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Osburn MR, Selensky MJ, Beddows PA, Jacobson A, DeFranco K, Merediz-Alonso G. Microbial biogeography of the eastern Yucatán carbonate aquifer. Appl Environ Microbiol 2023; 89:e0168223. [PMID: 37916826 PMCID: PMC10701671 DOI: 10.1128/aem.01682-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The extensive Yucatán carbonate aquifer, located primarily in southeastern Mexico, is pockmarked by numerous sinkholes (cenotes) that lead to a complex web of underwater caves. The aquifer hosts a diverse yet understudied microbiome throughout its highly stratified water column, which is marked by a meteoric lens floating on intruding seawater owing to the coastal proximity and high permeability of the Yucatán carbonate platform. Here, we present a biogeographic survey of bacterial and archaeal communities from the eastern Yucatán aquifer. We apply a novel network analysis software that models ecological niche space from microbial taxonomic abundance data. Our analysis reveals that the aquifer community is composed of several distinct niches that follow broader regional and hydrological patterns. This work lays the groundwork for future investigations to characterize the biogeochemical potential of the entire aquifer with other systems biology approaches.
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Affiliation(s)
- Magdalena R. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Matthew J. Selensky
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Patricia A. Beddows
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Andrew Jacobson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Karyn DeFranco
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Gonzalo Merediz-Alonso
- Amigos de Sian Ka'an, and Consejo de Cuenca de la Península de Yucatán, Cancún, Quintana Roo, Mexico
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Kujur RRA, Ghosh M, Basak S, Das SK. Phylogeny and structural insights of lipase from Halopseudomonas maritima sp. nov., isolated from sea sand. Int Microbiol 2023; 26:1021-1031. [PMID: 37076723 DOI: 10.1007/s10123-023-00362-0] [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: 01/07/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
A Gram-negative, aerobic bacterial strain RR6T was isolated from the sea sand to produce lipase and proposed as a novel species of Halopseudomonas. The optimum growth occurred at 28-37 °C, and the pH was 6.0-8.0. The optimum growth occurred at 3.0 -6.5% (w/v) NaCl. The major cellular fatty acids were C10:0 3OH, C12:0, C16:1 ω7c/16:1 ω6c, 18:1 ω7c and/or 18:1 ω6c, and C16:0. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid, and unidentified lipids. The genome is 3.93 Mb, and the G + C content is 61.3%. The 16S rRNA gene sequences shared 99.73-99.87% sequence similarity with the closely related type strains of Halopseudomonas. The average nucleotide identity and average amino acid identity of strain RR6T with reference type strains were below 95-96%, and the corresponding in-silico DNA-DNA hybridization values were below 70%. Strain RR6T clustered with Halopseudomonas gallaeciensis V113T and Halopseudomonas pachastrellae CCUG 46540 T in the phylogenetic tree. Further, lipase produced by this bacterium belongs to α/β hydrolase lipase family and exhibits structural similarity to the lactonizing lipase. Based on the polyphasic analysis, the new isolates RR6T represent a novel species of Halopseudomonas for which Halopseudomonas maritima sp. nov. is proposed. The type strain is RR6T (= NBRC 115418 T = TBRC 15628 T).
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Affiliation(s)
- Ritu Rani Archana Kujur
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar, 751023, India
- Regional Center of Biotechnology, NCR Biotech Science Cluster, 3Rd Milestone, Faridabad, Haryana (NCR Delhi), India
| | - Manisha Ghosh
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700 010, India
| | - Surajit Basak
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700 010, India
| | - Subrata K Das
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar, 751023, India.
- Regional Center of Biotechnology, NCR Biotech Science Cluster, 3Rd Milestone, Faridabad, Haryana (NCR Delhi), India.
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3
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Rafieyan S, Amoozegar MA, Makzum S, Salimi-Ashtiani M, Nikou MM, Ventosa A, Sanchez-Porro C. Marinobacter iranensis sp. nov., a slightly halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2023; 73. [PMID: 37889849 DOI: 10.1099/ijsem.0.006083] [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: 10/29/2023] Open
Abstract
A novel halophilic bacterium, strain 71-iT, was isolated from Inche-Broun hypersaline lake in Golestan province, in the north of Iran. It was a Gram-stain-negative, non-endospore forming, rod-shaped bacterium. It grew at 4-40 °C (optimum 30 °C), pH 6.0-11.0 (optimum pH 7.5) and with 0.5-15 % (w/v) NaCl [optimum 3 % (w/v) NaCl]. The results of phylogenetic analyses based on the 16S rRNA gene sequence comparison indicated its affiliation to the genus Marinobacter and the low percentage of identity with the most closely related species (97.5 %), indicated its placement as a novel species within this genus. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) analyses of this strain against closely related species confirmed its condition of novel taxon. On the other hand, the percentage of the average amino acid identity (AAI) affiliated strain 71-iT within the genus Marinobacter. The DNA G+C content of this isolate was 57.7 mol%. The major fatty acids were C16 : 0 and C16 : 1ω7c and/or C16 : 1 ω6c. Ubiquinone-9 was the major isoprenoid quinone and diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) were the main polar lipids of this strain. On the basis of the phylogenomic and phenotypic (including chemotaxonomic) features, we propose strain 71-iT (= IBRC M 11023T = CECT 30160T = LMG 29252T) as the type strain of a novel species within the genus Marinobacter, with the name Marinobacter iranensis sp. nov. Genomic detections of this strain in various metagenomic databases indicate that it is a relatively abundant species in environments with low salinities (approximately 5 % salinity), but not in hypersaline habitats with high salt concentrations.
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Affiliation(s)
- Shokufeh Rafieyan
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran-Iran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Somaye Makzum
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran-Iran, Tehran, Iran
| | - Mahsa Salimi-Ashtiani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran-Iran, Tehran, Iran
| | - Mahdi Moshtaghi Nikou
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran-Iran, Tehran, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sanchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142622. [PMID: 36719221 PMCID: PMC9945501 DOI: 10.1128/jcm.01426-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.
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Kijewska A, Koroza A, Grudlewska-Buda K, Kijewski T, Wiktorczyk-Kapischke N, Zorena K, Skowron K. Molluscs-A ticking microbial bomb. Front Microbiol 2023; 13:1061223. [PMID: 36699600 PMCID: PMC9868776 DOI: 10.3389/fmicb.2022.1061223] [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: 10/04/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Bivalve shellfish consumption (ark shells, clams, cockles, and oysters) has increased over the last decades. Following this trend, infectious disease outbreaks associated with their consumption have been reported more frequently. Molluscs are a diverse group of organisms found wild and farmed. They are common on our tables, but unfortunately, despite their great taste, they can also pose a threat as a potential vector for numerous species of pathogenic microorganisms. Clams, in particular, might be filled with pathogens because of their filter-feeding diet. This specific way of feeding favors the accumulation of excessive amounts of pathogenic microorganisms like Vibrio spp., including Vibrio cholerae and V. parahaemolyticus, Pseudomonas aeruginosa, Escherichia coli, Arcobacter spp., and fecal coliforms, and intestinal enterococci. The problems of pathogen dissemination and disease outbreaks caused by exogenous bacteria in many geographical regions quickly became an unwanted effect of globalized food supply chains, global climate change, and natural pathogen transmission dynamics. Moreover, some pathogens like Shewanella spp., with high zoonotic potential, are spreading worldwide along with food transport. These bacteria, contained in food, are also responsible for the potential transmission of antibiotic-resistance genes to species belonging to the human microbiota. Finally, they end up in wastewater, thus colonizing new areas, which enables them to introduce new antibiotic-resistance genes (ARG) into the environment and extend the existing spectrum of ARGs already present in local biomes. Foodborne pathogens require modern methods of detection. Similarly, detecting ARGs is necessary to prevent resistance dissemination in new environments, thus preventing future outbreaks, which could threaten associated consumers and workers in the food processing industry.
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Affiliation(s)
- Agnieszka Kijewska
- Department of Immunobiology and Environmental Microbiology, Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Koroza
- Department of Climate and Ocean Research and Education Laboratory, Institute of Oceanology Polish Academy of Science, Sopot, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland
| | - Tomasz Kijewski
- Department of Climate and Ocean Research and Education Laboratory, Institute of Oceanology Polish Academy of Science, Sopot, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland
| | - Katarzyna Zorena
- Department of Immunobiology and Environmental Microbiology, Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland,*Correspondence: Krzysztof Skowron,
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Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules. Mar Drugs 2022; 20:md20100617. [DOI: 10.3390/md20100617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.
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Rudra B, Gupta RS. Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 2021; 71. [PMID: 34546867 DOI: 10.1099/ijsem.0.005011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas. Within this large cluster 18-30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae. This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans. Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas, which has priority over the name Oblitimonas. We are also proposing transfer of the deep-branching Pseudomonas hussainii, for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas, respectively. In addition, we are also reclassifying 'Pseudomonas acidophila' as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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8
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Saati-Santamaría Z, Peral-Aranega E, Velázquez E, Rivas R, García-Fraile P. Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera. BIOLOGY 2021; 10:782. [PMID: 34440014 PMCID: PMC8389581 DOI: 10.3390/biology10080782] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022]
Abstract
Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
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Pang Y, Zhang Y, Chen M, Lu W, Chen M, Yan Y, Lin M, Zhang W, Zhou Z. Pseudomonas nanhaiensis sp. nov., a lipase-producing bacterium isolated from deep-sea sediment of the South China Sea. Antonie van Leeuwenhoek 2021; 114:1791-1804. [PMID: 34392431 DOI: 10.1007/s10482-021-01639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/05/2021] [Indexed: 11/28/2022]
Abstract
A bacterial lipase producing bacterium, designated SCS 2-3, was isolated from deep-sea sediment of the South China Sea. Phylogenetic analysis based on the 16S rRNA sequence revealed that strain SCS2-3 belonged to the genus Pseudomonas and had 98.56% similarity to P. xinjiangensis NRRL B-51270T as the closest relative strain. MLSA using four protein-coding genes (dnaK, gyrA, recA, and rpoB) showed strain SCS 2-3 to form a separate branch. ANI and in silico DDH values between strain SCS 2-3 and related type strains of Pseudomonas were less than 81.51% and 23.80%, respectively. Genome comparison showed that strain SCS 2-3 shared 1875 core gene families with other eight closely related type strains in Pseudomonas, and the number of strain-unique genes was 263. Through gene annotations, genes related to lipase were found in the genome. Furthermore, a combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SCS 2-3 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nanhaiensis sp. nov. is proposed. The type strain is SCS 2-3T (= GDMCC 1.2219T = JCM 34440T).
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Affiliation(s)
- Yu Pang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yage Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mengru Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Hongxia M, Jingfeng F, Jiwen L, Zhiyi W, Yantao W, Dongwei L, Mengfei L, Tingting S, Yuan J, Huiling H, Jixue S. Full-length 16S rRNA gene sequencing reveals spatiotemporal dynamics of bacterial community in a heavily polluted estuary, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116567. [PMID: 33578312 DOI: 10.1016/j.envpol.2021.116567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Understanding the bacterial community structure of the river estuary could provide insights into the resident microorganisms in response to environmental pollution. In this study, the bacterial community structure of Liaohe Estuary was investigated using single-molecule real-time sequencing (SMRT). A total of 57 samples were collected and grouped according to habitat, space, season, and lifestyle. In seawater, regardless of whether it is particle-attached (PA) or free-living (FL) bacteria, the area with higher alpha diversity is the nearshore area in the dry season, while it is the midstream area in the wet season. The bacterial communities in sediment and seawater samples were different at the genus level in the nearshore area, and habitat type was the main factor. A marked difference in the bacterial community was observed in the dry season between different lifestyles but not in the wet season, which resulted from lifestyle transitions of bacterioplankton. Bacterial community varied spatially but not seasonally in sediment samples. In seawater, both FL and PA bacterial communities varied spatially during the wet season. Seasonal differences were only observed in FL bacterial community. Zn and sand were the principal determining factors of the bacterial community in the sediment, Cu and salinity were the main environmental factors for FL bacteria, and Cu, salinity, Zn and temperature were the main environmental factors for PA bacteria. Besides, the tide and nutrients were also the main drivers of the bacterial community in seawater. The indicative taxa, related to Cyanobium_PCC-6307, Pseudomonas and Vibrio, further evidenced the presence of possible bloom, crude oil and pathogen contamination. Overall, our results can contribute to the knowledge of the bacterial community and anthropogenic impacts on the Liaohe Estuary.
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Affiliation(s)
- Ming Hongxia
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Fan Jingfeng
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China.
| | - Liu Jiwen
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wan Zhiyi
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Wang Yantao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Ocean University, Dalian, 116023, China
| | - Li Dongwei
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Maritime University, Dalian, 116026, China
| | - Li Mengfei
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Ocean University, Dalian, 116023, China
| | - Shi Tingting
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jin Yuan
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Huang Huiling
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Ocean University, Dalian, 116023, China
| | - Song Jixue
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
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11
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Li J, Wang LH, Xiang FG, Ding WL, Xi LJ, Wang MQ, Xiao ZJ, Liu JG. Pseudomonas phragmitis sp. nov., isolated from petroleum polluted river sediment. Int J Syst Evol Microbiol 2020; 70:364-372. [PMID: 31661054 DOI: 10.1099/ijsem.0.003763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium, motile by means of a single polar flagellum, designated S-6-2T, was isolated from petroleum polluted river sediment in Huangdao, Shandong Province, PR China. The 16S rRNA gene sequence analysis revealed that S-6-2T represented a member of the genus Pseudomonas, sharing the highest sequence similarities with Pseudomonas parafulva (97.5 %) and Pseudomonas fulva (97.5 %). Phylogenetic analysis based on 16S rRNA gene, concatenated 16S rRNA, gyrB, rpoB and rpoD genes and genome core-genes indicated that S-6-2T was affiliated with the members of the Pseudomonas pertucinogena group. The average nucleotide identity (ANI) and genome-to-genome distance between the whole genome sequences of S-6-2T and closely related species of the genus Pseudomonas within the P. pertucinogena group were less than 77.94 % and 20.5 %, respectively. Differences in phenotypic characteristics were also found between S-6-2T and the closely related species. The major cellular fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ C18 : 1ω6c), C16 : 0, C17 : 0cyclo and C12 : 0. The predominant respiratory quinone was ubiquinone 9. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified lipid (L1), two unidentified phospholipids (PL1 and PL2) and an aminophospholipid (APL). The DNA G+C content of the genome of S-6-2T was 60.1 mol%. On the basis of the evidence from the polyphasic taxonomic study, strain S-6-2T can be classified as representative of a novel species of the genus Pseudomonas, for which the name Pseudomonas phragmitis sp. nov. is proposed. The type strain is S-6-2T (=CGMCC 1.15798T=KCTC 52539T).
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Affiliation(s)
- Jing Li
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Lin-Hui Wang
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Fan-Gqin Xiang
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Wen-Long Ding
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Li-Jun Xi
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Ming-Qing Wang
- Shandong Peanut Research Institute, Qingdao 266100, PR China.,State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Zi-Jun Xiao
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Jian-Guo Liu
- State Key Laboratory of Heavy Oil Processing & Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
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12
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Bollinger A, Thies S, Katzke N, Jaeger K. The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena. Microb Biotechnol 2020; 13:19-31. [PMID: 29943398 PMCID: PMC6922532 DOI: 10.1111/1751-7915.13288] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 01/20/2023] Open
Abstract
Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.
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Affiliation(s)
- Alexander Bollinger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Nadine Katzke
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum Jülich GmbHD‐52425JülichGermany
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13
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Wang MQ, Wang Z, Yu LN, Zhang CS, Bi J, Sun J. Pseudomonas qingdaonensis sp. nov., an aflatoxin-degrading bacterium, isolated from peanut rhizospheric soil. Arch Microbiol 2019; 201:673-678. [DOI: 10.1007/s00203-019-01636-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/18/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
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14
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Wei Y, Mao H, Xu Y, Zou W, Fang J, Blom J. Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:2462-2467. [DOI: 10.1099/ijsem.0.002785] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuli Wei
- 2National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
- 3The Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Haiyan Mao
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yunping Xu
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Wencai Zou
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- 4Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
- 5Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Jochen Blom
- 6Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
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15
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Mulet M, Sánchez D, Rodríguez AC, Nogales B, Bosch R, Busquets A, Gomila M, Lalucat J, García-Valdés E. Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 2018; 41:340-347. [DOI: 10.1016/j.syapm.2018.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
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16
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Draft Genome Sequence of Pseudomonas oceani DSM 100277 T, a Deep-Sea Bacterium. GENOME ANNOUNCEMENTS 2018; 6:6/15/e00254-18. [PMID: 29650573 PMCID: PMC5897802 DOI: 10.1128/genomea.00254-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas oceani DSM 100277T was isolated from deep seawater in the Okinawa Trough at 1390 m. P. oceani belongs to the Pseudomonas pertucinogena group. Here, we report the draft genome sequence of P. oceani, which has an estimated size of 4.1 Mb and exhibits 3,790 coding sequences, with a G+C content of 59.94 mol%.
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Suzuki M, Tachibana Y, Oba K, Takizawa R, Kasuya KI. Microbial degradation of poly(ε-caprolactone) in a coastal environment. Polym Degrad Stab 2018. [DOI: 10.1016/j.polymdegradstab.2018.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Anwar N, Rozahon M, Zayadan B, Mamtimin H, Abdurahman M, Kurban M, Abdurusul M, Mamtimin T, Abdukerim M, Rahman E. Pseudomonas tarimensis sp. nov., an endophytic bacteria isolated from Populus euphratica. Int J Syst Evol Microbiol 2017; 67:4372-4378. [DOI: 10.1099/ijsem.0.002295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nusratgul Anwar
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Manziram Rozahon
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Bolatkhan Zayadan
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Hormathan Mamtimin
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Mehfuzem Abdurahman
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Marygul Kurban
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Mihribangul Abdurusul
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Tursunay Mamtimin
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Muhtar Abdukerim
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Erkin Rahman
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
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19
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A rapid and simple method for identifying bacterial polar lipid components in wet biomass. J Microbiol 2017; 55:635-639. [DOI: 10.1007/s12275-017-7092-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/17/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
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20
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González-Rocha G, Muñoz-Cartes G, Canales-Aguirre CB, Lima CA, Domínguez-Yévenes M, Bello-Toledo H, Hernández CE. Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective. PLoS One 2017. [PMID: 28632790 PMCID: PMC5478107 DOI: 10.1371/journal.pone.0179390] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.
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Affiliation(s)
- Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Gabriel Muñoz-Cartes
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Cristian B. Canales-Aguirre
- Laboratorio de Ecología Evolutiva y Filoinformática. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue 6 km, Puerto Montt, Chile
| | - Celia A. Lima
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Mariana Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Cristián E. Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- * E-mail:
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Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540 T, a Deep-Sea Bacterium. GENOME ANNOUNCEMENTS 2017; 5:5/14/e00136-17. [PMID: 28385850 PMCID: PMC5383898 DOI: 10.1128/genomea.00136-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas pachastrellae strain CCUG 46540T (KMM 330T) was isolated from a deep-sea sponge specimen collected in the Philippine Sea at a depth of 750 m. The draft genome has an estimated size of 4.0 Mb, exhibits a G+C content of 61.2 mol%, and is predicted to encode 3,592 proteins, including pathways for the degradation of aromatic compounds.
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Wang MQ, Sun L. Pseudomonas oceani sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:4250-4255. [PMID: 27468709 DOI: 10.1099/ijsem.0.001343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we identified a novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, strain KX 20T, isolated from the deep seawater in Okinawa Trough, northwestern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KX 20T was related to members of the genus Pseudomonas and shares the highest sequence identities with Pseudomonas aestusnigri CECT 8317T (99.4 %) and Pseudomonas pachastrellae JCM 12285T (98.5 %). The 16S rRNA gene sequence identities between strain KX 20T and other members of the genus Pseudomonaswere below 96.6 %. The gyrB and rpoD genes of strain KX 20T shared 82.0 to 89.3 % sequence identity with the gyrB and rpoD genes of the closest phylogenetic neighbours of KX 20T. The predominant cellular fatty acids of strain KX 20T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (29.2 %), C16 : 0 (24.5 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (21.5 %) and C12 : 0 (8.2 %). The major polar lipids of strain KX 20T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids. The genomic DNA G+C content of strain KX 20T was 62.9 mol%. On the basis of phylogenetic analysis and phenotypic characteristics, a novel species, Pseudomonas oceani sp. nov. is proposed. The type strain is KX 20T (=CGMCC 1.15195T=DSM 100277T).
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Affiliation(s)
- Ming-Qing Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.,Function Laboratory for Marine Biology and Biotechnology, Qingdao National Oceanography Laboratory, Qingdao, PR China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.,Function Laboratory for Marine Biology and Biotechnology, Qingdao National Oceanography Laboratory, Qingdao, PR China
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Chang DH, Rhee MS, Kim JS, Lee Y, Park MY, Kim H, Lee SG, Kim BC. Pseudomonas kribbensis sp. nov., isolated from garden soils in Daejeon, Korea. Antonie van Leeuwenhoek 2016; 109:1433-1446. [PMID: 27460204 DOI: 10.1007/s10482-016-0743-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
Two bacterial strains, 46-1 and 46-2T, were isolated from garden soil. These strains were observed to be aerobic, Gram-stain negative, rod-shaped, non-spore-forming, motile and catalase and oxidase positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains shared 100 % sequence similarity with each other and belong to the genus Pseudomonas in the class Gammaproteobacteria. The concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences further confirmed that the isolates belong to the Pseudomonas koreensis subgroup (SG), with P. koreensis Ps 9-14T, Pseudomonas moraviensis 1B4T and Pseudomonas granadensis F-278,770T as their close relatives (>96 % pairwise similarity). DNA-DNA hybridization with the closely related type strain P. koreensis SG revealed a low level of relatedness (<50 %). A cladogram constructed using whole-cell matrix-assisted laser desorption/ionization time-of-flight (WC-MALDI-TOF) MS analysis showed the isolates formed a completely separate monophyletic group. The isolates were negative for utilization of glycogen, D-psicose, α-keto butyric acid, α-keto valeric acid, succinamic acid and D, L-α-glycerol phosphate. In contrast, all these reactions were positive in P. koreensis JCM 14769T and P. moraviensis DSM 16007T. The fatty acid C17:0 cyclo was detected as one of the major cellular fatty acids (>15 %) in the isolates but it was a minor component (<4 %) in both reference type strains. In contrast, the fatty acid, C12:0 was not observed in the isolates but was present in both reference strains. Based on differences such as phylogenetic position, low-level DNA-DNA hybridization, WC-MALDI-TOF MS analysis, fluorescence pigmentation, fatty acid profiles, and substrate utilization, we propose that the isolates 46-1 and 46-2T represent a novel species of the genus Pseudomonas, for which the name Pseudomonas kribbensis sp. nov. is proposed; the type strain is 46-2T (=KCTC 32541T = DSM 100278T).
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Affiliation(s)
- Dong-Ho Chang
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Moon-Soo Rhee
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ji-Sun Kim
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yookyung Lee
- National Institute of Animal Science, 1500 Kongjwipatjwi-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-Do, 55365, Republic of Korea
| | - Mi Young Park
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea. .,University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Byoung-Chan Kim
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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Das S, Ganeriwal S, Mangwani N, Patel B. Survival and expression of DNA repair genes in marine bacteria Pseudomonas pseudoalcaligenes NP103 and P. aeruginosa N6P6 in response to environmental stressors. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715050057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Carrascosa C, Millán R, Jaber JR, Lupiola P, del Rosario-Quintana C, Mauricio C, Sanjuán E. Blue pigment in fresh cheese produced by Pseudomonas fluorescens. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.12.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Romanenko LA, Tanaka N, Svetashev VI, Mikhailov VV. Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity. Arch Microbiol 2015; 197:693-9. [PMID: 25787010 DOI: 10.1007/s00203-015-1103-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/26/2015] [Accepted: 03/10/2015] [Indexed: 11/30/2022]
Abstract
An aerobic, Gram-negative, motile, rod-shaped bacterium designated KMM 9500(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis affiliated strain KMM 9500(T) to the genus Pseudomonas as a distinct subline clustered with Pseudomonas marincola KMM 3042(T) and Pseudomonas segetis KCTC 12331(T) sharing the highest similarities of 98 and 97.9 %, respectively. Strain KMM 9500(T) was characterized by mainly possessing ubiquinone Q-9, and by the predominance of C18:1 ω7c, C16:1 ω7c, and C16:0 followed by C12:0 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, and unknown phospholipids. Strain KMM 9500(T) was found to inhibit growth of Gram-negative and Gram-positive indicatory microorganisms. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain 9500(T) is concluded to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas glareae sp. nov. is proposed. The type strain of the species is strain KMM 9500(T) (=NRIC 0939(T)).
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Affiliation(s)
- Lyudmila A Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok, 690022, Russia,
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27
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Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, Matsui M. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater. BMC Microbiol 2014; 14:318. [PMID: 25539583 PMCID: PMC4326521 DOI: 10.1186/s12866-014-0318-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host. Results A total of 76 putative phaC PCR fragments were amplified from the whole genome amplified seawater DNA. Of these 55 clones contained conserved PhaC domains and were classified into 20 genetic groups depending on their sequence similarity. Eleven genetic groups have undisclosed PhaC activity based on their distinct phylogenetic lineages from known PHA producers. Three complete DNA coding sequences were determined by IAN-PCR, and one PhaC was able to produce poly(3-hydroxybutyrate) in recombinant Cupriavidus necator PHBˉ4 (PHB-negative mutant). Conclusions A new functional PhaC that has close identity to Marinobacter sp. was discovered in this study. Phylogenetic classification for all the phaC genes isolated from uncultured bacteria has revealed that seawater and other environmental resources harbor a great diversity of PhaCs with activities that have not yet been investigated. Functional evaluation of these in silico-based PhaCs via genome walking has provided new insights into the polymerizing ability of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0318-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Choon Pin Foong
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Nyok-Sean Lau
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Shigeru Deguchi
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Takashi Toyofuku
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Todd D Taylor
- Laboratory for Integrated Bioinformatics, Core for Precise Measuring and Modeling, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Minami Matsui
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan.
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Amoozegar MA, Shahinpei A, Sepahy AA, Makhdoumi-Kakhki A, Seyedmahdi SS, Schumann P, Ventosa A. Pseudomonas salegens sp. nov., a halophilic member of the genus Pseudomonas isolated from a wetland. Int J Syst Evol Microbiol 2014; 64:3565-3570. [PMID: 25062699 DOI: 10.1099/ijs.0.062935-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, non-endospore-forming, non-pigmented, rod-shaped, slightly halophilic bacterium, designated GBPy5(T), was isolated from aquatic plants of the Gomishan wetland, Iran. Cells of strain GBPy5(T) were motile. Growth occurred with between 1 and 10% (w/v) NaCl and the isolate grew optimally with 3% (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 8.0 and 30 °C, respectively, while it was able to grow over a pH range of 6.5-9.0 and a temperature range of 4-35 °C. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain GBPy5(T) is a member of the genus Pseudomonas forming a monophyletic branch. The novel strain exhibited 16S rRNA gene sequence similarity of 95.4% with type strains of Pseudomonas guariconensis PCAVU11(T) and Pseudomonas sabulinigri J64(T), respectively. The major cellular fatty acids of the isolate were C18:1ω7c (37.8%), C16:0 (14.9%), C16:1ω7c (12.9%), C12:0 3-OH (7.1%) and C12:0 (7.0%). The polar lipid pattern of strain GBPy5(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The G+C content of the genomic DNA of strain GBPy5(T) was 59.2 mol%. On the basis of the phenotypic and phylogenetic data, strain GBPY5(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salegens sp. nov. is proposed. The type strain is GBPy5(T) ( = IBRC-M 10762(T) = CECT 8338(T)).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Azadeh Shahinpei
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - Abbas Akhavan Sepahy
- Department of Microbiology, Faculty of Biological Sciences, Islamic Azad University North Tehran Branch, Tehran, Iran.,Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Kennedy J, Flemer B, Jackson SA, Morrissey JP, O'Gara F, Dobson ADW. Evidence of a putative deep sea specific microbiome in marine sponges. PLoS One 2014; 9:e91092. [PMID: 24670421 PMCID: PMC3966782 DOI: 10.1371/journal.pone.0091092] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/06/2014] [Indexed: 02/01/2023] Open
Abstract
The microbiota of four individual deep water sponges, Lissodendoryx diversichela, Poecillastra compressa, Inflatella pellicula, and Stelletta normani, together with surrounding seawater were analysed by pyrosequencing of a region of the 16S rRNA gene common to Bacteria and Archaea. Due to sampling constraints at depths below 700 m duplicate samples were not collected. The microbial communities of L. diversichela, P. compressa and I. pellicula were typical of low microbial abundance (LMA) sponges while S. normani had a community more typical of high microbial abundance (HMA) sponges. Analysis of the deep sea sponge microbiota revealed that the three LMA-like sponges shared a set of abundant OTUs that were distinct from those associated with sponges from shallow waters. Comparison of the pyrosequencing data with that from shallow water sponges revealed that the microbial communities of all sponges analysed have similar archaeal populations but that the bacterial populations of the deep sea sponges were distinct. Further analysis of the common and abundant OTUs from the three LMA-like sponges placed them within the groups of ammonia oxidising Archaea (Thaumarchaeota) and sulphur oxidising γ-Proteobacteria (Chromatiales). Reads from these two groups made up over 70% of all 16S rRNA genes detected from the three LMA-like sponge samples, providing evidence of a putative common microbial assemblage associated with deep sea LMA sponges.
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Affiliation(s)
- Jonathan Kennedy
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
| | - Burkhardt Flemer
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Stephen A. Jackson
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
| | - John P. Morrissey
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Ferghal O'Gara
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
- BIOMERIT Research Centre, University College Cork, Cork, Ireland
- School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Alan D. W. Dobson
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail:
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30
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Sánchez D, Mulet M, Rodríguez AC, David Z, Lalucat J, García-Valdés E. Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 2014; 37:89-94. [DOI: 10.1016/j.syapm.2013.09.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
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31
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Pseudomonas sihuiensis sp. nov., isolated from a forest soil in South China. Antonie van Leeuwenhoek 2014; 105:781-90. [DOI: 10.1007/s10482-014-0134-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
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32
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Paenibacillus profundus sp. nov., a deep sediment bacterium that produces isocoumarin and peptide antibiotics. Arch Microbiol 2013; 195:247-54. [DOI: 10.1007/s00203-013-0873-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/08/2012] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
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33
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Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Chen WM, Shen FT, Young CC. Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2012. [PMID: 23178721 DOI: 10.1099/ijs.0.045567-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped bacterium with a single polar flagellum, designated CC-OPY-1(T), was isolated from an oil-contaminated site in Taiwan. CC-OPY-1(T) produces siderophores, and can grow at temperatures of 25-37 °C and pH 5.0-9.0 and tolerate <5 % (w/v) NaCl. The 16S rRNA gene sequence analysis of CC-OPY-1(T) showed high pairwise sequence similarity to Pseudomonas alcaligenes BCRC 11893(T) (97.1 %), Pseudomonas. alcaliphila DSM 17744(T) (97.1 %), Pseudomonas tuomuerensis JCM 14085(T) (97.1 %), Pseudomonas toyotomiensis JCM 15604(T) (96.9 %) and lower sequence similarity to remaining species of the genus Pseudomonas. The phylogenetic trees reconstructed based on gyrB and rpoB gene sequences supported the classification of CC-OPY-1(T) as a novel member of the genus Pseudomonas. The predominant quinone system of strain CC-OPY-1T was ubiquinone (Q-9) and the DNA G+C content was 68.4 ± 0.3 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0 cyclo and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC) and two unknown phospholipids (PL1-2). Due to distinct phylogenetic, phenotypic and chemotaxonomic features, CC-OPY-1(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas sagittaria sp. nov. is proposed. The type strain is CC-OPY-1(T) ( = BCRC 80399(T) = JCM 18195(T)).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wen-Ming Chen
- Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University, Kaohsiung, Taiwan, ROC
| | - Fo-Ting Shen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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He WH, Wang YN, Du X, Zhou Y, Jia B, Bian J, Liu SJ, Chen GC. Pseudomonas linyingensis sp. nov.: a novel bacterium isolated from wheat soil subjected to long-term herbicides application. Curr Microbiol 2012; 65:595-600. [PMID: 22878554 DOI: 10.1007/s00284-012-0187-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/29/2012] [Indexed: 11/25/2022]
Abstract
A strain of genus Pseudomonas, LYBRD3-7(T) was isolated from long-term sulfonylurea herbicides applied wheat-field soil in Linying located in Henan province of China. This strain is a strictly aerobic and Gram-negative short rod-shaped bacterium with single flagellum. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of Pseudomonas, and most closely to Pseudomonas tuomuerensis CGMCC 1.1365(T) (97.1 %) and P. alcaligenes IAM12411(T) (97.1 %). Morphological characters and chemotaxonomic data confirmed the affiliation of strain LYBRD3-7(T) to the genus Pseudomonas. The results of phylogenetic analysis, physiological and biochemical studies, and DNA-DNA hybridization allowed the differentiation of genotype and phenotype between strain LYBRD3-7(T) and the phylogenetic closest species with valid names. The name proposed for the new species is Pseudomonas linyingensis sp. nov. The type strain is LYBRD3-7(T) (=CGMCC 1.10701(T ) =LMG 25967(T)).
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Affiliation(s)
- Wei-Hong He
- Henan Key Laboratory of Microbial Engineering, Institute of Biology, Henan Academy of Sciences, Zhengzhou, China
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35
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Jackson SA, Kennedy J, Morrissey JP, O'Gara F, Dobson ADW. Pyrosequencing reveals diverse and distinct sponge-specific microbial communities in sponges from a single geographical location in Irish waters. MICROBIAL ECOLOGY 2012; 64:105-116. [PMID: 22281804 DOI: 10.1007/s00248-011-0002-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/22/2011] [Indexed: 05/31/2023]
Abstract
Marine sponges are host to numerically vast and phylogenetically diverse bacterial communities, with 26 major phyla to date having been found in close association with sponge species worldwide. Analyses of these microbial communities have revealed many sponge-specific novel genera and species. These endosymbiotic microbes are believed to play significant roles in sponge physiology including the production of an array of bioactive secondary metabolites. Here, we report on the use of culture-based and culture-independent (pyrosequencing) techniques to elucidate the bacterial community profiles associated with the marine sponges Raspailia ramosa and Stelligera stuposa sampled from a single geographical location in Irish waters and with ambient seawater. To date, little is known about the microbial ecology of sponges of these genera. Culture isolation grossly underestimated sponge-associated bacterial diversity. Four bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) were represented amongst ~200 isolates, compared with ten phyla found using pyrosequencing. Long average read lengths of ~430 bp (V1-V3 region of 16S rRNA gene) allowed for robust resolution of sequences to genus level. Bacterial OTUs (2,109 total), at 95% sequence similarity, from ten bacterial phyla were recovered from R. ramosa, 349 OTUs were identified in S. stuposa representing eight phyla, while 533 OTUs from six phyla were found in surrounding seawater. Bacterial communities differed significantly between sponge species and the seawater. Analysis of the data for sponge-specific taxa revealed that 2.8% of classified reads from the sponge R. ramosa can be defined as sponge-specific, while 26% of S. stuposa sequences represent sponge-specific bacteria. Novel sponge-specific clusters were identified, whereas the majority of previously reported sponge-specific clusters (e.g. Poribacteria) were absent from these sponge species. This deep and robust analysis provides further evidence that the microbial communities associated with marine sponge species are highly diverse and divergent from one another and appear to be host-selected through as yet unknown processes.
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Affiliation(s)
- Stephen A Jackson
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
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36
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Romanenko LA, Tanaka N, Svetashev VI, Falsen E. Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina. Int J Syst Evol Microbiol 2012; 63:288-297. [PMID: 22427450 DOI: 10.1099/ijs.0.036863-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of five Gram-negative, aerobic, halotolerant, non-pigmented bacteria isolated from shallow sediment samples and invertebrate specimens collected from the Gulf of Alaska and the Sea of Japan was subjected to taxonomic study. On the basis of 16S rRNA gene sequence analysis, the novel isolates were affiliated to the genus Cobetia, sharing the highest sequence similarity of 99.3-99.9 % with Cobetia marina DSM 4741(T). DNA-DNA hybridization experiments between and among the novel strains and C. marina DSM 4741(T) and Cobetia crustatorum JCM 15644(T) revealed that the five strains represent three separate genospecies, which could be differentiated in their morphological, physiological and biochemical characteristics. Halomonas halodurans NBRC 15607(T) was included in this study as it has recently been reported to exhibit high 16S rRNA gene sequence similarity to C. marina DSM 4741(T), and it showed a high DNA relatedness value of 96 % with C. marina DSM 4741(T), indicating that they belong to the same species. On the basis of phylogenetic analysis, DNA-DNA hybridization and phenotypic characterization, three novel species are proposed, named Cobetia amphilecti sp. nov. (type strain KMM 1561(T) = NRIC 0815(T) = CCUG 49560(T)), Cobetia litoralis sp. nov. (type strain KMM 3880(T) =NRIC 0814(T) =CCUG 49563(T)) and Cobetia pacifica sp. nov. (type strain KMM 3879(T) = NRIC 0813(T) = CCUG 49562(T)). It is also proposed that Halomonas halodurans is a later heterotypic synonym of Cobetia marina, and emended descriptions of the genus Cobetia and the species Cobetia marina are provided.
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Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Vladivostoku 159 Prospect 100 Let, Vladivostok 690022, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Vassilii I Svetashev
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 6 17 Palchevsky Street, Vladivostok 690041, Russia
| | - Enevold Falsen
- Culture Collection, Department of Clinical Bacteriology, University of Göteborg, SE-405 30 Göteborg, Sweden
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Pascual J, Lucena T, Ruvira MA, Giordano A, Gambacorta A, Garay E, Arahal DR, Pujalte MJ, Macián MC. Pseudomonas litoralis sp. nov., isolated from Mediterranean seawater. Int J Syst Evol Microbiol 2012; 62:438-444. [DOI: 10.1099/ijs.0.029447-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains 2SM5T and 2SM6, two strictly aerobic chemo-organotrophic gammaproteobacteria, were isolated from Mediterranean seawater off the coast of Vinaroz, Castellón, Spain, in February, 1990. They were extensively characterized by a polyphasic study that placed them in the genus Pseudomonas. Phylogenetic analysis of 16S rRNA gene sequences showed that both strains shared 100 % sequence similarity and were closely related to members of the Pseudomonas pertucinogena clade, with less than 97.3 % similarity to strains of established species; Pseudomonas xiamenensis was the closest relative. Analysis of sequences of three housekeeping genes, rpoB, rpoD and gyrB, further confirmed the phylogenetic assignment of the Mediterranean isolates. Chemotaxonomic traits such as quinone and polar lipid composition also corroborated the placement of strains 2SM5T and 2SM6 in the gammaproteobacteria. Other phenotypic traits, including fatty acid composition, enabled clear differentiation of both isolates from other species of Pseudomonas. We therefore conclude that strains 2SM5T and 2SM6 represent a novel species of Pseudomonas, for which the name Pseudomonas litoralis is proposed; the type strain is 2SM5T ( = CECT 7670T = KCTC 23093T).
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Affiliation(s)
- Javier Pascual
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
| | - Teresa Lucena
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
| | - María A. Ruvira
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
| | | | | | - Esperanza Garay
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
| | - David R. Arahal
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
| | - María J. Pujalte
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
| | - M. Carmen Macián
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, 46980 Paterna (Valencia), Spain
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38
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Poseidonocella pacifica gen. nov., sp. nov. and Poseidonocella sedimentorum sp. nov., novel alphaproteobacteria from the shallow sandy sediments of the Sea of Japan. Arch Microbiol 2011; 194:113-21. [DOI: 10.1007/s00203-011-0736-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 06/27/2011] [Accepted: 07/12/2011] [Indexed: 10/17/2022]
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Romanenko LA, Tanaka N, Svetashev VI, Mikhailov VV. Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments. Int J Syst Evol Microbiol 2011; 61:1572-1578. [DOI: 10.1099/ijs.0.025551-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018T, were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives were Marinovum algicola FF3T (95.8 and 95.9 %, respectively) and members of the genera Leisingera (95.7–95.1 and 95.8–95.2 %), Phaeobacter (95.0–94.2 and 95.1–94.2 %) and Thalassobius (96.3–94.8 and 96.2–94.7 %) of the class Alphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018T were positioned as a distinct phylogenetic line adjacent to Marinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C18 : 1ω7c, followed by 11-methyl C18 : 1ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018T were 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018T represent a novel species in a novel genus, for which the name Primorskyibacter sedentarius gen. nov., sp. nov. is proposed. The type strain of Primorskyibacter sedentarius is strain KMM 9018T ( = NRIC 0784T = JCM 16874T).
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Affiliation(s)
- Lyudmila A. Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Vasily I. Svetashev
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Valery V. Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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40
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Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI. Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment. Int J Syst Evol Microbiol 2011; 61:1375-1381. [DOI: 10.1099/ijs.0.026047-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, non-pigmented, non-motile bacterium, strain KMM 9031T, was isolated from a sandy sediment sample collected from the shore of the Sea of Japan and subjected to phenotypic and phylogenetic analysis. Based on comparative 16S rRNA gene sequence analysis, strain KMM 9031T constituted a separate phylogenetic line within the Roseobacter clade of the class Alphaproteobacteria, sharing highest sequence similarities with members of the genera Roseovarius (92.7–95.3 %), Pseudoruegeria (94.5 %), Sulfitobacter (92.7–94.4 %) and Thalassobacter (94.2–94.3 %). The predominant fatty acid of strain KMM 9031T was C18 : 1ω7c, with C16 : 0, C10 : 0 3-OH and C12 : 1 3-OH present in lesser amounts. The DNA G+C content of the isolate was 52.6 mol%. The major isoprenoid quinone was Q-10 and polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and two unknown lipids. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KMM 9031T represents a novel species in a new genus, for which the name Pacificibacter maritimus gen. nov., sp. nov. is proposed; the type strain is KMM 9031T ( = NRIC 0785T = JCM 17096T).
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Affiliation(s)
- Lyudmila A. Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Vasily I. Svetashev
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Nataliya I. Kalinovskaya
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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Romanenko LA, Tanaka N, Frolova GM, Svetashev VI, Mikhailov VV. Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore. Int J Syst Evol Microbiol 2011; 61:148-154. [DOI: 10.1099/ijs.0.019513-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, strictly aerobic, non-motile bacteria designated strains KMM 3851T and KMM 3842T were respectively isolated from a marine snail specimen (Umbonium costatum) and from surrounding sediments collected simultaneously from the shore of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains KMM 3851T and KMM 3842T were affiliated with the Roseobacter lineage of the class Alphaproteobacteria as a separate phylogenetic line adjacent to the members of the genus Thalassobacter. These novel isolates shared 98.5 % 16S rRNA gene sequence similarity and 15 % DNA–DNA relatedness. The major isoprenoid quinone of both strains was Q-10 and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and aminophospholipids. In addition, strain KMM 3851T contained two unknown lipids, whereas strain KMM 3842T contained diphosphatidylglycerol. Fatty acid analysis revealed C18 : 1
ω7c and C16 : 0 as major components and small amounts of C18 : 2. The DNA G+C contents were 60.4 mol% (KMM 3851T) and 58.5 mol% (KMM 3842T). Based on distinctive phenotypic characteristics, DNA–DNA hybridization data and phylogenetic distance, strains KMM 3851T and KMM 3842T should be classified as representatives of two novel species in a new genus, Litoreibacter gen. nov., with the type species Litoreibacter albidus sp. nov. (type strain KMM 3851T =NRIC 0773T =JCM 16493T) and a second species Litoreibacter janthinus sp. nov. (type strain KMM 3842T =NRIC 0772T =JCM 16492T).
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Affiliation(s)
- Lyudmila A. Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Galina M. Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Vassilii I. Svetashev
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Valery V. Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment. Int J Syst Evol Microbiol 2010; 60:1832-1836. [DOI: 10.1099/ijs.0.017194-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1
ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1
ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).
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Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2010; 60:1613-1619. [DOI: 10.1099/ijs.0.016147-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, greyish–yellowish-pigmented, stenohaline, rod-shaped, non-motile bacterium, strain KMM 3900T, was isolated from a coastal seawater sample collected from the Sea of Japan. Based on phylogenetic analysis, strain KMM 3900T was positioned within the Gammaproteobacteria on a separate branch adjacent to members of the genera Reinekea and Kangiella, sharing less than 88 % 16S rRNA gene sequence similarity with all recognized species of the Gammaproteobacteria. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown phospholipids. Fatty acid analysis revealed iso-C15 : 0, C16 : 1
ω7c and C16 : 0 as the dominant components. The DNA G+C content was 43.8 mol%. Based on its unique phenotypic characteristics and phylogenetic remoteness, marine isolate KMM 3900T is considered to represent a novel genus and species, for which the name Marinicella litoralis gen. nov., sp. nov. is proposed. The type strain of Marinicella litoralis is KMM 3900T (=NRIC 0758T =JCM 16154T).
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Affiliation(s)
- Lyudmila A. Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Galina M. Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Valery V. Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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Santos OCS, Pontes PVML, Santos JFM, Muricy G, Giambiagi-deMarval M, Laport MS. Isolation, characterization and phylogeny of sponge-associated bacteria with antimicrobial activities from Brazil. Res Microbiol 2010; 161:604-12. [PMID: 20600863 DOI: 10.1016/j.resmic.2010.05.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 05/17/2010] [Accepted: 05/22/2010] [Indexed: 12/29/2022]
Abstract
Bacteria associated with marine sponges represent a rich source of bioactive metabolites. The aim of this study was to isolate and characterize bacteria with antimicrobial activities from Brazilian sponges. A total of 158 colony-forming units were isolated from nine sponge species. Among these, 12 isolates presented antimicrobial activities against pathogenic bacteria. Based on comparative sequence analysis of their 16S rRNA genes, the sponge-associated bacterial strains could be subdivided into three phylogenetically different clusters. Five strains were affiliated with Firmicutes (genera Bacillus and Virgibacillus), three with alpha-Proteobacteria (Pseudovibrio sp.) and four with gamma-Proteobacteria (genera Pseudomonas and Stenotrophomonas). The sponge-associated bacterial strains Pseudomonas fluorescens H40 and H41 and Pseudomonas aeruginosa H51 exhibited antimicrobial activity against both Gram-negative and Gram-positive bacteria, including strains such as vancomycin-resistant Enterococcus faecium and multiresistant Klebsiella pneumoniae. Bacillus pumilus Pc31 and Pc32, Pseudovibrio ascidiaceicola Pm31 and Ca31 and Pseudovibrio denitrificans Mm37 strains were more effective against Gram-positive bacteria. These findings suggest that the identified strains may contribute to the search for new sources of antimicrobial substances, an important strategy for developing alternative therapies to treat infections caused by multidrug-resistant bacteria.
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Affiliation(s)
- Olinda C S Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil.
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Abstract
Pseudomonas fulva has not yet been isolated from humans as a pathogen. Herein, we report the first case of P. fulva bacteremia in a patient hospitalized due to trauma. The species was identified using biochemical and molecular genetic analyses of the 16S rRNA, gyrB, rpoB, and rpoD genes.
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Darabpour E, Ardakani MR, Motamedi H, Ghezelbash G, Ronagh MT. Isolation of an antibiotic producer Pseudomonas sp. from the Persian Gulf. ASIAN PAC J TROP MED 2010. [DOI: 10.1016/s1995-7645(10)60077-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Tanaka N, Romanenko LA, Iino T, Frolova GM, Mikhailov VV. Cocleimonas flava gen. nov., sp. nov., a gammaproteobacterium isolated from sand snail (Umbonium costatum). Int J Syst Evol Microbiol 2010; 61:412-416. [PMID: 20348322 DOI: 10.1099/ijs.0.020263-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, yellow-pigmented, heterotrophic, sulfur-oxidizing, non-motile, rod-shaped bacterium, designated KMM 3898(T), was isolated from an internal tissue of the sand snail Umbonium costatum, collected from the shallow sediments of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KMM 3898(T) formed a distinct phylogenetic lineage within the class Gammaproteobacteria and was most closely related to Leucothrix mucor DSM 2157(T) (89.2 % 16S rRNA gene sequence similarity) and members of the genus Thiothrix (86.7-88.5 %). Chemotaxonomically, strain KMM 3898(T) contained the isoprenoid quinone Q-8, the polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid and the fatty acids C(18 : 1)ω7c, C(16 : 1)ω7c and C(16 : 0) as predominant components (>10 %). The DNA G+C content of strain KMM 3898(T) was 43.4 mol%. On the basis of phenotypic features and phylogenetic analysis, strain KMM 3898(T) represents a novel genus and species, for which the name Cocleimonas flava gen. nov., sp. nov. is proposed. The type strain is KMM 3898(T) (=NRIC 0757(T) =JCM 16494(T)).
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Affiliation(s)
- Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Galina M Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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Fendri I, Chaari A, Dhouib A, Jlassi B, Abousalham A, Carrière F, Sayadi S, Abdelkafi S. Isolation, identification and characterization of a new lipolytic pseudomonas sp., strain AHD-1, from Tunisian soil. ENVIRONMENTAL TECHNOLOGY 2010; 31:87-95. [PMID: 20232682 DOI: 10.1080/09593330903369994] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A novel, lipid-degrading bacterium (strain AHD-1) was isolated from soil regularly contaminated with washing-machine wastewater in Sfax, Tunisia. When this strain was grown in a medium containing 2% triacylglycerol, the hydrolysis products were found to be diacylglycerols, monoacylglycerols and free fatty acids. This strain was an aerobic, mesophilic, Gram-negative, motile, non-sporulating bacterium, capable of growing optimally at pH 7 and 27 degrees C. The predominant fatty acids were found to be C16:1omega7c (31%), C16:0 (28.1%), C18:1 omega7c (16.3%) and C17:0 (5.8%). Phylogenetic analysis of the 16S rRNA gene showed that this isolate is a new strain belonging to the genus Pseudomonas. Strain AHD-1 was found to be closely related to Pseudomonas azotoformans IAM 1603T, Pseudomonas gessardii CIP 105469T and Pseudomonas libanensis CIP 105460T with 99.7%, 99.56% and 99.54% of similarity, respectively.
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Affiliation(s)
- Imen Fendri
- Laboratoire des Bioprocédés, Pôle d'Excellence Régionale A UF, (PER-LBP), Centre de Biotechnologie de Sfax, Sfax, Tunisia
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Simon-Colin C, Alain K, Raguénès G, Schmitt S, Kervarec N, Gouin C, Crassous P, Costa B, Guezennec JG. Biosynthesis of medium chain length poly(3-hydroxyalkanoates) (mcl PHAs) from cosmetic co-products by Pseudomonas raguenesii sp. nov., isolated from Tetiaroa, French Polynesia. BIORESOURCE TECHNOLOGY 2009; 100:6033-6039. [PMID: 19632827 DOI: 10.1016/j.biortech.2009.06.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/18/2009] [Accepted: 06/22/2009] [Indexed: 05/28/2023]
Abstract
A new bacterium, designated as strain TE9 was isolated from a microbial mat in French Polynesia and was studied for its ability to synthesize medium chain length poly-beta-hydroxyalkanoates (mcl PHAs) during cultivation on cosmetics co-products. The composition of PHAs was analysed by coupled gas chromatography mass spectroscopy (GC/MS), nuclear magnetic resonance (NMR) and Fourier Transform InfraRed (FTIR) spectroscopy. PHAs were composed of C6-C14 3-hydroxyacids monomers, with a predominance of 3-hydroxyoctanoate (3HO), 3-hydroxydecanoate (3HD) and 3-hydroxydodecanoate (3HDD). Differential scanning calorimetry (DSC) experiments allowed the characterization of elastomeric materials with a melting point T(m) near 50 degrees C, enthalpy of fusion DeltaH(m) from 27 to 32 J/g, and glass transition temperature T(g) of -43 degrees C. Molecular weights ranged from 175,000 to 358,000 g/mol. On the basis of the phenotypical features and genotypic investigations, strain TE9 was assigned to the Pseudomonas genus and the name of Pseudomonas raguenesii sp. nov. is proposed.
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Affiliation(s)
- C Simon-Colin
- Institut Français de Recherche pour l'Exploitation de la Mer, Centre de Brest, BIOMAR/BMM, B.P. 70, 29280 Plouzané, France.
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Peix A, Ramírez-Bahena MH, Velázquez E. Historical evolution and current status of the taxonomy of genus Pseudomonas. INFECTION GENETICS AND EVOLUTION 2009; 9:1132-47. [DOI: 10.1016/j.meegid.2009.08.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 08/02/2009] [Accepted: 08/18/2009] [Indexed: 10/20/2022]
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