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Mohy-Ud-Din W, Bashir S, Akhtar MJ, Asghar HMN, Ghafoor U, Hussain MM, Niazi NK, Chen F, Ali Q. Glyphosate in the environment: interactions and fate in complex soil and water settings, and (phyto) remediation strategies. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2023; 26:816-837. [PMID: 37994831 DOI: 10.1080/15226514.2023.2282720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Glyphosate (Gly) and its formulations are broad-spectrum herbicides globally used for pre- and post-emergent weed control. Glyphosate has been applied to terrestrial and aquatic ecosystems. Critics have claimed that Gly-treated plants have altered mineral nutrition and increased susceptibility to plant pathogens because of Gly ability to chelate divalent metal cations. Still, the complete resistance of Gly indicates that chelation of metal cations does not play a role in herbicidal efficacy or have a substantial impact on mineral nutrition. Due to its extensive and inadequate use, this herbicide has been frequently detected in soil (2 mg kg-1, European Union) and in stream water (328 µg L-1, USA), mostly in surface (7.6 µg L-1, USA) and groundwater (2.5 µg L-1, Denmark). International Agency for Research on Cancer (IARC) already classified Gly as a category 2 A carcinogen in 2016. Therefore, it is necessary to find the best degradation techniques to remediate soil and aquatic environments polluted with Gly. This review elucidates the effects of Gly on humans, soil microbiota, plants, algae, and water. This review develops deeper insight toward the advances in Gly biodegradation using microbial communities. This review provides a thorough understanding of Gly interaction with mineral elements and its limitations by interfering with the plants biochemical and morphological attributes.
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Affiliation(s)
- Waqas Mohy-Ud-Din
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad Pakistan
- Department of Soil and Environmental Sciences, Ghazi University, D. G. Khan Pakistan
- Institute of Marine and Environmental Technology, University of MD Center for Environmental Science, Baltimore, MD, USA
| | - Safdar Bashir
- Department of Soil and Environmental Sciences, Ghazi University, D. G. Khan Pakistan
| | - Muhammad Javed Akhtar
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad Pakistan
| | | | - Umber Ghafoor
- Pesticide Residue Laboratory, Kala Shah Kaku, Pakistan
| | | | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad Pakistan
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of MD Center for Environmental Science, Baltimore, MD, USA
| | - Qasim Ali
- Department of Soil Science, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Pakistan
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2
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Kumari K, Sharma PK, Shikha S, Singh RP. Molecular characterization and in-depth genome analysis of Enterobacter sp. S-16. Funct Integr Genomics 2023; 23:245. [PMID: 37460717 DOI: 10.1007/s10142-023-01161-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Shweta Shikha
- Shyama Prasad Mukherjee University, Ranchi, Jharkhand, India
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India.
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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3
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Chen Y, Chen WJ, Huang Y, Li J, Zhong J, Zhang W, Zou Y, Mishra S, Bhatt P, Chen S. Insights into the microbial degradation and resistance mechanisms of glyphosate. ENVIRONMENTAL RESEARCH 2022; 215:114153. [PMID: 36049517 DOI: 10.1016/j.envres.2022.114153] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Glyphosate, as one of the broad-spectrum herbicides for controlling annual and perennial weeds, is widely distributed in various environments and seriously threatens the safety of human beings and ecology. Glyphosate is currently degraded by abiotic and biotic methods, such as adsorption, photolysis, ozone oxidation, and microbial degradation. Of these, microbial degradation has become the most promising method to treat glyphosate because of its high efficiency and environmental protection. Microorganisms are capable of using glyphosate as a phosphorus, nitrogen, or carbon source and subsequently degrade glyphosate into harmless products by cleaving C-N and C-P bonds, in which enzymes and functional genes related to glyphosate degradation play an indispensable role. There have been many studies on the abiotic and biotic treatment technologies, microbial degradation pathways and intermediate products of glyphosate, but the related enzymes and functional genes involved in the glyphosate degradation pathways have not been further discussed. There is little information on the resistance mechanisms of bacteria and fungi to glyphosate, and previous investigations of resistance mechanisms have mainly focused on how bacteria resist glyphosate damage. Therefore, this review explores the microorganisms, enzymes and functional genes related to the microbial degradation of glyphosate and discusses the pathways of microbial degradation and the resistance mechanisms of microorganisms to glyphosate. This review is expected to provide reference for the application and improvement of the microbial degradation of glyphosate in microbial remediation.
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Affiliation(s)
- Yongsheng Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianfeng Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Sandhya Mishra
- Environmental Technologies Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, 47906, USA.
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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4
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Zhou Z, Wu H, Li D, Zeng W, Huang J, Wu Z. Comparison of gut microbiome in the Chinese mud snail ( Cipangopaludina chinensis) and the invasive golden apple snail ( Pomacea canaliculata). PeerJ 2022; 10:e13245. [PMID: 35402093 PMCID: PMC8992660 DOI: 10.7717/peerj.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3-V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
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Affiliation(s)
- Zihao Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Hongying Wu
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Dinghong Li
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Wenlong Zeng
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Jinlong Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China,College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
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Smits THM, Arend LNVS, Cardew S, Tång-Hallbäck E, Mira MT, Moore ERB, Sampaio JLM, Rezzonico F, Pillonetto M. Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae. Eur J Clin Microbiol Infect Dis 2022; 41:547-558. [PMID: 35169969 PMCID: PMC8934334 DOI: 10.1007/s10096-022-04413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family.
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Affiliation(s)
- Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
| | - Lavinia N V S Arend
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil
| | - Sofia Cardew
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Erika Tång-Hallbäck
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil
| | - Edward R B Moore
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Disease, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge L M Sampaio
- Faculdade de Ciências Farmacêuticas - University of São Paulo and Fleury Medicina Diagnóstica, São Paulo, SP, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Marcelo Pillonetto
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil. .,Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil.
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6
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Niu Q, Liu S, Yin M, Lei S, Rezzonico F, Zhang L. Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor. Pathogens 2022; 11:pathogens11010082. [PMID: 35056030 PMCID: PMC8778419 DOI: 10.3390/pathogens11010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/04/2022] Open
Abstract
Symbiotic microorganisms in the intestinal tract can influence the general fitness of their hosts and contribute to protecting them against invading pathogens. In this study, we obtained isolate Phytobacter diazotrophicus SCO41 from the gut of free-living nematode Caenorhabditis elegans that displayed strong colonization-resistance against invading biocontrol bacterium Bacillus nematocida B16. The colonization-resistance phenotype was found to be mediated by a 37-kDa extracellular protein that was identified as flagellin (FliC). With the help of genome information, the fliC gene was cloned and heterologously expressed in E. coli. It could be shown that the B. nematocida B16 grows in chains rather than in planktonic form in the presence of FliC. Scanning Electronic Microscopy results showed that protein FliC-treated B16 bacterial cells are thinner and longer than normal cells. Localization experiments confirmed that the protein FliC is localized in both the cytoplasm and the cell membrane of B16 strain, in the latter especially at the position of cell division. ZDOCK analysis showed that FliC could bind with serine/threonine protein kinase, membrane protein insertase YidC and redox membrane protein CydB. It was inferred that FliC interferes with cell division of B. nematocidal B16, therefore inhibiting its colonization of C. elegans intestines in vivo. The isolation of P. diazotrophicus as part of the gut microbiome of C. elegans not only provides interesting insights about the lifestyle of this nitrogen-fixing bacterium, but also reveals how the composition of the natural gut microbiota of nematodes can affect biological control efforts by protecting the host from its natural enemies.
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Affiliation(s)
- Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Suyao Liu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Mingshen Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Shengwei Lei
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | - Lin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
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7
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Zhang Z, Li D, Shi X, Zhai Y, Guo Y, Zheng Y, Zhao L, He Y, Chen Y, Wang Z, Su J, Kang Y, Gao Z. Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient. BMC Genomics 2020; 21:297. [PMID: 32293254 PMCID: PMC7156906 DOI: 10.1186/s12864-020-6720-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/05/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause. RESULTS The isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumoniae. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial-resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18, which could serve as targets for novel antimicrobial strategies. CONCLUSIONS Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.
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Affiliation(s)
- Zhao Zhang
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China.,Department of Respiratory & Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Daixi Li
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China.,Department of Respiratory and Critical Care Medicine, Zhongshan Hospital Xiamen University, Xiamen, 361004, Fujian, China
| | - Xing Shi
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Beijing, China
| | - Yao Zhai
- University of Technology Sydney, Ultimo, NSW, Australia
| | - Yatao Guo
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China.,Department of Respiratory & Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yali Zheng
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China.,Department of Respiratory, Critical Care and Sleep Medicine, Xiamen University Xiang'an Hospital, Xiamen, Fujian, China
| | - Lili Zhao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China
| | - Yukun He
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China
| | - Yusheng Chen
- Department of Respiratory & Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Zhanwei Wang
- Laboratory Medicine, Peking University People's Hospital, Beijing, China
| | - Jianrong Su
- Department of Clinical Laboratory Center, Beijing Friendship Hospital, Beijing, Beijing, China
| | - Yu Kang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Beijing, China.
| | - Zhancheng Gao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, Beijing, China.
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Treatment of Low Biodegradability Leachates in a Serial System of Aged Refuse-Filled Bioreactors. SUSTAINABILITY 2019. [DOI: 10.3390/su11113193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This paper presents a technology based on the use of aged refuse that has proven to be highly effective in the treatment of low biodegradability leachates. The tests were developed using two filled bioreactors arranged in series and operated at steady state. The aged refuse used as filling material was extracted from a city located in the southeast of Mexico and characterized by particle size, humidity, volatile solids, and volumetric weight. On the other hand, bacterial characterization made it possible to identify the presence of species related to the degradation and mineralization of organic compounds, as well as to processes of nitrification or reduction of phosphates and Cr (VI). The bioreactor system was operated under four hydraulic loads (10, 20, 35, and 50 L/m3·d). Maximum removal efficiencies of 85, 86.1, 87.9, 98.6, 97.8, and 97.4% were achieved in COD, BOD5, Color, TP, TN, and N-NH3, respectively, complying with Mexican regulations (NOM-001-SEMARNAT-1996). The system also proved to be stable against shock loads, such as organic load fluctuations in the influent or pH variations. The results of this study show that, in countries such as Mexico, aged refuse extracted from landfills represents a promising option as a sustainable alternative for leachate treatment.
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9
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Zhan H, Feng Y, Fan X, Chen S. Recent advances in glyphosate biodegradation. Appl Microbiol Biotechnol 2018; 102:5033-5043. [PMID: 29705962 DOI: 10.1007/s00253-018-9035-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 02/01/2023]
Abstract
Glyphosate has emerged as the most widespread herbicide to control annual and perennial weeds. Massive use of glyphosate for decades has resulted in its ubiquitous presence in the environment, and poses a threat to humans and ecosystem. Different approaches such as adsorption, photocatalytic degradation, and microbial degradation have been studied to break down glyphosate in the environment. Among these, microbial degradation is the most effective and eco-friendly method. During its degradation, various microorganisms can use glyphosate as a sole source of phosphorus, carbon, and nitrogen. Major glyphosate degradation pathways and its metabolites have been frequently investigated, but the related enzymes and genes have been rarely studied. There are many reviews about the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid. However, there is lack of reviews on biodegradation and bioremediation of glyphosate. The aims of this review are to summarize the microbial degradation of glyphosate and discuss the potential of glyphosate-degrading microorganisms to bioremediate glyphosate-contaminated environments. This review will provide an instructive direction to apply glyphosate-degrading microorganisms in the environment for bioremediation.
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Affiliation(s)
- Hui Zhan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yanmei Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xinghui Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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10
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Pillonetto M, Arend LN, Faoro H, D'Espindula HRS, Blom J, Smits THM, Mira MT, Rezzonico F. Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov. Int J Syst Evol Microbiol 2017; 68:176-184. [PMID: 29125457 DOI: 10.1099/ijsem.0.002477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol189 (2008), 431-439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA-DNA hybridization support the existence of a second species within the genus Phytobacter. All isolates from the recent Brazilian outbreak, along with some older American clinical strains, were found to belong to the already described species Phytobacterdiazotrophicus, whereas three clinical strains retrieved in the USA over a time span of almost four decades, could be assigned to a new Phytobacter species. Implementation of an extended set of biochemical tests showed that the two Phytobacter species could phenotypically be discriminated from each other by the ability to utilize l-sorbose and d-serine. This feature was limited to the strains of the novel species described herein, for which the name Phytobacter ursingii sp. nov. is proposed, with ATCC 27989T (=CNCTC 5729T) as the designated type strain. An emended description of the species Phytobacter diazotrophicus and of the genus Phytobacter is also provided.
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Affiliation(s)
- Marcelo Pillonetto
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil.,Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil
| | - Lavinia N Arend
- Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil
| | | | - Helena R S D'Espindula
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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11
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Andrés-Barrao C, Lafi FF, Alam I, de Zélicourt A, Eida AA, Bokhari A, Alzubaidy H, Bajic VB, Hirt H, Saad MM. Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium. Front Microbiol 2017; 8:2023. [PMID: 29163376 PMCID: PMC5664417 DOI: 10.3389/fmicb.2017.02023] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea. SA187 could survive in the rhizosphere as well as in association with different plant species, and was able to provide abiotic stress tolerance to Arabidopsis thaliana. The genome sequence of SA187 was obtained by using Pacific BioScience (PacBio) single-molecule sequencing technology, with average coverage of 275X. The genome of SA187 consists of one single 4,429,597 bp chromosome, with an average 56% GC content and 4,347 predicted protein coding DNA sequences (CDS), 153 ncRNA, 7 rRNA, and 84 tRNA. Functional analysis of the SA187 genome revealed a large number of genes involved in uptake and exchange of nutrients, chemotaxis, mobilization and plant colonization. A high number of genes were also found to be involved in survival, defense against oxidative stress and production of antimicrobial compounds and toxins. Moreover, different metabolic pathways were identified that potentially contribute to plant growth promotion. The information encoded in the genome of SA187 reveals the characteristics of a dualistic lifestyle of a bacterium that can adapt to different environments and promote the growth of plants. This information provides a better understanding of the mechanisms involved in plant-microbe interaction and could be further exploited to develop SA187 as a biological agent to improve agricultural practices in marginal and arid lands.
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Affiliation(s)
- Cristina Andrés-Barrao
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Feras F Lafi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Axel de Zélicourt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abdul A Eida
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ameerah Bokhari
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hanin Alzubaidy
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maged M Saad
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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