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Galván V, Pascutti F, Sandoval NE, Lanfranconi MP, Lozada M, Arabolaza AL, Mac Cormack WP, Alvarez HM, Gramajo HC, Dionisi HM. High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments. PLoS One 2023; 18:e0288509. [PMID: 37459319 PMCID: PMC10351704 DOI: 10.1371/journal.pone.0288509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
The wax ester (WE) and triacylglycerol (TAG) biosynthetic potential of marine microorganisms is poorly understood at the microbial community level. The goal of this work was to uncover the prevalence and diversity of bacteria with the potential to synthesize these neutral lipids in coastal sediments of two high latitude environments, and to characterize the gene clusters related to this process. Homolog sequences of the key enzyme, the wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) were retrieved from 13 metagenomes, including subtidal and intertidal sediments of a Subantarctic environment (Ushuaia Bay, Argentina), and subtidal sediments of an Antarctic environment (Potter Cove, Antarctica). The abundance of WS/DGAT homolog sequences in the sediment metagenomes was 1.23 ± 0.42 times the abundance of 12 single-copy genes encoding ribosomal proteins, higher than in seawater (0.13 ± 0.31 times in 338 metagenomes). Homolog sequences were highly diverse, and were assigned to the Pseudomonadota, Actinomycetota, Bacteroidota and Acidobacteriota phyla. The genomic context of WS/DGAT homologs included sequences related to WE and TAG biosynthesis pathways, as well as to other related pathways such as fatty-acid metabolism, suggesting carbon recycling might drive the flux to neutral lipid synthesis. These results indicate the presence of abundant and taxonomically diverse bacterial populations with the potential to synthesize lipid storage compounds in marine sediments, relating this metabolic process to bacterial survival.
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Affiliation(s)
- Virginia Galván
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Federico Pascutti
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Natalia E. Sandoval
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana P. Lanfranconi
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana Lozada
- Instituto de Biología de Organismos Marinos (IBIOMAR-CONICET), Puerto Madryn, Chubut, Argentina
| | - Ana L. Arabolaza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Walter P. Mac Cormack
- Instituto de Nanobiotecnología (NANOBIOTEC-UBA-CONICET), San Martín, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Antártico Argentino (IAA), San Martín, Buenos Aires, Argentina
| | - Héctor M. Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Hugo C. Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Hebe M. Dionisi
- Centro para el Estudio de Sistemas Marinos (CESIMAR-CONICET), Puerto Madryn, Chubut, Argentina
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Gupta A, Sinha DK, Nair S. Shifts in Pseudomonas species diversity influence adaptation of brown planthopper to changing climates and geographical locations. iScience 2022; 25:104550. [PMID: 35754716 PMCID: PMC9218508 DOI: 10.1016/j.isci.2022.104550] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/29/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
The brown planthopper (BPH) is a monophagous sap-sucking pest of rice that causes immense yield loss. The rapid build-up of pesticide resistance combined with the ability of BPH populations to quickly overcome host plant resistance has rendered conventional control strategies ineffective. One of the likely ways in which BPH adapts to novel environments is by undergoing rapid shifts in its microbiome composition. To elucidate the rapid adaptation to novel environments and the contributions of Pseudomonas toward insect survival, we performed Pseudomonas-specific 16S rRNA gut-microbiome profiling of BPH populations. Results revealed the differential occurrence of Pseudomonas species in BPH populations with changing climates and geographical locations. Further, the observed variation in Pseudomonas species composition and abundance correlated with BPH survivability. Collectively, this study, while adding to our current understanding of symbiont-mediated insect adaptation, also demonstrated a complex interplay between insect physiology and microbiome dynamics, which likely confers BPH its rapid adaptive capacity. BPH, a major pest of rice, undergoes seasonal shifts in its microbiome composition Pseudomonas sp. in BPH microbiome varied with seasons and geographical locations Pseudomonas sp. composition and abundance correlated with BPH survivability Environment-guided microbial shifts drive rapid stress adaptations in BPH
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He AL, Li HR, Li HP, Gou JY, Chen J, Zhao Q, Zhang JL. Taxonomic description of Pseudomonas rhizovicinus sp. nov., isolated from the rhizosphere of a desert shrub Haloxylon ammodendron. Antonie van Leeuwenhoek 2021; 114:1443-1452. [PMID: 34272636 DOI: 10.1007/s10482-021-01612-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 06/30/2021] [Indexed: 11/30/2022]
Abstract
A Gram-negative aerobic bacterium, strain M30-35 T, was isolated from the rhizosphere of Haloxylon ammodendron in Tengger desert, Gansu province, northwest China. Our previous research indicated that strain M30-35 T can promote the growth of ryegrass (Lolium perenne L.). In this study, strain M30-35 T was subjected to a polyphasic taxonomic study. Phylogenetic analysis of the 16S rRNA gene and two other housekeeping genes (gyrB, rpoD) showed that strain M30-35 T is a member of Pseudomonas anguilliseptica group. The average nucleotide identity (ANI) scores for strains KMM 3042 T and FR1439T were 76.5% and 83.7%, respectively, and DNA-DNA hybridization (DDH) were 21.6% and 26.6%, respectively, and the rates were less than the threshold range for species determination. The dominant cellular fatty acids of strain M30-35 T were C16:0 (22.7%), summed feature 3 (C16:1ω7c and/or C16:1ω6c; 18.5%), summed feature 8 (C18:1ω7c and/or C18:1ω6c; 23.1%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and aminophospholipid and the predominant respiratory quinone was ubiquinone (Q9). On the basis of above data, it can be concluded that strain M30-35 T represents a novel species in the genus Pseudomonas, for which the name Pseudomonas rhizovicinus sp. nov. is proposed. The type strain is M30-35 T (= MCCC 1K03247T = KCTC 52664 T).
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Affiliation(s)
- Ao-Lei He
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hui-Ru Li
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hui-Ping Li
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jing-Yi Gou
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jia Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Qi Zhao
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| | - Jin-Lin Zhang
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Mining lipolytic enzymes in community DNA from high Andean soils using a targeted approach. Antonie van Leeuwenhoek 2017; 110:1035-1051. [DOI: 10.1007/s10482-017-0877-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 04/18/2017] [Indexed: 12/23/2022]
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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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Lin SY, Hameed A, Hung MH, Liu YC, Hsu YH, Young LS, Young CC. Pseudomonas matsuisoli sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2015; 65:902-909. [DOI: 10.1099/ijs.0.000035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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 and polar-flagellated bacterium, designated strain CC-MHH0089T, was isolated from a soil sample taken on Matsu Island (Taiwan). Strain CC-MHH0089T grew at 15–30 °C and pH 5.0–10.0 and tolerated ≤8 % (w/v) NaCl. 16S rRNA gene sequence analysis showed high pairwise sequence similarity to
Pseudomonas azotifigens
6H33bT (97.3 %) and
Pseudomonas balearica
SP1402T (96.7 %) and lower sequence similarity to other strains (<96.0 %). In DNA–DNA reassociation experiments, the relatedness of strain CC-MHH0089T to
P. azotifigens
JCM 12708T was 38.3 % (reciprocal value 19.5 %). Evolutionary trees reconstructed on the basis of 16S rRNA, gyrB and rpoB gene sequences revealed a varying phylogenetic neighbourhood of strain CC-MHH0089T with regard to the most closely related type strains. The predominant quinone system was ubiquinone 9 (Q-9) and the DNA G+C content was 63.6 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0, C19 : 0 cyclo ω8c and summed features 2 (C14 : 0 3-OH/iso-C16 : 1 I), 3 (C16 : 1ω7c/C16 : 1ω6c) and 8 (C18 : 1ω7c/C18 : 1ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. According to its distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-MHH0089T is proposed to represent a novel species within the genus
Pseudomonas
, for which the name Pseudomonas matsuisoli sp. nov. is proposed. The type strain is CC-MHH0089T ( = BCRC 80771T = JCM 30078T).
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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
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Li-Sen Young
- Department of Biotechnology, College of Applied Arts and Sciences, National Formosa University, Yunlin, Taiwan
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
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Hameed A, Shahina M, Lin SY, Liu YC, Young CC. Pseudomonas hussainii sp. nov., isolated from droppings of a seashore bird, and emended descriptions of Pseudomonas pohangensis, Pseudomonas benzenivorans and Pseudomonas segetis. Int J Syst Evol Microbiol 2014; 64:2330-2337. [PMID: 24744016 DOI: 10.1099/ijs.0.060319-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-staining-negative, aerobic, rod-shaped, non-spore-forming bacterial strains that are motile by a monopolar flagellum, designated CC-AMH-11(T) and CC-AMHZ-5, were isolated from droppings of a seashore bird off the coast of Hualien, Taiwan. The strains showed 99.7% mutual pairwise 16S rRNA gene sequence similarity, while exhibiting <96.2% sequence similarity to strains of other species of the genus Pseudomonas (95.7-95.9% similarity with type species, Pseudomonas aeruginosa LMG 1242T), and formed a distinct co-phyletic lineage in the phylogenetic trees. The common major fatty acids (>5% of the total) were C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8), C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3), C16 : 0 and C12 : 0. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine, an unidentified lipid and an unidentified phospholipid were detected as common polar lipids. The DNA G+C contents of strains CC-AMH-11(T) and CC-AMHZ-5 were 61.1 and 61.6 mol%, respectively. The common major respiratory quinone was ubiquinone 9 (Q-9), and the predominant polyamine was putrescine. The DNA-DNA hybridization obtained between the two strains was 79.0% (reciprocal value 89.4% using CC-AMHZ-5 DNA as the probe). The very high 16S rRNA gene sequence similarity and DNA-DNA relatedness and the poorly distinguishable phenotypic features witnessed between CC-AMH-11(T) and CC-AMHZ-5 suggested unambiguously that they are two distinct strains of a single genomic species. However, the strains also showed several genotypic and phenotypic characteristics that distinguished them from other closely related species of Pseudomonas. Thus, the strains are proposed to represent a novel species of Pseudomonas, for which the name Pseudomonas hussainii sp. nov. is proposed. The type strain is CC-AMH-11(T) ( = JCM 19513(T) = BCRC 80696(T)); a second strain of the same species is CC-AMHZ-5 ( = JCM 19512 = BCRC 80697). In addition, emended descriptions of the species Pseudomonas pohangensis, Pseudomonas benzenivorans and Pseudomonas segetis are also proposed.
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Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - You-Cheng Liu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan.,Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
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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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Nair D, Fernández-Acero FJ, García-Luque E, Riba I, Del Valls TA. Isolation and characterization of naphthalene-degrading bacteria from sediments of Cadiz area (SW Spain). ENVIRONMENTAL TOXICOLOGY 2008; 23:576-582. [PMID: 18528908 DOI: 10.1002/tox.20408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Petroleum hydrocarbon contamination of harbor sediments from shipping activity, fuel oil spills, and runoffs are becoming a great concern because of the toxicity and recalcitrance of many of the fuel components. Polycyclic aromatic hydrocarbons (PAHs) are of most concern due to their toxicity, low volatility, resistance to degradation, and high affinity for sediments. Microorganisms, especially bacteria, play an important role in the biodegradation of these hydrocarbons. The objective of the present study was to characterize and isolate PAH-(naphthalene) degrading bacteria in the coastal sediments of Cadiz (SW Spain), since this area is mostly polluted by PAH occurrence. A total of 16 naphthalene-utilizing bacteria were isolated from these sites. Introduction of bacteria isolated from contaminated sediments into mineral medium contributed to the increased rate of hydrocarbon utilization. The bacterial isolates obtained from these sites are very potent in utilizing naphthalene and crude oil. It would be interesting to assess if the selected naphthalene-degrading isolates may degrade other compounds of similar structure. Hence these isolates could be very helpful in bioremediating the PAH-contaminated sites. Further pursue on this work might represent eco-friendly solution for oil contamination on sea surface and coastal area.
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Affiliation(s)
- D Nair
- Cátedra UNESCO/UNITWIN/WiCop, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Polígono Río San Pedro s/n 11510 Puerto Real (Cádiz), España
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