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Su W, Yu Q, Yang J, Han Q, Wang S, Heděnec P, Wang X, Wan-Yan R, Li H. Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River. J Environ Sci (China) 2024; 142:236-247. [PMID: 38527889 DOI: 10.1016/j.jes.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 03/27/2024]
Abstract
The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.
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Affiliation(s)
- Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Petr Heděnec
- Institute for Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Ruijun Wan-Yan
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China.
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Sorokin DY, Merkel AY, Kolganova TV, Bale NJ, Sinninghe Damsté JS. Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria. Syst Appl Microbiol 2024; 47:126519. [PMID: 38759530 DOI: 10.1016/j.syapm.2024.126519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
The genus Natronospira is represented by a single species of extremely salt-tolerant aerobic alkaliphilic proteolytic bacterium, isolated from hypersaline soda lakes. When cells of Gram-positive cocci were used as a substrate instead of proteins at extremely haloalkaline conditions, two new members of this genus were enriched and isolated in pure culture from the same sites. Strains AB-CW1 and AB-CW4 are obligate aerobic heterotrophic proteolytic bacteria able to feed on both live and dead cells of staphylococci and a range of proteins and peptides. Similar to the type species, N. proteinivora, the isolates are extremely salt-tolerant obligate alkaliphiles. However, N. proteinivora was unable to use bacterial cells as a substrate. Electron microscopy showed direct contact between the prey and predator cells. Functional analysis of the AB-CW1 and AB-CW4 genomes identified two sets of genes coding for extracellular enzymes potentially involved in the predation and proteolysis, respectively. The first set includes several copies of lysozyme-like GH23 peptidoglycan-lyase and murein-specific M23 [Zn]-di-peptidase enabling the cell wall degradation. The second set features multiple copies of secreted serine and metallopeptidases apparently allowing for the strong proteolytic phenotype. Phylogenomic analysis placed the isolates into the genus Natronospira as two novel species members, and furthermore indicated that this genus forms a deep-branching lineage of a new family (Natronospiraceae) and order (Natronospirales) within the class Gammaproteobacteria. On the basis of distinct phenotypic and genomic properties, strain AB-CW1T (JCM 335396 = UQM 41579) is proposed to be classified as Natronospira elongata sp. nov., and AB-CW4T (JCM 335397 = UQM 41580) as Natronospira bacteriovora sp. nov.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, TU Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana V Kolganova
- Skryabin Insitutute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
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Kuppusamy S, Venkateswarlu K, Megharaj M. Tetracycline and fluoroquinolone antibiotics contamination in agricultural soils fertilized long-term with chicken litter: Trends and ravages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174286. [PMID: 38942301 DOI: 10.1016/j.scitotenv.2024.174286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 06/30/2024]
Abstract
We investigated the potential accumulation of tetracyclines (TCs) such as chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC), and fluoroquinolones (FQs) like enrofloxacin (ENR) and ciprofloxacin (CIP) in chicken litter and agricultural soils fertilized over short-term to long-term (<1-30 yrs) with chicken litter in a poultry hub for the first time from Tamil Nadu, India. CTC, OTC, DC, CIP, and ENR were detected in 46-92 % of the selected chicken litter samples, with mean levels ranging from 2.90 to 23.30 μg kg-1. Higher concentrations of TCs and FQs were observed in freshly collected chicken litter from poultry sheds than in those stockpiled in cultivated lands. CTC was the prevalent antibiotic in chicken litter. The overall occurrence, as well as the ecological risks of TCs and FQs, changed over a 30-yr period. The accumulation of veterinary antibiotics (VAs) (in μg kg-1) in short-term (>1 yr) to medium-term (1-3 yrs) chicken litter-fertilized soils reached a maximum of 11.60 for CTC, 6.50 for OTC, 0.80 for DC, 3.70 for CIP, and 3.60 for ENR, but decreased in long-term (10-30 yrs) fertilized soils. Ecological risk assessment revealed a Risk Quotient (RQ) of ≤0.10 for CTC, OTC, and DC in all soils, while an average risk (RQ >0.10-<1.0) was evident with CIP and ENR in short-term and medium-term fertilized soils. Antibiotic resistance genes (ARGs), including tetA, tetB, qnrA, qnrB and qnrS were detected in most of the chicken litter samples and litter-fertilized soils. Thus, it is critical to develop and adopt effective mitigation strategies before applying chicken litter in farmlands to decrease VAs and ARGs, reducing their associated risks to public health and ecosystems in India considering 'One Health' approach. Future investigations on the occurrence of other VAs and ARGs in soils fertilized with poultry litter at regional scale are required for effective risk mitigation of the widely used VAs.
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Affiliation(s)
- Saranya Kuppusamy
- Centre for Environmental Studies, Department of Civil Engineering, College of Engineering Guindy, Anna University, Chennai 600 025, India.
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu 515 003, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (crcCARE), ATC Building, Callaghan, NSW 2308, Australia
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4
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Le Geay M, Mayers K, Küttim M, Lauga B, Jassey VEJ. Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO 2 fixation. Environ Microbiol 2024; 26:e16666. [PMID: 38889760 DOI: 10.1111/1462-2920.16666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.
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Affiliation(s)
- Marie Le Geay
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRE, IRD, Toulouse INP, Université Toulouse 3-Paul Sabatier (UT3), Toulouse, France
| | - Kyle Mayers
- NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Martin Küttim
- Institute of Ecology, School of Natural Sciences and Health, Tallinn University, Tallinn, Estonia
| | - Béatrice Lauga
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Vincent E J Jassey
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRE, IRD, Toulouse INP, Université Toulouse 3-Paul Sabatier (UT3), Toulouse, France
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5
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Boltyanskaya Y, Zhilina T, Grouzdev D, Detkova E, Pimenov N, Kevbrin V. Halanaerobium polyolivorans sp. nov.-A Novel Halophilic Alkalitolerant Bacterium Capable of Polyol Degradation: Physiological Properties and Genomic Insights. Microorganisms 2023; 11:2325. [PMID: 37764169 PMCID: PMC10536098 DOI: 10.3390/microorganisms11092325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/16/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
A search for the microorganisms responsible for the anaerobic degradation of osmoprotectants in soda lakes resulted in the isolation of a novel halophilic and alkalitolerant strain, designated Z-7514T. The cells were Gram-stain-negative and non-endospore-forming rods. Optimal growth occurs at 1.6-2.1 M Na+, pH 8.0-8.5, and 31-35 °C. The strain utilized mainly sugars, low molecular polyols, and ethanolamine as well. The G+C content of the genomic DNA of strain Z-7514T was 33.3 mol%. Phylogenetic and phylogenomic analyses revealed that strain Z-7514T belongs to the genus Halanaerobium. On the basis of phenotypic properties and the dDDH and ANI values with close validly published species, it was proposed to evolve strain Z-7514T within the genus Halanaerobium into novel species, for which the name Halanaerobium polyolivorans sp. nov. was proposed. The type strain was Z-7514T (=KCTC 25405T = VKM B-3577T). For species of the genus Halanaerobium, the utilization of ethylene glycol, propylene glycol, and ethanolamine were shown for the first time. The anaerobic degradation of glycols and ethanolamine by strain Z-7514T may represent a novel metabiotic pathway within the alkaliphilic microbial community. Based on a detailed genomic analysis, the main pathways of catabolism of most of the used substrates have been identified.
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Affiliation(s)
- Yulia Boltyanskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Tatjana Zhilina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | | | - Ekaterina Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Nikolay Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Vadim Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
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6
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Elizabeth George S, Wan Y. Microbial functionalities and immobilization of environmental lead: Biogeochemical and molecular mechanisms and implications for bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131738. [PMID: 37285788 PMCID: PMC11249206 DOI: 10.1016/j.jhazmat.2023.131738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.
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Affiliation(s)
- S Elizabeth George
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA
| | - Yongshan Wan
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA.
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Wang X, Han Q, Yu Q, Wang S, Yang J, Su W, Wan-Yan R, Sun X, Li H. Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil. ENVIRONMENTAL RESEARCH 2023; 225:115653. [PMID: 36898422 DOI: 10.1016/j.envres.2023.115653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.
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Affiliation(s)
- Xiaochen Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Ruijun Wan-Yan
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaofang Sun
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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8
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Boltyanskaya YV, Kevbrin VV, Grouzdev DS, Detkova EN, Koziaeva VV, Novikov AA, Zhilina TN. Halonatronomonas betaini gen. nov., sp. nov., a haloalkaliphilic isolate from soda lake capable of betaine degradation and proposal of Halarsenatibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the order Halanaerobiales. Syst Appl Microbiol 2023; 46:126407. [PMID: 36906934 DOI: 10.1016/j.syapm.2023.126407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
A search for the organisms responsible for anaerobic betaine degradation in soda lakes resulted in isolation of a novel bacterial strain, designated Z-7014T. The cells were Gram-stain-negative, non-endospore-forming rods. Growth occurred at 8-52 °C (optimum 40-45 °C), pH 7.1-10.1 (optimum pH 8.1-8.8) and 1.0-3.5 M Na+ (optimum 1.8 M), i.e. it can be regarded as a haloalkaliphile. The strain utilized a limited range of substrates, mostly peptonaceous but not amino acids, and was able to degrade betaine. Growth on betaine occurred only in the presence of peptonaceous substances which could not be replaced by vitamins. The G + C content of the genomic DNA of strain Z-7014T was 36.1 mol%. The major cellular fatty acids (>5% of the total) were C16:0 DMA, C18: 0 DMA, C16:1ω8, C16:0, C18:1 DMA, C16:1 DMA, C18:1ω9, and C18:0. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Z-7014T formed a distinct evolutionary lineage in the order Halanaerobiales with the highest similarity to Halarsenitibacter silvermanii SLAS-1T (83.6%), Halothermothrix orenii H168T (85.6%), and Halocella cellulosilytica DSM 7362T (85.6%). AAI and POCP values between strain Z-7014T and type strains of the order Halanaerobiales were 51.7-57.8%, and 33.8-58.3%, respectively. Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain Z-7014T represents a novel species of a new genus, for which the name Halonatronomonas betaini gen. nov., sp. nov. is proposed. The type strain is Z-7014T (=KCTC 25237T = VKM B-3506T). On the basis of phylogenomic data, it is also proposed to evolve two novel families Halarsenitibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the current order Halanaerobiales.
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Affiliation(s)
- Yulia V Boltyanskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Vadim V Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia.
| | | | - Ekaterina N Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Veronika V Koziaeva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | | | - Tatjana N Zhilina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
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Moopantakath J, Imchen M, Anju VT, Busi S, Dyavaiah M, Martínez-Espinosa RM, Kumavath R. Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications. Front Microbiol 2023; 14:1113540. [PMID: 37065149 PMCID: PMC10102575 DOI: 10.3389/fmicb.2023.1113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - V. T. Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- Rosa María Martínez-Espinosa,
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- *Correspondence: Ranjith Kumavath, ,
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Chaudhary DR, Kumar M, Kalla V. Sediment microbial community structure, enzymatic activities and functional gene abundance in the coastal hypersaline habitats. Arch Microbiol 2023; 205:56. [PMID: 36607455 DOI: 10.1007/s00203-022-03398-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Salt marsh vegetation, mudflat and salt production are common features in worldwide coastal areas; however, their influence on microbial community composition and structure has been poorly studied and rarely compared. In the present study, microbial community composition (phospholipid fatty acid (PLFA) profiling and 16S rRNA gene sequencing (bacterial and archaeal)) and structure, enzymatic activities and abundance of functional genes in the sediments of salt ponds (crystallizer, condenser and reservoir), mudflat and vegetated mudflat were determined. Enzyme activities (β-glucosidase, urease and alkaline phosphatase) were considerably decreased in saltpan sediments because of elevated salinity while sediment of vegetated mudflat sediments showed the highest enzyme activities. Concentrations of total microbial biomarker PLFAs (total bacterial, Gram-positive, Gram-negative, fungal and actinomycetes) were the highest in vegetated mudflat sediments and the lowest in crystallizer sediments. Nonmetric-multidimensional scaling (NMDS) analysis of PLFA data revealed that the microbial community of crystallizer, mudflat and vegetated mudflat was significantly different from each other as well as different from condenser and reservoir. The most predominant phyla within the classified bacterial fractions were Proteobacteria followed by Firmicutes, Bacteroidetes and Planctomycetes, while Euryarchaeota and Crenarchaeota phyla dominated the classified archaeal fraction. Cyanobacterial genotypes were the most dominant in the condenser. Mudflat and vegetated mudflat supported a greater abundance of Bacteroidetes and Actinobacteria, respectively. The results of the present study suggest that salt ponds had significantly decreased the microbial and enzyme activities in comparison to mudflat and vegetated mudflat sediments due to very high salinity, ionic concentrations and devoid of vegetation. The present study expands our understanding of microbial resource utilization and adaptations of microorganisms in a hypersaline environment.
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Affiliation(s)
- Doongar R Chaudhary
- Division of Plant Omics, CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Madhav Kumar
- Division of Plant Omics, CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vandana Kalla
- Lachoo Memorial College of Science and Technology, Shastri Nagar, Sec. A, Jodhpur, 342001, Rajasthan, India
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11
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Medina-de la Rosa G, García-Oliva F, Alpuche-Solís ÁG, Ovando-Vázquez C, López-Lozano NE. The nutrient-improvement bacteria selected by Agave lechuguilla T. and their role in the rhizosphere community. FEMS Microbiol Ecol 2021; 97:6380485. [PMID: 34601598 DOI: 10.1093/femsec/fiab137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
Agave lechuguilla has one of the widest distributions among other agave species in the Chihuahuan Desert. Their capacity to grow in poorly developed soils and harsh conditions has been related to their association with plant growth-promoting rhizobacteria. In this work, we explored how soil properties and plant growth stage influence the composition of the rhizobacterial communities, their interactions, and the enzymatic activity and abundance of nitrogen-fixing bacteria and organic phosphorus-mineralizing bacteria in two subregions of the Chihuahuan Desert. We found that mature plants of lechuguilla stimulated the activity and abundance of nutrient-improvement rhizobacteria, and these soil samples had a higher content of total organic carbon, ammonium (NH4) and nitrite + nitrate (NO2+NO3). Nutrient availability seems to be an essential driver of the bacterial community's structure since the genera with more connections (hubs) were those with known mechanisms related to the availability of nutrients, such as env. OPS17 (Bacteroidetes), Gemmatimonadaceae uncultured, S0134terrestrial group, BD211terrestrial group (Gemmatimonadetes), Chthoniobacteracea and Candidatus Udaeobacter (Verrucomicrobia). This work shows that the late growth stages of lechuguilla recruit beneficial bacteria that favor its establishment and tolerance to harsh conditions of the arid lands.
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Affiliation(s)
- Guadalupe Medina-de la Rosa
- CONACyT- Division de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190 Morelia, Mich., Mexico
| | - Ángel G Alpuche-Solís
- Division de Biologia Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
| | - Cesaré Ovando-Vázquez
- Division de Biologia Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico.,CONACyT-Centro Nacional de Supercómputo, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
| | - Nguyen E López-Lozano
- CONACyT- Division de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
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12
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Wang Q, Han Y, Lan S, Hu C. Metagenomic Insight Into Patterns and Mechanism of Nitrogen Cycle During Biocrust Succession. Front Microbiol 2021; 12:633428. [PMID: 33815315 PMCID: PMC8009985 DOI: 10.3389/fmicb.2021.633428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
The successional ecology of nitrogen cycling in biocrusts and the linkages to ecosystem processes remains unclear. To explore this, four successional stages of natural biocrust with five batches of repeated sampling and three developmental stages of simulated biocrust were studied using relative and absolute quantified multi-omics methods. A consistent pattern across all biocrust was found where ammonium assimilation, mineralization, dissimilatory nitrite to ammonium (DNiRA), and assimilatory nitrate to ammonium were abundant, while denitrification medium, N-fixation, and ammonia oxidation were low. Mathematic analysis showed that the nitrogen cycle in natural biocrust was driven by dissolved organic N and NO3–. pH and SO42– were the strongest variables affecting denitrification, while C:(N:P) was the strongest variable affecting N-fixation, DNiRA, nitrite oxidation, and dissimilatory nitrate to nitrite. Furthermore, N-fixation and DNiRA were closely related to elemental stoichiometry and redox balance, while assimilatory nitrite to ammonium (ANiRA) and mineralization were related to hydrological cycles. Together with the absolute quantification and network models, our results suggest that responsive ANiRA and mineralization decreased during biocrust succession; whereas central respiratory DNiRA, the final step of denitrification, and the complexity and interaction of the whole nitrogen cycle network increased. Therefore, our study stresses the changing environmental functions in the biocrust N-cycle, which are succession-dependent.
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Affiliation(s)
- Qiong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingchun Han
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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13
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Abstract
The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.
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14
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Chen RW, Li C, He YQ, Cui LQ, Long LJ, Tian XP. Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea. Int J Syst Evol Microbiol 2020; 70:5576-5585. [PMID: 32941125 DOI: 10.1099/ijsem.0.004449] [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
Two novel Gram-stain-positive bacteria, designated as SCSIO 52909T and SCSIO 52915T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909T and SCSIO 52915T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909T (=KCTC 49412T=CGMCC 1.13853T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915T (=KCTC 49411T=CGMCC 1.13852T), are proposed.
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Affiliation(s)
- Rou-Wen Chen
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cun Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Yuan-Qiu He
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Lin-Qing Cui
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
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15
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Singh JK. Structural characteristics of mangrove forest in different coastal habitats of Gulf of Khambhat arid region of Gujarat, west coast of India. Heliyon 2020; 6:e04685. [PMID: 32817898 PMCID: PMC7426573 DOI: 10.1016/j.heliyon.2020.e04685] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/16/2020] [Accepted: 08/07/2020] [Indexed: 11/30/2022] Open
Abstract
Tropical mangroves are most productive and highly sensitive to environmental change and act as good bio-indicators of the environmental quality and health of any coastal ecosystem. The present study initiated to know the current ecological status of mangrove species at four selected study sites namely Bhavnagar (Ghogha coast), Bharuch (Dahej coast), Surat (Dumas beach) and Navsari (Purna estuaries), Gulf of Khambhat, Gujarat, India. Observation for a period of one year from January 2014 to December 2014. Mangroves were evaluated for their community structures at each site by standard quadrant method and different diversity indices were used for characterize the species diversity in a mangrove community. The mangrove forest habitat supports the occurrence of a total 16 species (6 mangrove species and 10 associated plant species), 15 species occurred at Navsari, whereas 7, 6 and 10 species occurred at Bhavnagar, Bharuch and Surat respectively. Out of six mangrove species, Avicennia marina was found to be most dominant and abundant mangroves occurring among all the four study locations. The most abundant and dominant mangrove associates were Suaeda maritima and Sesuvium portulacastrum. Simpson's diversity index was varied at a range of zero to 0.6538, showing the presence of less mangrove diversity. Navsari site presented higher diversity with Shannon and Wiener Species Diversity Index of 1.179 in comparison to other sites. The present study revealed that the species abundance, density and diversity of flora associates depend upon species density and diversity of mangroves. Therefore, mangrove forest habitats need to be protected and regular assess.
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Affiliation(s)
- Jitendra Kumar Singh
- School of Environment and Sustainable Development, Central University of Gujarat, Gandhinagar, India, 382030
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16
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Lavrentyeva EV, Erdyneeva EB, Banzaraktsaeva TG, Kotsyurbenko OR, Baturina OA, Khakhinov VV, Kozyreva LP. Prokaryotic Diversity in the Biotopes of the Gudzhirganskoe Saline Lake (Barguzin Valley, Russia). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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17
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Alexander A, Singh VK, Mishra A, Jha B. Plant growth promoting rhizobacterium Stenotrophomonas maltophilia BJ01 augments endurance against N2 starvation by modulating physiology and biochemical activities of Arachis hypogea. PLoS One 2019; 14:e0222405. [PMID: 31513643 PMCID: PMC6742461 DOI: 10.1371/journal.pone.0222405] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/28/2019] [Indexed: 12/21/2022] Open
Abstract
Arachis hypogea (Peanut) is one of the most important crops, and it is harvested and used for food and oil production. Being a legume crop, the fixation of atmospheric nitrogen is achieved through symbiotic association. Nitrogen deficiency is one of the major constrains for loss of crop productivity. The bacterium Stenotrophomonas maltophilia is known for interactions with plants. In this study, characteristics that promote plant growth were explored for their ability to enhance the growth of peanut plants under N2 deficit condition. In the presence of S. maltophilia, it was observed that fatty acid composition of peanut plants was influenced and increased contents of omega-7 monounsaturated fatty acid and omega-6 fatty acid (γ-Linolenic acid) were detected. Plant growth was increased in plants co-cultivated with PGPR (Plant Growth Promoting Rhizobacteria) under normal and stress (nitrogen deficient) condition. Electrolyte leakage, lipid peroxidation, and H2O2 content reduced in plants, co-cultivated with PGPR under normal (grown in a media supplemented with N2 source; C+) or stress (nitrogen deficient N+) conditions compared to the corresponding control plants (i.e. not co-cultivated with PGPR; C-or N-). The growth hormone auxin, osmoprotectants (proline, total soluble sugars and total amino acids), total phenolic-compounds and total flavonoid content were enhanced in plants co-cultivated with PGPR. Additionally, antioxidant and free radical scavenging (DPPH, hydroxyl and H2O2) activities were increased in plants that were treated with PGPR under both normal and N2 deficit condition. Overall, these results indicate that plants co-cultivated with PGPR, S. maltophilia, increase plant growth, antioxidant levels, scavenging, and stress tolerance under N2 deficit condition. The beneficial use of bacterium S. maltophilia could be explored further as an efficient PGPR for growing agricultural crops under N2 deficit conditions. However, a detail agronomic study would be prerequisite to confirm its commercial role.
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Affiliation(s)
- Ankita Alexander
- Biotechnology and Phycology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad, India
| | - Vijay Kumar Singh
- Biotechnology and Phycology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, India
| | - Avinash Mishra
- Biotechnology and Phycology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad, India
| | - Bhavanath Jha
- Biotechnology and Phycology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad, India
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18
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Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India. Gene 2019; 701:55-64. [DOI: 10.1016/j.gene.2019.02.099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 11/23/2022]
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19
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Xiao H, Li Z, Deng C, Liu L, Chen J, Huang B, Nie X, Liu C, Wang D, Jiang J. Autotrophic Bacterial Community and Microbial CO2 Fixation Respond to Vegetation Restoration of Eroded Agricultural Land. Ecosystems 2019. [DOI: 10.1007/s10021-019-00369-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Cole JK, Morton BR, Cardamone HC, Lake HRR, Dohnalkova AC, Kim YM, Kyle JE, Maezato Y, Dana KL, Metz TO, Romine MF, Nelson WC, Lindemann SR. Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae. Int J Syst Evol Microbiol 2018; 68:2116-2123. [PMID: 29855404 DOI: 10.1099/ijsem.0.002807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109T (=JCM 31876T=DSM 102886T). In addition, examination of the phylogenetics of strain HL-109T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).
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Affiliation(s)
- Jessica K Cole
- Scientific and Computing Operations, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Beau R Morton
- Risk and Decision Sciences, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hayley C Cardamone
- Present address: Center for Infectious Disease Research, Seattle, WA, USA.,Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hannah R R Lake
- Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alice C Dohnalkova
- Environmental Dynamics and Simulations, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yukari Maezato
- Present address: U.S. Naval Research Laboratory, Washington, DC, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl L Dana
- Present address: Nova Research, Inc., Alexandria, VA, USA.,Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret F Romine
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William C Nelson
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephen R Lindemann
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
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21
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Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L. Towards robust and repeatable sampling methods in eDNA-based studies. Mol Ecol Resour 2018; 18:940-952. [PMID: 29802793 DOI: 10.1111/1755-0998.12907] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/28/2023]
Abstract
DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.
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Affiliation(s)
- Ian A Dickie
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Stephane Boyer
- Institut de Recherche sur la Biologie de l'Insecte - UMR 7261 CNRS, Université de Tours, Tours, France
- Applied Molecular Solutions Research Group, Environmental and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, CHARS Campus, Cambridge Bay, NU, Canada
| | | | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Andreas Makiola
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
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22
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Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae. Int J Syst Evol Microbiol 2018; 68:1591-1598. [DOI: 10.1099/ijsem.0.002715] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Dholakiya RN, Kumar R, Mishra A, Mody KH, Jha B. Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat. Front Microbiol 2017; 8:2420. [PMID: 29270160 PMCID: PMC5725476 DOI: 10.3389/fmicb.2017.02420] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/22/2017] [Indexed: 02/02/2023] Open
Abstract
Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15–C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria (Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria (Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H2O2 scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria, isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising antibacterial activities. However, fractionation and further characterization of active compounds from S. variabilis RD-5 are needed for their optimum utilization toward antibacterial purposes.
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Affiliation(s)
- Riddhi N Dholakiya
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Raghawendra Kumar
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Avinash Mishra
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Kalpana H Mody
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
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Zhang Y, Yang Q, Ling J, Van Nostrand JD, Shi Z, Zhou J, Dong J. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing. Front Microbiol 2017; 8:2032. [PMID: 29093705 PMCID: PMC5651520 DOI: 10.3389/fmicb.2017.02032] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/04/2017] [Indexed: 11/18/2022] Open
Abstract
Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.
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Affiliation(s)
- Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Zhou Shi
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China
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25
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Singh VK, Mishra A, Jha B. Anti-quorum Sensing and Anti-biofilm Activity of Delftia tsuruhatensis Extract by Attenuating the Quorum Sensing-Controlled Virulence Factor Production in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2017; 7:337. [PMID: 28798903 PMCID: PMC5526841 DOI: 10.3389/fcimb.2017.00337] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/10/2017] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistance bacteria commonly use cell-to-cell communication that leads to biofilm formation as one of the mechanisms for developing resistance. Quorum sensing inhibition (QSI) is an effective approach for the prevention of biofilm formation. A Gram-negative bacterium, Delftia tsuruhatensis SJ01, was isolated from the rhizosphere of a species of sedge (Cyperus laevigatus) grown along the coastal-saline area. The isolate SJ01 culture and bacterial crude extract showed QSI activity in the biosensor plate containing the reference strain Chromobacterium violaceum CV026. A decrease in the violacein production of approximately 98% was detected with the reference strain C. violaceum CV026. The bacterial extract (strain SJ01) exhibited anti-quorum sensing activity and inhibited the biofilm formation of clinical isolates wild-type Pseudomonas aeruginosa PAO1 and P. aeruginosa PAH. A non-toxic effect of the bacterial extract (SJ01) was detected on the cell growth of the reference strains as P. aeruginosa viable cells were present within the biofilm. It is hypothesized that the extract (SJ01) may change the topography of the biofilm and thus prevent bacterial adherence on the biofilm surface. The extract also inhibits the motility, virulence factors (pyocyanin and rhamnolipid) and activity (elastase and protease) in P. aeruginosa treated with SJ01 extract. The potential active compound present was identified as 1,2-benzenedicarboxylic acid, diisooctyl ester. Microarray and transcript expression analysis unveiled differential expression of quorum sensing regulatory genes. The key regulatory genes, LasI, LasR, RhlI, and RhlR were down-regulated in the P. aeruginosa analyzed by quantitative RT-PCR. A hypothetical model was generated of the transcriptional regulatory mechanism inferred in P. aeruginosa for quorum sensing, which will provide useful insight to develop preventive strategies against the biofilm formation. The potential active compound identified, 1,2-benzenedicarboxylic acid, diisooctyl ester, has the potential to be used as an anti-pathogenic drug for the treatment of biofilm-forming pathogenic bacteria. For that, a detailed study is needed to investigate the possible applications.
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Affiliation(s)
- Vijay K Singh
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
| | - Avinash Mishra
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
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Ziegler M, Roik A, Porter A, Zubier K, Mudarris MS, Ormond R, Voolstra CR. Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea. MARINE POLLUTION BULLETIN 2016; 105:629-40. [PMID: 26763316 DOI: 10.1016/j.marpolbul.2015.12.045] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/25/2015] [Accepted: 12/22/2015] [Indexed: 05/20/2023]
Abstract
Coral-associated bacteria play an increasingly recognized part in coral health. We investigated the effect of local anthropogenic impacts on coral microbial communities on reefs near Jeddah, the largest city on the Saudi Arabian coast of the central Red Sea. We analyzed the bacterial community structure of water and corals (Pocillopora verrucosa and Acropora hemprichii) at sites that were relatively unimpacted, exposed to sedimentation & local sewage, or in the discharge area of municipal wastewaters. Coral microbial communities were significantly different at impacted sites: in both corals the main symbiotic taxon decreased in abundance. In contrast, opportunistic bacterial families, such as e.g. Vibrionaceae and Rhodobacteraceae, were more abundant in corals at impacted sites. In conclusion, microbial community response revealed a measurable footprint of anthropogenic impacts to coral ecosystems close to Jeddah, even though the corals appeared visually healthy.
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Affiliation(s)
- Maren Ziegler
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Adam Porter
- College of Life and Environmental Sciences: Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Khalid Zubier
- Faculty of Marine Science, King Abdulaziz University, PO Box 80207, Jeddah 21589, Saudi Arabia
| | - Mohammed S Mudarris
- Faculty of Marine Science, King Abdulaziz University, PO Box 80207, Jeddah 21589, Saudi Arabia
| | - Rupert Ormond
- Faculty of Marine Science, King Abdulaziz University, PO Box 80207, Jeddah 21589, Saudi Arabia; Centre for Marine Biotechnology and Biodiversity, School of Life Sciences, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS, Scotland, United Kingdom
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.
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