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Almuzara M, Cittadini R, Traglia G, Haim MS, De Belder D, Alvarez C, de Lourdes Reynal O'Connor Z, Ocampo CV, Barberis C, Prieto M, Campos J, Vay C. Phytobacter spp: the emergence of a new genus of healthcare-associated Enterobacterales encoding carbapenemases in Argentina: a case series. Infect Prev Pract 2024; 6:100379. [PMID: 39006243 PMCID: PMC11245914 DOI: 10.1016/j.infpip.2024.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/02/2024] [Indexed: 07/16/2024] Open
Abstract
Members of the genus Phytobacter (order Enterobacterales) are isolated from the natural environment and clinical settings. Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories. In this study we describe the first three clinical cases associated with Phytobacter spp. reported in Argentina. We describe the identification, the molecular analysis using whole genome sequencing and the potential clinical relevance.
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Affiliation(s)
- Marisa Almuzara
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
| | | | - Germán Traglia
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Salto, Universidad de La República, Uruguay
| | - María Sol Haim
- Unidad Operativa Centro Nacional de Genómica y Bioinformática ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Denise De Belder
- Unidad Operativa Centro Nacional de Genómica y Bioinformática ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Carla Alvarez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
| | | | | | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
| | - Mónica Prieto
- Laboratorio de Bacteriología Especial, ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Carlos Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
- Sanatorio Mater Dei, CABA, Argentina
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2
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Lin J, Wu J, Gong L, Li X, Wang G. Sepsis caused by Phytobacter diazotrophicus complicated with galactosemia type 1 in China: a case report. BMC Infect Dis 2024; 24:599. [PMID: 38898413 PMCID: PMC11186240 DOI: 10.1186/s12879-024-09458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Phytobacter diazotrophicus (P. diazotrophicus) is an opportunistic pathogen that causes nosocomial outbreaks and sepsis. However, there are no reports of P. diazotrophicus isolated from human blood in China. CASE PRESENTATION A 27-day-old female infant was admitted to our hospital with fever and high bilirubin levels. The clinical features included jaundice, abnormal coagulation, cholestasis, fever, convulsions, weak muscle tension, sucking weakness, ascites, abnormal tyrosine metabolism, cerebral oedema, abnormal liver function, clavicle fracture, and haemolytic anaemia. The strain isolated from the patient's blood was identified as P. diazotrophicus by whole-genome sequencing (WGS). Galactosemia type 1 (GALAC1) was diagnosed using whole-exome sequencing (WES). Based on drug sensitivity results, 10 days of anti-infective treatment with meropenem combined with lactose-free milk powder improved symptoms. CONCLUSION P. diazotrophicus was successfully identified in a patient with neonatal sepsis combined with galactosemia. Galactosemia may be an important factor in neonatal sepsis. This case further expands our understanding of the clinical characteristics of GALAC1.
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Affiliation(s)
- Jiansheng Lin
- Microbiology Laboratory, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
- The Affiliated Women's and Children's Hospital of Huaqiao University, Quanzhou, People's Republic of China
| | - Junfeng Wu
- Infection Disease Department, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
- The Affiliated Women's and Children's Hospital of Huaqiao University, Quanzhou, People's Republic of China
| | - Lan Gong
- St George and Sutherland Clinical Campus, UNSW Microbiome Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia
- School of Medicine, Huaqiao University, Quanzhou, 362021, China
| | - Xiaoqing Li
- Neonatal Department, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China.
- The Affiliated Women's and Children's Hospital of Huaqiao University, Quanzhou, People's Republic of China.
| | - Gaoxiong Wang
- Research Administration Office, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China.
- The Affiliated Women's and Children's Hospital of Huaqiao University, Quanzhou, People's Republic of China.
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3
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Choice S, Sherman A, Holder K, Harrington E. Gram-negative sepsis caused by a rare pathogen Phytobacter ursingii. BMJ Case Rep 2024; 17:e258384. [PMID: 38627051 PMCID: PMC11029423 DOI: 10.1136/bcr-2023-258384] [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] [Accepted: 03/24/2024] [Indexed: 04/19/2024] Open
Abstract
This case reviews the clinical course of an elderly woman on chronic total parenteral nutrition who developed sepsis secondary to a rare, newly described gram-negative rod known as Phytobacter ursingii The patient noticed a leak in her Hickman catheter when infusing her nutrition. 24 hours after a new catheter was replaced, the patient developed fevers, chills and weakness. She presented to the hospital with hypotension and tachycardia, meeting shock criteria. Blood cultures grew P. ursingii, and the diagnosis of septic shock was confirmed. Susceptibilities informed antibiotic coverage, and she ultimately improved within the next 48 hours.
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Affiliation(s)
- Samuel Choice
- Internal Medicine, UI Carver College of Medicine, Iowa City, Iowa, USA
| | - Ashten Sherman
- Department of Internal Medicine, The University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Katherine Holder
- Department of Internal Medicine, The University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Elaine Harrington
- Infectious Diseases, UI Carver College of Medicine, Iowa City, Iowa, USA
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4
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Huang Z, Zhang G, Zheng Z, Lou X, Cao F, Zeng L, Wang D, Yu K, Li J. Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens Kluyvera and Phytobacter. Front Cell Infect Microbiol 2024; 14:1376289. [PMID: 38577620 PMCID: PMC10991690 DOI: 10.3389/fcimb.2024.1376289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction Kluyvera is a Gram-negative, flagellated, motile bacillus within the Enterobacteriaceae. The case reports of clinical infections shed light on the importance of this organism as an emerging opportunistic pathogen. The genus Phytobacter, which often be misidentified with Kluyvera, is also an important clinically relevant member of the Enterobacteriaceae. However, the identification of Kluyvera and Phytobacter is problematic, and their phylogenetic relationship remains unclear. Methods Here, 81 strains of Kluyvera and 16 strains of Phytobacter were collected. A series of comparative genomics approaches were applied to the phylogenetic relationship reconstruction, virulence related genes profiles description, and antibiotic resistance genes prediction. Results Using average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH), we offered reliable species designations of 97 strains, in which 40 (41.24%) strains were incorrectly labeled. A new Phytobacter genomospecies-1 were defined. Phytobacter and Kluyvera show great genome plasticity and inclusiveness, which may be related to their diverse ecological niches. An intergenomic distances threshold of 0.15875 was used for taxonomy reassignments at the phylogenomic-group level. Further principal coordinates analysis (PCoA) revealed 11 core genes of Kluyvera (pelX, mdtL, bglC, pcak-1, uhpB, ddpA-2, pdxY, oppD-1, cptA, yidZ, csbX) that could be served as potential identification targets. Meanwhile, the Phytobacter specific virulence genes clbS, csgA-C, fliS, hsiB1_vipA and hsiC1_vipB, were found to differentiate from Kluyvera. We concluded that the evolution rate of Kluyvera was 5.25E-6, approximately three times higher than that of Phytobacter. Additionally, the co-existence of ESBLs and carbapenem resistance genes were present in approximately 40% strains, suggesting the potential development of extensively drug-resistant or even fully drug-resistant strains. Discussion This work provided a better understanding of the differences between closely related species Kluyvera and Phytobacter. Their genomes exhibited great genome plasticity and inclusiveness. They not only possess a potential pathogenicity threat, but also a risk of multi-drug resistance. The emerging pathogens Kluyvera and Phytobacter warrant close attention.
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Affiliation(s)
- Zhenzhou Huang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Guozhong Zhang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Zhibei Zheng
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Xiuqin Lou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Feifei Cao
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Lingyi Zeng
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Li
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
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Barretto LAF, Van PKT, Fowler CC. Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae. Microb Genom 2024; 10:001215. [PMID: 38502064 PMCID: PMC11004495 DOI: 10.1099/mgen.0.001215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Two-component regulatory systems (TCSs) are a major mechanism used by bacteria to sense and respond to their environments. Many of the same TCSs are used by biologically diverse organisms with different regulatory needs, suggesting that the functions of TCS must evolve. To explore this topic, we analysed the amino acid sequence divergence patterns of a large set of broadly conserved TCS across different branches of Enterobacteriaceae, a family of Gram-negative bacteria that includes biomedically important genera such as Salmonella, Escherichia, Klebsiella and others. Our analysis revealed trends in how TCS sequences change across different proteins or functional domains of the TCS, and across different lineages. Based on these trends, we identified individual TCS that exhibit atypical evolutionary patterns. We observed that the relative extent to which the sequence of a given TCS varies across different lineages is generally well conserved, unveiling a hierarchy of TCS sequence conservation with EnvZ/OmpR as the most conserved TCS. We provide evidence that, for the most divergent of the TCS analysed, PmrA/PmrB, different alleles were horizontally acquired by different branches of this family, and that different PmrA/PmrB sequence variants have highly divergent signal-sensing domains. Collectively, this study sheds light on how TCS evolve, and serves as a compendium for how the sequences of the TCS in this family have diverged over the course of evolution.
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Affiliation(s)
- Luke A. F. Barretto
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2E9, Canada
| | - Patryc-Khang T. Van
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2E9, Canada
| | - Casey C. Fowler
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2E9, Canada
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Kubota H, Nakayama T, Ariyoshi T, Uehara S, Uchitani Y, Tsuchida S, Nishiyama H, Morioka I, Koshinaga T, Kusabuka A, Nakatsubo N, Yamagishi T, Tabuchi Y, Okuno R, Kobayashi K, Mitobe M, Yokoyama K, Shinkai T, Suzuki J, Sadamasu K. Emergence of Phytobacter diazotrophicus carrying an IncA/C 2 plasmid harboring bla NDM-1 in Tokyo, Japan. mSphere 2023; 8:e0014723. [PMID: 37449846 PMCID: PMC10449528 DOI: 10.1128/msphere.00147-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Phytobacter diazotrophicus is an Enterobacterales species that was originally identified as a plant growth-promoting, Gram-negative bacterium. Recently, this species has been recognized as relevant to opportunistic human and nosocomial infections in clinical settings. Its frequent misidentification as other Enterobacterales species from clinical examination occasionally causes a delay in the identification of nosocomial outbreaks. Here, we report the emergence of New Delhi metallo-β-lactamase (NDM)-producing P. diazotrophicus isolated from hospitalized pediatric patients and hospital environments in Tokyo, Japan. In our case, these isolates were found during an investigation of carbapenem-resistant Enterobacterales in relation to nosocomial infections. Whole-genome sequencing is useful for overcoming the difficulty of species identification. Furthermore, we found that bla NDM-1 was carried by an IncA/C2 plasmid (approximately 170 kbp), which was transferrable from the clinical isolates to the recipient strain Escherichia coli J53. Our study demonstrated that P. diazotrophicus behaves as a carrier of bla NDM-harboring plasmids, potentially disseminating resistance to carbapenems among Enterobacterales. IMPORTANCE Early detection of nosocomial outbreaks is important to minimize the spread of bacteria. When an outbreak is caused by multidrug-resistant bacteria such as carbapenem-resistant Enterobacterales, a delay in findings makes it difficult to control it because such bacteria often spread not only among human patients but also in hospital environments. Phytobacter diazotrophicus, an Enterobacterales species that has recently been found to be relevant to clinical settings, is often misidentified as other bacteria in clinical laboratories. Here, we found NDM-producing P. diazotrophicus in hospitalized pediatric patients and their environment in Tokyo, Japan. Given that the isolates carried bla NDM-1-harboring transferrable plasmids, the influence of such bacteria could be greater with the mediation of horizontal transfer of carbapenem resistance. Our findings suggest that P. diazotrophicus should be recognized as an NDM-carrier, for which more attention should be paid in clinical settings.
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Affiliation(s)
- Hiroaki Kubota
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Tomohiro Nakayama
- Division of Laboratory Medicine and Companion Diagnostics, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Tsukasa Ariyoshi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Satomi Uehara
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Yumi Uchitani
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Sachio Tsuchida
- Division of Laboratory Medicine and Companion Diagnostics, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiroyuki Nishiyama
- Clinical Laboratory Department, Surugadai Nihon University Hospital, Chiyoda-ku, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Oyaguchi, Itabashi-ku, Tokyo, Japan
| | - Tsugumichi Koshinaga
- Department of Pediatric Surgery, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Akiko Kusabuka
- Department of Planning and Coordination, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Naoki Nakatsubo
- Department of Planning and Coordination, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Takuya Yamagishi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Yuri Tabuchi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Rumi Okuno
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Kai Kobayashi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Morika Mitobe
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Keiko Yokoyama
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Takayuki Shinkai
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Jun Suzuki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
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Gorrasi S, Pasqualetti M, Muñoz-Palazon B, Novello G, Mazzucato A, Campiglia E, Fenice M. Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich "Sun Black" and Wild-Type Tomatoes under Organic and Conventional Farming. Microorganisms 2022; 10:2240. [PMID: 36422310 PMCID: PMC9694333 DOI: 10.3390/microorganisms10112240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 07/30/2023] Open
Abstract
Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79-91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3-47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.
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Affiliation(s)
- Susanna Gorrasi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Marcella Pasqualetti
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Laboratory of Ecology of Marine Fungi, CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Barbara Muñoz-Palazon
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Institute of Water Research, University of Granada, 18071 Granada, Spain
| | - Giorgia Novello
- Department of Science, Technology and Innovation (DISIT), Università del Piemonte Orientale, Viale Teresa Michel, 11, 15121 Alessandria, Italy
| | - Andrea Mazzucato
- Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Enio Campiglia
- Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Massimiliano Fenice
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Laboratory of Applied Marine Microbiology, CoNISMa, University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
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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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9
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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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Rios-Galicia B, Villagómez-Garfias C, De la Vega-Camarillo E, Guerra-Camacho JE, Medina-Jaritz N, Arteaga-Garibay RI, Villa-Tanaca L, Hernández-Rodríguez C. The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria. 3 Biotech 2021; 11:447. [PMID: 34631348 DOI: 10.1007/s13205-021-02983-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/04/2021] [Indexed: 01/02/2023] Open
Abstract
The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co2+, Fe3+, Mo2 +, V5+, Zn2+), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.
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Affiliation(s)
- Bibiana Rios-Galicia
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Catalina Villagómez-Garfias
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Esaú De la Vega-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Jairo Eder Guerra-Camacho
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Nora Medina-Jaritz
- Departamento de Botánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Ramón Ignacio Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Boulevard de la Biodiversidad No. 400, Rancho Las Cruces, 47600 Tepatitlán de Morelos, Jalisco Mexico
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
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11
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Li W, Li F, Zeng H, Ma L, Qi L, Wang X, Wang W, Peng Z, Degen AA, Bai Y, Zhang T, Huang M, Han J, Shang Z. Diversity and Variation of Asymbiotic Nitrogen-Fixing Microorganisms in Alpine Grasslands on the Tibetan Plateau. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.702848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Asymbiotic nitrogen-fixing (ANF) bacteria contribute a substantial amount of nitrogen in ecosystems, especially in those with low symbiotic nitrogen fixation (SNF) capability. Degradation of alpine grassland is widespread on the Tibetan Plateau and sown grassland has become one of the main strategies for grassland restoration. However, the diversity and community structure of ANF bacteria in different grassland types remain unknown. The aim of this study was to fill this gap. Soil samples were obtained from 39 grassland plots selected from three counties in the eastern Tibetan Plateau. The plots were classified as natural grassland (NG), sown grassland (SG), lightly degraded grassland (LDG), and severely degraded grassland (SDG). ANF microbial communities of the four grassland types were compared at the level of community and species diversity by 16S rRNA high-throughput sequencing technology. The phylum Proteobacteria accounted for >72% of the ANF bacteria. The community structures of soil ANF bacteria differed significantly (p < 0.01) among grassland types. We concluded that: (1) planting gramineous forage could possibly mitigate the decrease in diversity of soil ANF bacteria caused by grassland degradation; and (2) the diversity of soil ANF bacteria in alpine grassland of the Tibetan Plateau is closely related to grassland degradation and restoration.
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12
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Bianco C, Andreozzi A, Romano S, Fagorzi C, Cangioli L, Prieto P, Cisse F, Niangado O, Sidibé A, Pianezze S, Perini M, Mengoni A, Defez R. Endophytes from African Rice ( Oryza glaberrima L.) Efficiently Colonize Asian Rice ( Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll. Microorganisms 2021; 9:microorganisms9081714. [PMID: 34442793 PMCID: PMC8398951 DOI: 10.3390/microorganisms9081714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.
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Affiliation(s)
- Carmen Bianco
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
- Correspondence: ; Tel.: +39-081-613-2610
| | - Anna Andreozzi
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
| | - Silvia Romano
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Lisa Cangioli
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Pilar Prieto
- Departamento de Mejora Genética, Campus ‘Alamedadel Obispo’, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain;
| | - Fousseyni Cisse
- Institut d’Economie Rurale, Rue Mohamed V Bamako, Bamako B.P. 258, Mali; (F.C.); (A.S.)
| | - Oumar Niangado
- Syngenta Foundation for Sustainable Agriculture, Bamako B.P.E. 1449, Mali;
| | - Amadou Sidibé
- Institut d’Economie Rurale, Rue Mohamed V Bamako, Bamako B.P. 258, Mali; (F.C.); (A.S.)
| | - Silvia Pianezze
- Fondazione Edmund Mach, Via Mach 1, 38098 San Michele All’Adige, Italy; (S.P.); (M.P.)
- Environmental and Animal Sciences DI4A, Università degli Studi di Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Matteo Perini
- Fondazione Edmund Mach, Via Mach 1, 38098 San Michele All’Adige, Italy; (S.P.); (M.P.)
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Roberto Defez
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
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13
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Medina-Cordoba LK, Chande AT, Rishishwar L, Mayer LW, Valderrama-Aguirre LC, Valderrama-Aguirre A, Gaby JC, Kostka JE, Jordan IK. Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields. Sci Rep 2021; 11:9187. [PMID: 33911103 PMCID: PMC8080613 DOI: 10.1038/s41598-021-88380-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/07/2021] [Indexed: 01/26/2023] Open
Abstract
Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.
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Affiliation(s)
- Luz K Medina-Cordoba
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Leonard W Mayer
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lina C Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, INCAUCA S.A.S., Cali, Valle del Cauca, Colombia
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Universidad Santiago de Cali, Cali, Colombia
| | - John Christian Gaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Dr NW, Atlanta, GA, 30332, USA.
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,Applied Bioinformatics Laboratory, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, Atlanta, GA, 30332, USA.
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14
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The Flora Compositions of Nitrogen-Fixing Bacteria and the Differential Expression of nifH Gene in Pennisetum giganteum z.x.lin Roots. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568845. [PMID: 33981770 PMCID: PMC8088366 DOI: 10.1155/2021/5568845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/05/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022]
Abstract
The flora compositions of nitrogen-fixing bacteria in roots of Pennisetum giganteum z.x.lin at different growth stages and the expression and copy number of nitrogen-fixing gene nifH were studied by Illumina Miseq second-generation sequencing technology and qRT-PCR. The results showed that there were more than 40,000~50,000 effective sequences in 5 samples from the roots of P. giganteum, with Proteobacteria and Cyanobacteria as the dominant nitrogen-fixing bacteria based on the OTU species annotations for each sample and Bradyrhizobium as the core bacterial genera. The relative expression and quantitative change of nifH gene in roots of P. giganteum at different growth stages were consistent with the changes in the flora compositions of nitrogen-fixing microbia. Both revealed a changing trend with an initial increase and a sequential decrease, as well as changing order as jointing stage>maturation stage>tillering stage>seedling stage>dying stage. The relative expression and copy number of nifH gene were different in different growth stages, and the difference among groups basically reached a significant level (p < 0.05). The relative expression and copy number of nifH gene at the jointing stage were the highest, and the 2-△△CT value was 4.43 folds higher than that at the seedling stage, with a copy number of 1.32 × 107/g. While at the dying stage, it was the lowest, and the 2-△△CT value was 0.67 folds, with a copy number of 0.31 × 107/g.
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15
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Effects of Selected Functional Bacteria on Maize Growth and Nutrient Use Efficiency. Microorganisms 2020; 8:microorganisms8060854. [PMID: 32517011 PMCID: PMC7356773 DOI: 10.3390/microorganisms8060854] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 01/09/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR), which include isolates from genera Paraburkholderia, Burkholderia and Serratia, have received attention due to their numerous plant growth-promoting mechanisms such as their ability to solubilize insoluble phosphates and nitrogen-fixation. However, there is a dearth of information on the potential plant growth-promoting effects of these three groups of bacteria on non-legumes such as maize. This study determined the influences of the aforementioned strains on soil properties, maize growth, nutrient uptake and nutrient use efficiency. A pot trial using maize as a test crop was done using a randomized complete block design with 7 treatments each replicated 7 times. The treatments used in this study were: Control (no fertilizer), chemical fertilizer (CF), organic-chemical fertilizers combination without inoculum (OCF) and with inocula consisting of single strains [cellulolytic bacteria (TC), organic fertilizer and chemical fertilizer with N-fixing bacteria (TN), organic fertilizer and chemical fertilizer with P-solubilizing bacteria (TP)) and three-strain inocula (TCNP), respectively. The variables measured included plant growth and nutrient content, soil nutrient content and functional rhizospheric bacterial populations. Paraburkholderia nodosa NB1 and Burkholderia cepacia PB3 showed comparable effects on maize biomass and also improved N and P use efficiencies when compared to full chemical fertilization. Nitrogen-fixing rhizobacteria had a positive effect on above-ground biomass of maize. Paraburkholderia nodosa NB1 improved soil total C and organic matter contents, besides being the only bacterial treatment that improved K use efficiency compared to OCF. The results suggest that P. nodosa NB1 and B. cepacia PB3 have potential usage in bio-fertilizers. In contrast, treatments with Serratia nematodiphila C46d and consortium strains showed poorer maize nutrient uptake and use efficiency than the other single strain treatments. Bacterial treatments generally showed comparable or higher overall N and P use efficiencies than full chemical fertilization. These findings suggest that at least half the amounts of N and P fertilizers could be reduced through the use of combined fertilization together with beneficial bacteria.
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16
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Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability. Antonie van Leeuwenhoek 2020; 113:1075-1107. [PMID: 32488494 DOI: 10.1007/s10482-020-01429-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/22/2020] [Indexed: 10/24/2022]
Abstract
Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles in the growth, development, fitness, and diversification of plants. The plant-endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combat a diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus-thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.
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17
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Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov. Curr Microbiol 2020; 77:1945-1954. [PMID: 32350604 DOI: 10.1007/s00284-020-02004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The genus Metakosakonia, as the closest phylogenetic neighbor of the genus Kosakonia within the family Enterobacteriaceae, when proposed in 2017, consisted of M. massiliensis JC163T and Metakosakonia spp. strains CAV1151 and GT-16. The strain CAV1151 was later classified into a novel species Phytobacter ursingii. Here, we show that the strain GT-16 shares a digital DNA-DNA hybridization (DDH) similarity of 91.0% with P. diazotrophicus DSM 17806 T and thus also belongs to P. diazotrophicus. M. massiliensis and the strains within the genus Phytobacter formed a monophyletic cluster on a phylogenomic tree based on the core proteins of the family Enterobacteriaceae and on a phylogenetic tree based on the 16S rRNA genes. M. massiliensis and the genus Phytobacter share average amino acid identities of 86.80‒87.41% above the threshold (86%) for genus delimitation within the family Enterobacteriaceae. Moreover, they share conserved signature indels in the intracellular growth protein IgaA and the outer membrane assembly protein AsmA. Therefore, we propose to unite the genus Metakosakonia and the genus Phytobacter to a single genus. Because the genus Phytobacter was validly published earlier in 2017 than the genus Metakosakonia in 2017, the genus name Phytobacter has priority over Metakosakonia. We propose to unite the two genera under the name Phytobacter with the type species P. diazotrophicus and reclassify M. massiliensis as P. massiliensis comb. nov. In addition, the analyses of genome relatedness and phylogenomic relationship identified one potential novel species within the genus Phytobacter and three potential novel species within the genus Kosakonia.
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18
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Madhaiyan M, Saravanan VS, Blom J, Smits THM, Rezzonico F, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 2020; 70:841-848. [DOI: 10.1099/ijsem.0.003834] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wadenswil, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wadenswil, Switzerland
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
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19
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Liu L, Yuan T, An Q, Yang M, Mao X, Mo C, Tan Z, Peng G. Azotobacter bryophylli sp. nov., isolated from the succulent plant Bryophyllum pinnatum. Int J Syst Evol Microbiol 2019; 69:1986-1992. [PMID: 31046894 DOI: 10.1099/ijsem.0.003412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
A Gram-stain-negative, aerobic, nitrogen-fixing bacterium, designated strain L461T, was isolated from leaves of Bryophyllum pinnatum growing at the South China Agricultural University. Phylogenetic analysis of the 16S rRNA gene sequence indicated it as a member of the genus Azotobacter closely related to Azotobacter beijerinckii JCM 20725T (97.82 % similarity) and Azotobacter chroococcum ATCC 9043T (97.34 %). Its major fatty acid components were C16 : 1 ω9c and C16 : 0. Its predominant isoprenoid quinone was Q-9. Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, phospholipid and one unknown lipid. Its DNA G+C content was 64.9 mol% (Tm). DNA-DNA relatedness values between strain L461T and the reference strains of A. beijerinckii and A. chroococcum were 46.43 and 28.23 %, respectively. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting, and comparison of cellular fatty acids distinguished strain L461T from the closely related Azotobacter species. Based on these data, the novel species Azotobacter bryophylli sp. nov. is proposed, with the type strain L461T (=KCTC 62195T=GDMCC 1.1250T).
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Affiliation(s)
- Lihui Liu
- 1Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, PR China
| | - Tao Yuan
- 1Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, PR China
| | - Qianli An
- 2State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Meiyan Yang
- 1Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiaoyun Mao
- 3College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - Cehui Mo
- 4School of Enviroment, Jinan University, Guangzhou, PR China
| | - Zhiyuan Tan
- 1Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, PR China
| | - Guixiang Peng
- 3College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China.,5Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, PR China
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20
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Pillonetto M, Arend L, Gomes SMT, Oliveira MAA, Timm LN, Martins AF, Barth AL, Mazzetti A, Hersemann L, Smits THM, Mira MT, Rezzonico F. Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil. BMC Infect Dis 2018; 18:397. [PMID: 30103698 PMCID: PMC6090600 DOI: 10.1186/s12879-018-3287-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Background Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. Methods We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. Results The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970’s. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. Conclusion This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans. Electronic supplementary material The online version of this article (10.1186/s12879-018-3287-2) contains supplementary material, which is available to authorized users.
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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. .,Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José dos Pinhais, PR, Brazil.
| | - Lavinia Arend
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José dos Pinhais, PR, Brazil
| | - Suzie M T Gomes
- Brazilian Health Surveillance Agency - ANVISA, Brasília, DF, Brazil
| | - Marluce A A Oliveira
- Ezequiel Dias Foundation, Central Public Health Laboratory - State of Minas Gerais, Bacteriology Division, Belo Horizonte, MG, Brazil
| | - Loeci N Timm
- Central Public Health Laboratory - State of Rio Grande do Sul, Bacteriology Division, Porto Alegre, RS, Brazil
| | - Andreza F Martins
- Research Laboratory on Bacterial Resistance (LABRESIS), Federal University of Rio Grande do Sul, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Afonso L Barth
- Research Laboratory on Bacterial Resistance (LABRESIS), Federal University of Rio Grande do Sul, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Alana Mazzetti
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Lena Hersemann
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.,Present Address: Scientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - 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
| | - 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 (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
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Paenibacillus bryophyllum sp. nov., a nitrogen-fixing species isolated from Bryophyllum pinnatum. Antonie Van Leeuwenhoek 2018; 111:2267-2273. [PMID: 29971704 DOI: 10.1007/s10482-018-1117-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/16/2018] [Indexed: 10/28/2022]
Abstract
A nitrogen-fixing, endospore-forming bacterium, designated strain L201T was isolated from the leaves of Bryophyllum pinnatum growing in South China Agricultural University. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain L201T is affiliated with the genus Paenibacillus, and closely related to Paenibacillus albidus Q4-3T (97.4%), Paenibacillus odorifer DSM 15391T (97.3%) and Paenibacillus borealis DSM 13188T (97.2%). The main fatty acids components was anteiso-C15:0 (48.1%). The predominant isoprenoid quinone was MK-7. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The G+C content of strain L201T was 43.9%. DNA-DNA relatedness between L201T and the reference strain was 29.8%. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting and comparison of cellular fatty acids distinguished strain L201T from the closely related Paenibacillus species. Based on these data, the novel species Paenibacillus bryophyllum sp. nov. is proposed, with the type strain L201T(= KCTC 33951 T = GDMCC 1.1251 T).
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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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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:1095-1098. [PMID: 28581921 DOI: 10.1099/ijsem.0.001986] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Nicolau Korres AM, Aquije GMDFV, Buss DS, Ventura JA, Fernandes PMB, Fernandes AAR. Comparison of biofilm and attachment mechanisms of a phytopathological and clinical isolate of Klebsiella pneumoniae Subsp. pneumoniae. ScientificWorldJournal 2013; 2013:925375. [PMID: 24222755 PMCID: PMC3809605 DOI: 10.1155/2013/925375] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 09/16/2013] [Indexed: 12/01/2022] Open
Abstract
Some bacterial species can colonize humans and plants. It is almost impossible to prevent the contact of clinically pathogenic bacteria with food crops, and if they can persist there, they can reenter the human food chain and cause disease. On the leaf surface, microorganisms are exposed to a number of stress factors. It is unclear how they survive in such different environments. By increasing adhesion to diverse substrates, minimizing environmental differences, and providing protection against defence mechanisms, biofilms could provide part of the answer. Klebsiella pneumoniae subsp. pneumoniae is clinically important and also associated with fruit diseases, such as "pineapple fruit collapse." We aimed to characterize biofilm formation and adhesion mechanisms of this species isolated from pineapple in comparison with a clinical isolate. No differences were found between the two isolates quantitatively or qualitatively. Both tested positive for capsule formation and were hydrophobic, but neither produced adherence fibres, which might account for their relatively weak adhesion compared to the positive control Staphylococcus epidermidis ATCC 35984. Both produced biofilms on glass and polystyrene, more consistently at 40°C than 35°C, confirmed by atomic force and high-vacuum scanning electron microscopy. Biofilm formation was maintained in an acidic environment, which may be relevant phytopathologically.
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Affiliation(s)
- Adriana Marcia Nicolau Korres
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Avenida Marechal Campos 1468, 29040-090 Vitória, ES, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo, Campus Vitória, Avenida Vitória 1729, 29040-780 Vitória, ES, Brazil
| | - Gloria Maria de Farias V. Aquije
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Avenida Marechal Campos 1468, 29040-090 Vitória, ES, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo, Campus Vila Velha, Avenida Ministro Salgado Filho S/Nº, 29106-010 Vila Velha, ES, Brazil
| | - David S. Buss
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Avenida Marechal Campos 1468, 29040-090 Vitória, ES, Brazil
| | - Jose Aires Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Avenida Marechal Campos 1468, 29040-090 Vitória, ES, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do Espírito Santo, INCAPER, Rua Afonso Sarlo 160, 29052-010 Vitória, ES, Brazil
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Yuan ZL, Su ZZ, Mao LJ, Peng YQ, Yang GM, Lin FC, Zhang CL. Distinctive endophytic fungal assemblage in stems of wild rice (Oryza granulata) in China with special reference to two species of Muscodor (Xylariaceae). J Microbiol 2011; 49:15-23. [PMID: 21369974 DOI: 10.1007/s12275-011-0213-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 09/11/2010] [Indexed: 12/30/2022]
Abstract
Ecological niches in the rhizosphere and phyllosphere of grasses capable of sustaining endophytes have been extensively studied. In contrast, little information regarding the identity and functions of endophytic fungi in stems is available. In this study, we investigated the taxonomic affinities, diversity, and host specificities of culturable endophytes in stems of wild rice (Oryza granulata) in China. Seventy-four isolates were recovered. Low recovery rate (11.7%) indicated that there were relatively few sites for fungal infection. Identification using morphology, morphospecies sorting, and molecular techniques resulted in classification into 50 taxa, 36 of which were recovered only once. Nucleotide sequence similarity analysis indicated that 30% of the total taxa recovered were highly divergent from known species and thus may represent lineages new to science. Most of the taxa were classified as members of the classes Sordariomycetes or Dothideomycetes (mainly in Pleosporales). The presence of Arthrinium and Magnaporthaceae species, most often associated with poaceous plants, suggested a degree of host specificity. A polyphasic approach was employed to identify two Muscodor taxa based on (i) ITS and RPB2 phylogenies, (ii) volatile compounds produced, and (iii) an in vitro bioassay of antifungal activity. This to our knowledge is only the second report regarding the isolation of Muscodor spp. in China. Therefore, we hypothesize that wild plants represent a huge reservoir of unknown fungi. The prevalence, novelty, and species-specificity of unique isolates necessitate a reevaluation of their contribution to ecosystem function and fungal biodiversity.
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Affiliation(s)
- Zhi-lin Yuan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, 310029, PR China
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