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Yu Y, Zhang Q, Kang J, Xu N, Zhang Z, Deng Y, Gillings M, Lu T, Qian H. Effects of organic fertilizers on plant growth and the rhizosphere microbiome. Appl Environ Microbiol 2024; 90:e0171923. [PMID: 38193672 PMCID: PMC10880660 DOI: 10.1128/aem.01719-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jian Kang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yu Deng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, New South Wales, Australia
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, China
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2
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Zhang Q, Lei C, Jin M, Qin G, Yu Y, Qiu D, Wang Y, Zhang Z, Zhang Z, Lu T, Peijnenburg WJGM, Gillings M, Yao Z, Qian H. Glyphosate Disorders Soil Enchytraeid Gut Microbiota and Increases Its Antibiotic Resistance Risk. J Agric Food Chem 2024; 72:2089-2099. [PMID: 38235689 DOI: 10.1021/acs.jafc.3c05436] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 01/19/2024]
Abstract
Pesticides promote the stable development of intensive global agriculture. Nevertheless, their residues in the soil can cause ecological and human health risks. Glyphosate is a popular herbicide and is generally thought to be ecologically safe and nontoxic, but this conclusion has been questioned. Herein, we investigated the interaction among soil fauna (Enchytraeus crypticus) exposed to glyphosate and found that glyphosate induced oxidative stress and detoxification responses in E. crypticus and disturbed their lipid metabolism and digestive systems. We further demonstrated that glyphosate disordered the gut microbiota of E. crypticus and increased the abundance of resistance determinants with significant human health risks. Empirical tests and structural equation models were then used to confirm that glyphosate could cause E. crypticus to generate reactive oxygen species, indirectly interfering with their gut microbiota. Our study provides important implications for deciphering the mechanisms of the ecotoxicity of pesticides under the challenge of worldwide pesticide contamination.
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Affiliation(s)
- Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Mingkang Jin
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, RA Leiden 2300, The Netherlands
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven 3720 BA, The Netherlands
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales 2109, Australia
| | - Ziang Yao
- College of Life Science, Dalian Minzu University, Dalian, Liaoning 116600, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
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3
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Zhang Q, Xu N, Lei C, Chen B, Wang T, Ma Y, Lu T, Penuelas J, Gillings M, Zhu Y, Fu Z, Qian H. Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome. Adv Sci (Weinh) 2023; 10:e2303925. [PMID: 37870180 PMCID: PMC10667823 DOI: 10.1002/advs.202303925] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/09/2023] [Indexed: 10/24/2023]
Abstract
The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.
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Affiliation(s)
- Qi Zhang
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Nuohan Xu
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Chaotang Lei
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Bingfeng Chen
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhou310012P. R. China
| | - Yunting Ma
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhou310012P. R. China
| | - Tao Lu
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Josep Penuelas
- CSICGlobal Ecology Unit CREAF‐CSIC‐UABBellaterraBarcelonaCatalonia08193Spain
- CREAFCampus Universitat Autònoma de BarcelonaCerdanyola del VallèsBarcelonaCatalonia08193Spain
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic BiologySchool of Natural SciencesMacquarie UniversitySydneyNSW2109Australia
| | - Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021P. R. China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐environmental SciencesChinese Academy of SciencesBeijing100085P. R. China
| | - Zhengwei Fu
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
- College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou310032P. R. China
| | - Haifeng Qian
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
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4
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Xu N, Qiu D, Zhang Z, Wang Y, Chen B, Zhang Q, Wang T, Hong W, Zhou NY, Penuelas J, Gillings M, Zhu YG, Qian H. A global atlas of marine antibiotic resistance genes and their expression. Water Res 2023; 244:120488. [PMID: 37604017 DOI: 10.1016/j.watres.2023.120488] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/23/2023] [Revised: 07/18/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023]
Abstract
Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia 08193, Spain; CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia 08193, Spain
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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5
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Chen B, Zhang Z, Zhang Q, Xu N, Lu T, Wang T, Hong W, Fu Z, Penuelas J, Gillings M, Qian H. Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants. Environ Sci Technol 2023; 57:7698-7708. [PMID: 37161271 DOI: 10.1021/acs.est.3c01664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.
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Affiliation(s)
- Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, P. R. China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, P. R. China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
- CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
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6
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Khushalani N, Shue H, Gedye C, Mazumder A, Sharma S, Eastgate M, Majem Tarruella M, Antonanzas Basa M, Montaudie H, Marais-Nieman R, de la Cruz Merino L, Clements A, Mortier L, Jameson M, Shojaei F, Ning J, Aiyer L, Gillings M, Kabbinavar F, Ascierto P. 42TiP A multicenter, randomized, double-blind phase III study of HBI-8000 combined with nivolumab versus placebo with nivolumab in patients with unresectable or metastatic melanoma not previously treated with PD-1 or PD-L1 inhibitors. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
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7
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Zhang Z, Wang Y, Chen B, Lei C, Yu Y, Xu N, Zhang Q, Wang T, Gao W, Lu T, Gillings M, Qian H. Xenobiotic pollution affects transcription of antibiotic resistance and virulence factors in aquatic microcosms. Environ Pollut 2022; 306:119396. [PMID: 35525510 DOI: 10.1016/j.envpol.2022.119396] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 02/22/2022] [Revised: 04/08/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.
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Affiliation(s)
- Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Wenwen Gao
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, NSW, 2109, Australia
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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8
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Castillo-Ramírez S, Ghaly T, Gillings M. Non-clinical settings - the understudied facet of antimicrobial drug resistance. Environ Microbiol 2021; 23:7271-7274. [PMID: 34773441 DOI: 10.1111/1462-2920.15841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Timothy Ghaly
- ARC Centre of Excellence in Synthetic Biology and Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology and Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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9
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Kim WS, Rai S, Ando K, Choi I, Izutsu K, Tsukamoto N, Yokoyama M, Tsukasaki K, Kuroda J, Ando J, Hidaka M, Koh Y, Shibayama H, Uchida T, Yang DH, Ishitsuka K, Ishizawa K, Kim JS, Lee HG, Minami H, Eom HS, Nagai H, Kurosawa M, Lee JH, Lee WS, Shindo T, Yoon DH, Yoshida S, Gillings M, Onogi H, Tobinai K. A PHASE 2B OPEN‐LABEL SINGLE ARM STUDY TO EVALUATE THE EFFICACY AND SAFETY OF HBI‐8000 (TUCIDINOSTAT) IN PATIENTS WITH RELAPSED OR REFRACTORY PERIPHERAL T‐CELL LYMPHOMA (PTCL). Hematol Oncol 2021. [DOI: 10.1002/hon.121_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- W. S. Kim
- Samsung Medical Center Division of Hematology‐Oncology Seoul Korea
| | - S. Rai
- Kindai University Hospital Department of Hematology and Rheumatology Faculty of Medicine Osakasayama Japan
| | - K. Ando
- Tokai University Hospital Department of Hematology and Oncology Isehara Japan
| | - I. Choi
- National Hospital Organization Kyushu Cancer Center Department of Hematology Fukuoka Japan
| | - K. Izutsu
- National Cancer Center Hospital Department of Hematology Tokyo Japan
| | - N. Tsukamoto
- Gunma University Hospital Oncology Center Maebashi Japan
| | - M. Yokoyama
- The Cancer Institute Hospital of Japanese Foundation for Cancer Research Department of Hematology and Oncology Tokyo Japan
| | - K. Tsukasaki
- International Medical Center Saitama Medical University Department of Hematology Saitama Japan
| | - J. Kuroda
- Kyoto Prefectural University of Medicine Division of Hematology and Oncology Kyoto Japan
| | - J. Ando
- Juntendo University Hospital Department of Hematology Tokyo Japan
| | - M. Hidaka
- National Hospital Organization Kumamoto Medical Center Department of Hematology Kumamoto Japan
| | - Y. Koh
- Seoul National University Hospital Department of Internal Medicine Seoul Korea
| | - H. Shibayama
- Osaka University Hospital Department of Hematology and Oncology Suita Japan
| | - T. Uchida
- Japanese Red Cross Nagoya Daini Hospital Department of Hematology and Oncology Nagoya Japan
| | - D. H. Yang
- Chonnam National University Hwasun Hospital Department of Hematology Hwasun Korea
| | - K. Ishitsuka
- Kagoshima University Hospital Department of Hematology and Rheumatology Kagoshima Japan
| | - K. Ishizawa
- Yamagata University Hospital Department of Third Internal Medicine Yamagata Japan
| | - J. S. Kim
- Yonsei University College of Medicine Severance Hospital Division of Hematology Department of Internal Medicine Seoul Korea
| | - H. G. Lee
- Konkuk University Medical Center Department of Hematology & Oncology Seoul Korea
| | - H. Minami
- Kobe University Graduate School of Medicine and Hospital Department of Medical Oncology/Hematology Kobe Japan
| | - H. S. Eom
- National Cancer Center Center for Hematologic Malignancy Goyang‐si Korea
| | - H. Nagai
- National Hospital Organization Nagoya Medical Center Clinical Research Center Nagoya Japan
| | - M. Kurosawa
- National Hospital Organization Hokkaido Cancer Center Department of Hematology Sapporo Japan
| | - J. H. Lee
- Gachon University Gil Medical Center Division of Hematology Incheon Korea
| | - W. S. Lee
- Inje University Busan Paik Hospital Department of Internal Medicine Busan Korea
| | - T. Shindo
- Kyoto University Hospital Department of Hematology and Oncology Kyoto Japan
| | - D. H. Yoon
- Asan Medical Center University of Ulsan College of Medicine Department of Oncology Seoul Korea
| | - S. Yoshida
- National Hospital Organization Nagasaki Medical Center Department of Hematology Omura Japan
| | - M. Gillings
- HUYA Bioscience International LLC, CEO & Executive Chair CA USA
| | - H. Onogi
- HUYA Bioscience International Executive Vice President, Head of Clinical Development‐Japan Tokyo Japan
| | - K. Tobinai
- National Cancer Center Hospital Department of Hematology Tokyo Japan
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10
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Izutsu K, Utsunomiya A, Jo T, Yoshida S, Ando K, Choi I, Imaizumi Y, Kato K, Kurosawa M, Kusumoto S, Miyagi T, Ohtsuka E, Sasaki O, Shibayama H, Shimoda K, Takamatsu Y, Takano K, Tsukasaki K, Makita S, Yonekura K, Taguchi J, Gillings M, Onogi H, Tobinai K. A PHASE 2B STUDY TO EVALUATE THE EFFICACY AND SAFETY OF TUCIDINOSTAT (HBI‐8000) IN JAPANESE PATIENTS WITH RELAPSED OR REFRACTORY ADULT T‐CELL LEUKEMIA‐LYMPHOMA (ATL). Hematol Oncol 2021. [DOI: 10.1002/hon.122_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- K. Izutsu
- National Cancer Center Hospital Department of Hematology Tokyo Japan
| | - A. Utsunomiya
- Imamura General Hospital Department of Hematology Kagoshima Japan
| | - T. Jo
- Japanese Red Cross Nagasaki Genbaku Hospital Department of Hematology Nagasaki Japan
| | - S. Yoshida
- National Hospital Organization Nagasaki Medical Center Department of Hematology Omura Japan
| | - K. Ando
- Tokai University Hospital Department of Hematology/Oncology Kanagawa Japan
| | - I. Choi
- National Hospital Organization Kyushu Cancer Center Department of Hematology Fukuoka Japan
| | - Y. Imaizumi
- Nagasaki University Hospital Department of Hematology Nagasaki Japan
| | - K. Kato
- Kyushu University Hospital Department of Hematology Oncology & Cardiovascular medicine Fukuoka Japan
| | - M. Kurosawa
- National Hospital Organization Hokkaido Cancer Center Department of Hematology Sapporo Japan
| | - S. Kusumoto
- Nagoya City University Hospital Division of Hematology and Oncology Aichi Japan
| | - T. Miyagi
- Heartlife Hospital Department of Hematology Okinawa Japan
| | - E. Ohtsuka
- Oita Prefectural Hospital Department of Hematology Oita Japan
| | - O. Sasaki
- Miyagi Cancer Center Division of Hematology Miyagi Japan
| | - H. Shibayama
- Osaka University Hospital Department of Hematology and Oncology Osaka Japan
| | - K. Shimoda
- University of Miyazaki Hospital Department of Hematology Miyazaki Japan
| | - Y. Takamatsu
- Fukuoka University Hospital Department of Medical Oncology Hematology and Infectious Diseases Fukuoka Japan
| | - K. Takano
- Oita University Department of Medical Oncology and Hematology Faculty of Medicine Oita Japan
| | - K. Tsukasaki
- International Medical Center Saitama Medical University Department of Hematology Saitama Japan
| | - S. Makita
- National Cancer Center Hospital Department of Hematology Tokyo Japan
| | - K. Yonekura
- Imamura General Hospital Department of Dermatology Kagoshima Japan
| | - J. Taguchi
- Japanese Red Cross Nagasaki Genbaku Hospital Department of Hematology Nagasaki Japan
| | - M. Gillings
- HUYA Bioscience International LLC CEO & Executive Chair San Diego USA
| | - H. Onogi
- HUYA Bioscience International LLC Executive Vice President, Head of Clinical Development‐Japan Tokyo Japan
| | - K. Tobinai
- National Cancer Center Hospital Department of Hematology Tokyo Japan
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11
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Ke M, Ye Y, Zhang Z, Gillings M, Qu Q, Xu N, Xu L, Lu T, Wang J, Qian H. Synergistic effects of glyphosate and multiwall carbon nanotubes on Arabidopsis thaliana physiology and metabolism. Sci Total Environ 2021; 769:145156. [PMID: 33477045 DOI: 10.1016/j.scitotenv.2021.145156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/09/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
Agricultural chemicals have the potential to become pollutants that adversely affect plant growth. Interactions between these compounds are likely, but potential synergies are under-researched. Multiwall carbon nanotubes are increasingly finding novel uses in agriculture, as delivery mechanisms and as slow-release fertilizers. There is potential for nanotubes to interact with other agricultural chemicals in unpredictable ways. To investigate this possibility, we examined interactions with glyphosate, a widely used herbicide that is also attracting increasing concern over its potential for non-target effects. Here we examined potential synergistic effects on hydroponically grown Arabidopsis thaliana. Single treatments did not affect plant growth significantly, or did only mildly. However, combined treatment significantly affected both plant root and shoot growth. High-level content of malondialdehyde and up-regulated of metabolic antioxidant molecules in plant indicated that combined group caused the strong oxidative damage, while the decreased of antioxidant enzyme activities indicated an imbalance between reactive oxygen species (ROS)and the antioxidant defense system due to the continuously generated ROS. Besides, several intermediate metabolites of unsaturated fatty acids synthesis pathways were up-regulated in combined treatment, which clarified that combined group changed membrane components. The increase of intermediate metabolites in combined group also reflected more energy consumption in the repairment of the disrupt of combined treatment. The synergistic effect observed was attributed to the accumulation of glyphosate resulting from permeability and transportability of the carbon nanotubes. Overall, the risk of nanotube-herbicide interaction suggests a caution use of nanotubes in agricultural applications.
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Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yizhi Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lusheng Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jiade Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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12
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Zhu G, Wang X, Yang T, Su J, Qin Y, Wang S, Gillings M, Wang C, Ju F, Lan B, Liu C, Li H, Long XE, Wang X, Jetten MSM, Wang Z, Zhu YG. Air pollution could drive global dissemination of antibiotic resistance genes. ISME J 2021; 15:270-281. [PMID: 32963346 PMCID: PMC7852678 DOI: 10.1038/s41396-020-00780-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [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: 04/22/2020] [Revised: 08/13/2020] [Accepted: 09/14/2020] [Indexed: 11/08/2022]
Abstract
Antibiotic-resistant pathogens pose a significant threat to human health. Several dispersal mechanisms have been described, but transport of both microbes and antibiotic resistance genes (ARGs) via atmospheric particles has received little attention as a pathway for global dissemination. These atmospheric particles can return to the Earth's surface via rain or snowfall, and thus promote long-distance spread of ARGs. However, the diversity and abundance of ARGs in fresh snow has not been studied and their potential correlation with particulate air pollution is not well explored. Here, we characterized ARGs in 44 samples of fresh snow from major cities in China, three in North America, and one in Europe, spanning a gradient from pristine to heavily anthropogenically influenced ecosystems. High-throughput qPCR analysis of ARGs and mobile genetic elements (MGEs) provided strong indications that dissemination of ARGs in fresh snow could be exacerbated by air pollution, severely increasing the health risks of both air pollution and ARGs. We showed that snowfall did effectively spread ARGs from point sources over the Earth surface. Together our findings urge for better pollution control to reduce the risk of global dissemination of antibiotic resistance genes.
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Affiliation(s)
- Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ting Yang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yu Qin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Cheng Wang
- South China Sea Institution, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Feng Ju
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Bangrui Lan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chunlei Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Xi-En Long
- School of Geographic Sciences, Nantong University, Nantong, 226007, China
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, 36525, AJ, Nijmegen, The Netherlands
| | - Zifa Wang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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13
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Campbell SJ, Ashley W, Gil-Fernandez M, Newsome TM, Di Giallonardo F, Ortiz-Baez AS, Mahar JE, Towerton AL, Gillings M, Holmes EC, Carthey AJR, Geoghegan JL. Red fox viromes in urban and rural landscapes. Virus Evol 2020; 6:veaa065. [PMID: 33365150 PMCID: PMC7744383 DOI: 10.1093/ve/veaa065] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans whilst remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live at higher densities, and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To investigate this possibility, we used a meta-transcriptomic approach to characterise the virome of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. We identified ten potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae, and Picornaviridae as well as rabbit haemorrhagic disease virus-2. This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human–wildlife interface.
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Affiliation(s)
- Sarah J Campbell
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Wilbur Ashley
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Margarita Gil-Fernandez
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Thomas M Newsome
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jackie E Mahar
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alison L Towerton
- Greater Sydney Local Land Services, Sydney, New South Wales 2750, Australia
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexandra J R Carthey
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.,Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.,Institute of Environmental Science and Research, Wellington 5018, New Zealand
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14
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Abstract
Globalization accelerates the mobilization of microorganisms via international trade and transport. Growth in population, increasing connectivity, and rapid urbanization all exacerbate the consequent risk of pandemics of zoonotic diseases. Global problems require global solutions, particularly the co-ordination of international research in biomedical sciences, global ecology, and sustainability.
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Affiliation(s)
- Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Michael Gillings
- ARC Centre of Excellence for Synthetic Biology and Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia 08913, Spain.,CREAF, Cerdanyola del Vallès, Catalonia 08913, Spain
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15
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Zhu YG, Zhao Y, Zhu D, Gillings M, Penuelas J, Ok YS, Capon A, Banwart S. Soil biota, antimicrobial resistance and planetary health. Environ Int 2019; 131:105059. [PMID: 31374443 DOI: 10.1016/j.envint.2019.105059] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [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: 03/27/2019] [Revised: 06/21/2019] [Accepted: 07/23/2019] [Indexed: 05/07/2023]
Abstract
The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air.
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Affiliation(s)
- Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Yi Zhao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark
| | - Dong Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Yong Sik Ok
- Korea Biochar Research Center, Division of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Anthony Capon
- Planetary Health Platform, University of Sydney, Sydney, NSW, Australia
| | - Steve Banwart
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, United Kingdom
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16
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Smalla K, Cook K, Djordjevic SP, Klümper U, Gillings M. Environmental dimensions of antibiotic resistance: assessment of basic science gaps. FEMS Microbiol Ecol 2019; 94:5114257. [PMID: 30277517 DOI: 10.1093/femsec/fiy195] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 09/28/2018] [Indexed: 02/01/2023] Open
Abstract
Antibiotic resistance is one of the major problems facing medical practice in the 21st century. Historical approaches to managing antibiotic resistance have often focused on individual patients, specific pathogens and particular resistance phenotypes. However, it is increasingly recognized that antibiotic resistance is a complex ecological and evolutionary problem. As such, understanding the dynamics of antibiotic resistance requires integration of data on the diverse mobile genetic elements often associated with antibiotic resistance genes, and their dissemination by various mechanisms of horizontal gene transfer between bacterial cells and environments. Most important is understanding the fate and effects of antibiotics at sub-inhibitory concentrations, and co-selection. This opinion paper identifies key knowledge gaps in our understanding of resistance phenomena, and outlines research needs that should be addressed to help us manage resistance into the future.
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Affiliation(s)
- Kornelia Smalla
- Julius Kühn-Institut Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research center, 950 College Station Road, Athens GA 306052720, USA
| | - Steven P Djordjevic
- ithree institute, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007 Australia
| | - Uli Klümper
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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17
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Lu T, Ke M, Lavoie M, Jin Y, Fan X, Zhang Z, Fu Z, Sun L, Gillings M, Peñuelas J, Qian H, Zhu YG. Rhizosphere microorganisms can influence the timing of plant flowering. Microbiome 2018; 6:231. [PMID: 30587246 PMCID: PMC6307273 DOI: 10.1186/s40168-018-0615-0] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/17/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant phenology has crucial biological, physical, and chemical effects on the biosphere. Phenological drivers have largely been studied, but the role of plant microbiota, particularly rhizosphere microbiota, has not been considered. RESULTS We discovered that rhizosphere microbial communities could modulate the timing of flowering of Arabidopsis thaliana. Rhizosphere microorganisms that increased and prolonged N bioavailability by nitrification delayed flowering by converting tryptophan to the phytohormone indole acetic acid (IAA), thus downregulating genes that trigger flowering, and stimulating further plant growth. The addition of IAA to hydroponic cultures confirmed this metabolic network. CONCLUSIONS We document a novel metabolic network in which soil microbiota influenced plant flowering time, thus shedding light on the key role of soil microbiota on plant functioning. This opens up multiple opportunities for application, from helping to mitigate some of the effects of climate change and environmental stress on plants (e.g. abnormal temperature variation, drought, salinity) to manipulating plant characteristics using microbial inocula to increase crop potential.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Michel Lavoie
- Quebec-Ocean and Takuvik Joint International Research Unit, Université Laval, Québec, G1VOA6 Canada
| | - Yujian Jin
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Xiaoji Fan
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Barcelona, Catalonia Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia Spain
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 People’s Republic of China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 People’s Republic of China
- State Key Lab of Urban and Regional Ecology, Research Center for Ecoenvironmental Sciences, Chinese Academy of Sciences, Beijing, 100085 People’s Republic of China
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18
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Zhou ZC, Feng WQ, Han Y, Zheng J, Chen T, Wei YY, Gillings M, Zhu YG, Chen H. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ Int 2018; 121:1155-1161. [PMID: 30420129 DOI: 10.1016/j.envint.2018.10.032] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [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: 07/14/2018] [Revised: 09/12/2018] [Accepted: 10/02/2018] [Indexed: 06/09/2023]
Abstract
The transmission routes for antibiotic resistance genes (ARGs) and microbiota between humans and water environments is poorly characterized. Here, we used high-throughput qPCR analyses and 16S rRNA gene sequencing to examine the occurrence and abundance of antibiotic resistance genes and microbiota in both healthy humans and associated water environments from a Chinese village. Humans carried the most diverse assemblage of ARGs, with 234 different ARGs being detected. The total abundance of ARGs in feces, on skin, and in the effluent from domestic sewage treatment systems were approximately 23, 2, and 7 times higher than their abundance in river samples. In total, 53 ARGs and 28 bacteria genera that were present in human feces could also be found in the influent and effluent of rural sewage treatment systems, and also downstream of the effluent release point. We identified the bacterial taxa that showed a significant association with ARGs (P < 0.01, r > 0.8) by network analysis, supporting the idea that these bacteria could carry some ARGs and transfer between humans and the environment. Analysis of ARGs and microbiota in humans and in water environments helps to define the transmission routes and dynamics of antibiotic resistance within these environments. This study highlights human contribution to the load of ARGs into the environment and suggests means to prevent such dissemination.
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Affiliation(s)
- Zhen-Chao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wan-Qiu Feng
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yue Han
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ji Zheng
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tao Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuan-Yuan Wei
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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19
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Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S, Penuelas J. Human dissemination of genes and microorganisms in Earth's Critical Zone. Glob Chang Biol 2018; 24:1488-1499. [PMID: 29266645 DOI: 10.1111/gcb.14003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 09/27/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.
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Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Université de Lyon, Lyon, France
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Steven Banwart
- Department of Geography, The University of Sheffield, Sheffield, UK
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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20
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Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratory Ampère, UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Écully cedex, France
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Steve Banwart
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Josep Penuelas
- Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit, Centre for Ecological Research and Forestry Applications (CREAF)-CSIC-Universitat Autonoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Catalonia, Spain.,CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
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21
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Penesyan A, Gillings M, Paulsen IT. Antibiotic discovery: combatting bacterial resistance in cells and in biofilm communities. Molecules 2015; 20:5286-98. [PMID: 25812150 PMCID: PMC6272253 DOI: 10.3390/molecules20045286] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [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: 02/12/2015] [Revised: 03/11/2015] [Accepted: 03/18/2015] [Indexed: 12/26/2022] Open
Abstract
Bacterial resistance is a rapidly escalating threat to public health as our arsenal of effective antibiotics dwindles. Therefore, there is an urgent need for new antibiotics. Drug discovery has historically focused on bacteria growing in planktonic cultures. Many antibiotics were originally developed to target individual bacterial cells, being assessed in vitro against microorganisms in a planktonic mode of life. However, towards the end of the 20th century it became clear that many bacteria live as complex communities called biofilms in their natural habitat, and this includes habitats within a human host. The biofilm mode of life provides advantages to microorganisms, such as enhanced resistance towards environmental stresses, including antibiotic challenge. The community level resistance provided by biofilms is distinct from resistance mechanisms that operate at a cellular level, and cannot be overlooked in the development of novel strategies to combat infectious diseases. The review compares mechanisms of antibiotic resistance at cellular and community levels in the light of past and present antibiotic discovery efforts. Future perspectives on novel strategies for treatment of biofilm-related infectious diseases are explored.
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Affiliation(s)
- Anahit Penesyan
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
| | - Michael Gillings
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
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22
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Penton CR, Gupta VVSR, Tiedje JM, Neate SM, Ophel-Keller K, Gillings M, Harvey P, Pham A, Roget DK. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. PLoS One 2014; 9:e93893. [PMID: 24699870 PMCID: PMC3974846 DOI: 10.1371/journal.pone.0093893] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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: 08/20/2013] [Accepted: 03/11/2014] [Indexed: 01/09/2023] Open
Abstract
Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.
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Affiliation(s)
- C. Ryan Penton
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | | | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Stephen M. Neate
- Department of Agriculture, Fisheries and Forestry, Queensland, Leslie Research Centre, Towoomba, Queensland, Australia
| | | | - Michael Gillings
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul Harvey
- CSIRO Ecosystem Sciences, Glen Osmond, South Australia, Australia
| | - Amanda Pham
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - David K. Roget
- CSIRO Ecosystem Sciences, Glen Osmond, South Australia, Australia
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Ajani P, Murray S, Hallegraeff G, Lundholm N, Gillings M, Brett S, Armand L. The diatom genus Pseudo-nitzschia (Bacillariophyceae) in New South Wales, Australia: morphotaxonomy, molecular phylogeny, toxicity, and distribution. J Phycol 2013; 49:765-785. [PMID: 27007209 DOI: 10.1111/jpy.12087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/19/2013] [Indexed: 06/05/2023]
Abstract
Species belonging to the potentially harmful diatom genus Pseudo-nitzschia, isolated from 16 localities (31 sampling events) in the coastal waters of south-eastern Australia, were examined. Clonal isolates were characterized by (i) light and transmission electron microscopy; (ii) phylogenies, based on sequencing of nuclear-encoded ribosomal deoxyribonucleic acid (rDNA) regions and, (iii) domoic acid (DA) production as measured by liquid chromatography-mass spectrometry (LC-MS/MS). Ten taxa were unequivocally confirmed as Pseudo-nitzschia americana, P. arenysensis, P. calliantha, P. cuspidata, P. fraudulenta, P. hasleana, P. micropora, P. multiseries, P. multistriata, and P. pungens. An updated taxonomic key for south-eastern Australian Pseudo-nitzschia is presented. The occurrence of two toxigenic species, P. multistriata (maximum concentration 11 pg DA per cell) and P. cuspidata (25.4 pg DA per cell), was documented for the first time in Australia. The Australian strains of P. multiseries, a consistent producer of DA in strains throughout the world, were nontoxic. Data from 5,888 water samples, collected from 31 oyster-growing estuaries (2,000 km coastline) from 2005 to 2009, revealed 310 regulatory exceedances for "Total Pseudo-nitzschia," resulting in six toxic episodes. Further examination of high-risk estuaries revealed that the "P. seriata group" had highest cell densities in the austral summer, autumn, or spring (species dependent), and lowest cell densities in the austral winter, while the "P. delicatissima group" had highest in winter and spring.
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Affiliation(s)
- Penelope Ajani
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, 2109, Australia
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, New South Wales, 2088, Australia
| | - Shauna Murray
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, New South Wales, 2088, Australia
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, PO Box 123, Broadway, Sydney, New South Wales, 2007, Australia
| | - Gustaaf Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tasmania, 7001, Australia
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, Copenhagen, 1307, Denmark
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, 2109, Australia
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, New South Wales, 2088, Australia
| | - Steve Brett
- Microalgal Services, 308 Tucker Road, Ormond, Victoria, 3204, Australia
| | - Leanne Armand
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, 2109, Australia
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, New South Wales, 2088, Australia
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Turnbull C, Wilson PD, Hoggard S, Gillings M, Palmer C, Smith S, Beattie D, Hussey S, Stow A, Beattie A. Primordial enemies: fungal pathogens in thrips societies. PLoS One 2012; 7:e49737. [PMID: 23185420 PMCID: PMC3504084 DOI: 10.1371/journal.pone.0049737] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/12/2012] [Indexed: 11/24/2022] Open
Abstract
Microbial pathogens are ancient selective agents that have driven many aspects of multicellular evolution, including genetic, behavioural, chemical and immune defence systems. It appears that fungi specialised to attack insects were already present in the environments in which social insects first evolved and we hypothesise that if the early stages of social evolution required antifungal defences, then covariance between levels of sociality and antifungal defences might be evident in extant lineages, the defences becoming stronger with group size and increasing social organisation. Thus, we compared the activity of cuticular antifungal compounds in thrips species (Insecta: Thysanoptera) representing a gradient of increasing group size and sociality: solitary, communal, social and eusocial, against the entomopathogen Cordyceps bassiana. Solitary and communal species showed little or no activity. In contrast, the social and eusocial species killed this fungus, suggesting that the evolution of sociality has been accompanied by sharp increases in the effectiveness of antifungal compounds. The antiquity of fungal entomopathogens, demonstrated by fossil finds, coupled with the unequivocal response of thrips colonies to them shown here, suggests two new insights into the evolution of thrips sociality: First, traits that enabled nascent colonies to defend themselves against microbial pathogens should be added to those considered essential for social evolution. Second, limits to the strength of antimicrobials, through resource constraints or self-antibiosis, may have been overcome by increase in the numbers of individuals secreting them, thus driving increases in colony size. If this is the case for social thrips, then we may ask: did antimicrobial traits and microbes such as fungal entomopathogens play an integral part in the evolution of insect sociality in general?
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Affiliation(s)
- Christine Turnbull
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Peter D. Wilson
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephen Hoggard
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Chris Palmer
- Department of Natural Resources, Northern Territory Government, Alice Springs, Northern Territory, Australia
| | - Shannon Smith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Doug Beattie
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sam Hussey
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Andrew Beattie
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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25
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Abstract
The Lake Eacham rainbowfish (Melanotaenia eachamensis) was once thought to be confined to its type locality within the Lake Eacham World Heritage National Park. M. eachamensis disappeared from the lake following the translocation of several species into the lake and the species was pronounced extinct in the wild in 1987. In a 2007 survey we noticed that rainbowfish were present in the lake once again. We used a molecular marker to identify these fish and the likely source population. Analysis of the D-loop region of mitochondrial DNA revealed that the species now present in the lake is Melanotaenia splendida, and is most closely related to several M. splendida populations in the immediate vicinity. Here we explore a range of scenarios that may have led to this colonisation event and highlight the dangers associated with translocation.
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Turnbull C, Hoggard S, Gillings M, Palmer C, Stow A, Beattie D, Briscoe D, Smith S, Wilson P, Beattie A. Antimicrobial strength increases with group size: implications for social evolution. Biol Lett 2010; 7:249-52. [PMID: 20880858 DOI: 10.1098/rsbl.2010.0719] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We hypothesize that aggregations of animals are likely to attract pathogenic micro-organisms and that this is especially the case for semisocial and eusocial insects where selection ultimately led to group sizes in the thousands or even millions, attracting the epithet 'superorganism'. Here, we analyse antimicrobial strength, per individual, in eight thrips species (Insecta: Thysanoptera) that present increasing innate group sizes and show that species with the largest group size (100-700) had the strongest antimicrobials, those with smaller groups (10-80) had lower antimicrobial activity, while solitary species showed none. Species with large innate group sizes showed strong antimicrobial activity while the semisocial species showed no activity until group size increased sufficiently to make activity detectable. The eusocial species behaved in a similar way, with detectable activity appearing once group size exceeded 120. These analyses show that antimicrobial strength is determined by innate group size. This suggests that the evolution of sociality that, by definition, increases group size, may have had particular requirements for defences against microbial pathogens. Thus, increase in group size, accompanied by increased antibiotic strength, may have been a critical factor determining the 'point of no return', early in the evolution of social insects, beyond which the evolution of social anatomical and morphological traits was irreversible. Our data suggest that traits that increase group size in general are accompanied by increased antimicrobial strength and that this was critical for transitions from solitary to social and eusocial organization.
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Affiliation(s)
- Christine Turnbull
- Department of Biological Sciences, Macquarie University, New South Wales, Australia
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27
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Stow A, Turnbull C, Gillings M, Smith S, Holley M, Silberbauer L, Wilson PD, Briscoe D, Beattie A. Differential antimicrobial activity in response to the entomopathogenic fungus Cordyceps in six Australian bee species. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1440-6055.2010.00749.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Young JM, Allen C, Coutinho T, Denny T, Elphinstone J, Fegan M, Gillings M, Gottwald TR, Graham JH, Iacobellis NS, Janse JD, Jacques MA, Lopez MM, Morris CE, Parkinson N, Prior P, Pruvost O, Neto JR, Scortichini M, Takikawa Y, Upper CD. Plant-pathogenic bacteria as biological weapons - real threats? Phytopathology 2008; 98:1060-1065. [PMID: 18943451 DOI: 10.1094/phyto-98-10-1060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
At present, much attention is being given to the potential of plant pathogens, including plant-pathogenic bacteria, as biological weapons/bioterror weapons. These two terms are sometimes used interchangeably and there is need for care in their application. It has been claimed that clandestine introduction of certain plant-pathogenic bacteria could cause such crop losses as to impact so significantly on a national economy and thus constitute a threat to national security. As a separate outcome, it is suggested that they could cause serious public alarm, perhaps constituting a source of terror. Legislation is now in place to regulate selected plant-pathogenic bacteria as potential weapons. However, we consider it highly doubtful that any plant-pathogenic bacterium has the requisite capabilities to justify such a classification. Even if they were so capable, the differentiation of pathogens into a special category with regulations that are even more restrictive than those currently applied in quarantine legislation of most jurisdictions offers no obvious benefit. Moreover, we believe that such regulations are disadvantageous insofar as they limit research on precisely those pathogens most in need of study. Whereas some human and animal pathogens may have potential as biological or bioterror weapons, we conclude that it is unlikely that any plant-pathogenic bacterium realistically falls into this category.
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29
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Stow A, Briscoe D, Gillings M, Holley M, Smith S, Leys R, Silberbauer T, Turnbull C, Beattie A. Antimicrobial defences increase with sociality in bees. Biol Lett 2007; 3:422-4. [PMID: 17504731 PMCID: PMC2390670 DOI: 10.1098/rsbl.2007.0178] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [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: 11/12/2022] Open
Abstract
Evidence for the antiquity and importance of microbial pathogens as selective agents is found in the proliferation of antimicrobial defences throughout the animal kingdom. Social insects, typified by crowding and often by low genetic variation, have high probabilities of disease transmission and eusocial Hymenoptera may be particularly vulnerable because of haplodiploidy. Mechanisms they employ to reduce the risk of disease include antimicrobial secretions which are particularly important primary barriers to infection. However, until now, whether or not there is selection for stronger antimicrobial secretions when the risk of disease increases because of sociality has not been tested. Here, we present evidence that the production of progressively stronger antimicrobial compounds was critical to the evolution of sociality in bees. We found that increases in group size and genetic relatedness were strongly correlated with increasing antimicrobial strength. The antimicrobials of even the most primitive semi-social species were an order of magnitude stronger that those of solitary species, suggesting a point of no return, beyond which disease control was essential. Our results suggest that selection by microbial pathogens was critical to the evolution of sociality and required the production of strong, front-line antimicrobial defences.
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Affiliation(s)
- Adam Stow
- Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia.
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30
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Stow A, Zenger K, Briscoe D, Gillings M, Peddemors V, Otway N, Harcourt R. Isolation and genetic diversity of endangered grey nurse shark (Carcharias taurus) populations. Biol Lett 2007; 2:308-11. [PMID: 17148390 PMCID: PMC1618890 DOI: 10.1098/rsbl.2006.0441] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [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: 11/12/2022] Open
Abstract
Anthropogenic impacts are believed to be the primary threats to the eastern Australian population of grey nurse sharks (Carcharias taurus), which is listed as critically endangered, and the most threatened population globally. Analyses of 235 polymorphic amplified fragment length polymorphisms (AFLP) loci and 700 base pairs of mitochondrial DNA control region provide the first account of genetic variation and geographical partitioning (east and west coasts of Australia, South Africa) in C. taurus. Assignment tests, analysis of relatedness and Fst values all indicate that the Australian populations are isolated from South Africa, with negligible migration between the east and west Australian coasts. There are significant differences in levels of genetic variation among regions. Australian C. taurus, particularly the eastern population, has significantly less AFLP variation than the other sampling localities. Further, the eastern Australian sharks possess only a single mitochondrial haplotype, also suggesting a small number of founding individuals. Therefore, historical, rather than anthropogenic processes most likely account for their depauperate genetic variation. These findings have implications for the viability of the eastern Australian population of grey nurse sharks.
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Affiliation(s)
- Adam Stow
- Macquarie University, Department of Biological Sciences, Sydney, NSW 2109, Australia.
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31
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Ferrari BC, Binnerup SJ, Gillings M. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 2006; 71:8714-20. [PMID: 16332866 PMCID: PMC1317317 DOI: 10.1128/aem.71.12.8714-8720.2005] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [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: 11/20/2022] Open
Abstract
Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously "unculturable" organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used.
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Affiliation(s)
- Belinda C Ferrari
- Department of Biological Sciences, Division of Environmental and Life Sciences, Macquarie University, Sydney 2109, NSW, Australia.
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32
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Green JL, Holmes AJ, Westoby M, Oliver I, Briscoe D, Dangerfield M, Gillings M, Beattie AJ. Spatial scaling of microbial eukaryote diversity. Nature 2005; 432:747-50. [PMID: 15592411 DOI: 10.1038/nature03034] [Citation(s) in RCA: 309] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 09/14/2004] [Indexed: 11/08/2022]
Abstract
Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity of life and the complexity of ecosystems. Although microorganisms may comprise much of the Earth's biodiversity and have critical roles in biogeochemistry and ecosystem functioning, little is known about their spatial diversification. Here we present quantitative estimates of microbial community turnover at local and regional scales using the largest spatially explicit microbial diversity data set available (> 10(6) sample pairs). Turnover rates were small across large geographical distances, of similar magnitude when measured within distinct habitats, and did not increase going from one vegetation type to another. The taxa-area relationship of these terrestrial microbial eukaryotes was relatively flat (slope z = 0.074) and consistent with those reported in aquatic habitats. This suggests that despite high local diversity, microorganisms may have only moderate regional diversity. We show how turnover patterns can be used to project taxa-area relationships up to whole continents. Taxa dissimilarities across continents and between them would strengthen these projections. Such data do not yet exist, but would be feasible to collect.
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Affiliation(s)
- Jessica L Green
- Key Centre for Biodiversity and Bioresources, Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia.
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33
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Holmes AJ, Holley MP, Mahon A, Nield B, Gillings M, Stokes HW. Recombination activity of a distinctive integron-gene cassette system associated with Pseudomonas stutzeri populations in soil. J Bacteriol 2003; 185:918-28. [PMID: 12533467 PMCID: PMC142810 DOI: 10.1128/jb.185.3.918-928.2003] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [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
Class 1 integrons have strongly influenced the evolution of multiple antibiotic resistance. Diverse integrons have recently been detected directly in a range of natural environments. In order to characterize the properties of these environmental integrons, we sought to isolate organisms containing integrons from soils, which resulted in the isolation of Pseudomonas stutzeri strain Q. Further isolation efforts targeted at this species resulted in recovery of two other strains (P and BAM). 16S rRNA sequences and chromosome mapping showed that these three strains are very closely related clonal variants in a single genomovar of P. stutzeri. Only strains Q and BAM were found to contain an integron and an associated gene cassette array. The intI and attI components of these strains showed 99 and 90% identity, respectively. The structure of these integrons and their associated gene cassettes was similar to that reported previously for other integron classes. The two integrons contained nonoverlapping sets of cassette-associated genes. In contrast, many of the cassette-associated recombination sites in the two integrons were similar and were considered to constitute a distinct subfamily consisting of 59-base element (59-be) recombination sites (the Pseudomonas subfamily). The recombination activity of P. stutzeri integron components was tested in cointegrate assays. IntIPstQ was shown to catalyze site-specific recombination between its cognate attI site and 59-be sites from antibiotic resistance gene cassettes. While IntIPstQ did not efficiently mediate recombination between members of the Pseudomonas 59-be subfamily and other 59-be types, the former sites were functional when they were tested with IntI1. We concluded that integrons present in P. stutzeri possess recombination activity and represent a hot spot for genomic diversity in this species.
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Affiliation(s)
- Andrew J Holmes
- Key Centre for Biodiversity and Bioresources, Macquarie University, Sydney NSW 2109, Australia.
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34
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Abstract
Antibiotics were discovered over 50 years ago, providing a long sought after treatment for infectious diseases. These drugs effectively suppressed diseases such as tuberculosis and infections such as those caused by Staphylococcus aureus.
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35
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Nouwens AS, Cordwell SJ, Larsen MR, Molloy MP, Gillings M, Willcox MD, Walsh BJ. Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1. Electrophoresis 2000. [PMID: 11271498 DOI: 10.1002/1522-2683(200011)21] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
With the completion of many genome projects, a shift is now occurring from the acquisition of gene sequence to understanding the role and context of gene products within the genome. The opportunistic pathogen Pseudomonas aeruginosa is one organism for which a genome sequence is now available, including the annotation of open reading frames (ORFs). However, approximately one third of the ORFs are as yet undefined in function. Proteomics can complement genomics, by characterising gene products and their response to a variety of biological and environmental influences. In this study we have established the first two-dimensional gel electrophoresis reference map of proteins from the membrane fraction of P. aeruginosa strain PA01. A total of 189 proteins have been identified and correlated with 104 genes from the P. aeruginosa genome. Annotated membrane proteins could be grouped into three distinct categories: (i) those with functions previously characterised in P. aeruginosa (38%); (ii) those with significant sequence similarity to proteins with assigned function or hypothetical proteins in other organisms (46%); and (iii) those with unknown function (16%). Transmembrane prediction algorithms showed that each identified protein sequence contained at least one membrane-spanning region. Furthermore, the current methodology used to isolate the membrane fraction was shown to be highly specific since no contaminating cytosolic proteins were characterised. Preliminary analysis showed that at least 15 gel spots may be glycosylated in vivo, including three proteins that have not previously been functionally characterised. The reference map of membrane proteins from this organism is now the basis for determining surface molecules associated with antibiotic resistance and efflux, cell-cell signalling and pathogen-host interactions in a variety of P. aeruginosa strains.
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Affiliation(s)
- A S Nouwens
- Australian Proteome Analysis Facility, Macquarie University, Sydney.
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36
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Abstract
With the completion of many genome projects, a shift is now occurring from the acquisition of gene sequence to understanding the role and context of gene products within the genome. The opportunistic pathogen Pseudomonas aeruginosa is one organism for which a genome sequence is now available, including the annotation of open reading frames (ORFs). However, approximately one third of the ORFs are as yet undefined in function. Proteomics can complement genomics, by characterising gene products and their response to a variety of biological and environmental influences. In this study we have established the first two-dimensional gel electrophoresis reference map of proteins from the membrane fraction of P. aeruginosa strain PA01. A total of 189 proteins have been identified and correlated with 104 genes from the P. aeruginosa genome. Annotated membrane proteins could be grouped into three distinct categories: (i) those with functions previously characterised in P. aeruginosa (38%); (ii) those with significant sequence similarity to proteins with assigned function or hypothetical proteins in other organisms (46%); and (iii) those with unknown function (16%). Transmembrane prediction algorithms showed that each identified protein sequence contained at least one membrane-spanning region. Furthermore, the current methodology used to isolate the membrane fraction was shown to be highly specific since no contaminating cytosolic proteins were characterised. Preliminary analysis showed that at least 15 gel spots may be glycosylated in vivo, including three proteins that have not previously been functionally characterised. The reference map of membrane proteins from this organism is now the basis for determining surface molecules associated with antibiotic resistance and efflux, cell-cell signalling and pathogen-host interactions in a variety of P. aeruginosa strains.
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Affiliation(s)
- A S Nouwens
- Australian Proteome Analysis Facility, Macquarie University, Sydney.
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37
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Abstract
The mannanase (endo-beta-1,4-mannanase; E.C. 3.2.1.78) and xylanase (endo-beta-1,4-xylanase; E.C. 3.2.1.8) activity of five microfungal isolates from Antarctica were characterized at different temperatures and pH. In general, the hemicellulase activity of the antarctic strains occurred at least 10 degrees C and as much as 30 degrees C lower than that of a mesophilic reference strain. At 0 degrees C, two strains, a Phoma and a Penicillium, produced in excess of 40% of their measured maximum activity of mannanase. All strains had maximum hemicellulase activity in the range pH 4-5, with Penicillium, Phoma and Alternaria strains exhibiting high (in excess of 80% of maximum) mannanase activity at pH 10. Three of the antarctic isolates exhibited high levels of xylanase activity over a pH range of 3-11.
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39
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Affiliation(s)
- J L Robinson
- Department of Animal Sciences, University of Illinois, Urbana 61801, USA
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40
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Gillings M, Holley M. Amplification of anonymous DNA fragments using pairs of long primers generates reproducible DNA fingerprints that are sensitive to genetic variation. Electrophoresis 1997; 18:1512-8. [PMID: 9378113 DOI: 10.1002/elps.1150180904] [Citation(s) in RCA: 38] [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] [Indexed: 02/05/2023]
Abstract
The reproducibility and potential applications of anonymous amplification protocols can be improved by using pairs of primers, each of 18 to 24 bases, to replace the single 8 to 10 base primers normally used in randomly amplified polymorphic DNA (RAPD) or DNA amplification fingerprinting (DAF) methods. Amplification using large primer pairs (LP-RAPD) generates 5 to 30 bands that can be resolved on standard agarose gels. Complex fingerprints can be readily generated from viruses, bacteria, fungi, plants, invertebrates and vertebrates. We also present evidence that a number of polymerase chain reaction (PCR) methods, including those based on the use of enterobacterial repetitive intergenic consensus (ERIC-PCR) or microsatellite primed (MP-PCR) sequence, may in essence operate by the same mechanism as LP-RAPD. Using standard LP-RAPD protocols, reproducible fingerprints can be generated from a single specimen using different thermocyclers, regardless of the mechanism used for thermocycling (air-cooled, Peltier effect, or robotic arm). LP-RAPD is sensitive to intraspecific and interspecific genetic variation, demonstrated here by analysis of mites and apple cultivars. Approximately 50% of LP-RAPD products are expected to have different primers at either end. Polymorphic bands with this arrangement can be recovered from the gel and directly sequenced using the LP-RAPD primers themselves. The efficiency of sequencing is improved by the length of the LP-RAPD primers. This method has the potential to allow the production of allele-specific species markers in less than two days.
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Affiliation(s)
- M Gillings
- Key Centre for Biodiversity and Bioresources, School of Biological Sciences, Macquarie University, Sydney, NSW, Australia.
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Gillings M, Holley M. Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements. Lett Appl Microbiol 1997; 25:17-21. [PMID: 9248074 DOI: 10.1046/j.1472-765x.1997.00162.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.2] [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: 02/04/2023]
Abstract
We examined the use of enterobacterial repetitive intergenic consensus (ERIC) sequences in PCR on the DNAs of various bacteria, bacteriophage, invertebrates, fungi, plants and vertebrates and have shown that complex ERIC-PCR patterns can be readily produced from all of these target organisms. A range of annealing temperatures was tested, from 52 degrees C (the commonly used annealing temperature) to 66 degrees C (the approximate Tm of ERIC primers). At the higher temperatures, most bands failed to amplify, the exception being a subset of bands from enterobacterial targets. It was concluded that ERIC-PCR does not necessarily direct amplification from genuine ERIC sequences.
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Affiliation(s)
- M Gillings
- Key Centre for Biodiversity and Bioresources, School of Biological Sciences, Macquarie University, Sydney, NSW, Australia.
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Gillings M, Broadbent P, Indsto J, Lee R. Characterisation of isolates and strains of citrus tristeza closterovirus using restriction analysis of the coat protein gene amplified by the polymerase chain reaction. J Virol Methods 1993; 44:305-17. [PMID: 7903310 DOI: 10.1016/0166-0934(93)90065-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Citrus Tristeza Virus (CTV) exists as a large number of distinct strains differing in biological properties and with different distributions in citrus producing countries. Strategies such as eradication or cross protection, aimed at controlling severe variants of the pathogen, require procedures to identify virus strains accurately and reliably. To fill the need for a rapid, reproducible assay, we have investigated the use of restriction analysis of the CTV coat protein gene amplified using the polymerase chain reaction (PCR). The primers 5' ATG GAC GAC GAA ACA AAG 3' and 5' TCA ACG TGT GTT GAA TTT 3' amplified a DNA copy of the CTV coat protein gene (approx. 670 base pairs) when used in a reverse transcriptase PCR assay. Amplifications were carried out using dsRNA prepared from field and indicator plants, or from single-stranded RNA prepared from crude PEG precipitates of intact virions. All 51 CTV isolates tested produced an amplified product of the same size, regardless of country of origin or biological properties. Digestion of the amplified coat protein genes with the restriction enzymes Hinf1 or Rsa1 revealed sequence variation in the PCR products. Hinf1 provided the best discrimination between strains, defining seven Restriction Fragment Length Polymorphism (RFLP) groups, some of which circumscribed sets of isolates with similar biological properties. Limited analysis of field isolates using this method showed that individual trees could contain mixtures of CTV strains, as assessed by the recovery of several RFLP types from individual reactions. Single aphid transmissions of isolates usually, but not always, generated apparently pure single strains judged by the recovery of single RFLP groups.
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Affiliation(s)
- M Gillings
- Plant Pathology Branch, Biological and Chemical Research Institute, NSW Agriculture, Rydalmere, Australia
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Gillings M, Fahy P, Davies C. Restriction analysis of an amplified polygalacturonase gene fragment differentiates strains of the phytopathogenic bacterium Pseudomonas solanacearum. Lett Appl Microbiol 1993; 17:44-8. [PMID: 7765308 DOI: 10.1111/j.1472-765x.1993.tb01432.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [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: 01/27/2023]
Abstract
Amplification of a polygalacturonase gene fragment using the polymerase chain reaction (PCR) formed a rapid, sensitive and portable method for detecting and differentiating strains of Pseudomonas solanacearum, a taxonomically complex bacterial species. Primers 5'CAG CAG AAC CCG CGC CTG ATC CAG 3' and 5'ATC GGA CTT GAT GCG CAG GCC GTT 3' were used to amplify a 504 base pair polygalacturonase gene fragment from 57 Ps. solanacearum isolates. Digestion of these products with Hae III defined groups which reflected the known genetic divisions within the species.
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Affiliation(s)
- M Gillings
- Biological and Chemical Research Institute, Rydalmere, NSW, Australia
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