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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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102
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Point-Counterpoint: What's in a Name? Clinical Microbiology Laboratories Should Use Nomenclature Based on Current Taxonomy. J Clin Microbiol 2023; 61:e0173222. [PMID: 36625570 PMCID: PMC9879091 DOI: 10.1128/jcm.01732-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION The mnemonic SPICE (Serratia, Pseudomonas, indole-positive Proteus, Citrobacter, and Enterobacter) has served as a reminder to consider when a Gram-negative organism may carry a chromosomal copy of blaampC, with the associated risk of developing resistance to first-, second-, and third-generation cephalosporins. However, in 2017, there was a well-founded proposal to rename Enterobacter aerogenes to Klebsiella aerogenes, based on whole-genome sequencing (WGS), and the SPICE mnemonic lost its relevance. With the increased use of WGS for taxonomy, it seems like bacteria and fungi are undergoing constant name changes. These changes create unique challenges for clinical microbiology laboratories, who would like to issue reports that are readily understood and that help clinicians determine empirical antibiotic therapy, interpret antimicrobial resistance, and understand clinical significance. In this Point-Counterpoint, Drs. Karen Carroll and Erik Munson discuss the pros of updating bacterial taxonomy and why clinical labs must continue to update reporting, while Drs. Susan Butler-Wu and Sheila Patrick argue for caution in adopting new names for microorganisms.
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103
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Xue H, Tu Y, Ma T, Jiang N, Piao C, Li Y. Taxonomic Study of Three Novel Paenibacillus Species with Cold-Adapted Plant Growth-Promoting Capacities Isolated from Root of Larix gmelinii. Microorganisms 2023; 11:microorganisms11010130. [PMID: 36677422 PMCID: PMC9867441 DOI: 10.3390/microorganisms11010130] [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: 11/20/2022] [Revised: 12/24/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Exploration of the novel species of the genus Paenibacillus with plant-growth promoting characteristics at the low-temperature environment is of great significance for the development of psychrotolerant biofertilizer in forestry and agriculture. During the course of isolation of root endophytes of Larix gmelinii in the island frozen soil, three strains designated as T3-5-0-4, N1-5-1-14 and N5-1-1-5 were isolated. The three strains showed plant growth-promoting properties at the low temperature, such as phosphate solubilization, indole-3-acetic acid biosynthesis and siderophore production. According to pairwise sequence analyses of the 16S rRNA genes, the three strains represent putatively novel taxa within the genus Paenibacillus. The strains have typical chemotaxonomic characteristics of the genus Paenibacillus by having meso-diaminopimelic acid as diagnostic diamino acid, anteiso-C15:0 as the predominant fatty acid and MK-7 as the predominant menaquinone. The polar lipid profiles of all strains contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The sizes of the genomes of the stains ranged from 5.66 to 9.07 Mb and the associated G+C contents ranged from 37.9% to 44.7%. Polyphasic taxonomic study including determination of genome relatedness indices revealed that the strains are representatives of three novel species in the genus Paenibacillus. Consequently, isolates T3-5-0-4, N1-5-1-14 and N5-1-1-5 are proposed as novel species for which the names of Paenibacillus endoradicis sp. nov. (CFCC15691T = KCTC43441T), Paenibacillus radicibacter sp. nov, (CFCC15694T = KCTC43442T) and Paenibacillus radicis sp. nov. (CFCC15710T = KCTC43173T), respectively. Moreover, analysis for biosynthetic genes showed that the strains have potential for plant growth-promoting characteristics, plant rhizospheres colonization and low-temperature adaption, most of which are consistent with the results of the bioactivity test.
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Affiliation(s)
| | | | | | | | | | - Yong Li
- Correspondence: ; Tel.: +861062889587
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104
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Shevtsov A, Cloeckaert A, Berdimuratova K, Shevtsova E, Shustov AV, Amirgazin A, Karibayev T, Kamalova D, Zygmunt MS, Ramanculov Y, Vergnaud G. Brucella abortus in Kazakhstan, population structure and comparison with worldwide genetic diversity. Front Microbiol 2023; 14:1106994. [PMID: 37032899 PMCID: PMC10073595 DOI: 10.3389/fmicb.2023.1106994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/01/2023] [Indexed: 04/11/2023] Open
Abstract
Brucella abortus is the main causative agent of brucellosis in cattle, leading to severe economic consequences in agriculture and affecting public health. The zoonotic nature of the infection increases the need to control the spread and dynamics of outbreaks in animals with the incorporation of high resolution genotyping techniques. Based on such methods, B. abortus is currently divided into three clades, A, B, and C. The latter includes subclades C1 and C2. This study presents the results of whole-genome sequencing of 49 B. abortus strains isolated in Kazakhstan between 1947 and 2015 and of 36 B. abortus strains of various geographic origins isolated from 1940 to 2004. In silico Multiple Locus Sequence Typing (MLST) allowed to assign strains from Kazakhstan to subclades C1 and to a much lower extend C2. Whole-genome Single-Nucleotide Polymorphism (wgSNP) analysis of the 46 strains of subclade C1 with strains of worldwide origins showed clustering with strains from neighboring countries, mostly North Caucasia, Western Russia, but also Siberia, China, and Mongolia. One of the three Kazakhstan strains assigned to subclade C2 matched the B. abortus S19 vaccine strain used in cattle, the other two were genetically close to the 104 M vaccine strain. Bayesian phylodynamic analysis dated the introduction of B. abortus subclade C1 into Kazakhstan to the 19th and early 20th centuries. We discuss this observation in view of the history of population migrations from Russia to the Kazakhstan steppes.
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Affiliation(s)
- Alexandr Shevtsov
- National Center for Biotechnology, Astana, Kazakhstan
- *Correspondence: Alexandr Shevtsov,
| | | | | | | | | | | | | | | | | | - Yerlan Ramanculov
- National Center for Biotechnology, Astana, Kazakhstan
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Gilles Vergnaud
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Gilles Vergnaud,
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105
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Pereira CR, de Jesus Sousa T, Lima da Silva A, Gonçalves Dos Santos R, Minharro S, Costa Custódio DA, Pickard DJ, O'Callaghan D, Foster JT, de Castro Soares S, Juca Ramos RT, Góes-Neto A, Matiuzzi da Costa M, Lage AP, Azevedo V, Seles Dorneles EM. First report and whole-genome sequencing of Pseudochrobactrum saccharolyticum in Latin America. Microbes Infect 2023; 25:105018. [PMID: 35940401 DOI: 10.1016/j.micinf.2022.105018] [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: 02/17/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023]
Abstract
The Brucellaceae family comprises microorganisms similar both phenotypically and genotypically, making it difficult to identify the etiological agent of these infections. This study reports the first isolation, identification, and characterization of Pseudochrobactrum saccharolyticum (strain 115) from Latin America. Strain 115 was isolated in 2007 from a bovine in Brazil and was initially classified as Brucella spp. by classical microbiological tests and bcsp31 PCR. The antimicrobial susceptibility of strain 115 was tested against drugs used to treat human brucellosis by minimal inhibitory concentration test. Subsequently, the whole genome of the strain was sequenced, assembled, and characterized. Phylogenetic trees built from 16S rRNA and recA gene sequences enabled the classification of strain 115 as Pseudochrobactrum spp. Phylogenomic analysis using Single Nucleotide Polymorphisms and Average Nucleotide Identity allowed the classification of the strain as P. saccharolyticum. Additionally, a Tetra Correlation Search identified one related genome from the same species, which was compared with strain 115 by analyzing genomic islands. This is the first identification and whole-genome sequence of P. saccharolyticum in Latin America and highlights a challenge in the diagnosis of bovine brucellosis, which could be solved by including the sequencing of 16S rRNA and recA genes in routine diagnostics.
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Affiliation(s)
- Carine Rodrigues Pereira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alessandra Lima da Silva
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roselane Gonçalves Dos Santos
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sílvia Minharro
- Centro de Ciência da Saúde - Medicina - Araguaína, Universidade Federal de Tocantins, Tocantins, Brazil
| | - Dirceia Aparecida Costa Custódio
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Derek J Pickard
- Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - David O'Callaghan
- IVBIC, INSERM, Universite de Montpellier, Nimes, France; CNR Brucella, Laboratoire de Microbiologie, CHU Nimes, Nimes, France
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Siomar de Castro Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Ciências Naturais, Universidade Federal Do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Rommel Thiago Juca Ramos
- Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - Aristóteles Góes-Neto
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mateus Matiuzzi da Costa
- Universidade Federal Do Vale Do São Francisco, Departamento de Zootecnia, Petrolina, Pernambuco, Brazil
| | - Andrey Pereira Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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106
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Pascual DW, Goodwin ZI, Bhagyaraj E, Hoffman C, Yang X. Activation of mucosal immunity as a novel therapeutic strategy for combating brucellosis. Front Microbiol 2022; 13:1018165. [PMID: 36620020 PMCID: PMC9814167 DOI: 10.3389/fmicb.2022.1018165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Brucellosis is a disease of livestock that is commonly asymptomatic until an abortion occurs. Disease in humans results from contact of infected livestock or consumption of contaminated milk or meat. Brucella zoonosis is primarily caused by one of three species that infect livestock, Bacillus abortus in cattle, B. melitensis in goats and sheep, and B. suis in pigs. To aid in disease prophylaxis, livestock vaccines are available, but are only 70% effective; hence, improved vaccines are needed to mitigate disease, particularly in countries where disease remains pervasive. The absence of knowing which proteins confer complete protection limits development of subunit vaccines. Instead, efforts are focused on developing new and improved live, attenuated Brucella vaccines, since these mimic attributes of wild-type Brucella, and stimulate host immune, particularly T helper 1-type responses, required for protection. In considering their development, the new mutants must address Brucella's defense mechanisms normally active to circumvent host immune detection. Vaccination approaches should also consider mode and route of delivery since disease transmission among livestock and humans is believed to occur via the naso-oropharyngeal tissues. By arming the host's mucosal immune defenses with resident memory T cells (TRMs) and by expanding the sources of IFN-γ, brucellae dissemination from the site of infection to systemic tissues can be prevented. In this review, points of discussion focus on understanding the various immune mechanisms involved in disease progression and which immune players are important in fighting disease.
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107
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Azospirillum Endophyticum sp. nov., an Endophyte of Paris Polyphylla Smith var. Yunnanensis. Curr Microbiol 2022; 80:34. [PMID: 36508041 DOI: 10.1007/s00284-022-03142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
A Gram-negative, facultative anaerobic bacterial strain, designated YIM B02556T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, southwest China. By using a polyphasic approach, its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02556T belonged to the genus Azospirillum and the 16S rRNA gene sequence similarity values of strain YIM B02556T to the type strains of members of this genus ranged from 94.9 to 98.3%. Overall genome relatedness index (OGRI) analysis estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between YIM B02556T and other Azospirillum species type strains were <90.8% and <37.8%, lower than the limit of species circumscription. Cells of the strain were characterized as oxidase- and catalase-positive, with motility provided by flagella. The growth conditions of the strain were found to occur at 20-40 °C (optimum, 35 °C), and pH 6.0-9.5 (optimum, pH 7.5). Strain YIM B02556T can tolerate 2% NaCl concentration. Strain YIM B02556T contained Q-10 as the major ubiquinone. The major fatty acids were C18:1 ω7c and summed feature three (C16:1 ω7c and/or C16:1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Based on polyphasic analysis, strain YIM B02556T could be differentiated genotypically and phenotypically from recognized species of the genus Azospirillum. Therefore, the isolate represents a novel species, for which the name Azospirillum endophyticum is proposed. The type strain is YIM B02556T (=JCM 34631T=CGMCC 1.18654T).
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108
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Spanka DT, Grützner J, Jäger A, Klug G. A Small RNA, UdsC, Interacts with the R poHII mRNA and Affects the Motility and Stress Resistance of Rhodobacter sphaeroides. Int J Mol Sci 2022; 23:ijms232415486. [PMID: 36555125 PMCID: PMC9779115 DOI: 10.3390/ijms232415486] [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: 10/26/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
sRNAs have an important role in the regulation of bacterial gene expression. The sRNA, UdsC, of Rhodobacter sphaeroides is derived from the 3' UTR of the RSP_7527 mRNA, which encodes a hypothetical protein. Here, we showed the effect of UdsC on the resistance of Rhodobacter sphaeroides to hydrogen peroxide and on its motility. In vitro binding assays supported the direct interaction of UdsC with the 5' UTR of the rpoHII mRNA. RpoHII is an alternative sigma factor with an important role in stress responses in R. sphaeroides, including its response to hydrogen peroxide. We also demonstrated that RpoHII controls the expression of the torF gene, which encodes an important regulator of motility genes. This strongly suggested that the observed effect of UdsC on TorF expression is indirect and mediated by RpoHII.
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109
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Göker M. Filling the gaps: missing taxon names at the ranks of class, order and family. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748602 DOI: 10.1099/ijsem.0.005638] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. However, it turned out that a number of names at the ranks of class, order and family are either not validly published or are validly published but illegitimate, although these names occur in the literature and are based on the type genus of a phylum with a validly published name. A closer examination of the literature for these and similar cases indicates that the names are unavailable under the ICNP either because of minor formal errors in the original descriptions, because another name should have been adopted for the taxon when the name was proposed, because of taxonomic uncertainties that were settled in the meantime, or because the names were placed on the list of rejected names. The purpose of this article is to fill the gaps by providing the missing formal descriptions and to ensure that the resulting taxon names are attributed to the original authors who did the taxonomic work.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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110
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Delgadillo-Ordoñez N, Raimundo I, Barno AR, Osman EO, Villela H, Bennett-Smith M, Voolstra CR, Benzoni F, Peixoto RS. Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review. Microorganisms 2022; 10:microorganisms10122340. [PMID: 36557593 PMCID: PMC9787610 DOI: 10.3390/microorganisms10122340] [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: 08/28/2022] [Revised: 10/12/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Inês Raimundo
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Adam R. Barno
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Eslam O. Osman
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Helena Villela
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Morgan Bennett-Smith
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Christian R. Voolstra
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Francesca Benzoni
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Raquel S. Peixoto
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Correspondence:
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111
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Sugo Y, Tamura H, Ishikita H. Electron Transfer Route between Quinones in Type-II Reaction Centers. J Phys Chem B 2022; 126:9549-9558. [PMID: 36374126 PMCID: PMC9707520 DOI: 10.1021/acs.jpcb.2c05713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/28/2022] [Indexed: 11/16/2022]
Abstract
In photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II (PSII), the photoinduced charge separation is terminated by an electron transfer between the primary (QA) and secondary (QB) quinones. Here, we investigate the electron transfer route, calculating the superexchange coupling (HQA-QB) for electron transfer from QA to QB in the protein environment. HQA-QB is significantly larger in PbRC than in PSII. In superexchange electron tunneling, the electron transfer via unoccupied molecular orbitals of the nonheme Fe complex (QA → Fe → QB) is pronounced in PbRC, whereas the electron transfer via occupied molecular orbitals (Fe → QB followed by QA → Fe) is pronounced in PSII. The significantly large HQA-QB is caused by a water molecule that donates the H-bond to the ligand Glu-M234 in PbRC. The corresponding water molecule is absent in PSII due to the existence of D1-Tyr246. HQA-QB increases in response to the Ser-L223···QB H-bond formation caused by an extension of the H-bond network, which facilitates charge delocalization over the QB site. This explains the observed discrepancy in the QA-to-QB electron transfer between PbRC and PSII, despite their structural similarity.
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Affiliation(s)
- Yu Sugo
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
| | - Hiroyuki Tamura
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
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112
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Anianabacter salinae gen. nov., sp. nov. ASV31T, a Facultative Alkaliphilic and Extremely Halotolerant Bacterium Isolated from Brine of a Millennial Continental Saltern. DIVERSITY 2022. [DOI: 10.3390/d14111009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
During a prokaryotic diversity study in Añana Salt Valley, a new Rhodobacteraceae member, designated ASV31T, was isolated from Santa Engracia spring water. It was extremely halotolerant, tolerating up to 23% NaCl, and facultatively alkaliphilic, growing at pH 6.5–9.5 (optimum at 7.0–9.5). The isolate was a Gram-negative, rod-shaped, aerobic and non-motile bacterium that formed beige-to-pink colonies on marine agar. According to a 16S rRNA gene-based phylogenetic analysis, strain ASV31T forms a distinct branch of the family Rhodobacteraceae, with Thioclava pacifica DSM 10166T being its closest type strain (95.3%). This was confirmed with a phylogenomic tree and the values of ANI (73.9%), dDDH (19.3%), AAI (63.5%) and POCP (56.0%), which were below the genus/species level boundary. Additionally, an ability to degrade aromatic compounds and biosynthesise secondary metabolites was suggested by the genome of strain ASV31T. Distinguishing fatty acid profiles and polar lipid content were also observed. The genome size was 3.6 Mbp, with a DNA G+C content of 65.7%. Based on the data obtained, it was considered that strain ASV31T (=CECT 30309T = LMG 32242T) represents a new species of a new genus in the family Rhodobacteraceae, for which the name Anianabacter salinae gen. nov., sp. nov. is proposed.
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113
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Behrendt U, Spanner T, Augustin J, Zak DH, Horn MA, Kolb S, Ulrich A. Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.). Microorganisms 2022; 10:microorganisms10112304. [PMID: 36422374 PMCID: PMC9697520 DOI: 10.3390/microorganisms10112304] [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: 10/11/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N2O) are gaining increasing attention in the development of strategies to control N2O emissions. Non-denitrifying N2O reducers are of particular interest because they can provide a real sink without contributing to N2O release. The bacterial strain under investigation (IGB 4-14T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N2O under anoxic conditions. However, consumption activity is considerably affected by the O2 level. The reduction of N2O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N2O consumption of strain IGB 4-14T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N2O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14T = LMG 29709T = DSM 103580T).
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Affiliation(s)
- Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
- Correspondence: (U.B.); (A.U.); Tel.: +49-33432-82460 (U.B.); +49-33432-82345 (A.U.)
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Jürgen Augustin
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Dominik H. Zak
- Institute for Ecoscience, Aarhus University, C.F. Møllersvej, Bygning 1331, 8000 Aarhus, Denmark
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Müggelseedamm 301, D-12587 Berlin, Germany
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Steffen Kolb
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
- Correspondence: (U.B.); (A.U.); Tel.: +49-33432-82460 (U.B.); +49-33432-82345 (A.U.)
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114
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Heo J, Sombolestani AS, Laureys D, De Clippeleer J, Won M, Vandamme P, Kwon SW. Acetobacter vaccinii sp. nov., a novel acetic acid bacterium isolated from blueberry fruit ( Vaccinium corymbosum L.). Int J Syst Evol Microbiol 2022; 72. [PMID: 36748597 DOI: 10.1099/ijsem.0.005614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Strain C17-3T was isolated from blueberry fruits collected from a farmland located in Damyang-gun, Jeollanam-do, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain C17-3T to the genus Acetobacter, where it occupied a rather isolated line of descent with Acetobacter ghanensis 430AT and Acetobacter lambici LMG 27439T as the nearest neighbours (98.9 % sequence similarity to both species). The highest average nucleotide identity and digital DNA-DNA hybridization values were 76.3 % and 21.7 % with Acetobacter garciniae TBRC 12339T; both values were well below the cutoff values for species delineation. Cells are strictly aerobic, Gram-stain-negative rods, catalase-positive and oxidase-negative. The DNA G+C content calculated from the genome sequence was 59.2 %. Major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C19 : 0cyclo ω8c. The major isoprenoid quinone was ubiquinone 9. On the basis of the results of phylogenetic analyses, phenotypic features and genomic comparisons, it is proposed that strain C17-3T represents a novel species of the genus Acetobacter and the name Acetobacter vaccinii sp. nov. is proposed. The type strain is C17-3T (= KACC 21233T = LMG 31758T).
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - David Laureys
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Jessika De Clippeleer
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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115
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Foligné B, Menetrey Q, Titécat M. Letter to the Editor: Focus on Zymomonas spp for the sake of clarity. Compr Rev Food Sci Food Saf 2022; 21:4507-4508. [PMID: 36349466 DOI: 10.1111/1541-4337.13078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Benoit Foligné
- Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Quentin Menetrey
- Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Marie Titécat
- Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
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116
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Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M. Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:977-988. [PMID: 35876747 DOI: 10.1094/mpmi-05-22-0116-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Omri M Finkel
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
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He W, Fan J, Ya T, Zhang M, Zhang T, Wang X. Response of microbial interactions in activated sludge to chlortetracycline. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120035. [PMID: 36030958 DOI: 10.1016/j.envpol.2022.120035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/30/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Chlortetracycline (CTC) has attracted increasing attention due to its potential environmental risks. However, its effects on bacterial communities and microbial interactions in activated sludge systems remain unclear. To verify these issues, a lab-scale sequencing batch reactor (SBR) exposed to different concentrations of CTC (0, 0.05, 0.5, 1 mg/L) was carried out for 106 days. The results showed that the removal efficiencies of COD, TN, and TP were negatively affected, and the system functions could gradually recover at low CTC concentrations (≤0.05 mg/L), but high CTC concentrations (≥0.5 mg/L) caused irreversible damage. CTC significantly altered bacterial diversity and the overall bacterial community structure, and stimulated the emergence of many taxa with antibiotic resistance. Molecular ecological network analysis showed that low concentrations of CTC increased network complexity and enhanced microbial interactions, while high concentrations of CTC had the opposite effect. Sub-networks analysis of dominant phyla (Bacteriodota, Proteobacteria, and Actionobacteriota) and dominant genera (Propioniciclava, a genus from the family Pleomorphomonadaceae and WCHB1-32) also showed the same pattern. In addition, keystone species identified by Z-P analysis had low relative abundance, but they were important in maintaining the stable performance of the system. In summary, low concentrations of CTC enhanced the complexity and stability of the activated sludge system. While high CTC concentrations destabilized the stability of the overall network and then caused effluent water quality deterioration. This study provides insights into our understanding of response in the bacteria community and their network interactions under tetracycline antibiotics in activated sludge system.
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Affiliation(s)
- Wenshan He
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingkai Fan
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Tao Ya
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Minglu Zhang
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China
| | - Tingting Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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118
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Endophytic Bosea spartocytisi sp. nov. Coexists with rhizobia in root nodules of Spartocytisus supranubius growing in soils of Teide National Park (Canary Islands). Syst Appl Microbiol 2022; 45:126374. [DOI: 10.1016/j.syapm.2022.126374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
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119
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Sun X, Lin D, Han Y, Sun J, Ye J, Chen B, Tang K. Roseovarius carneus sp. nov., a novel bacterium isolated from a coastal phytoplankton bloom in Xiamen. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
A Gram-stain-negative, non-motile, ovoid or short rod shaped and aerobic marine bacterium, designated as strain LXJ103T, was isolated from a coastal phytoplankton bloom in Xiamen, PR China. Cells were oxidase- and catalase-positive. Strain LXJ103T grew at 4–40 °C (optimum, 28–37 °C), at pH 6–10 (optimum, pH 8.5) and with 1–15 % (w/v) NaCl (optimum, 3 %). The major cellular fatty acids (>10 %) were iso-C18 : 1
ω7c/iso-C18 : 1
ω6c (70.2 %) and C16 : 0 (10.3 %). The following polar lipids were found to be present: phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and five unknown glycolipids. The predominant respiratory quinone was ubiquinone-10. Strain LXJ103T exhibited the highest 16S rRNA gene sequence similarity to
Roseovarius litorisediminis
D1-W8T (96.97 %). The phylogenetic trees based on 16S rRNA gene sequences showed that strain LXJ103T was a member of the genus
Roseovarius
. The draft genome size of strain LXJ103T is 3.05 Mb with a genomic G+C content of 61.22 mol%. The digital DNA–DNA genome hybridization value of strain LXJ103T compared with the most similar type strain
R. litorisediminis
CECT 8287T was 18.80 %. The average nucleotide identity value between strain LXJ103T and
R. litorisediminis
CECT 8287T was 72.60 %. On the basis of polyphasic data, strain LXJ103T represents a novel species of the genus
Roseovarius
, for which the name Roseovarius carneus sp. nov. is proposed. The type strain is LXJ103T (=CGMCC 1.19168T=MCCC 1K06527T=JCM 34778T).
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Affiliation(s)
- Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, PR China
| | - Dan Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, PR China
| | - Yu Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, PR China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, PR China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, PR China
| | - Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, PR China
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120
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Slobodkina G, Ratnikova N, Merkel A, Kevbrin V, Kuchierskaya A, Slobodkin A. Lithoautotrophic lifestyle of the widespread genus Roseovarius revealed by physiological and genomic characterization of Roseovarius autotrophicus sp. nov. FEMS Microbiol Ecol 2022; 98:6724241. [PMID: 36166357 DOI: 10.1093/femsec/fiac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/13/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
The genus Roseovarius, a member of the ecologically important Roseobacter-clade, is widespread throughout the world. A facultatively anaerobic lithoautotrophic bacterium (strain SHN287T), belonging to the genus Roseovarius, was isolated with molecular hydrogen as an electron donor and nitrate as an electron acceptor from a terrestrial mud volcano. Strain SHN287T possessed metabolic features not reported for Roseovarius such as chemolithoautotrophic growth with oxidation of molecular hydrogen or sulfur compounds, anaerobic growth and denitrification. Based on the phenotypic and phylogenetic characteristics, the new isolate is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius autotrophicus sp. nov. is proposed. The type strain is SHN287T (= KCTC 15916T = VKM B-3404T). An amended description of the genus Roseovarius is provided. Comparison of 46 Roseovarius genomes revealed that (i) a full set of genes for the Calvin-Benson cycle is present only in two strains: SHN287T and Roseovarius salinarum; (ii) respiratory H2-uptake [NiFe] hydrogenases are specific for a phylogenetically distinct group, including SHN287T-related strains; (iii) the Sox enzymatic complex is encoded in most of the studied genomes; and (iv) denitrification genes are widespread and randomly distributed among the genus. The metabolic characteristics found in R. autotrophicus sp. nov. expand the ecological role of the genus Roseovarius.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Nataliya Ratnikova
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Vadim Kevbrin
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | | | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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121
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Devosia litorisediminis sp. nov., isolated from a sand dune. Arch Microbiol 2022; 204:623. [DOI: 10.1007/s00203-022-03181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/03/2022] [Accepted: 01/19/2022] [Indexed: 11/02/2022]
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122
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Vasilyeva L, Grouzdev D, Koziaeva V, Berestovskaya Y, Novikov A, Pimenov N. Prosthecodimorpha staleyi gen. nov., sp. nov., Novel Prosthecate Bacteria within the Family Ancalomicrobiaceae and Reclassification of the Polyphyletic Genus Prosthecomicrobium. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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123
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Tian J, Xu L, Zhang X, Sun JQ. Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum. Int J Syst Evol Microbiol 2022; 72. [PMID: 36251750 DOI: 10.1099/ijsem.0.005521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
A 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing, Gram-stain-negative, strictly aerobic, non-motile, yellow-reddish, oval-shaped bacterial strain, designated M5D2P5T, was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, PR China. M5D2P5T grew at 10-40 °C (optimum 30-35 °C), pH 5.0-10.0 (optimum pH 8.0) and with 0-7% NaCl (optimum 3.0 %). The strain was positive for catalase and oxidase. The phylogenetic trees based on 16S rRNA gene sequences indicated that M5D2P5T clustered with Acuticoccus yangtzensis JL1095T, and shared 98.0, 97.3, 97.2, 96.9 and less than 96.9 % 16S rRNA gene similarities to A. yangtzensis JL1095T, Acuticoccus mangrovi B2012T, Acuticoccus sediminis PTG4-2T, Acuticoccus kandeliae J103T, and all the other type strains, respectively. However, the phylogenomic tree showed it clustered with A. kandeliae J103T. M5D2P5T contained Q-10 as the major respiratory quinone, as well as two minor respiratory quinones, Q-7 and Q-8. Its major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid, and four unidentified lipids. The genomic DNA G+C content was 66.5 %. The digital DNA-DNA hybridization score and the average nucleotide identity based on blast values of M5D2P5T to A. yangtzensis JL1095T, A. kandeliae J103T, A. mangrovi B2012T, and A. sediminis PTG4-2T, were 20.8, 23.7, 20.7, and 21.5 %, and 73.3, 79.5, 74.4, and 73.7 %, respectively. The phylogenetic and phenotypic characteristics allowed the discrimination of M5D2P5T from its phylogenetic relatives. The novel species Acuticoccus kalidii sp. nov. is therefore proposed, and the type strain is M5D2P5T (=CGMCC 1.19149T=KCTC 92132T).
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Affiliation(s)
- Jing Tian
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xu Zhang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
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Duhamel S, Hamilton CW, Pálsson S, Björnsdóttir SH. Microbial Response to Increased Temperatures Within a Lava-Induced Hydrothermal System in Iceland: An Analogue for the Habitability of Volcanic Terrains on Mars. ASTROBIOLOGY 2022; 22:1176-1198. [PMID: 35920884 DOI: 10.1089/ast.2021.0124] [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: 06/15/2023]
Abstract
Fossil hydrothermal systems on Mars are important exploration targets because they may have once been habitable and could still preserve evidence of microbial life. We investigated microbial communities within an active lava-induced hydrothermal system associated with the 2014-2015 eruption of Holuhraun in Iceland as a Mars analogue. In 2016, the microbial composition in the lava-heated water differed substantially from that of the glacial river and spring water sources that fed into the system. Several taxonomic and metabolic groups were confined to the water emerging from the lava and some showed the highest sequence similarities to subsurface ecosystems, including to the predicted thermophilic and deeply branching Candidatus Acetothermum autotrophicum. Measurements show that the communities were affected by temperature and other environmental factors. In particular, comparing glacial river water incubated in situ (5.7°C, control) with glacial water incubated within a lava-heated stream (17.5°C, warm) showed that microbial abundance, richness, and diversity increased in the warm treatment compared with the control, with the predicted major metabolism shifting from lithotrophy toward organotrophy and possibly phototrophy. In addition, thermophilic bacteria isolated from the lava-heated water and a nearby acidic hydrothermal system included the known endospore-formers Geobacillus stearothermophilus and Paenibacillus cisolokensis as well as a potentially novel taxon within the order Hyphomicrobiales. Similar lava-water interactions on Mars could therefore have generated habitable environments for microbial communities.
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Affiliation(s)
- Solange Duhamel
- Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
- Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | | | - Snæbjörn Pálsson
- Department of Biology, University of Iceland, Reykjavík, Iceland
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Fufina TY, Tretchikova OA, Khristin AM, Khatypov RA, Vasilieva LG. Properties of Mutant Photosynthetic Reaction Centers of Purple Non-Sulfur Bacteria Cereibacter sphaeroides with M206 Ile→Gln Substitution. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1149-1158. [PMID: 36273883 DOI: 10.1134/s000629792210008x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/14/2022] [Accepted: 08/14/2022] [Indexed: 06/16/2023]
Abstract
In the structure of photosynthetic reaction center (RC) of the purple bacterium Cereibacter sphaeroides the highly conserved amino acid residue Ile-M206 is located near the bacteriochlorophyll dimer P, which is the primary electron donor, and the monomeric bacteriochlorophyll BA, which is the nearest electron acceptor. Since Ile-M206 is close to the C2-acetyl group of bacteriochlorophyll PB, the hydroxyl group of Tyr-M210, and to the C9-keto group of bacteriochlorophyll BA, as well as to the water molecule near the latter group, this site can be used for introducing mutations in order to study mechanisms of primary photochemical processes in the RC. Previously it was shown that the Ile→Glu substitution at the M204 position (analog of M206 in the RC of C. sphaeroides) in the RC of the closely related purple non-sulfur bacterium Rhodobacter capsulatus significantly affected kinetics of the P+HA- state formation, whereas the M204 Ile→Gln substitution led to the loss of BChl BA molecule from the complex structure. In the present work, it is shown that the single I(M206)Q or double I(M206)Q + F(M208)A amino acid substitutions in the RC of C. sphaeroides do not change the pigment composition and do not markedly influence redox potential of the primary electron donor. However, substitution of Ile M206 by Gln affected positions and amplitudes of the absorption bands of bacteriochlorophylls, increased lifetime of the primary electron donor P* excited state from 3.1 ps to 22 ps, and decreased quantum yield of the P+QA- state formation to 60%. These data suggest significant changes in the pigment-protein interactions in the vicinity of the primary electron donor P and the nearest electron acceptor BA. A considerable decrease was also noticed in the resistance of the mutant RC to thermal denaturation, which was more pronounced in the RC with the double substitution I(M206)Q + F(M208)A. This was likely associated with the disruption of the dense packing of the protein near bacteriochlorophylls PB and BA. Possible reasons for different effects of identical mutations on the properties of two highly homologous RCs from closely related purple non-sulfur bacteria are discussed.
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Affiliation(s)
- Tatiana Yu Fufina
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Olga A Tretchikova
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Anton M Khristin
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ravil A Khatypov
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Lyudmila G Vasilieva
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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126
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Timsy T, Behrendt U, Ulrich A, Foesel BU, Spanner T, Neumann-Schaal M, Wolf J, Schloter M, Horn MA, Kolb S. Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36861375 DOI: 10.1099/ijsem.0.005581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.
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Affiliation(s)
- Timsy Timsy
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Bärbel U Foesel
- Research Unit Molecular Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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127
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Hu Z, Chen Y, Lai Q, Yu Z, Shao Z, Dong C. Zavarzinia marina sp. nov., a novel hydrocarbon-degrading bacterium isolated from deep chlorophyll maximum layer seawater of the West Pacific Ocean and emended description of the genus Zavarzinia. Int J Syst Evol Microbiol 2022; 72. [PMID: 36251753 DOI: 10.1099/ijsem.0.005527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
A Gram-stain-negative, motile, non-spore-forming, strictly aerobic and rod-shaped bacterial strain, Adcm-6AT, was isolated from a seawater sample collected from the deep chlorophyll maximum layer in the West Pacific Ocean. Strain Adcm-6AT grew at 20-37 °C (optimum, 28-32 °C), at pH 6-11 (pH 7) and in the presence of 0-6 % (1-2 %) NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it belonged to the genus Zavarzinia and had 97.7 and 96.9 % sequence similarity to Zavarzinia compransoris DSM 1231T and Zavarzinia aquatilis JCM 32263T, respectively. Digital DNA-DNA hybridization and average nucleotide identity values between strain Adcm-6AT and the two type strains were 22.2-22.9 % and 79.7-80.4 %, respectively. The principal fatty acids were C19:0 cyclo ω8c, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and C16:0. The predominant respiratory quinone was Q-10. The polar lipids were diphosphatidylglycerol, two phosphatidylethanolamines, two phosphatidyglycerols and an unidentified lipid. The genomic DNA G+C content of strain Adcm-6AT was 67.7 %. Based on phylogenetic analysis and genomic-based relatedness indices, as well as phenotypic and genotypic characteristics, strain Adcm-6AT represents a novel species within the genus Zavarzinia, for which the name Zavarzinia marina sp. nov. is proposed. The type strain is Adcm-6AT (=MCCC M24951T=KCTC 82849T).
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Affiliation(s)
- Ziyan Hu
- College of Life Sciences, Hunan Normal University, Changsha 410081, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yongqing Chen
- College of Life Sciences, Hunan Normal University, Changsha 410081, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Ziquan Yu
- College of Life Sciences, Hunan Normal University, Changsha 410081, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
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128
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Díaz Rodríguez CA, Díaz-García L, Bunk B, Spröer C, Herrera K, Tarazona NA, Rodriguez-R LM, Overmann J, Jiménez DJ. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation. ISME COMMUNICATIONS 2022; 2:89. [PMID: 37938754 PMCID: PMC9723784 DOI: 10.1038/s43705-022-00176-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2023]
Abstract
The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.
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Affiliation(s)
- Carlos Andrés Díaz Rodríguez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, Sheffield, UK
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katherine Herrera
- Department of Civil and Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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129
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Sandhu M, Paul AT, Proćków J, de la Lastra JMP, Jha PN. PCB-77 biodegradation potential of biosurfactant producing bacterial isolates recovered from contaminated soil. Front Microbiol 2022; 13:952374. [PMID: 36225351 PMCID: PMC9549355 DOI: 10.3389/fmicb.2022.952374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants widely distributed in the environment and possess deleterious health effects. The main objective of the study was to obtain bacterial isolates from PCB-contaminated soil for enhanced biodegradation of PCB-77. Selective enrichment resulted in the isolation of 33 strains of PCB-contaminated soil nearby Bhilai steel plant, Chhattisgarh, India. Based on the prominent growth using biphenyl as the sole carbon source and the confirmation of its degradation by GC-MS/MS analysis, four isolates were selected for further study. The isolates identified by 16S rRNA gene sequencing were Pseudomonas aeruginosa MAPB-2, Pseudomonas plecoglossicida MAPB-6, Brucella anthropi MAPB-9, and Priestia megaterium MAPB-27. The isolate MAPB-9 showed a degradation of 66.15% biphenyl, while MAPB-2, MAPB-6, and MAPB-27 showed a degradation of 62.06, 57.02, and 56.55%, respectively in 48 h. Additionally, the degradation ability of these strains was enhanced with addition of co-metabolite glucose (0.2%) in the culture medium. Addition of glucose showed 100% degradation of biphenyl by MAPB-9, in 48 h, while MAPB-6, MAPB-2, and MAPB-27 showed 97.1, 67.5, and 53.3% degradation, respectively as analyzed by GC-MS/MS. Furthermore, in the presence of inducer, PCB-77 was found to be 59.89, 30.49, 27.19, and 4.43% degraded by MAPB-6, MAPB-9, MAPB-2, and MAPB-27, respectively in 7 d. The production of biosurfactants that aid in biodegradation process were observed in all the isolates. This was confirmed by ATR-FTIR analysis that showed the presence of major functional groups (CH2, CH3, CH, = CH2, C–O–C, C-O) of the biosurfactant. The biosurfactants were further identified by HPTLC and GC-MS/MS analysis. Present study is the first to report PCB-77 degradation potential of Pseudomonas aeruginosa, B. anthropi, Pseudomonas plecoglossicida, and Priestia megaterium. Similarly, this is the first report on Pseudomonas plecoglossicida and Priestia megaterium for PCB biodegradation. Our results suggest that the above isolates can be used for the biodegradation of biphenyl and PCB-77 in PCB-contaminated soil.
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Affiliation(s)
- Monika Sandhu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Atish T. Paul
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - José Manuel Pérez de la Lastra
- Biotecnología de Macromoléculas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
- José Manuel Pérez de la Lastra,
| | - Prabhat N. Jha
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
- *Correspondence: Prabhat N. Jha,
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130
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Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
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Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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131
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Lopez Marin MA, Suman J, Jani K, Ulbrich P, Cajthaml T, Pajer P, Wolf J, Neumann-Schaal M, Strejcek M, Uhlik O. Pedomonas mirosovicensis gen. nov., sp. nov., a bacterium isolated from soil with the aid of Micrococcus luteus culture supernatant containing resuscitation-promoting factor. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An orange-golden iridescent culture, designated A1X5R2T, was isolated from a compost soil suspension which was amended with
Micrococcus luteus
NCTC 2665T culture supernatant. The cells were non-motile, Gram-stain-negative, 0.4–0.5 µm wide and 0.7–1.4 µm long. The 16S rRNA-based phylogenetic and whole-genome analyses revealed that strain A1X5R2T forms a distinct lineage within the family
Sphingosinicellaceae
and is closely related to members of the genus
Sphingoaurantiacus
(
S. capsulatus
, 93.04 % similarity, and
S. polygranulatus
, 92.77 %). The organism grew at 22–47 °C (optimal at 37 °C), salinity <3 % (optimal at 1.5 %) and at pH 7. The major respiratory quinone was ubiquinone-10, but a small quantity of ubiquinone-9 was also detected The major polyamine was homospermidine, but a small quantity of putrescine was also detected. The strain contained C18 : 1ω7c, C16 : 0, C16 : 1 ω7c and C18 : 0 as the major fatty acids. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, sphingoglycolipid, diphosphatidylglycerol, two unidentified phospholipids and three unidentified amino lipids. The DNA G+C content was 64.9 mol%. According to the results of phylogenetic and phylogenomic analyses, as well as its physiological characteristics, strain A2X5R2T represents the type species of a novel genus within the family
Sphingosinicellaceae
. The name Pedomonas mirosovicensis gen. nov., sp. nov. is proposed, with the type strain being A1X5R2T (=NCCB 100839T=DSM 112829T).
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Affiliation(s)
- Marco A. Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Pavel Ulbrich
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02, Prague, Czech Republic
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7 B, 38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7 B, 38124, Braunschweig, Germany
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
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132
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Goldberg SR, Haltli BA, Correa H, Kerr RG. Pseudovibrio flavus sp. nov. isolated from the sea sponge Verongula gigantea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, rod-shaped marine bacterium, designated RKSG542T, was isolated from the sea sponge Verongula gigantea collected at a depth of 20 m off the west coast of San Salvador, The Bahamas. Phylogenetic analyses based on 16S rRNA gene and genome sequences place RKSG542T in a monophyletic clade with members of the genus
Pseudovibrio
. Strain RKSG542T shared <96.7 % 16S rRNA gene sequence similarity,<72.2 % average nucleotide identity,<66.7 % average amino acid identity, and <24.8 % digital DNA–DNA hybridization with type strains of the family
Stappiaceae
. Growth occurred at 22–37 °C (22–30 °C optimum), at pH 7–9 (pH 7 optimum), and with 0.5–5 % (w/v) NaCl (2 % optimum). The predominant fatty acids (>10 %) were summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c), C18 : 0 and C16 : 0, and the respiratory lipoquinone was Q-10. The polar lipid composition comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unknown aminolipids, six unknown phospholipids and four unknown lipids. The DNA G+C content of the genome sequence was 52.5 mol%. Based on the results of biochemical, phylogenetic and genomic analyses, RKSG542T (=TSD-76T=LMG 29867T) is presented here as the type strain of a novel species within the genus
Pseudovibrio
(family
Stappiaceae
, order
Hyphomicrobiales
, class
Alphaproteobacteria
), for which the name Pseudovibrio flavus sp. nov. is proposed.
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Affiliation(s)
- Stacey R. Goldberg
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Brad A. Haltli
- Nautilus Biosciences Croda, Duffy Research Centre, Charlottetown, Prince Edward Island, Canada
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Hebelin Correa
- Nautilus Biosciences Croda, Duffy Research Centre, Charlottetown, Prince Edward Island, Canada
| | - Russell G. Kerr
- Nautilus Biosciences Croda, Duffy Research Centre, Charlottetown, Prince Edward Island, Canada
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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133
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Maszenan AM, Bessarab I, Williams RBH, Petrovski S, Seviour RJ. The phylogeny, ecology and ecophysiology of the glycogen accumulating organism (GAO) Defluviicoccus in wastewater treatment plants. WATER RESEARCH 2022; 221:118729. [PMID: 35714465 DOI: 10.1016/j.watres.2022.118729] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/22/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
This comprehensive review looks critically what is known about members of the genus Defluviicoccus, an example of a glycogen accumulating organism (GAO), in wastewater treatment plants, but found also in other habitats. It considers the operating conditions thought to affect its performance in activated sludge plants designed to remove phosphorus microbiologically, including the still controversial view that it competes with the polyphosphate accumulating bacterium Ca. Accumulibacter for readily biodegradable substrates in the anaerobic zone receiving the influent raw sewage. It looks at its present phylogeny and what is known about it's physiology and biochemistry under the highly selective conditions of these plants, where the biomass is recycled continuously through alternative anaerobic (feed); aerobic (famine) conditions encountered there. The impact of whole genome sequence data, which have revealed considerable intra- and interclade genotypic diversity, on our understanding of its in situ behaviour is also addressed. Particular attention is paid to the problems in much of the literature data based on clone library and next generation DNA sequencing data, where Defluviicoccus identification is restricted to genus level only. Equally problematic, in many publications no attempt has been made to distinguish between Defluviicoccus and the other known GAO, especially Ca. Competibacter, which, as shown here, has a very different ecophysiology. The impact this has had and continues to have on our understanding of members of this genus is discussed, as is the present controversy over its taxonomy. It also suggests where research should be directed to answer some of the important research questions raised in this review.
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Affiliation(s)
- Abdul M Maszenan
- E2S2, NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 117456, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 117456, Singapore
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, 3086 Victoria, Australia
| | - Robert J Seviour
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, 3086 Victoria, Australia.
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dos Santos Ferreira N, Coniglio A, Puente M, Sant’Anna FH, Maroniche G, García J, Molina R, Nievas S, Volpiano CG, Ambrosini A, Passaglia LMP, Pedraza RO, Reis VM, Zilli JÉ, Cassan F. Genome-based reclassification of Azospirillum brasilense Az39 as the type strain of Azospirillum argentinense sp. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain Az39T of
Azospirillum
is a diazotrophic plant growth-promoting bacterium isolated in 1982 from the roots of wheat plants growing in Marcos Juárez, Córdoba, Argentina. It produces indole-3-acetic acid in the presence of l-tryptophan as a precursor, grows at 20–38 °C (optimal 38 °C), and the cells are curved or spiral-shaped, with diameters ranging from 0.5–0.9 to 1.8–2.2 µm. They contain C16 : 0, C18 : 0 and C18 : 1
ω7c/ω6c as the main fatty acids. Phylogenetic analysis of its 16S rRNA gene sequence confirmed that this strain belongs to the genus
Azospirillum
, showing a close relationship with
Azospirillum baldaniorum
Sp245T,
Azospirillum brasilense
Sp7T and
Azospirillum formosense
CC-Nfb-7T. Housekeeping gene analysis revealed that Az39T, together with five strains of the genus (Az19, REC3, BR 11975, MTCC4035 and MTCC4036), form a cluster apart from
A. baldaniorum
Sp245T,
A. brasilense
Sp7T and
A. formosense
CC-Nfb-7T. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between Az39T and the aforementioned type strains revealed values below 96 %, the circumscription limit for the species delineation (ANI: 95.3, 94.1 and 94.0 %; dDDH: 62.9, 56.3 and 55.6 %). Furthermore, a phylogeny evaluation of the core proteome, including 809 common shared proteins, showed an independent grouping of Az39T, Az19, REC3, BR 11975, MTCC4035 and MTCC4036. The G+C content in the genomic DNA of these six strains varied from 68.3 to 68.5 %. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we consider that strain Az39T, along with strains Az19, REC3, BR 11975, MTCC4035 and MTCC4036, are members of a new
Azospirillum
species, for which the name Azospirillum argentinense sp. nov. is proposed. The type strain is Az39T (=LBPCV39T=BR 148428T=CCCT 22.01T).
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Affiliation(s)
- Natália dos Santos Ferreira
- Programa de Pós-Graduação em Agronomia-Ciência do Solo, Universidade Federal Rural do Rio de Janeiro, BR 465 Km 7, 23890-000 Seropédica, Rio de Janeiro, Brazil
| | - Anahí Coniglio
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Mariana Puente
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, Nicolás Repetto y de los Reseros, Hurlingham 1686, Buenos Aires, Argentina
| | | | - Guillermo Maroniche
- Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Mar del Plata, km 73.5, km 73.5, 20 B7620, Buenos Aires, Argentina
| | - Julia García
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, Nicolás Repetto y de los Reseros, Hurlingham 1686, Buenos Aires, Argentina
| | - Romina Molina
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Sofia Nievas
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Camila Gazolla Volpiano
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil
| | - Adriana Ambrosini
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil
| | - Luciane M. P. Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil
| | - Raul O. Pedraza
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, Av. Kirchner 1900. (4000) 24 San Miguel de Tucumán, Tucumán, Argentina
| | | | - Jerri Édson Zilli
- Embrapa Agrobiologia, BR 465 Km 7, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | - Fabricio Cassan
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
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Leducq JB, Sneddon D, Santos M, Condrain-Morel D, Bourret G, Cecilia Martinez-Gomez N, Lee JA, Foster JA, Stolyar S, Jesse Shapiro B, Kembel SW, Sullivan JM, Marx CJ. Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity. Genome Biol Evol 2022; 14:6652236. [PMID: 35906926 PMCID: PMC9364378 DOI: 10.1093/gbe/evac123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer. We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.
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Affiliation(s)
- Jean-Baptiste Leducq
- Université Laval - Quebec City (QC) Canada.,University of Idaho - Moscow (ID) US
| | | | | | | | | | | | | | | | | | - B Jesse Shapiro
- Université de Montréal - Montreal (QC) Canada.,McGill University - Montreal (QC) Canada
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136
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Morrow KM, Pankey MS, Lesser MP. Community structure of coral microbiomes is dependent on host morphology. MICROBIOME 2022; 10:113. [PMID: 35902906 PMCID: PMC9331152 DOI: 10.1186/s40168-022-01308-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. RESULTS The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. CONCLUSIONS The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.
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Affiliation(s)
- Kathleen M Morrow
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
- Present address: Thomas Jefferson High School for Science and Technology, 6560 Braddock Rd, Alexandria, VA, 22312, USA
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Michael P Lesser
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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137
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Du J, Liu Y, Pei T, Li A, Zhu H. Ruegeria alba sp. nov., Isolated from a Tidal Flat Sediment. Curr Microbiol 2022; 79:267. [PMID: 35881206 DOI: 10.1007/s00284-022-02968-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
A novel Gram-staining-negative, aerobic, rod-shaped, and white-colored bacterium designated as 1NDH52CT was isolated from a tidal flat sediment and its taxonomic position was determined using a polyphasic taxonomic approach. The microorganism was found to grow at 10-37 °C, pH 6.0-9.0, and in the presence of 0-2% (w/v) NaCl, and to hydrolyze gelatin and aesculin. The major cellular fatty acid of strain 1NDH52CT was summed feature 8 (C19:1 ω7c and/or C18:1 ω6c); the polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, and a lipid; the respiratory quinone was ubiquinone-10. The 16S rRNA gene-based phylogenetic analysis showed that strain 1NDH52CT was closely related to members of the genus Ruegeria with the identity of 98.2% to the type strain Ruegeria pomeroyi DSM 15711T. The genome DNA G + C content of strain 1NDH52CT was 63.6%. The phylogenomic analysis indicated that strain 1NDH52CT formed an independent branch distinct from reference type strains of species within this genus. Digital DNA-DNA hybridization and average nucleotide identity values between strain 1NDH52CT and reference strains were, respectively, 19.1-41.5% and 78.3-91.3%, which are far below the thresholds of 70% and 95-96% for species definition, respectively, indicating that strain 1NDH52CT represents a novel genospecies of the genus Ruegeria. Based on phenotypic and genotypic data, strain 1NDH52CT is concluded to represent a novel species of the genus Ruegeria, for which the name Ruegeria alba sp. nov., is proposed. The type strain of the species is 1NDH52CT (= GDMCC 1.2382T = KCTC 82664T).
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Affiliation(s)
- Juan Du
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Tao Pei
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Anzhang Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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138
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Comparative Analysis of Brucepastera parasyntrophica gen. nov., sp. nov. and Teretinema zuelzerae gen. nov., comb. nov. ( Treponemataceae) Reveals the Importance of Interspecies Hydrogen Transfer in the Energy Metabolism of Spirochetes. Appl Environ Microbiol 2022; 88:e0050322. [PMID: 35862663 PMCID: PMC9317865 DOI: 10.1128/aem.00503-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Most members of the family Treponemataceae (Spirochaetales) are associated with vertebrate hosts. However, a diverse clade of uncultured, putatively free-living treponemes comprising several genus-level lineages is present in other anoxic environments. The only cultivated representative to date is Treponema zuelzerae, isolated from freshwater mud. Here, we describe the isolation of strain RmG11 from the intestinal tract of cockroaches. The strain represents a novel genus-level lineage of Treponemataceae and is metabolically distinct from T. zuelzerae. While T. zuelzerae grows well on various sugars, forming acetate and H2 as major fermentation products, strain RmG11 grew poorly on glucose, maltose, and starch, forming mainly ethanol and only small amounts of acetate and H2. In contrast to the growth of T. zuelzerae, that of strain RmG11 was strongly inhibited at high H2 partial pressures but improved considerably when H2 was removed from the headspace. Cocultures of strain RmG11 with the H2-consuming Methanospirillum hungatei produced acetate and methane but no ethanol. Comparative genomic analysis revealed that strain RmG11 possesses only a single, electron-confurcating hydrogenase that forms H2 from NADH and reduced ferredoxin, whereas T. zuelzerae also possesses a second, ferredoxin-dependent hydrogenase that allows the thermodynamically more favorable formation of H2 from ferredoxin via the Rnf complex. In addition, we found that T. zuelzerae utilizes xylan and possesses the genomic potential to degrade other plant polysaccharides. Based on phenotypic and phylogenomic evidence, we describe strain RmG11 as Brucepastera parasyntrophica gen. nov., sp. nov. and Treponema zuelzerae as Teretinema zuelzerae gen. nov., comb. nov. IMPORTANCE Spirochetes are widely distributed in various anoxic environments and commonly form molecular hydrogen as a major fermentation product. Here, we show that two closely related members of the family Treponemataceae differ strongly in their sensitivity to high hydrogen partial pressure, and we explain the metabolic mechanisms that cause these differences by comparative genome analysis. We demonstrate a strong boost in the growth of the hydrogen-sensitive strain and a shift in its fermentation products to acetate during cocultivation with a H2-utilizing methanogen. Our results add a hitherto unrecognized facet to the fermentative metabolism of spirochetes and also underscore the importance of interspecies hydrogen transfer in not-obligately-syntrophic interactions among fermentative and hydrogenotrophic guilds in anoxic environments.
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139
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Core Genome Multilocus Sequence Typing Scheme for Improved Characterization and Epidemiological Surveillance of Pathogenic Brucella. J Clin Microbiol 2022; 60:e0031122. [PMID: 35852343 PMCID: PMC9387271 DOI: 10.1128/jcm.00311-22] [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] [Indexed: 11/30/2022] Open
Abstract
Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of Brucella strains. Core genome multilocus sequence typing (cgMLST) is a powerful genotyping system commonly used to delineate pathogen transmission routes for disease surveillance and control. Except for Brucella melitensis, cgMLST schemes for Brucella species are currently not established. Here, we describe a novel cgMLST scheme that covers multiple Brucella species. We first determined the phylogenetic breadth of the genus using 612 Brucella genomes. We selected 1,764 genes that were particularly well conserved and typeable in at least 98% of these genomes. We tested the new scheme on 600 genomes and found high agreement with the whole-genome-based single nucleotide polymorphism (SNP) analysis. Next, we applied the scheme to reanalyze the genome of Brucella strains from epidemiologically linked outbreaks. We demonstrated the applicability of the new scheme for high-resolution typing required in outbreak investigations as previously reported with whole-genome SNP methods. We also used the novel scheme to define the global population structure of the genus using 1,322 Brucella genomes. Finally, we demonstrated the possibility of tracing distribution of Brucella strains by performing cluster analysis of cgMLST profiles and found nearly identical cgMLST profiles in different countries. Our results show that sequencing depth of more than 40-fold is optimal for allele calling with this scheme. In summary, this study describes a novel Brucella-wide cgMLST scheme that is applicable in Brucella molecular epidemiology and helps in accurately tracking and thus controlling the sources of infection. The scheme is publicly accessible and should represent a valuable resource for laboratories with limited computational resources and bioinformatics expertise.
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Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles 2022; 26:24. [PMID: 35829965 PMCID: PMC9279279 DOI: 10.1007/s00792-022-01271-2] [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: 09/01/2021] [Accepted: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
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Mendoza-Hoffmann F, Zarco-Zavala M, Ortega R, Celis-Sandoval H, Torres-Larios A, García-Trejo JJ. Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF 1 Subunits of the F 1F O-ATPase as Related to the Endosymbiotic Origin of Mitochondria. Microorganisms 2022; 10:microorganisms10071372. [PMID: 35889091 PMCID: PMC9317440 DOI: 10.3390/microorganisms10071372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/03/2022] [Accepted: 07/03/2022] [Indexed: 12/10/2022] Open
Abstract
The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1FO-ATPase activity, several different inhibitory proteins or domains in bacteria (ε and ζ subunits), mitochondria (IF1), and chloroplasts (ε and γ disulfide) emerged to block the F1FO-ATPase activity selectively. In this study, we analyze how these F1FO-ATPase inhibitory proteins have evolved. The phylogeny of the α-proteobacterial ε showed that it diverged in its C-terminal side, thus losing both the inhibitory function and the ATP-binding/sensor motif that controls this inhibition. The losses of inhibitory function and the ATP-binding site correlate with an evolutionary divergence of non-inhibitory α-proteobacterial ε and mitochondrial δ subunits from inhibitory bacterial and chloroplastidic ε subunits. Here, we confirm the lack of inhibitory function of wild-type and C-terminal truncated ε subunits of P. denitrificans. Taken together, the data show that ζ evolved to replace ε as the primary inhibitor of the F1FO-ATPase of free-living α-proteobacteria. However, the ζ inhibitory function was also partially lost in some symbiotic α-proteobacteria and totally lost in some strictly parasitic α-proteobacteria such as the Rickettsiales order. Finally, we found that ζ and IF1 likely evolved independently via convergent evolution before and after the endosymbiotic origin mitochondria, respectively. This led us to propose the ε and ζ subunits as tracer genes of the pre-endosymbiont that evolved into the actual mitochondria.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California (UABC)—Campus Tijuana, Tijuana C.P. 22390, Baja California, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
| | - Mariel Zarco-Zavala
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Alfredo Torres-Larios
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
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142
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Neoroseomonas marina sp. nov., Isolated from a Beach Sand. Curr Microbiol 2022; 79:233. [PMID: 35767156 DOI: 10.1007/s00284-022-02917-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/25/2022] [Indexed: 11/03/2022]
Abstract
A pink-pigmented bacterium (strain JC162T = KCTC 32190T) was isolated from a beach sand sample. Cells were Gram-stain-negative, coccoid, non-motile, and strictly aerobic. EzBioCloud BLAST search of 16S rRNA gene sequence showed that strain KCTC 32190T had the highest sequence identity to the members of the genus Neoroseomonas and was closely related to N. oryzicola YC6724T (99.8%), N. sediminicola FW-3T (98.5%), N. soli 5N26T (98.2%), and other members of the genus Neoroseomonas (< 97.9%) in the family Acetobacteriaceae within the class of Alphaproteobacteria. Chemo-organoheterotrophy was the only growth mode and growth was possible on a wide range of organic substrates. Strain KCTC 32190T was positive for catalase and oxidase. Fatty acid composition of strain KCTC 32190T includes (in decreasing %) C18:1ω7c, cyclo-C19:0ω8c, C18:02-OH, C16:0, C18:03-OH, C16:1ω7c/C16:1ω6c, C16:02-OH and C16:1ω5c. Polar lipids comprised of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, and three unidentified lipids. The genomic DNA G+C content of the strain KCTC 32190T was 70.9 mol%. Strain KCTC 32190T has a low ANI value of < 92.7% and genome reassociation (based on digital DNA-DNA hybridization) value of < 48.8% with the nearest type strains. The genome relatedness is supported by other polyphasic taxonomic data to propose strain KCTC 32190T as a new species in the genus Neoroseomonas with the name Neoroseomonas marina sp. nov. The type strain is strain JC162T (KCTC 32190T = CGMCC1.12364T).
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143
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Zhang X, Feng GD, Zhen X, Zhang Y, Deng X, Zhu H, Yao Q. Microvirga terricola sp. nov. and Microvirga solisilvae sp. nov, isolated from forest soil. Arch Microbiol 2022; 204:423. [PMID: 35750895 DOI: 10.1007/s00203-022-02963-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/10/2022] [Indexed: 12/01/2022]
Abstract
Two Gram-staining-negative, aerobic and rod-shaped strains, designated c23x22T and sex2T, were isolated from forest soil collected from Chebaling National Nature Reserve in Guangdong Province and Limu Mountain National Forest Park in Hainan Province, P. R. China, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that they belonged to the genus Microvirga, and strain c23 x22T was most closely related to 'Microvirga alba' KCTC 72385, while strain sex2T showed close relationship with Microvirga guangxiensis CGMCC 1.7666T. The average nucleotide identity and digital DNA-DNA hybridization values between strains c23 x22T and sex2T and their close relatives, 'M. alba' KCTC 72385 and M. guangxiensis CGMCC 1.7666T, were all below the threshold values for species delimitation. The predominant quinones of the two novel strains were ubiquinone 10, and the major fatty acids contained C19:0 cyclo ω8c and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Their predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The phenotypic, genotypic and chemotaxonomic analyses clearly supported that strains c23 x 22T and sex2T represent two novel species of the genus Microvirga, for which the name Microvirga terricola sp. nov. (type strain c23 x 22T = GDMCC 1.1700T = KCTC 62432T) and Microvirga solisilvae sp. nov. (type strain sex2T = GDMCC 1.1651T = KACC 21311T) are proposed, respectively.
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Affiliation(s)
- Xianjiao Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.,Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Guang-Da Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Xiangling Zhen
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Yulian Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Xiaoqin Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Kuzmanović N, Biondi E, Overmann J, Puławska J, Verbarg S, Smalla K, Lassalle F. Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis). BMC Genomics 2022; 23:462. [PMID: 35733110 PMCID: PMC9219206 DOI: 10.1186/s12864-022-08662-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/17/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverse All. vitis strains to get insights into their diversification and taxonomy. RESULTS Pairwise genome comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description of All. vitis, which now refers to a restricted group of strains within the All. vitis species complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species, All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the current type strain of All. vitis, K309T. The type strain of All. ampelinum sp. nov. is S4T. We also identified sets of gene clusters specific to the All. vitis species complex, All. vitis sensu stricto and All. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate. All. vitis species complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly, All. vitis sensu stricto-specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid. All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification, All. vitis sensu stricto and All. ampelinum were clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated that Allorhizobium is clearly separated from other genera of the family Rhizobiaceae. CONCLUSIONS Comparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy of Allorhizobium vitis species complex, supporting our redefinition of All. vitis sensu stricto and description of All. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
- Present address, Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Messeweg 11-12, 38104, Braunschweig, Germany.
| | - Enrico Biondi
- Department of Agricultural and Food Sciences (DISTAL), Plant Pathology, Alma Mater Studiorum-University of Bologna, Viale G. Fanin, 42, 40127, Bologna, Italy
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
| | - Joanna Puławska
- The National Institute of Horticultural Research, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | - Susanne Verbarg
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Florent Lassalle
- Department of Infectious Disease Epidemiology, Imperial College London, St-Mary's Hospital Campus, Praed Street, London, W2 1NY, UK.
- Imperial College London, St-Mary's Hospital Campus, MRC Centre for Global Infectious Disease Analysis, Praed Street, London, W2 1NY, UK.
- Wellcome Sanger Institute, Pathogens and Microbes Programme, Wellcome Genome Campus, Saffron Walden, Hinxton, CB10 1RQ, UK.
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145
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Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species.
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Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
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146
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Charoenyingcharoen P, Yukphan P, Malimas S, Likhitrattanapisal S, Tanasupawat S, Yamada Y. Neokomagataea anthophila sp. nov., an osmotolerant acetic acid bacterium isolated in Thailand and emended description of the genus Neokomagataea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, non-motile, aerobic bacterium isolated from a sea bean flower [Canavalia rosea (Sw.) DC.] collected in Surat Thani Province, Thailand, and designated as AH18T was characterized on the basis of polyphasic taxonomy. The phylogenetic analysis of 16S rRNA gene revealed that strain AH18T represented a member of the genus
Neokomagataea
. In the 16S rRNA gene sequence analysis, the strain's closest phylogenetic neighbour was
Neokomagataea thailandica
TBRC 376T. The draft genome size of strain AH18T was 2613495 bp, and its DNA G+C content was 52.0 mol%. The strain showed 90.3 and 76.3% pairwise-determined whole-genome average nucleotide identity and 39.8 and 19.6% digital DNA–DNA hybridization values with
N. thailandica
TBRC 376T and
N. tanensis
TBRC 7768T, respectively. The 16S rRNA gene sequences and phylogenomic analysis revealed that the strain clustered with the members of the genus
Neokomagataea
but was located in a distinct branch closely related to
N. thailandica
TBRC 376T. The predominant cellular fatty acids of the strain were summed feature 8 (C18:1
ω6c and/or C18:1
ω7c), C16:0 and C18:1 2OH (>5%). The major respiratory ubiquinone was Q-10. In addition, strain AH18T was substantiated by differences in several physiological characteristics and by MALDI-TOF profiling. On the basis of the results obtained from phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the strain clearly represented a novel species within the genus
Neokomagataea
, for which the name Neokomagataea anthophila sp. nov. (AH18T=TBRC 2177T=NBRC 115156T) is proposed. An emended description of the genus
Neokomagataea
is also given.
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Affiliation(s)
- Piyanat Charoenyingcharoen
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Pattaraporn Yukphan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Sukunphat Malimas
- Sukhunphat Malimas Microbiology Laboratory Biosafety level I, 52 M.9 Nongphua, Muangsuang, Roi-Et, 45220, Thailand
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Somsak Likhitrattanapisal
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Yuzo Yamada
- Laboratory of Applied Microbiology (Professor Emeritus), Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
- Japan International Cooperation Agency (JICA Senior Overseas Volunteer), Shibuya-ku, Tokyo 151-8558, Japan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
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Lakey BD, Myers KS, Alberge F, Mettert EL, Kiley PJ, Noguera DR, Donohue TJ. The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis. PLoS Genet 2022; 18:e1010270. [PMID: 35767559 PMCID: PMC9275681 DOI: 10.1371/journal.pgen.1010270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/12/2022] [Accepted: 05/20/2022] [Indexed: 12/13/2022] Open
Abstract
Bacterial two-component systems (TCSs) often function through the detection of an extracytoplasmic stimulus and the transduction of a signal by a transmembrane sensory histidine kinase. This kinase then initiates a series of reversible phosphorylation modifications to regulate the activity of a cognate, cytoplasmic response regulator as a transcription factor. Several TCSs have been implicated in the regulation of cell cycle dynamics, cell envelope integrity, or cell wall development in Escherichia coli and other well-studied Gram-negative model organisms. However, many α-proteobacteria lack homologs to these regulators, so an understanding of how α-proteobacteria orchestrate extracytoplasmic events is lacking. In this work we identify an essential TCS, CenKR (Cell envelope Kinase and Regulator), in the α-proteobacterium Rhodobacter sphaeroides and show that modulation of its activity results in major morphological changes. Using genetic and biochemical approaches, we dissect the requirements for the phosphotransfer event between CenK and CenR, use this information to manipulate the activity of this TCS in vivo, and identify genes that are directly and indirectly controlled by CenKR in Rb. sphaeroides. Combining ChIP-seq and RNA-seq, we show that the CenKR TCS plays a direct role in maintenance of the cell envelope, regulates the expression of subunits of the Tol-Pal outer membrane division complex, and indirectly modulates the expression of peptidoglycan biosynthetic genes. CenKR represents the first TCS reported to directly control the expression of Tol-Pal machinery genes in Gram-negative bacteria, and we predict that homologs of this TCS serve a similar function in other closely related organisms. We propose that Rb. sphaeroides genes of unknown function that are directly regulated by CenKR play unknown roles in cell envelope biosynthesis, assembly, and/or remodeling in this and other α-proteobacteria. The bacterial cell envelope is home to an array of important functions including energy conservation, motility, influx/efflux of nutrients and toxins, modulation of cell morphology and division, cell-cell interaction, and biofilm formation. Consequently, it is a major target of antibiotics and antimicrobial agents that inhibit these essential processes. Key to the recognition of environmental stressors or stimuli are bacterial TCSs, however systems that monitor or directly regulate cell envelope assembly and homeostasis are not widely conserved amongst bacteria. Here, we use Rhodobacter sphaeroides as a model to investigate the function of the CenKR TCS in this and other α-proteobacteria. We show that this essential TCS plays a key role in maintenance of the cell envelope through the regulation of outer membrane integrity and division, cell wall remodeling and homeostasis, and an alternate sigma factor that controls global cellular stress response. We provide evidence that this TCS and its function is widely conserved in α-proteobacteria and identify genes of unknown function as candidates for the study of cell envelope assembly in this and related bacteria.
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Affiliation(s)
- Bryan D. Lakey
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin S. Myers
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - François Alberge
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erin L. Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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148
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He X, Lu H, Hu W, Deng T, Gong X, Yang X, Song D, He M, Xu M. Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus
Novosphingobium
. The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of
Novosphingobium
species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1
ω7c, C18 : 0, C16 : 1
ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of
Novosphingobium
, for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.
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Affiliation(s)
- Xiaoling He
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, PR China
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Huibin Lu
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Wenzhe Hu
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Tongchu Deng
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Xiaofan Gong
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Xunan Yang
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Da Song
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Mei He
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, PR China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, PR China
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149
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Genetic Characterization of the Ibuprofen-Degradative Pathway of Rhizorhabdus wittichii MPO218. Appl Environ Microbiol 2022; 88:e0038822. [PMID: 35604231 PMCID: PMC9195938 DOI: 10.1128/aem.00388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ibuprofen is one of the most common drugs found as a contaminant in soils, sediments, and waters. Although several microorganisms able to metabolize ibuprofen have been described, the metabolic pathways and factors limiting biodegradation in nature remain poorly characterized. Among the bacteria able to grow on ibuprofen, three different strains belonging to Sphingomonadaceae and isolated from different geographical locations carry the same set of genes required for the upper part of the ibuprofen metabolic pathway. Here, we have studied the metabolic pathway of Rhizorhabdus wittichii MPO218, identifying new genes required for the lower part of the ibuprofen metabolic pathway. We have identified two new DNA regions in MPO218 involved in the metabolism of ibuprofen. One is located on the MPO218 chromosome and appears to be required for the metabolism of propionyl-CoA through the methylmalonyl-CoA pathway. Although involved in ibuprofen metabolism, this region is not strictly necessary for growing using ibuprofen. The second region belongs to the pIBU218 plasmid and comprises two gene clusters containing aromatic compound biodegradation genes, part of which are necessary for ibuprofen degradation. We have identified two genes required for the first two steps of the lower part of the ibuprofen metabolic pathway (ipfL and ipfM), and, based on our results, we propose the putative complete pathway for ibuprofen metabolism in strain MPO218. IMPORTANCE Ibuprofen, one of the most common pharmaceutical contaminants in natural environments, is toxic for some aquatic and terrestrial organisms. The main source of environmental ibuprofen is wastewater, so improving wastewater treatment is of relevant importance. Although several microorganisms capable of biodegrading ibuprofen have been described, the metabolic pathways and their genetic bases remain poorly understood. Three bacterial strains of the family Sphingomonadaceae capable of using ibuprofen as carbon and energy source have been described. Although the genes involved in the upper part of the degradation pathway (ipfABDEF cluster) have been identified, those required for the lower part of the pathway remained unknown. Here, we have confirmed the requirement of the ipf cluster for the generation of isobutyl catechol and have identified the genes involved in the subsequent transformation of the metabolic products. Identification of genes involved in ibuprofen degradation is essential to developing improved strains for the removal of this contaminant.
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150
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Jung GY, Nam IH, Kim SJ. Undibacter mobilis gen. nov., sp. nov. isolated from an artificial wetland in Okcheon, Korea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005369] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain GY_HT was isolated from an artificial wetland in Okcheon, Chungcheongbuk-do Province, Republic of Korea. Strain GY_HT was closely related to
Pseudolabrys taiwanensis
CC-BB4T based on 16S rRNA gene sequences (94.7 % similarity) and clustered within the family
Nitrobacteraceae
. Cells of the isolate were Gram-stain-negative, catalase-negative and oxidase-positive, and colonies were white or pale transparent. A flagellum was observed, and the isolate could respire both aerobically and anaerobically. Growth of GY_ HT was observed in the following conditions: 10–45 °C, pH 5–11 and 0–4 % NaCl. The optimal conditions for growth were 25 °C, pH 6.5–7.5 and 0.5–1.5 % NaCl. The major fatty acids were C19 : 0 cyclo ω8c (35.8 %) and summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c; 27.4 %). The major quinone was found to be ubiquinone-10. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The G+C content of the genome of GY_HT was 63.3 mol%. Based on its phylogenomic, physiological and biochemical attributes, strain GY_HT represents a novel species of a novel genus of the family
Nitrobacteraceae
. We propose the name as Undibacter mobilis gen. nov., sp. nov. The type strain is GY_HT (=KCTC 62792T=JCM 32856T).
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Affiliation(s)
- Gi-Yong Jung
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
- Mineral Resources Division, Korea Institute of Geoscience and Mineral resources, Daejeon 34132, Republic of Korea
| | - In-Hyun Nam
- Mineral Resources Division, Korea Institute of Geoscience and Mineral resources, Daejeon 34132, Republic of Korea
| | - So-Jeong Kim
- Mineral Resources Division, Korea Institute of Geoscience and Mineral resources, Daejeon 34132, Republic of Korea
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