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Grettenberger CL, Havig JR, Hamilton TL. Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site. BMC Microbiol 2020; 20:119. [PMID: 32423375 PMCID: PMC7236192 DOI: 10.1186/s12866-020-01768-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ferrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY. RESULTS Here we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis. CONCLUSIONS Previously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.
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Affiliation(s)
| | - Jeff R Havig
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, 218 Cargill Building, St. Paul, MN, 55108, USA.
- The BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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Rodríguez-Castro L, Méndez V, Durán RE, Seeger M. Long-chain flavodoxin FldX1 improves Paraburkholderia xenovorans LB400 tolerance to oxidative stress caused by paraquat and H2O2. PLoS One 2019; 14:e0221881. [PMID: 31469877 PMCID: PMC6716667 DOI: 10.1371/journal.pone.0221881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/17/2019] [Indexed: 11/26/2022] Open
Abstract
Flavodoxins are small electron transfer proteins containing flavin mononucleotide (FMN) as a prosthetic group, which play an important role during oxidative stress or iron limitation. The aims of this study were the identification and characterization of flavodoxins in the model aromatic-degrader Paraburkholderia xenovorans LB400 and the analyses of their protective effects during oxidative stress induced by paraquat and H2O2. Two genes (BxeA0278 and BxeB0391) encoding flavodoxins (hereafter referred to as fldX for flavodoxin from P. xenovorans), were identified at the LB400 major and minor chromosome. Genomic context of the flavodoxin-encoding genes showed genes encoding membrane proteins, transporters, and proteins involved in redox processes and biosynthesis of macromolecules. A secondary structure prediction of both LB400 flavodoxins showed the characteristic flavodoxin structure of five ß-sheets intercalated with five α-helices. FldX1 contains a loop intercalated in the fifth β-strand, which indicates that it belongs to the long-chain flavodoxins, whereas FldX2 is a short-chain flavodoxin. A phylogenetic analysis of 73 flavodoxins from 43 bacterial genera revealed eight clusters (I-VIII), while FldX1 and FldX2 grouped separately within a long-chain and a short-chain flavodoxin clades. FldX1 and FldX2 were overexpressed in P. xenovorans. Interestingly, the strain overexpressing the long-chain flavodoxin FldX1 (p2-fldX1) showed a faster growth in glucose than the control strain. The recombinant strain overexpressing the long-chain flavodoxin FldX1 (p2-fldx1) exposed to paraquat (20 mM) possessed lower susceptibility to growth inhibition on plates and higher survival in liquid medium than the control strain. The strains overexpressing the flavodoxins FldX1 and FldX2 showed higher survival during exposure to 1 mM paraquat (>95%) than the control strain (68%). Compared to the control strain, strains overexpressing FldX1 and FldX2 showed lower lipid peroxidation (>20%) after exposure to 1 mM paraquat and a lower protein carbonylation (~30%) after exposure to 1 mM H2O2 was observed. During exposure to paraquat, strain p2-fldx1 downregulated the katG4, hpf, trxB1 and ohr genes (> 2-fold), whereas strain p2-fldx2 upregulated the oxyR and ahpC1 genes (> 2-fold). In conclusion, the flavodoxins FldX1 and FldX2 of P. xenovorans LB400 conferred protection to cells exposed to the oxidizing agents paraquat and H2O2.
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Affiliation(s)
- Laura Rodríguez-Castro
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Roberto E. Durán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
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Wu W, Huang L, Mao Q, Wei J, Li J, Zhao Y, Zhang Q, Jia D, Wei T. Interaction of viral pathogen with porin channels on the outer membrane of insect bacterial symbionts mediates their joint transovarial transmission. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180320. [PMID: 30967020 PMCID: PMC6367154 DOI: 10.1098/rstb.2018.0320] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
Many hemipteran insects that can transmit plant viruses in a persistent and transovarial manner are generally associated with a common obligate bacterial symbiont Sulcia and its β-proteobacterial partner. Rice dwarf virus (RDV), a plant reovirus, can bind to the envelope of Sulcia through direct interaction of the viral minor outer capsid protein P2 with the bacterial outer membrane protein, allowing the virus to exploit the ancient oocyte entry path of Sulcia in rice leafhopper vectors. Here, we show that RDV can hitchhike with both Sulcia and its β-proteobacterial partner Nasuia to ensure their simultaneous transovarial transmission. Interestingly, RDV can move through the outer envelope of Nasuia and reside in the periplasmic space, which is mediated by the specific interaction of the viral major outer capsid protein P8 and the porin channel on the bacterial outer envelope. Nasuia porin-specific antibody efficiently interferes with the binding between RDV and the Nasuia envelope, thus strongly preventing viral transmission to insect offspring. Thus, RDV has evolved different strategies to exploit the ancient oocyte entry paths used by two obligate bacterial symbionts in rice leafhoppers. Our results thus reveal that RDV has formed complex, cooperative interactions with both Sulcia and Nasuia during their joint transovarial transmission. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
- Wei Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Lingzhi Huang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Qianzhuo Mao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Jing Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Jiajia Li
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Yu Zhao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Qian Zhang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Dongsheng Jia
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Taiyun Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
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García-Bonilla E, Brandão PFB, Pérez T, Junca H. Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida). Microb Ecol 2019; 77:25-36. [PMID: 29766224 DOI: 10.1007/s00248-018-1201-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.
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Affiliation(s)
- Erika García-Bonilla
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia
| | - Pedro F B Brandão
- Laboratorio de Microbiología Ambiental y Aplicada, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Avenida Carrera 30 No. 45-03, Bogotá, Colombia
| | - Thierry Pérez
- Station Marine d'Endoume SME - IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, UMR 7263 CNRS, Aix-Marseille Université, IRD, Avignon Université, Rue Batterie des Lions, 13007, Marseille, France
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia.
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5
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Mao M, Yang X, Bennett GM. Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host. Proc Natl Acad Sci U S A 2018; 115:E11691-E11700. [PMID: 30463949 PMCID: PMC6294904 DOI: 10.1073/pnas.1811932115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.
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Affiliation(s)
- Meng Mao
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343;
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Xiushuai Yang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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Kasbekar DP. A cross-eyed geneticist's view II. Riddles, wrapped in mysteries, inside … mealybugs. J Biosci 2018; 43:819-822. [PMID: 30541943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Durgadas P Kasbekar
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500 039, India,
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Muszyński A, Załęska-Radziwiłł M, Doskocz N. Factors affecting Accumulibacter population structure in full- and laboratory-scale biological reactors with nutrients removal. Water Sci Technol 2018; 77:2794-2802. [PMID: 30065131 DOI: 10.2166/wst.2018.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The structure of Accumulibacter lineage was examined over a three-year period in six full-scale wastewater treatment plants and compared to the population in a laboratory-scale reactor. The Accumulibacter lineage reached 69% of all bacteria in the laboratory-scale reactor and contained clades IA and IIA,C,D only. In full-scale plants, Accumulibacter constituted up to 12%, correlated with sludge loading with BOD, COD, N and P. Clade IA was more abundant after periods with low temperatures, whereas clades IIA,C,D presented opposite variations. The fraction, unrevealed by clade-specific probes, constituted 31-62% of the Accumulibacter lineage in all but one full-scale plant - the population in the plant with significant industrial contribution in the influent resembled the low diversity in the laboratory-scale reactor. Selection of specific clades in the laboratory-scale reactor was associated with its different performance, despite stable operational conditions being maintained through the study. It implies that high relative abundance of Accumulibacter in bacterial community is not enough for efficient P removal and the effectiveness may also be associated with the presence of specific clades. A considerable fraction of Accumulibacter in full-scale plants, which is not targeted by clade-specific probes, should be further investigated to better characterize clades that may affect effectiveness of phosphorus removal.
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Affiliation(s)
- A Muszyński
- Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, Nowowiejska 20, 00-653 Warsaw, Poland E-mail:
| | - M Załęska-Radziwiłł
- Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, Nowowiejska 20, 00-653 Warsaw, Poland E-mail:
| | - N Doskocz
- Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, Nowowiejska 20, 00-653 Warsaw, Poland E-mail:
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Gil R, Vargas-Chavez C, López-Madrigal S, Santos-García D, Latorre A, Moya A. Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. ISME J 2018; 12:124-135. [PMID: 28914880 PMCID: PMC5739004 DOI: 10.1038/ismej.2017.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/31/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023]
Abstract
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.
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Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Institute for Integrative Systems Biology, Universitat de València/CSIC, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. E-mail:
| | - Carlos Vargas-Chavez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
| | - Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Diego Santos-García
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
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Wang Y, Xu C, Tian M, Deng X, Cen Y, He Y. Genetic diversity of Diaphorina citri and its endosymbionts across east and south-east Asia. Pest Manag Sci 2017; 73:2090-2099. [PMID: 28374537 DOI: 10.1002/ps.4582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/15/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Diaphorina citri is the vector of 'Candidatus Liberibacter asiaticus', the most widespread pathogen associated huanglongbing, the most serious disease of citrus. To enhance our understanding of the distribution and origin of the psyllid, we investigated the genetic diversity and population structures of 24 populations in Asia and one from Florida based on the mtCOI gene. Simultaneously, genetic diversity and population structures of the primary endosymbiont (P-endosymbiont) 'Candidatus Carsonella ruddii' and secondary endosymbiont (S-endosymbiont) 'Candidatus Profftella armatura' of D. citri were determined with the housekeeping genes. RESULT AMOVA analysis indicated that populations of D. citri and its endosymbionts in east and south-east Asia were genetically distinct from populations in Pakistan and Florida. Furthermore, P-endosymbiont populations displayed a strong geographical structure across east and south-east Asia, while low genetic diversity indicated the absence of genetic structure among the populations of D. citri and its S-endosymbiont across these regions. CONCLUSION The 'Ca. C. ruddii' is more diverse and structured than the D. citri and the 'Ca. P. armatura' across east and south-east Asia. Multiple introductions of the psyllid have occurred in China. Management application for controlling the pest is proposed based on the genetic information of D. citri and its endosymbionts. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Yanjing Wang
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Changbao Xu
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Mingyi Tian
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Yurong He
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
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Mao M, Yang X, Poff K, Bennett G. Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis. Genome Biol Evol 2017; 9:1803-1815. [PMID: 28854637 PMCID: PMC5533117 DOI: 10.1093/gbe/evx134] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2017] [Indexed: 12/20/2022] Open
Abstract
Insect species in the Auchenorrhyncha suborder (Hemiptera) maintain ancient obligate symbioses with bacteria that provide essential amino acids (EAAs) deficient in their plant-sap diets. Molecular studies have revealed that two complementary symbiont lineages, "Candidatus Sulcia muelleri" and a betaproteobacterium ("Ca. Zinderia insecticola" in spittlebugs [Cercopoidea] and "Ca. Nasuia deltocephalinicola" in leafhoppers [Cicadellidae]) may have persisted in the suborder since its origin ∼300 Ma. However, investigation of how this pair has co-evolved on a genomic level is limited to only a few host lineages. We sequenced the complete genomes of Sulcia and a betaproteobacterium from the treehopper, Entylia carinata (Membracidae: ENCA), as the first representative from this species-rich group. It also offers the opportunity to compare symbiont evolution across a major insect group, the Membracoidea (leafhoppers + treehoppers). Genomic analyses show that the betaproteobacteria in ENCA is a member of the Nasuia lineage. Both symbionts have larger genomes (Sulcia = 218 kb and Nasuia = 144 kb) than related lineages in Deltocephalinae leafhoppers, retaining genes involved in basic cellular functions and information processing. Nasuia-ENCA further exhibits few unique gene losses, suggesting that its parent lineage in the common ancestor to the Membracoidea was already highly reduced. Sulcia-ENCA has lost the abilities to synthesize menaquinone cofactor and to complete the synthesis of the branched-chain EAAs. Both capabilities are conserved in other Sulcia lineages sequenced from across the Auchenorrhyncha. Finally, metagenomic sequencing recovered the partial genome of an Arsenophonus symbiont, although it infects only 20% of individuals indicating a facultative role.
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Affiliation(s)
- Meng Mao
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Xiushuai Yang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Kirsten Poff
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Gordon Bennett
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
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Niu L, Li Y, Wang P, Zhang W, Wang C, Cai W, Wang L. Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China. Sci Total Environ 2016; 559:38-44. [PMID: 27054491 DOI: 10.1016/j.scitotenv.2016.03.175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/24/2016] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
Microbial ecological information on the nitrogen removal processes in wastewater treatment plants (WWTPs) has been of considerable importance as a means for diagnosing the poor performance of nitrogen removal. In this study, the altitude-scale variations in the quantitative relationships and community structures of betaproteobacteria ammonia-oxidizing bacteria (βAOB) and nitrite-reducing bacteria containing the copper-containing nitrite reductase gene (nirK-NRB) and the cytochrome cd1-containing nitrite reductase gene (nirS-NRB) were investigated in 18 municipal WWTPs distributed along a 3660-masl altitude gradient in China. An altitude threshold associated with the proportions of NRB to total bacteria, NRB to βAOB and nirK-NRB to nirS-NRB was detected at approximately 1500m above sea level (masl). Compared with the stable proportions below 1500masl, the proportions exhibited a pronounced decreasing trend with increased altitude above 1500masl. Spearman correlation analysis indicated that the trend was significantly driven by altitude as well as multiple wastewater and operational variables. The community structure dissimilarity of βAOB, nirK-NRB and nirS-NRB showed significant and positive correlations with altitudinal distance between WWTPs. Redundancy analyses indicated that the variation in community structures above 1500masl were predominantly associated with wastewater, followed by operation and altitude. In summary, although the variations of nitrogen-removal bacterial community in WWTPs were driven dominantly by wastewater and operational variables, altitude was also an important variable influencing the quantitative relationships and community structures of nitrogen-removal bacteria in WWTPs particularly above 1500masl.
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Affiliation(s)
- Lihua Niu
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Peifang Wang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wenlong Zhang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Chao Wang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wei Cai
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Linqiong Wang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
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Szklarzewicz T, Grzywacz B, Szwedo J, Michalik A. Bacterial symbionts of the leafhopper Evacanthus interruptus (Linnaeus, 1758) (Insecta, Hemiptera, Cicadellidae: Evacanthinae). Protoplasma 2016; 253:379-91. [PMID: 25900723 PMCID: PMC4783452 DOI: 10.1007/s00709-015-0817-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/06/2015] [Indexed: 05/15/2023]
Abstract
Plant sap-feeding hemipterans harbor obligate symbiotic microorganisms which are responsible for the synthesis of amino acids missing in their diet. In this study, we characterized the obligate symbionts hosted in the body of the xylem-feeding leafhopper Evacanthus interruptus (Cicadellidae: Evacanthinae: Evacanthini) by means of histological, ultrastructural and molecular methods. We observed that E. interruptus is associated with two types of symbiotic microorganisms: bacterium 'Candidatus Sulcia muelleri' (Bacteroidetes) and betaproteobacterium that is closely related to symbionts which reside in two other Cicadellidae representatives: Pagaronia tredecimpunctata (Evacanthinae: Pagaronini) and Hylaius oregonensis (Bathysmatophorinae: Bathysmatophorini). Both symbionts are harbored in their own bacteriocytes which are localized between the body wall and ovaries. In E. interruptus, both Sulcia and betaproteobacterial symbionts are transovarially transmitted from one generation to the next. In the mature female, symbionts leave the bacteriocytes and gather around the posterior pole of the terminal oocytes. Then, they gradually pass through the cytoplasm of follicular cells surrounding the posterior pole of the oocyte and enter the space between them and the oocyte. The bacteria accumulate in the deep depression of the oolemma and form a characteristic 'symbiont ball'. In the light of the results obtained, the phylogenetic relationships within modern Cicadomorpha and some Cicadellidae subfamilies are discussed.
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Affiliation(s)
- Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland.
| | - Jacek Szwedo
- Department of Invertebrate Zoology and Parasitology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.
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Dossi FCA, da Silva EP, Cônsoli FL. Population dynamics and growth rates of endosymbionts during Diaphorina citri (Hemiptera, Liviidae) ontogeny. Microb Ecol 2014; 68:881-9. [PMID: 25037159 DOI: 10.1007/s00248-014-0463-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/04/2014] [Indexed: 05/26/2023]
Abstract
The infection density of symbionts is among the major parameters to understand their biological effects in host-endosymbionts interactions. Diaphorina citri harbors two bacteriome-associated bacterial endosymbionts (Candidatus Carsonella ruddii and Candidatus Profftella armatura), besides the intracellular reproductive parasite Wolbachia. In this study, the density dynamics of the three endosymbionts associated with the psyllid D. citri was investigated by real-time quantitative PCR (qPCR) at different developmental stages. Bacterial density was estimated by assessing the copy number of the 16S rRNA gene for Carsonella and Profftella, and of the ftsZ gene for Wolbachia. Analysis revealed a continuous growth of the symbionts during host development. Symbiont growth and rate curves were estimated by the Gompertz equation, which indicated a negative correlation between the degree of symbiont-host specialization and the time to achieve the maximum growth rate (t*). Carsonella densities were significantly lower than those of Profftella at all host developmental stages analyzed, even though they both displayed a similar trend. The growth rates of Wolbachia were similar to those of Carsonella, but Wolbachia was not as abundant. Adult males displayed higher symbiont densities than females. However, females showed a much more pronounced increase in symbiont density as they aged if compared to males, regardless of the incorporation of symbionts into female oocytes and egg laying. The increased density of endosymbionts in aged adults differs from the usual decrease observed during host aging in other insect-symbiont systems.
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Affiliation(s)
- Fabio Cleisto Alda Dossi
- Insect Interactions Laboratory, Department of Entomology and Acarology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil,
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Hou M, Xiong J, Wang K, Ye X, Ye R, Wang Q, Hu C, Zhang D. Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea. Mar Pollut Bull 2014; 86:147-153. [PMID: 25110045 DOI: 10.1016/j.marpolbul.2014.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/08/2014] [Accepted: 07/20/2014] [Indexed: 06/03/2023]
Abstract
Anthropogenic nitrogen (N) discharges has caused eutrophication in coastal zones. Ammonia-oxidizing bacteria (AOB) convert ammonia to nitrite and play important roles in N transformation. Here, we used pyrosequencing based on the amoA gene to investigate the response of the sediment AOB community to an N pollution gradient in the East China Sea. The results showed that AOB assemblages were primarily affiliated with Nitrosospira-like lineages, and only 0.4% of those belonged to Nitrosomonas-like lineage. The Nitrosospira-like lineage was separated into four clusters that were most similar to the sediment AOB communities detected in adjacent marine regions. Additionally, one clade was out grouped from the AOB lineages, which shared the high similarities with pmoA gene. The AOB community structures substantially changed along the pollution gradient, which were primarily shaped by NH4(+)-N, NO3(-)-N, SO4(2)(-)-S, TP and Eh. These results demonstrated that coastal pollution could dramatically influence AOB communities, which, in turn, may change ecosystem function.
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Affiliation(s)
- Manhua Hou
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China
| | - Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China
| | - Xiansen Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Ran Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Qiong Wang
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Changju Hu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China.
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Daskin JH, Bell SC, Schwarzkopf L, Alford RA. Cool temperatures reduce antifungal activity of symbiotic bacteria of threatened amphibians--implications for disease management and patterns of decline. PLoS One 2014; 9:e100378. [PMID: 24941262 PMCID: PMC4062522 DOI: 10.1371/journal.pone.0100378] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 05/27/2014] [Indexed: 11/18/2022] Open
Abstract
Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a widespread disease of amphibians responsible for population declines and extinctions. Some bacteria from amphibians' skins produce antimicrobial substances active against Bd. Supplementing populations of these cutaneous antifungal bacteria might help manage chytridiomycosis in wild amphibians. However, the activity of protective bacteria may depend upon environmental conditions. Biocontrol of Bd in nature thus requires knowledge of how environmental conditions affect their anti-Bd activity. For example, Bd-driven amphibian declines have often occurred at temperatures below Bd's optimum range. It is possible these declines occurred due to reduced anti-Bd activity of bacterial symbionts at cool temperatures. Better understanding of the effects of temperature on chytridiomycosis development could also improve risk evaluation for amphibian populations yet to encounter Bd. We characterized, at a range of temperatures approximating natural seasonal variation, the anti-Bd activity of bacterial symbionts from the skins of three species of rainforest tree frogs (Litoria nannotis, Litoria rheocola, and Litoria serrata). All three species declined during chytridiomycosis outbreaks in the late 1980s and early 1990s and have subsequently recovered to differing extents. We collected anti-Bd bacterial symbionts from frogs and cultured the bacteria at constant temperatures from 8 °C to 33 °C. Using a spectrophotometric assay, we monitored Bd growth in cell-free supernatants (CFSs) from each temperature treatment. CFSs from 11 of 24 bacteria showed reduced anti-Bd activity in vitro when they were produced at cool temperatures similar to those encountered by the host species during population declines. Reduced anti-Bd activity of metabolites produced at low temperatures may, therefore, partially explain the association between Bd-driven declines and cool temperatures. We show that to avoid inconsistent antifungal activity, bacteria evaluated for use in chytridiomycosis biocontrol should be tested over a range of environmental temperatures spanning those likely to be encountered in the field.
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Affiliation(s)
- Joshua H. Daskin
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia
- * E-mail:
| | - Sara C. Bell
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia
| | - Lin Schwarzkopf
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia
| | - Ross A. Alford
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia
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Chen Y, Zhen Y, He H, Lu X, Mi T, Yu Z. Diversity, abundance, and spatial distribution of ammonia-oxidizing β-proteobacteria in sediments from Changjiang Estuary and its adjacent area in East China Sea. Microb Ecol 2014; 67:788-803. [PMID: 24362769 DOI: 10.1007/s00248-013-0341-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.
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Affiliation(s)
- Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, 238 Songling Road, Qingdao, 266100, People's Republic of China
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Bressan A, Mulligan KL. Localization and morphological variation of three bacteriome-inhabiting symbionts within a planthopper of the genus Oliarus (Hemiptera: Cixiidae). Environ Microbiol Rep 2013; 5:499-505. [PMID: 23864562 DOI: 10.1111/1758-2229.12051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 03/18/2013] [Indexed: 06/02/2023]
Abstract
Many planthoppers of the family Cixiidae (Hemiptera: Fulgoroidea) host three bacteriome-inhabiting bacteria: a gammaproteobacterium: 'Ca.Purcelliella pentastirinorum', a betaproteobacterium: 'Ca. Vidania fulgoroidea', and a member of the bacteroidetes: 'Ca.Sulcia muelleri'. Through light microscopy observations, DGGE PCR and FISH analysis, we examined the morphology and localization of these three endosymbionts within the abdomens of females of the planthopper Oliarus filicicola. Our results indicate a complex distribution and variation in bacterial morphologies. 'Ca. Sulcia muelleri' singularly colonize one pair of bacteriomes and have cells of irregular shape with an average diameter of approximately 4-5 μm. 'Ca.Purcelliella pentastirinorum' bacteria are roughly globular and have an average diameter of approximately 1.5-2 μm in a pair of bacteriomes located near the posterior end of the abdomen, which are surrounded by giant and highly degenerated cells of 'Ca.Vidania fulgoroidea'. In addition, 'Ca.Vidania fulgoroidea' colonizes the 'rectal organ' (sensu Buchner) and the bacterial cells appear as a small, roughly globular with an average diameter of 3 μm; whereas, 'Ca.Purcelliella pentastirinorum' infects an additional two bacteriomes and the bacterial cells appear tightly packed and highly degenerated. All three endosymbionts colocalize in the forming eggs inside the host's ovaries. Based on the abdominal distribution of bacteriomes and bacterial morphologies, we suggest that 'Ca.Vidania fulgoroidea' and 'Ca.Purcelliella pentastirinorum' correspond to the symbionts described by Buchner as the 'x-' and the 'c + d symbiont' respectively.
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Affiliation(s)
- Alberto Bressan
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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López-Madrigal S, Latorre A, Porcar M, Moya A, Gil R. Mealybugs nested endosymbiosis: going into the 'matryoshka' system in Planococcus citri in depth. BMC Microbiol 2013; 13:74. [PMID: 23548081 PMCID: PMC3620526 DOI: 10.1186/1471-2180-13-74] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/25/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In all branches of life there are plenty of symbiotic associations. Insects are particularly well suited to establishing intracellular symbiosis with bacteria, providing them with metabolic capabilities they lack. Essential primary endosymbionts can coexist with facultative secondary symbionts which can, eventually, establish metabolic complementation with the primary endosymbiont, becoming a co-primary. Usually, both endosymbionts maintain their cellular identity. An exception is the endosymbiosis found in mealybugs of the subfamily Pseudoccinae, such as Planococcus citri, with Moranella endobia located inside Tremblaya princeps. RESULTS We report the genome sequencing of M. endobia str. PCVAL and the comparative genomic analyses of the genomes of strains PCVAL and PCIT of both consortium partners. A comprehensive analysis of their functional capabilities and interactions reveals their functional coupling, with many cases of metabolic and informational complementation. Using comparative genomics, we confirm that both genomes have undergone a reductive evolution, although with some unusual genomic features as a consequence of coevolving in an exceptional compartmentalized organization. CONCLUSIONS M. endobia seems to be responsible for the biosynthesis of most cellular components and energy provision, and controls most informational processes for the consortium, while T. princeps appears to be a mere factory for amino acid synthesis, and translating proteins, using the precursors provided by M. endobia. In this scenario, we propose that both entities should be considered part of a composite organism whose compartmentalized scheme (somehow) resembles a eukaryotic cell.
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Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, Valencia, 46020, Spain
| | - Manuel Porcar
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Fundació General de la Universitat de València, Apartado Postal 22085, València, 46071, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, Valencia, 46020, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
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Vargas M, Yuan Z, Pijuan M. Effect of long-term starvation conditions on polyphosphate- and glycogen-accumulating organisms. Bioresour Technol 2013; 127:126-131. [PMID: 23131632 DOI: 10.1016/j.biortech.2012.09.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 08/27/2012] [Accepted: 09/28/2012] [Indexed: 06/01/2023]
Abstract
Endogenous processes such as biomass decay and intracellular polymers degradation of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) were investigated. Cultures enriched in Accumulibacter (a well known PAO) or Competibacter (a well known GAO) were subjected to 21 and 26 days of alternating anaerobic/aerobic conditions respectively. The main energy source for PAOs during starvation was their intracellular polyphosphate released into the medium during the first 14 days of starvation. In contrast, GAOs used their intracellular glycogen during the 26 days of starvation. Biomass decay rates were 0.029 d(-1) for PAOs and almost negligible for GAOs. The reduction in acetate uptake rate during the starvation period, referred to as activity decay, was 0.25 and 0.047 d(-1) for PAOs and GAOs, respectively. Once wastewater was reintroduced, both populations recovered their initial substrate uptake rate after 1 day. The results obtained show that PAOs are more affected than GAOs by starvation conditions.
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Affiliation(s)
- M Vargas
- The University of Queensland, Advanced Water Management Centre, QLD 4072, Australia
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Zhang X, Lin L, Zhu Z, Yang X, Wang Y, An Q. Colonization and modulation of host growth and metal uptake by endophytic bacteria of Sedum alfredii. Int J Phytoremediation 2013; 15:51-64. [PMID: 23487985 DOI: 10.1080/15226514.2012.670315] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sedum alfredii Hance is a Zn and Cd co-hyperaccumulating plant species found in an old mining area in China. Four bacterial strains, Burkholderia sp. SaZR4, Burkholderia sp. SaMR10, Sphingomonas sp. SaMR12 and Variovorax sp. SaNR1, isolated from surface-sterilized S. alfredii plants were used to investigate their endophytic nature and root colonization patterns and effects on phytoextraction of Zn and Cd. Laser scanning confocal microscopy revealed that gfp-tagged SaZR4, SaMR12, and SaNR1 cells formed biofilms on roots and that SaZR4 and SaMR12 cells could invade root tissues. SaMR10 showed the lowest total population associated with S. alfredii and little effect on plant growth and phytoextraction. SaZR4 significantly promoted Zn-extraction but not Cd-extraction. SaMR12 and SaNR1 significantly promoted plant growth in substrates supplemented with Zn or Cd and phytoextraction of Zn and Cd. Together, this study have shown that the four native endophytic bacteria differently colonize the host plants and modulate metal uptake and growth of host plant, and that SaMR12 and SaNR1 strains are promising assistants of S. alfredii plants for phytoremediation of Zn/Cd-contaminated soil.
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Affiliation(s)
- Xincheng Zhang
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Zijingang Campus, Hangzhou, China
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Gatehouse LN, Sutherland P, Forgie SA, Kaji R, Christeller JT. Molecular and histological characterization of primary (betaproteobacteria) and secondary (gammaproteobacteria) endosymbionts of three mealybug species. Appl Environ Microbiol 2012; 78:1187-97. [PMID: 22156418 PMCID: PMC3273002 DOI: 10.1128/aem.06340-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/23/2011] [Indexed: 11/20/2022] Open
Abstract
Microscopic localization of endosymbiotic bacteria in three species of mealybug (Pseudococcus longispinus, the long-tailed mealybug; Pseudococcus calceolariae, the citrophilus mealybug; and Pseudococcus viburni, the obscure mealybug) showed these organisms were confined to bacteriocyte cells within a bacteriome centrally located within the hemocoel. Two species of bacteria were present, with the secondary endosymbiont, in all cases, living within the primary endosymbiont. DNA from the dissected bacteriomes of all three species of mealybug was extracted for analysis. Sequence data from selected 16S rRNA genes confirmed identification of the primary endosymbiont as "Candidatus Tremblaya princeps," a betaproteobacterium, and the secondary endosymbionts as gammaproteobacteria closely related to Sodalis glossinidius. A single 16S rRNA sequence of the primary endosymbiont was found in all individuals of each mealybug species. In contrast, the presence of multiple divergent strains of secondary endosymbionts in each individual mealybug suggests different evolutionary and transmission histories of the two endosymbionts. Mealybugs are known vectors of the plant pathogen Grapevine leafroll-associated virus 3. To examine the possible role of either endosymbiont in virus transmission, an extension of the model for interaction of proteins with bacterial chaperonins, i.e., GroEL protein homologs, based on mobile-loop amino acid sequences of their GroES homologs, was developed and used for analyses of viral coat protein interactions. The data from this model are consistent with a role for the primary endosymbiont in mealybug transmission of Grapevine leafroll-associated virus 3.
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Gyaneshwar P, Hirsch AM, Moulin L, Chen WM, Elliott GN, Bontemps C, Estrada-de Los Santos P, Gross E, Dos Reis FB, Sprent JI, Young JPW, James EK. Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe Interact 2011; 24:1276-88. [PMID: 21830951 DOI: 10.1094/mpmi-06-11-0172] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rhizobia form specialized nodules on the roots of legumes (family Fabaceae) and fix nitrogen in exchange for carbon from the host plant. Although the majority of legumes form symbioses with members of genus Rhizobium and its relatives in class Alphaproteobacteria, some legumes, such as those in the large genus Mimosa, are nodulated predominantly by betaproteobacteria in the genera Burkholderia and Cupriavidus. The principal centers of diversity of these bacteria are in central Brazil and South Africa. Molecular phylogenetic studies have shown that betaproteobacteria have existed as legume symbionts for approximately 50 million years, and that, although they have a common origin, the symbiosis genes in both subclasses have evolved separately since then. Additionally, some species of genus Burkholderia, such as B. phymatum, are highly promiscuous, effectively nodulating several important legumes, including common bean (Phaseolus vulgaris). In contrast to genus Burkholderia, only one species of genus Cupriavidus (C. taiwanensis) has so far been shown to nodulate legumes. The recent availability of the genome sequences of C. taiwanensis, B. phymatum, and B. tuberum has paved the way for a more detailed analysis of the evolutionary and mechanistic differences between nodulating strains of alpha- and betaproteobacteria. Initial analyses of genome sequences have suggested that plant-associated Burkholderia spp. have lower G+C contents than Burkholderia spp. that are opportunistic human pathogens, thus supporting previous suggestions that the plant- and human-associated groups of Burkholderia actually belong in separate genera.
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Affiliation(s)
- Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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Hedrich S, Lünsdorf H, Kleeberg R, Heide G, Seifert J, Schlömann M. Schwertmannite formation adjacent to bacterial cells in a mine water treatment plant and in pure cultures of Ferrovum myxofaciens. Environ Sci Technol 2011; 45:7685-7692. [PMID: 21838259 DOI: 10.1021/es201564g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Schwertmannite has previously been found in iron- and sulfate-rich mine waters at pH 2.8-4.5. In the present study, schwertmannite (Fe(8)O(8)(OH)(6)SO(4)) was shown to be the major mineral in a mine water treatment plant at pH 3, in which ferrous iron is mainly oxidized by bacteria belonging to the species Ferrovum myxofaciens. Strain EHS6, which is closely related to the type strain of Fv. myxofaciens, was isolated from the pilot plant and characterized as an acidophilic, iron-oxidizing bacterium. In contrast to the pilot plant, the mineral phase formed by a pure culture of Fv. myxofaciens EHS6 was a mixture of schwertmannite and jarosite (KFe(3)(SO(4))(2)(OH)(6)). In contrast to other reports of neutrophilic, iron-oxidizing bacteria, acidophilic microorganisms in the pilot plant and cultures of strain EHS6 did not show encrustation of the cell surface or deposition of minerals inside the cell, though a few cells appeared to be in contact with jarosite crystals. It was concluded that no direct biomineralization occurred in the pilot plant or in laboratory cultures. The lack of encrustation of bacterial cells in the pilot plant is considered advantageous since the cells are still able to get in contact with ferrous iron and the iron oxidation process in the mine water treatment plant can proceed.
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Affiliation(s)
- Sabrina Hedrich
- Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany.
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Marchal M, Briandet R, Halter D, Koechler S, DuBow MS, Lett MC, Bertin PN. Subinhibitory arsenite concentrations lead to population dispersal in Thiomonas sp. PLoS One 2011; 6:e23181. [PMID: 21876737 PMCID: PMC3158062 DOI: 10.1371/journal.pone.0023181] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 07/07/2011] [Indexed: 11/19/2022] Open
Abstract
Biofilms represent the most common microbial lifestyle, allowing the survival of microbial populations exposed to harsh environmental conditions. Here, we show that the biofilm development of a bacterial species belonging to the Thiomonas genus, frequently found in arsenic polluted sites and playing a key role in arsenic natural remediation, is markedly modified when exposed to subinhibitory doses of this toxic element. Indeed, arsenite [As(III)] exposure led to a considerable impact on biofilm maturation by strongly increasing the extracellular matrix synthesis and by promoting significant cell death and lysis within microcolonies. These events were followed by the development of complex 3D-biofilm structures and subsequently by the dispersal of remobilized cells observed inside the previously formed hollow voids. Our results demonstrate that this biofilm community responds to arsenite stress in a multimodal way, enhancing both survival and dispersal. Addressing this complex bacterial response to As(III) stress, which might be used by other microorganisms under various adverse conditions, may be essential to understand how Thiomonas strains persist in extreme environments.
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Affiliation(s)
- Marie Marchal
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS & Université de Strasbourg, Strasbourg, France
| | - Romain Briandet
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Massy, France
| | - David Halter
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS & Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS & Université de Strasbourg, Strasbourg, France
| | - Michael S. DuBow
- Université Paris-Sud 11, Institut de Génétique et Microbiologie, CNRS UMR 8621, Orsay, France
| | - Marie-Claire Lett
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS & Université de Strasbourg, Strasbourg, France
| | - Philippe N. Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS & Université de Strasbourg, Strasbourg, France
- * E-mail:
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Chen WM, Yang SH, Huang WC, Cheng CY, Sheu SY. Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2011; 62:1086-1091. [PMID: 21705448 DOI: 10.1099/ijs.0.031310-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, chitinolytic bacterium, strain KL-9(T), was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9(T) were gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15-40 °C (optimum, 30-37 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9(T) was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9(T) formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria, being most closely related to members of the genera Leeia, Chitinimonas, Silvimonas and Andreprevotia. Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9(T) is thus considered to represent a novel species of a new genus within the class Betaproteobacteria, for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9(T) ( = BCRC 80168(T) = LMG 25530(T)).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Shwu-Harn Yang
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Wei-Cheng Huang
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chih-Yu Cheng
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Niu GL, Zhang JJ, Zhao S, Liu H, Boon N, Zhou NY. Bioaugmentation of a 4-chloronitrobenzene contaminated soil with Pseudomonas putida ZWL73. Environ Pollut 2009; 157:763-771. [PMID: 19108939 DOI: 10.1016/j.envpol.2008.11.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 11/17/2008] [Accepted: 11/18/2008] [Indexed: 05/27/2023]
Abstract
The strain Pseudomonas putida ZWL73, which metabolizes 4-chloronitrobenzene (4CNB) by a partial-reductive pathway, was inoculated into lab-scale 4CNB-contaminated soil for bioaugmentation purposes in this study. The degradation of 4CNB was clearly stimulated, as indicated with the gradual accumulation of ammonium and chloride. Simultaneously, the diversity and quantity of cultivable heterotrophic bacteria decreased due to 4CNB contamination, while the quantity of 4CNB-resistant bacteria increased. During the bioaugmentation, denaturing gradient gel electrophoresis analysis showed the changes of diversity in dominant populations of intrinsic soil microbiota. The results showed that Alphaproteobacteria and Betaproteobacteria were not distinctly affected, but Actinobacteria were apparently stimulated. In addition, an interesting dynamic within Acidobacteria was observed, as well as an influence on ammonia-oxidizing bacteria population. These combined findings demonstrate that the removal of 4CNB in soils by inoculating strain ZWL73 is feasible, and that specific populations in soils rapidly changed in response to 4CNB contamination and subsequent bioaugmentation.
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Affiliation(s)
- Gui-Lan Niu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Schreiber F, Szewzyk U. Environmentally relevant concentrations of pharmaceuticals influence the initial adhesion of bacteria. Aquat Toxicol 2008; 87:227-233. [PMID: 18359104 DOI: 10.1016/j.aquatox.2008.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 02/04/2008] [Accepted: 02/07/2008] [Indexed: 05/26/2023]
Abstract
Pharmaceuticals are abundant at low concentrations (i.e. ng L(-1); microg L(-1)) in natural aquatic systems. However, very little is known about their effects on microorganisms. This study investigated the influence of the pharmaceuticals phenazone, amoxicillin and erythromycin, at low, non-toxic concentrations (i.e. 0.5-50 microg L(-1)), on the initial adhesion of bacteria to uncoated and iron-coated polystyrene. The influence of the pharmaceuticals on the initial adhesion of bacterial pure cultures (Escherichia coli, Aquabacterium commune, Bacillus subtilis) isolated from natural aquatic systems, was investigated with a plate assay. Initial adhesion of the pure cultures depended on the selected pharmaceutical, its concentration, the bacterial strain and the adhesion surface. Different combinations of these parameters resulted in inhibition, enhancement or had no effect on initial adhesion. In addition, a continuous flow system was used to investigate the influence of the pharmaceuticals on the initial adhesion of a drinking water microbial community. The drinking water community showed decreased adhesion in the presence of the pharmaceuticals regardless of adhesion surface. The results show that pharmaceuticals at environmentally relevant concentrations can influence the initial adhesion of bacteria. Thus, pharmaceutical compounds that are introduced to natural aquatic systems are able to exert subtle effects on bacteria.
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Affiliation(s)
- Frank Schreiber
- Department of Environmental Microbiology, Technical University Berlin, Franklin Str. 29, 10587 Berlin, Germany.
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Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat J. Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water. Int J Syst Evol Microbiol 2008; 57:2629-2635. [PMID: 17978231 DOI: 10.1099/ijs.0.65149-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99% with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3% 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA-DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA-DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.
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Affiliation(s)
- Margarita Gomila
- Área Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Botho Bowien
- Abt. Molekularphysiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Enevold Falsen
- CCUG, Culture Collection University of Göteborg, Department of Clinical Bacteriology, 41346 Göteborg, Sweden
| | - Edward R B Moore
- CCUG, Culture Collection University of Göteborg, Department of Clinical Bacteriology, 41346 Göteborg, Sweden
| | - Jorge Lalucat
- Área 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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Abstract
A freshwater bacterium, designated IMCC1728(T), was isolated from a eutrophic pond. The strain was Gram-negative, chemoheterotrophic and facultatively aerobic, forming non-motile rods that contained poly-beta-hydroxybutyrate granules. Based on 16S rRNA gene sequence comparisons, the most closely related species to strain IMCC1728(T) was Methylibium petroleiphilum (97.0 % similarity). Phylogenetic trees generated using 16S rRNA gene sequences showed that this isolate formed an independent phyletic line of the genus Methylibium clade of the class Betaproteobacteria. The DNA G+C content of the strain was 66.2+/-0.4 mol%. The predominant cellular fatty acid constituents were C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH (43.1 %), C(16 : 0) (20.3 %), C(12 : 0) (13.4 %) and C(10 : 0) 3-OH (7.3 %). The strain contained Q-8 as the predominant ubiquinone. Several phenotypic characteristics, including flagellation, temperature range for growth and carbon source utilization patterns, differentiated strain IMCC1728(T) from species of the genus Methylibium. Therefore, it is proposed that strain IMCC1728(T) represents a novel species, Methylibium aquaticum sp. nov. The type strain is IMCC1728(T) (=KCCM 42364(T)=NBRC 102349(T)).
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MESH Headings
- Aerobiosis/physiology
- Bacterial Typing Techniques
- Base Composition
- Betaproteobacteria/classification
- Betaproteobacteria/genetics
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- Cytoplasmic Granules/chemistry
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Flagella/physiology
- Fresh Water/microbiology
- Genes, rRNA
- Hydroxybutyrates/analysis
- Korea
- Molecular Sequence Data
- Organic Chemicals/metabolism
- Phylogeny
- Polyesters/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Temperature
- Ubiquinone/analysis
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Affiliation(s)
- Jaeho Song
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
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30
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Wertz JT, Breznak JA. Stenoxybacter acetivorans gen. nov., sp. nov., an acetate-oxidizing obligate microaerophile among diverse O2-consuming bacteria from termite guts. Appl Environ Microbiol 2007; 73:6819-28. [PMID: 17827334 PMCID: PMC2074940 DOI: 10.1128/aem.00786-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In termite hindguts, fermentative production of acetate--a major carbon and energy source for the insect--depends on efficient removal of inwardly diffusing oxygen by microbes residing on and near the hindgut wall. However, little is known about the identity of these organisms or about the substrate(s) used to support their respiratory activity. A cultivation-based approach was used to isolate O(2)-consuming organisms from hindguts of Reticulitermes flavipes. A consistently greater (albeit not statistically significant) number of colonies developed under hypoxia (2% [vol/vol] O(2)) than under air, and the increase coincided with the appearance of morphologically distinct colonies of a novel, rod-shaped, obligately microaerophilic beta-proteobacterium that was <95% similar (based on the 16S rRNA gene sequence) to its closest known relative (Eikenella corrodens). Nearly identical organisms (and/or their 16S rRNA genes) were obtained from geographically separated and genetically distinct populations of Reticulitermes. PCR-based procedures implied that the novel isolates were autochthonous to the hindgut of R. flavipes and comprised ca. 2 to 7% of the hindgut prokaryote community. Representative strain TAM-DN1 utilized acetate and a limited range of other organic and amino acids as energy sources and possessed catalase and superoxide dismutase. On solid medium, the optimal O(2) concentration for growth was about 2%, and no growth occurred with O(2) concentrations above 4% or under anoxia. However, cells in liquid medium could grow with higher O(2) concentrations (up to 16%), but only after proportionately extended lag phases. The genetic and physiological distinctiveness of TAM-DN1 and related strains supports their recognition as a new genus and species, for which the name Stenoxybacter acetivorans gen. nov., sp. nov. is proposed.
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Affiliation(s)
- John T Wertz
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA.
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31
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Abstract
Stenoxybacter acetivorans is a newly described, obligately microaerophilic beta-proteobacterium that is abundant in the acetate-rich hindgut of Reticulitermes. Here we tested the hypotheses that cells are located in the hypoxic, peripheral region of Reticulitermes flavipes hindguts and use acetate to fuel their O(2)-consuming respiratory activity in situ. Physical fractionation of R. flavipes guts, followed by limited-cycle PCR with S. acetivorans-specific 16S rRNA gene primers, indicated that cells of this organism were indeed located primarily among the microbiota colonizing the hindgut wall. Likewise, reverse transcriptase PCR of hindgut RNA revealed S. acetivorans-specific transcripts for acetate-activating enzymes that were also found in cell extracts (acetate kinase and phosphotransacetylase), as well as transcripts of ccoN, which encodes the O(2)-reducing subunit of high-affinity cbb(3)-type cytochrome oxidases. However, S. acetivorans strains did not possess typical enzymes of the glyoxylate cycle (isocitrate lyase and malate synthase A), suggesting that they may use an alternate pathway to replenish tricarboxylic acid cycle intermediates or they obtain such compounds (or their precursors) in situ. Respirometric measurements indicated that much of the O(2) consumption by R. flavipes worker larvae was attributable to their guts, and the potential contribution of S. acetivorans to O(2) consumption by extracted guts was about 0.2%, a value similar to that obtained for other hindgut bacteria examined. Similar measurements obtained with guts of larvae prefed diets to disrupt major members of the hindgut microbiota implied that most of the O(2) consumption observed with extracted guts was attributable to protozoans, a group of microbes long thought to be "strict anaerobes."
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Affiliation(s)
- John T Wertz
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA.
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Yoon MH, Ten LN, Im WT, Lee ST. Methylibium fulvum sp. nov., a member of the Betaproteobacteria isolated from ginseng field soil, and emended description of the genus Methylibium. Int J Syst Evol Microbiol 2007; 57:2062-2066. [PMID: 17766872 DOI: 10.1099/ijs.0.64909-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated Gsoil 322T and Gsoil 328, were isolated from soil of a ginseng field in Pocheon province (Republic of Korea). The strains were Gram-negative, motile, aerobic rods that showed nearly identical physiological profiles and similar chemotaxonomic profiles. The two strains were oxidase-positive but catalase-negative, reduced nitrate to nitrite and had fatty acid profiles in which C16 : 0, C17 : 0 cyclo and C16 : 1
ω7c/iso-C15 : 0 2-OH were predominant. The DNA G+C contents of Gsoil 322T and Gsoil 328 were 66.6 and 66.7 mol%, respectively. Q-8 was observed as the major quinone. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 322T belongs to the class Betaproteobacteria and was most closely related to Methylibium petroleiphilum ATCC BAA-1232T (97.5 % sequence similarity). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 322T (=KCTC 12591T =LMG 23394T) was classified in the genus Methylibium as the type strain of a novel species, for which the name Methylibium fulvum sp. nov. is proposed.
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MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Betaproteobacteria/classification
- Betaproteobacteria/genetics
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- Catalase/biosynthesis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Korea
- Locomotion/physiology
- Molecular Sequence Data
- Nitrates/metabolism
- Nitrites/metabolism
- Oxidation-Reduction
- Oxidoreductases/biosynthesis
- Panax
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- Min-Ho Yoon
- Department of BioEnvironmental Chemistry, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Leonid N Ten
- Department of Biology & Medicinal Sciences, Pai Chai University, Daejeon, 302-735, Republic of Korea
| | - Wan-Taek Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Sung-Taik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
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Saunders AM, Mabbett AN, McEwan AG, Blackall LL. Proton motive force generation from stored polymers for the uptake of acetate under anaerobic conditions. FEMS Microbiol Lett 2007; 274:245-51. [PMID: 17610509 DOI: 10.1111/j.1574-6968.2007.00839.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The bacteria facilitating enhanced biological phosphorus removal gain a selective advantage from intracellularly stored polymer-driven substrate uptake under anaerobic conditions during sequential anaerobic : aerobic cycling. Mechanisms for these unusual membrane transport processes were proposed and experimentally validated using selective inhibitors and highly-enriched cultures of a polyphosphate-accumulating organism, Accumulibacter, and a glycogen-accumulating organism, Competibacter. Acetate uptake by both Accumulibacter and Competibacter was driven by a proton motive force (PMF). Stored polymers were used to generate the PMF -Accumulibacter used phosphate efflux through the Pit transporter, while Competibacter generated a PMF by proton efflux through the ATPase and fumarate reductase in the reductive TCA cycle.
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Affiliation(s)
- Aaron M Saunders
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, Queensland, Australia
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Lechner U, Brodkorb D, Geyer R, Hause G, Härtig C, Auling G, Fayolle-Guichard F, Piveteau P, Müller RH, Rohwerder T. Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium. Int J Syst Evol Microbiol 2007; 57:1295-1303. [PMID: 17551046 DOI: 10.1099/ijs.0.64663-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains L10T, L108 and CIP I-2052 were originally obtained from methyl tert-butyl ether (MTBE)-contaminated groundwater and from a wastewater treatment plant, respectively. All share the ability to grow on tert-butanol, an intermediate of MTBE degradation. Cells are strictly aerobic, motile by a polar flagellum and exhibit strong pili formation. Poly β-hydroxybutyrate (PHB) granules are formed. The DNA G+C content is 69–70.5 mol% and the main ubiquinone is Q-8. The major cellular fatty acids are 16 : 1 cis-9 and 16 : 0 and the only hydroxy fatty acid is 10 : 0 3-OH. The major phospholipids are phosphatidylethanolamine (PE) 16 : 1/16 : 1 and phosphatidylglycerol 16 : 0/16 : 1. A significant amount of PE 17 : 0/16 : 1 is present. The 16S rRNA gene sequences of these strains are almost identical and form a separate line of descent in the Rubrivivax–Roseateles–Leptothrix–Ideonella–Aquabacterium branch of the Betaproteobacteria with 97 % similarity to 16S rRNA genes of the type strains of Rubrivivax gelatinosus, Leptothrix mobilis and Ideonella dechloratans. However, physiological properties, DNA–DNA relatedness values and the phospholipid and cellular fatty acid profiles distinguish the novel isolates from the three closely related genera. Therefore, it is concluded that strains L10T, L108 and CIP I-2052 represent a new genus and novel species for which the name Aquincola tertiaricarbonis gen. nov., sp. nov., is proposed. The type strain is strain L10T (=DSM 18512T=CIP 109243T).
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MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Betaproteobacteria/classification
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- Biodegradation, Environmental
- Cytoplasmic Granules/physiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fimbriae, Bacterial
- Flagella/physiology
- Genes, rRNA
- Hydroxybutyrates/metabolism
- Lipids/analysis
- Locomotion
- Metabolic Networks and Pathways
- Methyl Ethers/metabolism
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Polyesters/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Ubiquinone/analysis
- Water Microbiology
- tert-Butyl Alcohol/metabolism
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Affiliation(s)
- Ute Lechner
- Institut für Mikrobiologie, Kurt-Mothes-Str. 3, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany
| | - Danny Brodkorb
- Institut für Mikrobiologie, Kurt-Mothes-Str. 3, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany
| | - Roland Geyer
- Umweltforschungszentrum Leipzig-Halle, Department Umweltmikrobiologie, Permoserstr. 15, D-04318 Leipzig, Germany
| | - Gerd Hause
- Biozentrum, Weinbergweg 22, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany
| | - Claus Härtig
- Umweltforschungszentrum Leipzig-Halle, Department Umweltmikrobiologie, Permoserstr. 15, D-04318 Leipzig, Germany
| | - Georg Auling
- Institut für Mikrobiologie, Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | | | - Pascal Piveteau
- Institute Français du Pétrole, 1-4, avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Roland H Müller
- Umweltforschungszentrum Leipzig-Halle, Department Umweltmikrobiologie, Permoserstr. 15, D-04318 Leipzig, Germany
| | - Thore Rohwerder
- Umweltforschungszentrum Leipzig-Halle, Department Umweltmikrobiologie, Permoserstr. 15, D-04318 Leipzig, Germany
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Lim JM, Jeon CO, Lee GS, Park DJ, Kang UG, Park CY, Kim CJ. Leeia oryzae gen. nov., sp. nov., isolated from a rice field in Korea. Int J Syst Evol Microbiol 2007; 57:1204-1208. [PMID: 17551030 DOI: 10.1099/ijs.0.64582-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, non-spore-forming, Gram-negative bacterium, designated strain HW7T, was isolated from a rice field in Korea. Cells of strain HW7T were short rod-shaped and motile with single polar flagella. The major cellular fatty acids of strain HW7T were C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 56 mol% and the major isoprenoid quinone was Q-8. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HW7T forms a distinct lineage with respect to closely related genera within the class Betaproteobacteria and that the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the physiological and phylogenetic data, strain HW7T represents a novel genus and species of the Betaproteobacteria, for which the name Leeia oryzae gen. nov., sp. nov. is proposed. The type strain is HW7T (=KCTC 12585T=DSM 17879T).
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MESH Headings
- Aerobiosis
- Base Composition
- Betaproteobacteria/classification
- Betaproteobacteria/genetics
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Korea
- Locomotion
- Molecular Sequence Data
- Oryza
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Spores, Bacterial
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Affiliation(s)
- Jee-Min Lim
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Che Ok Jeon
- Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Gye Suk Lee
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Dong-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Ui-Gum Kang
- Yeongnam Agricultural Research Institute, 1085 Neidong, Milyang 627-803, Republic of Korea
| | - Chang-Young Park
- Yeongnam Agricultural Research Institute, 1085 Neidong, Milyang 627-803, Republic of Korea
| | - Chang-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
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Pernice M, Wetzel S, Gros O, Boucher-Rodoni R, Dubilier N. Enigmatic dual symbiosis in the excretory organ of Nautilus macromphalus (Cephalopoda: Nautiloidea). Proc Biol Sci 2007; 274:1143-52. [PMID: 17311780 PMCID: PMC2189564 DOI: 10.1098/rspb.2006.0353] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 01/23/2007] [Accepted: 01/23/2007] [Indexed: 12/13/2022] Open
Abstract
Symbiosis is an important driving force in metazoan evolution and the study of ancient lineages can provide an insight into the influence of symbiotic associations on morphological and physiological adaptations. In the 'living fossil' Nautilus, bacterial associations are found in the highly specialized pericardial appendage. This organ is responsible for most of the excretory processes (ultrafiltration, reabsorption and secretion) and secretes an acidic ammonia-rich excretory fluid. In this study, we show that Nautilus macromphalus pericardial appendages harbour a high density of a beta-proteobacterium and a coccoid spirochaete using transmission electron microscopy, comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH). These two bacterial phylotypes are phylogenetically distant from any known bacteria, with ammonia-oxidizing bacteria as the closest relatives of the beta-proteobacterium (above or equal to 87.5% sequence similarity) and marine Spirochaeta species as the closest relatives of the spirochaete (above or equal to 89.8% sequence similarity), and appear to be specific to Nautilus. FISH analyses showed that the symbionts occur in the baso-medial region of the pericardial villi where ultrafiltration and reabsorption processes take place, suggesting a symbiotic contribution to the excretory metabolism.
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Affiliation(s)
- Mathieu Pernice
- UMR 5178 Biologie des Organismes Marins et Ecosystèmes, Département Peuplements et Milieux Aquatiques, Muséum National d'Histoire Naturelle, 55 rue Buffon, 75005 Paris, France.
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La Duc MT, Dekas A, Osman S, Moissl C, Newcombe D, Venkateswaran K. Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments. Appl Environ Microbiol 2007; 73:2600-11. [PMID: 17308177 PMCID: PMC1855582 DOI: 10.1128/aem.03007-06] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4 degrees C to 65 degrees C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 10(6) cells/m(2). However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (alpha- and beta-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means of translocation of thermophiles, anaerobes, and halotolerant alkalophiles into these environments.
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Affiliation(s)
- Myron T La Duc
- Biotechnology and Planetary Protection Group, M/S 89, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
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Kasuga I, Shimazaki D, Kunikane S. Influence of backwashing on the microbial community in a biofilm developed on biological activated carbon used in a drinking water treatment plant. Water Sci Technol 2007; 55:173-80. [PMID: 17546984 DOI: 10.2166/wst.2007.256] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The influence of backwashing on the biofilm community developed on biological activated carbon (BAC) used in a drinking water treatment plant was investigated by means of bacterial cell enumeration and terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting analysis of bacterial and eukaryotic ribosomal RNA genes (rDNA). After backwashing, the attached bacterial abundance in the top layer of the BAC bed decreased to 64% of that before backwashing. The community level changes caused by backwashing were examined through the T-RFLP profiles. In the bacterial 16S rDNA analysis, the relative abundances of some terminal-restriction fragments (T-RFs) including the Planctomycetes-derived fragment increased; however, the relative abundances of some T-RFs including the Betaproteobacteria-derived fragments decreased. In the eukaryotic 18S rDNA analysis, the relative abundances of some T-RFs including the protozoan Cercozoa-derived fragments increased; however, the relative abundances of some T-RFs including the metazoan Chaetonotus- and Paratripyla-derived fragments decreased. The T-RFLP analysis suggests that backwashing can cause changes in the relative compositions of microorganisms in a BAC biofilm in the top layer of the bed.
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Affiliation(s)
- I Kasuga
- Department of Water Supply Engineering, National Institute of Public Health, 2-3-6 Minami, Wako City, Saitama 351-0197, Japan.
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Chou YJ, Sheu SY, Sheu DS, Wang JT, Chen WM. Schlegelella aquatica sp. nov., a novel thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2006; 56:2793-2797. [PMID: 17158979 DOI: 10.1099/ijs.0.64446-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately thermophilic bacterial strain designated wcf1T, isolated from a hot spring located in the Tainan area, southern Taiwan, was characterized using a polyphasic approach. The cells were Gram-negative, non-pigmented, rod-shaped, non-spore-forming and motile. Phylogenetic analysis using 16S rRNA gene sequences showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Schlegelella; its only close neighbour was the type strain of Schlegelella thermodepolymerans, K14T (97.8 %). The isolate was clearly distinguishable from other strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It was evident from the genotypic and phenotypic data that strain wcf1T represents a novel species in the genus Schlegelella, for which the name Schlegelella aquatica sp. nov. is proposed, with the type strain wcf1T (=BCRC 17557T=LMG 23380T).
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Affiliation(s)
- Yi-Ju Chou
- Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Road, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Road, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Der-Shyan Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Road, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Jih-Terng Wang
- Department of Biotechnology, Tajen University, Pingtung, Taiwan
| | - Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Road, Nan-Tzu, Kaohsiung City 811, Taiwan
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40
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França L, Rainey FA, Nobre MF, da Costa MS. Tepidicella xavieri gen. nov., sp. nov., a betaproteobacterium isolated from a hot spring runoff. Int J Syst Evol Microbiol 2006; 56:907-912. [PMID: 16585714 DOI: 10.1099/ijs.0.64193-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains TU-16T and TU-18, two non-pigmented bacterial isolates with an optimum growth temperature of about 45 degrees C and an optimum pH of about 8.5-9.0, were recovered from the Furnas geothermal area on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequence of these strains indicated that they represent a novel species in a new genus of the phylum Betaproteobacteria. The major fatty acids of strains TU-16T and TU-18 were 16 : 0 and 18 : 1omega7c. Ubiquinone 8 was the major respiratory quinone and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The novel isolates were aerobic; thiosulfate was oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strain TU-16T (=LMG 23030T = CIP 108724T) represents the type strain of a novel species in a new genus, Tepidicella xavieri gen. nov., sp. nov.
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Affiliation(s)
- Luis França
- Departamento de Bioquímica, Universidade de Coimbra, 3001-401 Coimbra, Portugal
| | - Fred A Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Fernanda Nobre
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Milton S da Costa
- Departamento de Bioquímica, Universidade de Coimbra, 3001-401 Coimbra, Portugal
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Kalyuzhnaya MG, De Marco P, Bowerman S, Pacheco CC, Lara JC, Lidstrom ME, Chistoserdova L. Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. Int J Syst Evol Microbiol 2006; 56:2517-2522. [PMID: 17082383 DOI: 10.1099/ijs.0.64422-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions and phylogenetic relationships of two new methylotrophic isolates from Lake Washington (USA) sediment, FAM5Tand 500, and the previously described methylotrophic strain EHg5 isolated from contaminated soil in Estarreja (Portugal) were investigated. All three strains were facultative methylotrophs capable of growth on a variety of C1and multicarbon compounds. Optimal growth occurred at pH 7.5–8 and 30–37 °C. The major fatty acids were C16 : 1ω7cand C16 : 0. The major quinone was ubiquinone Q8. Neither methanol dehydrogenase nor methanol oxidase activities were detectable in cells grown on methanol, suggesting an alternative, as-yet unknown, mechanism for methanol oxidation. The isolates assimilated C1units at the level of formaldehyde, via the serine cycle. The DNA G+C content of the strains ranged between 64 and 65 mol%. 16S rRNA gene sequence similarity between the three new isolates was 99.85–100 %, but was below 94 % with other members of theBetaproteobacteria, indicating that the isolates represent a novel taxon. Based on physiological, phenotypic and genomic characteristics of the three isolates, a new genus,Methyloversatilisgen. nov., is proposed within the familyRhodocyclaceae. The type strain ofMethyloversatilis universalisgen. nov., sp. nov. is FAM5T(=CCUG 52030T=JCM 13912T).
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MESH Headings
- Alcohol Oxidoreductases/analysis
- Betaproteobacteria/classification
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- Betaproteobacteria/ultrastructure
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Fresh Water/microbiology
- Genes, rRNA
- Geologic Sediments/microbiology
- Hydrogen-Ion Concentration
- Methanol/metabolism
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Phylogeny
- Portugal
- Quinones/analysis
- Quinones/chemistry
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Temperature
- United States
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Affiliation(s)
- Marina G Kalyuzhnaya
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Paolo De Marco
- Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Sarah Bowerman
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Catarina C Pacheco
- Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Jimmie C Lara
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Mary E Lidstrom
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
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Katayama Y, Uchino Y, Wood AP, Kelly DP. Confirmation of Thiomonas delicata (formerly Thiobacillus delicatus) as a distinct species of the genus Thiomonas Moreira and Amils 1997 with comments on some species currently assigned to the genus. Int J Syst Evol Microbiol 2006; 56:2553-2557. [PMID: 17082389 DOI: 10.1099/ijs.0.64299-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The transfer of Thiobacillus delicatus to the genus Thiomonas as a distinct species, Thiomonas delicata (type strain NBRC 14566T), is confirmed by its morphological and physiological properties, DNA–DNA hybridization and the grouping of its 16S rRNA gene sequence with those of other species of the genus. An emended formal description of Thiomonas delicata is given. The status of Thiomonas cuprina DSM 5495T as a member of the genus is reconsidered.
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Affiliation(s)
- Yoko Katayama
- Department of Environmental and Natural Resource Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yoshihito Uchino
- NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Ann P Wood
- Department of Microbiology, King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Floor 28 Guy's Tower, Guy's Campus, London SE1 9RT, UK
| | - Donovan P Kelly
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Kim BY, Weon HY, Yoo SH, Chen WM, Kwon SW, Go SJ, Stackebrandt E. Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 2006; 56:1761-1764. [PMID: 16902004 DOI: 10.1099/ijs.0.64163-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain R2A43-10(T) was isolated from a greenhouse soil in Korea. Cells were Gram-negative rods, motile by means of a single flagellum. Growth occurred at 10-40 degrees C and at pH 5-8. Ubiquinone-8 (Q-8) was the only respiratory lipoquinone. Major fatty acids were summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) and C(16 : 0). 16S rRNA gene sequence analysis revealed that strain R2A43-10(T) was closely related to Chitinimonas taiwanensis cf(T) (sequence similarity of 94.8 %), but it exhibited low sequence similarities (<92 %) to other members of the Betaproteobacteria. The G+C content of the genomic DNA of strain R2A43-10(T) was 65.0 mol%. The novel isolate could be differentiated from C. taiwanensis cf(T) by several physiological properties. On the basis of genomic and phenotypic data, it is concluded that R2A43-10(T) (=KACC 11467(T)=DSM 17726(T)) is the type strain of a novel species of the genus Chitinimonas, for which the name Chitinimonas koreensis sp. nov. is proposed.
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Affiliation(s)
- Byung-Yong Kim
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, Republic of Korea
| | - Hang-Yeon Weon
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon, Republic of Korea
| | - Seung-Hee Yoo
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, Republic of Korea
| | - Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, Republic of Korea
| | - Seung-Joo Go
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, Republic of Korea
| | - Erko Stackebrandt
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
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44
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Albuquerque L, Tiago I, Veríssimo A, da Costa MS. Tepidimonas thermarum sp. nov., a new slightly thermophilic betaproteobacterium isolated from the Elisenquelle in Aachen and emended description of the genus Tepidimonas. Syst Appl Microbiol 2006; 29:450-6. [PMID: 16410043 DOI: 10.1016/j.syapm.2005.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Indexed: 11/21/2022]
Abstract
Several non-pigmented bacterial isolates, with an optimum growth temperature of about 50-55 degrees C, were recovered from the Elisenquelle at Aachen, Germany. Phylogenetic analysis of the 16S rRNA gene sequence of strains AA-1(T) and AA-2 indicated that these organisms represent a new species of the genus Tepidimonas. The major fatty acids of strains AA-1(T) and AA-2 are 16:0 and 16:1 omega7c. Ubiquinone 8 is the major respiratory quinone, the major polar lipids are phosphotidylethanolamine and phosphotidylglycerol. The new isolates are aerobic; thiosulfate is oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strains AA-1(T) (=LMG 23094(T); =CIP 108777(T)) and AA-2 (=LMG 23095; =CIP 108778) represents a new species for which we recommend the name Tepidimonas thermarum.
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MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Betaproteobacteria/chemistry
- Betaproteobacteria/classification
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- Carbohydrate Metabolism
- Carboxylic Acids/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA
- Germany
- Molecular Sequence Data
- Oxidation-Reduction
- Phylogeny
- Polymers/metabolism
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Thiosulfates/metabolism
- Water Microbiology
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Affiliation(s)
- Luciana Albuquerque
- Departamento de Bioquímica and Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3001-401 Coimbra, Portugal
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45
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Abstract
Psyllids, whiteflies, aphids, and mealybugs are members of the suborder Sternorrhyncha and share a common property, namely the utilization of plant sap as their food source. Each of these insect groups has an obligatory association with a different prokaryotic endosymbiont, and the association is the result of a single infection followed by maternal, vertical transmission of the endosymbionts. The result of this association is the domestication of the free-living bacterium to serve the purposes of the host, namely the synthesis of essential amino acids. This domestication is probably in all cases accompanied by a major reduction in genome size. The different properties of the genomes and fragments of the genomes of these endosymbionts suggest that there are different constraints on the permissible evolutionary changes that are probably a function of the gene repertoire of the endosymbiont ancestor and the gene losses that occurred during the reduction of genome size.
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Affiliation(s)
- Paul Baumann
- Microbiology Section, University of California, Davis, California 95616,USA.
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46
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Kanzler BEM, Pfannes KR, Vogl K, Overmann J. Molecular characterization of the nonphotosynthetic partner bacterium in the consortium "Chlorochromatium aggregatum". Appl Environ Microbiol 2005; 71:7434-41. [PMID: 16269785 PMCID: PMC1287705 DOI: 10.1128/aem.71.11.7434-7441.2005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. The phototrophic consortium "Chlorochromatium aggregatum" consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. Although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of the beta-Proteobacteria but so far could not be characterized further. In the present study, "C. aggregatum" was enriched chemotactically, and the 16S rRNA gene sequence of the central bacterium was elucidated. Based on the sequence information, fluorescence in situ hybridization probes targeting four different regions of the 16S rRNA were designed and shown to hybridize exclusively to cells of the central bacterium. Phylogenetic analyses of the 1,437-bp-long sequence revealed that the central bacterium of "C. aggregatum" represents a so far isolated phylogenetic lineage related to Rhodoferax spp., Polaromonas vacuolata, and Variovorax paradoxus within the family Comamonadaceae. The majority of relatives of this lineage are not yet cultured and were found in low-temperature aquatic environments or aquatic environments containing xenobiotica or hydrocarbons. In CsCl-bisbenzimidazole equilibrium density gradients, genomic DNA of the central bacterium of "Chlorochromatium aggregatum" formed a distinct band which could be detected by quantitative PCR using specific primers. Using this method, the G+C content of the central bacterium was determined to be 55.6 mol%.
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Affiliation(s)
- Birgit E M Kanzler
- Bereich Mikrobiologie, Ludwig-Maximilians-Universitaet Muenchen, Maria-Ward-Strasse 1a, D-80638 Munich, Germany
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47
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Ko KS, Lee NY, Oh WS, Lee JH, Ki HK, Peck KR, Song JH. Tepidimonas arfidensis Sp. Nov., a Novel Gram-negative and thermophilic bacterium isolated from the bone marrow of a patient with leukemia in Korea. Microbiol Immunol 2005; 49:785-8. [PMID: 16113507 DOI: 10.1111/j.1348-0421.2005.tb03669.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A Gram-negative bacillus, SMC-6271(T), which was isolated from the bone marrow of a patient with leukemia but could not be identified by a conventional microbiologic method, was characterized by a genotypic analysis of 16S rRNA gene. Sequences of the 16S rRNA gene revealed that this bacterium was closely related to Tepidimonas ignava and other slightly thermophilic isolates but diverged distinctly from them. Analyses of cellular fatty acid composition and performance of biochemical tests confirmed that this bacterium is a distinct species from the other Tepidimonas species. Based on the evaluated phenotypic and genotypic characteristics, it is proposed that SMC-6271T (=ABB 0301T =KCTC 12412T =JCM 13232T) should be classified as a new species, namely Tepidimonas arfidensis sp. nov.
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Affiliation(s)
- Kwan Soo Ko
- Asian-Pacific Research Foundation for Infectious Diseases (ARFID), Seoul, Korea
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48
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Ghosh W, Bagchi A, Mandal S, Dam B, Roy P. Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India. Int J Syst Evol Microbiol 2005; 55:1779-1787. [PMID: 16166666 DOI: 10.1099/ijs.0.63595-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twelve chemolithotrophic strains were isolated from temperate orchard soil on reduced sulfur compounds as energy and electron sources and characterized on the basis of their physiological properties and ability to oxidize various reduced sulfur compounds. The new isolates could oxidize tetrathionate as well as thiosulfate, and oxidation of the latter involved conversion of thiosulfate to tetrathionate followed by its accumulation and eventual oxidation to sulfate, manifested in the production of acid. The mesophilic, neutrophilic, Gram-negative and coccoid bacteria had a respiratory metabolism. Physiologically and biochemically, all the strains were more or less similar, differing only in their growth rates and ability to utilize a few carbon compounds as single heterotrophic substrates. 16S rRNA gene sequence analysis was performed with five representative strains, which revealed a high degree of similarity (> or =99%) among them and placed the cluster in the 'Betaproteobacteria'. The strains showed low levels (93.5-95.3 %) of 16S rRNA gene sequence similarity to Pigmentiphaga kullae, Achromobacter xylosoxidans, Pelistega europaea and species belonging to the genera Alcaligenes, Taylorella and Bordetella. The taxonomic coherence of the new isolates was confirmed by DNA-DNA hybridization. On the basis of their uniformly low 16S rRNA gene sequence similarities to species of all the closest genera, unique fatty acid profile, distinct G+C content (54-55.2 mol%) and phenotypic characteristics that include efficient chemolithotrophic utilization of tetrathionate, the organisms were classified in a new genus, Tetrathiobacter gen. nov. In the absence of any significant discriminatory phenotypic or genotypic characteristics, all the new isolates are considered to constitute a single species, for which the name Tetrathiobacter kashmirensis sp. nov. (type strain WT001(T)=LMG 22695(T)=MTCC 7002(T)) is proposed.
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Affiliation(s)
- Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 C. I. T. Scheme, VII M, Kolkata - 700 054, India
| | - Angshuman Bagchi
- Bioinformatics Center, Bose Institute, P-1/12 C. I. T. Scheme, VII M, Kolkata - 700 054, India
| | - Sukhendu Mandal
- Department of Microbiology, Bose Institute, P-1/12 C. I. T. Scheme, VII M, Kolkata - 700 054, India
| | - Bomba Dam
- Department of Microbiology, Bose Institute, P-1/12 C. I. T. Scheme, VII M, Kolkata - 700 054, India
| | - Pradosh Roy
- Department of Microbiology, Bose Institute, P-1/12 C. I. T. Scheme, VII M, Kolkata - 700 054, India
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49
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Yun C, Amakata D, Matsuo Y, Matsuda H, Kawamukai M. New chitosan-degrading strains that produce chitosanases similar to ChoA of Mitsuaria chitosanitabida. Appl Environ Microbiol 2005; 71:5138-44. [PMID: 16151097 PMCID: PMC1214613 DOI: 10.1128/aem.71.9.5138-5144.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The betaproteobacterium Mitsuaria chitosanitabida (formerly Matsuebacter chitosanotabidus) 3001 produces a chitosanase (ChoA) that is classified in glycosyl hydrolase family 80. While many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the M. chitosanitabida 3001 chitosanase gene (choA). To investigate the phylogenetic distribution of chitosanases analogous to ChoA in nature, we identified 67 chitosan-degrading strains by screening and investigated their physiological and biological characteristics. We then searched for similarities to ChoA by Western blotting and Southern hybridization and selected 11 strains whose chitosanases showed the most similarity to ChoA. PCR amplification and sequencing of the chitosanase genes from these strains revealed high deduced amino acid sequence similarities to ChoA ranging from 77% to 99%. Analysis of the 16S rRNA gene sequences of the 11 selected strains indicated that they are widely distributed in the beta and gamma subclasses of Proteobacteria and the Flavobacterium group. These observations suggest that the ChoA-like chitosanases that belong to family 80 occur widely in a broad variety of bacteria.
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Affiliation(s)
- ChoongSoo Yun
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
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50
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Horn MA, Ihssen J, Matthies C, Schramm A, Acker G, Drake HL. Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa. Int J Syst Evol Microbiol 2005; 55:1255-1265. [PMID: 15879265 DOI: 10.1099/ijs.0.63484-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Earthworms emit nitrous oxide (N(2)O) via the activity of bacteria in their gut. Four N(2)O-producing facultative aerobes, ED1(T), ED5(T), MH21(T) and MH72, were isolated from the gut of the earthworm Aporrectodea caliginosa. The isolates produced N(2)O under conditions that simulated the microenvironment of the earthworm gut. ED1(T) and ED5(T) were Gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to N(2)) and contained membranous c-type cytochromes. ED1(T) grew optimally at 30 degrees C and pH 7. ED1(T) oxidized organic acids and reduced (per)chlorate, sulfate, nitrate and nitrite. The closest phylogenetic relative of ED1(T) was Dechloromonas agitata. ED5(T) grew optimally at 25 degrees C and pH 7. ED5(T) grew mainly on sugars, and nitrate and nitrite were used as alternative electron acceptors. The closest phylogenetic relatives of ED5(T) were Flavobacterium johnsoniae and Flavobacterium flevense. MH21(T) and MH72 were motile, spore-forming, rod-shaped bacteria with a three-layered cell wall. Sugars supported the growth of MH21(T) and MH72. Cells of MH21(T) grew in chains, were linked by connecting filaments and contained membranous b-type cytochromes. MH21(T) grew optimally at 30-35 degrees C and pH 7.7, grew by fermentation and reduced low amounts of nitrite to N(2)O. The closest phylogenetic relatives of MH21(T) were Paenibacillus borealis and Paenibacillus chibensis. Based on morphological, physiological and phylogenetic characteristics, ED1(T) (= DSM 15892(T) = ATCC BAA-841(T)), ED5(T) (= DSM 15936(T) = ATCC BAA-842(T)) and MH21(T) (=DSM 15890(T) = ATCC BAA-844(T)) are proposed as type strains of the novel species Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov. and Paenibacillus anaericanus sp. nov., respectively. MH72 is considered a new strain of Paenibacillus terrae.
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Affiliation(s)
- Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Julian Ihssen
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Carola Matthies
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Andreas Schramm
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Georg Acker
- Electron Microscopy Laboratory, University of Bayreuth, 95440 Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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