q) PCR were used to quantify differences in the relative abundance of Bacteroides-Prevotella and Prevotella bryantii. SSCP profiles revealed a significant influence of the forage source as well as of the feed particle size on the community structure of the Bacteroides-Prevotella group. Different, phylogenetically distinct, so far uncultured Prevotella species were detected by sequence analysis of several treatment-dependent occurring SSCP bands indicating different nutritional requirements of these organisms for growth. No quantitative differences in the occurrence of Bacteroides-Prevotella-related species were detected between diets by FISH with probe BAC303. However, real-time qPCR data revealed a higher abundance of P. bryantii with increasing grass silage to corn silage ratio, thus again indicating changes within the community composition of the Bacteroides-Prevotella group. As P. bryantii possesses high proteolytic activity its higher abundance may have been caused by the higher contents of crude protein in the grass silage containing diets. To conclude, results of this study show an influence of the forage source on the ruminal community of Bacteroides-Prevotella. Furthermore, they suggest an effect of the feed particle size on this bacterial group.
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Affiliation(s)
- M Witzig
- Universität Hohenheim, Institut für Tierernährung, Emil-Wolff-Strasse 10, Stuttgart, Germany.
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Biosynthesis and biodegradation of 3-hydroxypropionate-containing polyesters. Appl Environ Microbiol 2010; 76:4919-25. [PMID: 20543057 DOI: 10.1128/aem.01015-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3-Hydroxypropionate (3HP) is an important compound in the chemical industry, and the polymerized 3HP can be used as a bioplastic. In this review, we focus on polyesters consisting of 3HP monomers, including the homopolyester poly(3-hydroxypropionate) and copolyesters poly(3-hydroxybutyrate-co-3-hydroxypropionate), poly(3-hydroxypropionate-co-3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), poly(4-hydroxybutyrate-co-3-hydroxypropionate-co-lactate), and poly(3-hydroxybutyrate-co-3-hydroxypropionate-co-4-hydroxybutyrate-co-lactate). Homopolyesters like poly(3-hydroxybutyrate) are often highly crystalline and brittle, which limits some of their applications. The incorporation of 3HP monomers reduces the glass transition temperature, the crystallinity, and also, at up to 60 to 70 mol% 3HP, the melting point of the copolymer. This review provides a survey of the synthesis and physical properties of different polyesters containing 3HP.
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Gomila M, Pinhassi J, Falsen E, Moore ERB, Lalucat J. Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae. Int J Syst Evol Microbiol 2010; 60:809-814. [DOI: 10.1099/ijs.0.011478-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, Gram-negative bacterium, strain KIN192T, isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA–DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192T (=CCUG 53117T =CECT 7319T).
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Affiliation(s)
- Margarita Gomila
- CCUG – Culture Collection University of Göteborg, University of Göteborg, SE-413 46 Göteborg, Sweden
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Jarone Pinhassi
- Marine Microbiology, Department of Pure and Applied Natural Sciences, University of Kalmar, SE-391 82 Kalmar, Sweden
| | - Enevold Falsen
- CCUG – Culture Collection University of Göteborg, University of Göteborg, SE-413 46 Göteborg, Sweden
| | - Edward R. B. Moore
- Sahlgrenska University Hospital, University of Göteborg, SE-413 46 Göteborg, Sweden
- CCUG – Culture Collection University of Göteborg, University of Göteborg, SE-413 46 Göteborg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
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Benítez MS, Gardener BBM. Linking sequence to function in soil bacteria: sequence-directed isolation of novel bacteria contributing to soilborne plant disease suppression. Appl Environ Microbiol 2009; 75:915-24. [PMID: 19088312 PMCID: PMC2643568 DOI: 10.1128/aem.01296-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 12/09/2008] [Indexed: 01/09/2023] Open
Abstract
Microbial community profiling of samples differing in a specific ecological function, i.e., soilborne plant disease suppression, can be used to mark, recover, and ultimately identify the bacteria responsible for that specific function. Previously, several terminal restriction fragments (TRF) of 16S rRNA genes were statistically associated with damping-off disease suppression. This work presents the development of sequence-based TRF length polymorphism (T-RFLP)-derived molecular markers to direct the identification and isolation of novel bacteria involved in damping-off pathogen suppression. Multiple sequences matching TRF M139 and M141 were cloned and displayed identity to multiple database entries in the genera incertae sedis of the Burkholderiales. Sequences matching TRF M148, in contrast, displayed greater sequence diversity. A sequence-directed culturing strategy was developed using M139- and M141-derived markers and media reported to be selective for the genera identified within this group. Using this approach, we isolated and identified novel Mitsuaria and Burkholderia species with high levels of sequence similarity to the targeted M139 and M141 TRF, respectively. As predicted, these Mitsuaria and Burkholderia isolates displayed the targeted function by reducing fungal and oomycete plant pathogen growth in vitro and reducing disease severity in infected tomato and soybean seedlings. This work represents the first successful example of the use of T-RFLP-derived markers to direct the isolation of microbes with pathogen-suppressing activities, and it establishes the power of low-cost molecular screening to identify and direct the recovery of functionally important microbes, such as these novel biocontrol strains.
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MESH Headings
- Betaproteobacteria/classification
- Betaproteobacteria/genetics
- Betaproteobacteria/isolation & purification
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Solanum lycopersicum/microbiology
- Solanum lycopersicum/physiology
- Molecular Sequence Data
- Phylogeny
- Plant Diseases/microbiology
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Glycine max/microbiology
- Glycine max/physiology
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Affiliation(s)
- María-Soledad Benítez
- Department of Plant Pathology, The Ohio State University, OARDC, 1680 Madison Avenue, Wooster, OH 44691, USA
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