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Galván FS, Alonso-Reyes DG, Albarracín VH. From genes to nanotubes: exploring the UV-resistome in the Andean extremophile Exiguobacterium sp. S17. Extremophiles 2025; 29:17. [PMID: 39964557 DOI: 10.1007/s00792-025-01383-5] [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: 07/09/2024] [Accepted: 02/01/2025] [Indexed: 04/11/2025]
Abstract
Exiguobacterium sp. S17, a polyextremophile isolated from a High-Altitude Andean Lake, exhibits a multi-resistance profile against toxic arsenic concentrations, high UV radiation, and elevated salinity. Here, we characterize the mechanisms underlying the UV resistance of Exiguobacterium sp. S17 (UV-resistome) through comparative genomics within the Exiguobacterium genus and describe morphological and ultrastructural changes using Scanning (SEM) and Transmission (TEM) Electron Microscopy.UV-resistome in Exiguobacterium species ranges from 112 to 132 genes. While we anticipated Exiguobacterium sp. S17 to lead the non-HAAL UV-resistome, it ranked eleventh with 113 genes. This larger UV-resistome in Exiguobacterium spp. aligns with their known adaptation to extreme environments. With SEM/TEM analyses we observed the formation of nanotubes (NTs), a novel finding in Exiguobacterium spp., which increased with higher UV-B doses. These NTs, confirmed to be membranous structures through sensitivity studies and imaging, suggest a role in cellular communication and environmental sensing. Genomic evidence supports the presence of essential NT biogenesis genes in Exiguobacterium sp. S17, further elucidating its adaptive capabilities.Our study highlights the complex interplay of genetic and phenotypic adaptations enabling Exiguobacterium sp. S17 to thrive in extreme UV environments. The novel discovery of NTs under UV stress presents a new avenue for understanding bacterial survival strategies in harsh conditions.
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Affiliation(s)
- Fátima Silvina Galván
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía, Zootecnia y Veterinaria (FAZyV), UNT- CCT CONICET NOA SUR, CONICET, Tucumán, Argentina
| | - Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía, Zootecnia y Veterinaria (FAZyV), UNT- CCT CONICET NOA SUR, CONICET, Tucumán, Argentina
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía, Zootecnia y Veterinaria (FAZyV), UNT- CCT CONICET NOA SUR, CONICET, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Tucumán, Argentina.
- Centro Integral de Microscopía Electrónica (CIME, CONICET-UNT), Camino de Sirga S/N. FAZyV, Finca El Manantial, 4107, Yerba Buena, Tucumán, Argentina.
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Gilmore BF, White TA, Busetti A, McAteer MI, Maggs CA, Thompson TP. Exiguolysin, a Novel Thermolysin (M4) Peptidase from Exiguobacterium oxidotolerans. Microorganisms 2024; 12:2311. [PMID: 39597700 PMCID: PMC11596557 DOI: 10.3390/microorganisms12112311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 10/30/2024] [Accepted: 11/01/2024] [Indexed: 11/29/2024] Open
Abstract
This study details a comprehensive biochemical and structural characterization of exiguolysin, a novel thermolysin-like, caseinolytic peptidase secreted by a marine isolate of Exiguobacterium oxidotolerans strain BW26. Exiguolysin demonstrated optimal proteolytic activity at 37 °C and pH 3, retaining 85% activity at 50 °C, highlighting its potential stability under broad reaction conditions. SDS-PAGE and LC-MS analysis identified the enzyme as a 32 kDa M4-family metalloprotease. Exiguolysin activity was inhibited by 1,10-phenanthroline, confirming its dependence on metal ions for activity. Zymographic analysis and substrate specificity assays revealed selective hydrolysis of matrix metalloproteinase (MMP) substrates but no activity against elastase substrates. Analysis of the predicted gene sequence and structural predictions using AlphaFold identified the presence and position of HEXXH and Glu-Xaa-Xaa-Xaa-Asp motifs, crucial for zinc binding and catalytic activity, characteristic of 'Glu-zincins' and members of the M4 peptidase family. High-throughput screening of a 20 × 20 N-alpha mercaptoamide dipeptide inhibitor library against exiguolysin identified SH-CH2-CO-Met-Tyr-NH2 as the most potent inhibitor, with a Ki of 1.95 μM. Notably, exiguolysin selectively inhibited thrombin-induced PAR-1 activation in PC-3 cells, potentially indicating a potential mechanism of virulence in modulating PAR-1 signalling during infection by disarming PARs. This is the first detailed characterization of a peptidase of the M4 (thermolysin) family in the genus Exiguobacterium which may have industrial application potential and relevance as a putative virulence factor.
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Affiliation(s)
- Brendan F. Gilmore
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
- School of Medicine, University of Limerick, Limerick V94 T9PX, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Tracy A. White
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alessandro Busetti
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Matthew I. McAteer
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Christine A. Maggs
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Thomas P. Thompson
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
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Wang S, Dhulappa A, Quadri SR, Jin P, Wang K, Qiao H, Narsing Rao MP. Reclassification of Some Exiguobacterium Species Based on Genome Analysis. Curr Microbiol 2024; 81:186. [PMID: 38775831 DOI: 10.1007/s00284-024-03735-4] [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: 10/04/2023] [Accepted: 05/08/2024] [Indexed: 06/29/2024]
Abstract
The Exiguobacterium genus comprises Gram-stain-positive and facultatively anaerobic bacteria. Some Exiguobacterium species have previously shown significant high 16S rRNA gene sequence similarities with each other. This study evaluates the taxonomic classification of those Exiguobacterium species through comprehensive genome analysis. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were determined for various Exiguobacterium species pairs. The ANI and dDDH values between Exiguobacterium enclense and Exiguobacterium indicum, Exiguobacterium aquaticum and Exiguobacterium mexicanum, Exiguobacterium soli and Exiguobacterium antarcticum, and Exiguobacterium sibiricum and Exiguobacterium artemiae were above the cut-off level (95-96% for ANI and 70% for dDDH) for species delineation. Based on the findings, we propose to reclassify Exiguobacterium enclense as a later heterotypic synonym of Exiguobacterium indicum, Exiguobacterium aquaticum as a later heterotypic synonym of Exiguobacterium mexicanum, Exiguobacterium soli as a later heterotypic synonym of Exiguobacterium antarcticum and Exiguobacterium sibiricum as a later heterotypic synonym of Exiguobacterium artemiae.
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Affiliation(s)
- Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization/Heilongjiang Black Soil Conservation Engineering and Technology Research Center, Harbin, 150086, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Awalagaway Dhulappa
- Department of Microbiology, Maharani's Science College for Women, Bangalore, 560001, India
| | - Syed Raziuddin Quadri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar, 91431, Kingdom of Saudi Arabia
| | - Pinjiao Jin
- Heilongjiang Academy of Black Soil Conservation and Utilization/Heilongjiang Black Soil Conservation Engineering and Technology Research Center, Harbin, 150086, People's Republic of China
| | - Kangkang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization/Heilongjiang Black Soil Conservation Engineering and Technology Research Center, Harbin, 150086, People's Republic of China
| | - Hui Qiao
- Dengta City Development Reform Affairs Service Center, Dengta, 150499, People's Republic of China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, 3460000, Talca, Chile.
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Zada S, Khan M, Su Z, Sajjad W, Rafiq M. Cryosphere: a frozen home of microbes and a potential source for drug discovery. Arch Microbiol 2024; 206:196. [PMID: 38546887 DOI: 10.1007/s00203-024-03899-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
The world is concerned about the emergence of pathogens and the occurrence and spread of antibiotic resistance among pathogens. Drug development requires time to combat these issues. Consequently, drug development from natural sources is unavoidable. Cryosphere represents a gigantic source of microbes that could be the bioprospecting source of natural products with unique scaffolds as molecules or drug templates. This review focuses on the novel source of drug discovery and cryospheric environments as a potential source for microbial metabolites having potential medicinal applications. Furthermore, the problems encountered in discovering metabolites from cold-adapted microbes and their resolutions are discussed. By adopting modern practical approaches, the discovery of bioactive compounds might fulfill the demand for new drug development.
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Affiliation(s)
- Sahib Zada
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Mohsin Khan
- Department of Biological Sciences, Ohio University Athens, Athens, OH, USA
| | - Zheng Su
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, 87650, Pakistan.
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Shen L, Liu Y, Chen L, Lei T, Ren P, Ji M, Song W, Lin H, Su W, Wang S, Rooman M, Pucci F. Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group. THE ISME JOURNAL 2024; 18:wrad020. [PMID: 38365240 PMCID: PMC10837837 DOI: 10.1093/ismejo/wrad020] [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: 11/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu 241000, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tingting Lei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wei Su
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
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Nawaz S, Rafiq M, Pepper IL, Betancourt WQ, Shah AA, Hasan F. Prevalence and abundance of antibiotic-resistant genes in culturable bacteria inhabiting a non-polar passu glacier, karakorum mountains range, Pakistan. World J Microbiol Biotechnol 2023; 39:94. [PMID: 36754876 DOI: 10.1007/s11274-023-03532-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023]
Abstract
Natural pristine environments including cold habitats are thought to be the potent reservoirs of antibiotic-resistant genes and have been recurrently reported in polar glaciers' native bacteria, nevertheless, their abundance among the non-polar glaciers' inhabitant bacteria is mostly uncharted. Herein we evaluated antibiotic resistance profile, abundance of antibiotic-resistant genes plus class 1, 2, and 3 integron integrases in 65 culturable bacterial isolates retrieved from a non-polar glacier. The 16S rRNA gene sequencing analysis identified predominantly Gram-negative 43 (66.15%) and Gram-positive 22 (33.84%) isolates. Among the Gram-negative bacteria, Gammaproteobacteria were dominant (62.79%), followed by Betaproteobacteria (18.60%) and Alphaproteobacteria (9.30%), whereas Phyla Actinobacteria (50%) and Firmicutes (40.90%) were predominant among Gram-positive. The Kirby Bauer disc diffusion method evaluated significant antibiotic resistance among the isolates. PCR amplification revealed phylum Proteobacteria predominantly carrying 21 disparate antibiotic-resistant genes like; blaAmpC 6 (100%), blaVIM-1, blaSHV and blaDHA 5 (100%) each, blaOXA-1 1 (100%), blaCMY-4 4 (100%), followed by Actinobacteria 14, Firmicutes 13 and Bacteroidetes 11. Tested isolates were negative for blaKPC, qnrA, vanA, ermA, ermB, intl2, and intl3. Predominant Gram-negative isolates had higher MAR index values, compared to Gram-positive. Alignment of protein homology sequences of antibiotic-resistant genes with references revealed amino acid variations in blaNDM-1, blaOXA-1, blaSHV, mecA, aac(6)-Ib3, tetA, tetB, sul2, qnrB, gyrA, and intI1. Promising antibiotic-resistant bacteria, harbored with numerous antibiotic-resistant genes and class 1 integron integrase with some amino acid variations detected, accentuating the mandatory focus to evaluate the intricate transcriptome analysis of glaciated bacteria conferring antibiotic resistance.
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Affiliation(s)
- Sabir Nawaz
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Rafiq
- Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan.
| | - Ian L Pepper
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, 85745, Tucson, AZ, USA
| | - Walter Q Betancourt
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, 85745, Tucson, AZ, USA
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Aguilera-Torres C, Riveros G, Morales LV, Sierra-Almeida A, Schoebitz M, Hasbún R. Relieving your stress: PGPB associated with Andean xerophytic plants are most abundant and active on the most extreme slopes. Front Microbiol 2023; 13:1062414. [PMID: 36741893 PMCID: PMC9889642 DOI: 10.3389/fmicb.2022.1062414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Plants interact with plant growth-promoting bacteria (PGPB), especially under stress condition in natural and agricultural systems. Although a potentially beneficial microbiome has been found associated to plants from alpine systems, this plant- PGPB interaction has been scarcely studied. Nevados de Chillán Complex hold one of the southernmost xerophytic formations in Chile. Plant species living there have to cope with drought and extreme temperatures during the growing season period, microclimatic conditions that become harsher on equatorial than polar slopes, and where the interaction with PGPB could be key for plant survival. Our goal was to study the abundance and activity of different PGPB associated to two abundant plant species of Andean xerophytic formations on contrasting slopes. Methods Twenty individuals of Berberis empetrifolia and Azorella prolifera shrubs were selected growing on a north and south slope nearby Las Fumarolas, at 2,050 m elevation. On each slope, microclimate based on temperature and moisture conditions were monitored throughout the growing period (oct. - apr.). Chemical properties of the soil under plant species canopies were also characterized. Bacterial abundance was measured as Log CFU g-1 from soil samples collected from each individual and slope. Then, the most abundant bacterial colonies were selected, and different hormonal (indoleacetic acid) and enzymatic (nitrogenase, phosphatase, ACC-deaminase) mechanisms that promote plant growth were assessed and measured. Results and Discussion Extreme temperatures were observed in the north facing slope, recording the hottest days (41 vs. 36°C) and coldest nights (-9.9 vs. 6.6°C). Moreover, air and soil moisture were lower on north than on south slope, especially late in the growing season. We found that bacterial abundance was higher in soils on north than on south slope but only under B. empetrifolia canopy. Moreover, the activity of plant growth-promoting mechanisms varied between slopes, being on average higher on north than on south slope, but with plant species-dependent trends. Our work showed how the environmental heterogeneity at microscale in alpine systems (slope and plant species identity) underlies variations in the abundance and plant growth promoting activity of the microorganisms present under the plant canopy of the Andean xerophytic formations and highlight the importance of PGPB from harsh systems as biotechnological tools for restoration.
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Affiliation(s)
- Carla Aguilera-Torres
- Grupo de Ecofisiología Térmica, Facultad de Ciencias Naturales y Oceanográficas, Departamento de Botánica, Universidad de Concepción, Concepción, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile,Rizoma, Centro de Estudios Agroecológicos y Botánicos, Valparaíso, Chile
| | - Gustavo Riveros
- Laboratorio de Microbiología de Suelos, Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Concepción, Chile
| | - Loreto V. Morales
- Grupo de Ecofisiología Térmica, Facultad de Ciencias Naturales y Oceanográficas, Departamento de Botánica, Universidad de Concepción, Concepción, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile
| | - Angela Sierra-Almeida
- Grupo de Ecofisiología Térmica, Facultad de Ciencias Naturales y Oceanográficas, Departamento de Botánica, Universidad de Concepción, Concepción, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile,*Correspondence: Angela Sierra-Almeida,
| | - Mauricio Schoebitz
- Laboratorio de Microbiología de Suelos, Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Concepción, Chile,Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Rodrigo Hasbún
- Laboratorio de Epigenética Vegetal, Facultad de Ciencias Forestales, Departamento de Silvicultura, Universidad de Concepción, Concepción, Chile
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Ma Y, You F, Parry D, Urban A, Huang L. Adaptive growth and acidogenic fermentation performance of haloalkaliphilic bacterial communities enriched from biofilms colonising strongly alkaline and saline bauxite residue. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159131. [PMID: 36183768 DOI: 10.1016/j.scitotenv.2022.159131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The present study aimed to characterise the adaptive growth and acidogenic fermentation performance of haloalkaliphilic bacteria sourced from field biofilms colonising seawater-treated bauxite residue, under moderate and extremely alkaline pH conditions (8.5 to 10.8) and coupled saline (EC ≈ 50 mS/cm) conditions. The haloalkaliphilic bacterial communities demonstrated strong adaptiveness to the increasing pH from 8.5 to 10.8. The dominant groups were Exiguobacterales and Bacillales at pH 8.5 and 10, but Lactobacillales and Bacillales at pH 10.8. The exposure to pH 10.8 initially delayed bacterial growth in the first 24 h, but which rapidly recovered to a peak rate at 48 h similar to that in the pH 10 treatment. Correspondingly, lactic acid concentration at pH 10.8 rapidly rose to as high as >2000 mg/L at 48 h. Bacterial growth and organic acid production were positively related to carbohydrate supply. Overall, these bacterial groups fermented glucose to produce mainly lactic acid (>80 %) and other acids (such as acetic acid, formic acid, and succinic acid), leading to 0.5-2.0 units of pH reduction, despite the strong buffering capacity in the culture solution. The bacteria could up-regulate their phosphatase activity to mineralise the organic P in the basal nutrient broth, but increasing soluble phosphate-P at a 1:10 of glucose-C was beneficial. The biofilm-sourced bacteria communities contained redundant fermentative haloalkaliphilic groups which were adaptive to strongly alkaline pH and saline conditions.
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Affiliation(s)
- Yuanying Ma
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - David Parry
- Rio Tinto, Brisbane, Queensland 4000, Australia
| | - Anja Urban
- Queensland Alumina Limited, Gladstone, Queensland 4680, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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Krumbeck JA, Turner DD, Diesel A, Hoffman AR, Heatley JJ. Skin microbiota of quaker parrots (Myiopsitta monachus) with normal feathering or feather loss via next-generation sequencing technology. J Exot Pet Med 2022. [DOI: 10.1053/j.jepm.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Rodríguez-Castrejón UE, Serafin-Muñoz AH, Alvarez-Vargas A, Cruz-Jímenez G, Noriega-Luna B. Isolation and molecular identification of native As-resistant bacteria: As(III) and As(V) removal capacity and possible mechanism of detoxification. Arch Microbiol 2022; 204:191. [PMID: 35194697 DOI: 10.1007/s00203-022-02794-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022]
Abstract
The study of arsenic (As)-resistant microorganisms with high As removal capacity is fundamental for the development of economically sustainable technologies used for the treatment of water contaminated with metalloid. In the current study, four bacterial strains were isolated from As-contaminated water samples of the Xichu region, Mexico. Based on 16S rRNA gene sequencing and phylogenetic analysis of the isolated strains, Rhodococcus gordoniae, Microbacterium hydrocarbonoxydans, Exiguobacterium indicum, and Pseudomonas kribbensis were identified as potential As removal strains. R. gordoniae shows the highest growth capacity in both As(III) and As(V). R. gordoniae, M. hydrocarbonoxydans, and E. indicum removed approximately 81.6, 79.9, and 61.7% of As(III), as well as 77.2, 68.9, and 74.8% of As(V), respectively. P. kribbensis removed only about 80.2% of As(V). This study contributes to the possible detoxification mechanisms employed by these bacteria. Such insight could be crucial in the successful implementation of in situ bioremediation programs using these little-known bacteria.
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Affiliation(s)
- U E Rodríguez-Castrejón
- Division of Engineering, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
| | - A H Serafin-Muñoz
- Division of Engineering, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico.
| | - A Alvarez-Vargas
- Division of Natural and Exact Sciences, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
| | - G Cruz-Jímenez
- Division of Natural and Exact Sciences, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
| | - B Noriega-Luna
- Division of Engineering, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
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Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China. Microorganisms 2021; 10:microorganisms10010066. [PMID: 35056515 PMCID: PMC8779447 DOI: 10.3390/microorganisms10010066] [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: 11/25/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022] Open
Abstract
The genome of Exiguobacterium aurantiacum SW-20 (E. aurantiacum SW-20), a salt-tolerant microorganism with petroleum hydrocarbon-degrading ability isolated from the Changqing Oilfield, was sequenced and analyzed. Genomic data mining even comparative transcriptomics revealed that some genes existed in SW-20 might be related to the salt tolerance. Besides, genes related to petroleum hydrocarbon degradation discovered in genomic clusters were also found in the genome, indicating that these genes have a certain potential in the bioremediation of petroleum pollutants. Multiple natural product biosynthesis gene clusters were detected, which was critical for survival in the extreme conditions. Transcriptomic studies revealed that some genes were significantly up-regulated as salinity increased, implying that these genes might be related to the salt tolerance of SW-20 when living in a high salt environment. In our study, gene clusters including salt tolerance, heavy metal tolerance and alkane degradation were all compared. When the same functional gene clusters from different strains, it was discovered that the gene composition differed. Comparative genomics and in-depth analysis provided insights into the physiological features and adaptation strategies of E. aurantiacum SW-20 in the oilfield environment. Our research increased the understanding of niches adaption of SW-20 at genomic level.
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López MC, Galán B, Carmona M, Navarro Llorens JM, Peretó J, Porcar M, Getino L, Olivera ER, Luengo JM, Castro L, García JL. Xerotolerance: A New Property in Exiguobacterium Genus. Microorganisms 2021; 9:2455. [PMID: 34946057 PMCID: PMC8706201 DOI: 10.3390/microorganisms9122455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
The highly xerotolerant bacterium classified as Exiguobacterium sp. Helios isolated from a solar panel in Spain showed a close relationship to Exiguobacterium sibiricum 255-15 isolated from Siberian permafrost. Xerotolerance has not been previously described as a characteristic of the extremely diverse Exiguobacterium genus, but both strains Helios and 255-15 showed higher xerotolerance than that described in the reference xerotolerant model strain Deinococcus radiodurans. Significant changes observed in the cell morphology after their desiccation suggests that the structure of cellular surface plays an important role in xerotolerance. Apart from its remarkable resistance to desiccation, Exiguobacterium sp. Helios strain shows several polyextremophilic characteristics that make it a promising chassis for biotechnological applications. Exiguobacterium sp. Helios cells produce nanoparticles of selenium in the presence of selenite linked to its resistance mechanism. Using the Lactobacillus plasmid pRCR12 that harbors a cherry marker, we have developed a transformation protocol for Exiguobacterium sp. Helios strain, being the first time that a bacterium of Exiguobacterium genus has been genetically modified. The comparison of Exiguobacterium sp. Helios and E. sibiricum 255-15 genomes revealed several interesting similarities and differences. Both strains contain a complete set of competence-related DNA transformation genes, suggesting that they might have natural competence, and an incomplete set of genes involved in sporulation; moreover, these strains not produce spores, suggesting that these genes might be involved in xerotolerance.
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Affiliation(s)
- María Castillo López
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain;
| | - Beatriz Galán
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
| | - Manuel Carmona
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain;
| | - Juli Peretó
- Program for Applied Systems Biology and Synthetic Biology, Instituto de Biología Integrativa de Sistemas (I2SYSBIO) (UV-CSIC), Carrer del Catedràtic Agustín Escardino Benlloch s/n, 46980 Paterna, Spain; (J.P.); (M.P.)
- Department of Biochemistry and Molecular Biology, University of Valencia, 46100 Burjassot, Spain
| | - Manuel Porcar
- Program for Applied Systems Biology and Synthetic Biology, Instituto de Biología Integrativa de Sistemas (I2SYSBIO) (UV-CSIC), Carrer del Catedràtic Agustín Escardino Benlloch s/n, 46980 Paterna, Spain; (J.P.); (M.P.)
| | - Luis Getino
- Department of Molecular Biology, Facultades de Veterinaria y Biología, Universidad de León, 24007 León, Spain; (L.G.); (E.R.O.); (J.M.L.)
| | - Elías R. Olivera
- Department of Molecular Biology, Facultades de Veterinaria y Biología, Universidad de León, 24007 León, Spain; (L.G.); (E.R.O.); (J.M.L.)
| | - José M. Luengo
- Department of Molecular Biology, Facultades de Veterinaria y Biología, Universidad de León, 24007 León, Spain; (L.G.); (E.R.O.); (J.M.L.)
| | - Laura Castro
- Department of Applied Mathematics, Materials Science and Engineering and Electronic Technology, School of Experimental Sciences and Technology, Rey Juan Carlos University, 28933 Móstoles, Spain;
| | - José Luís García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
- Program for Applied Systems Biology and Synthetic Biology, Instituto de Biología Integrativa de Sistemas (I2SYSBIO) (UV-CSIC), Carrer del Catedràtic Agustín Escardino Benlloch s/n, 46980 Paterna, Spain; (J.P.); (M.P.)
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Chemical, Biological and Morphological Properties of Fine Particles during Local Rice Straw Burning Activities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18158192. [PMID: 34360485 PMCID: PMC8346042 DOI: 10.3390/ijerph18158192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022]
Abstract
Rice straw is commonly burned openly after harvesting in Malaysia and many other Asian countries where rice is the main crop. This operation emits a significant amount of air pollution, which can have severe consequences for indoor air quality, public health, and climate change. Therefore, this study focuses on determining the compositions of trace elements and the morphological properties of fine particles. Furthermore, the species of bacteria found in bioaerosol from rice burning activities were discovered in this study. For morphological observation of fine particles, FESEM-EDX was used in this study. Two main categories of particles were found, which were natural particles and anthropogenic particles. The zinc element was found during the morphological observation and was assumed to come from the fertilizer used by the farmers. ICP-OES identifies the concentration of trace elements in the fine particle samples. A cultured method was used in this study by using nutrient agar. From this study, several bacteria were identified: Exiguobavterium indicum, Bacillus amyloliquefaciens, Desulfonema limicola str. Jadabusan, Exiguobacterium acetylicum, Lysinibacillus macrolides, and Bacillus proteolyticus. This study is important, especially for human health, and further research on the biological composition of aerosols should be conducted to understand the effect of microorganisms on human health.
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Pham VHT, Ahn JY, Ro YH, Ravindran B, Kim JS, Chang SW, Shim JH, Chung WJ. The efficiency of potential food waste-degrading bacteria under harsh conditions. J Appl Microbiol 2021; 132:340-350. [PMID: 33900007 DOI: 10.1111/jam.15119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 11/27/2022]
Abstract
AIMS Investigate the impact of highly adapted bacterial strains and their ability in waste degradation under a wide range of temperatures. METHODS AND RESULTS Bacteria isolated from soil and food waste were grown in various media under fluctuated temperatures. After screening for organic compound degradation, the seven strongest bacterial strains have been selected for further experiments. Their enzyme activities were expressed in terms of the size of the hydrolysis zone in a wide temperature range of 2.5-70 ºC. The enzyme production assay was carried out for each protease, cellulase, and amylase. The waste degradation was determined with a maximum 80% decrease in the volume of food waste in 21 days compared to the control in lab-scale with enriched bacterial cultures and soil bacteria as additives at room temperature around 18 ºC-20 ºC. CONCLUSION These seven bacteria are promising candidates for food waste biodegradation in composting especially in the winter without heating expense for maintaining ambient temperature. SIGNIFICANCE AND IMPACT OF THE STUDY It is necessary to coax the uncultured bacteria from the various environments into the laboratory for investigating their valuable functions. Herein, using enrichment culture of consortium and additive of soil have illustrated the significant mean in food waste degradation.
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Affiliation(s)
- Van Hong Thi Pham
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Jeong Yoon Ahn
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Yeon Hee Ro
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Balasubramani Ravindran
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Jai Soo Kim
- Microbial Ecology Laboratory, Department of Life Science, Kyonggi University, South Korea
| | - Soon Woong Chang
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Jea Hong Shim
- Fertilizer Resources Lab, Soil and Fertilizer Management Division, National Institute of Agricultural Science, Rural Development Administration
| | - Woo Jin Chung
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
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Yasin MT, Ali Y, Ahmad K, Ghani A, Amanat K, Basheir MM, Faheem M, Hussain S, Ahmad B, Hussain A, Bokhari SAI. Alkaline lipase production by novel meso-tolerant psychrophilic Exiguobacterium sp. strain (AMBL-20) isolated from glacier of northeastern Pakistan. Arch Microbiol 2020; 203:1309-1320. [PMID: 33325000 DOI: 10.1007/s00203-020-02133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 11/30/2022]
Abstract
Lipase is an important commercial enzyme with unique and versatile biotechnological applications. This study was conducted to biosynthesize and characterizes alkaliphilic lipase by Exiguobacterium sp. strain AMBL-20T isolated from the glacial water samples of the northeastern (Gilgit-Baltistan) region of Pakistan. The isolated bacterium was identified as Exiguobaterium sp. strain AMBL-20T on the basis of morphological, biochemical, and phylogenetic analysis of 16S rRNA sequences with GenBank accession number MW229267. The bacterial strain was further screened for its lipolytic activity, biosynthesis, and characterization by different parameters with the aim of maximizing lipase activity. Results showed that 2% Olive oil, 0.2% peptone at 25 °C, pH 8, and 24 h of incubation time found optimal for maximum lipase production. The lipase enzyme was partially purified by ammonium sulphate precipitation and its activity was standardized at pH 8 under 30 °C temperature. The enzyme showed functional stability over a range of temperature and pH. Hence, extracellular alkaliphilic lipase from Exiguobacterium sp. is a potential candidate with extraordinary industrial applications, particularly in bio-detergent formulations.
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Affiliation(s)
- Muhammad Talha Yasin
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Yasir Ali
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Abdul Ghani
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Kinza Amanat
- Department of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Mudassir Basheir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Saddam Hussain
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Bashir Ahmad
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Adil Hussain
- Department of Biotechnology, University of Okara, Okara, 56130, Pakistan
| | - Syed Ali Imran Bokhari
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
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Srivastava AK, Srivastava R, Sharma A, Bharati AP, Tiwari PK, Singh AK, Srivastava AK, Chakdar H, Kashyap PL, Saxena AK. Pan-genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:639-650. [PMID: 32996243 DOI: 10.1111/1758-2229.12890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The stint of the bacterial species is convoluting, but the new algorithms to calculate genome-to-genome distance (GGD) and DNA-DNA hybridization (DDH) for comparative genome analysis have rejuvenated the exploration of species and sub-species characterization. The present study reports the first whole genome sequence of Exiguobacterium profundum PHM11. PHM11 genome consist of ~ 2.92 Mb comprising 48 contigs, 47.93% G + C content. Functional annotations revealed a total of 3033 protein coding genes and 33 non-protein coding genes. Out of these, only 2316 could be characterized and others reported as hypothetical proteins. The comparative analysis of predicted proteome of PHM11 with five other Exiguobacterium sp. identified 3806 clusters, out of which the PHM11 shared a total of 2723 clusters having 1664 common clusters, 131 singletons and 928 distributed between five species. The pan-genome analysis of 70 different genomic sequences of Exigubacterium strains devoid of a species taxon was done on the basis of GGD and the DDH which identified eight genomes analogous to the PHM11 at species level and may be characterized as E. profundum. The ANI value and phylogenetic tree analysis also support the same. The results regarding pan-genome analysis provide a convincing insight for delineation of these eight strains to species.
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Affiliation(s)
- Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Ruchi Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Anjney Sharma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Akhilendra Pratap Bharati
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Praveen Kumar Tiwari
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Alok Kumar Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Anchal Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
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Meng X, Chang YQ, Zhou LY, Du ZJ. Exiguobacterium flavidum sp. nov., isolated from the Red Maple Lake. Int J Syst Evol Microbiol 2020; 70:2359-2365. [PMID: 32065575 DOI: 10.1099/ijsem.0.004048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, motile, facultatively anaerobic, non-sporing, and rod-shaped bacterial strain, designated HF60T, was isolated from the Red Maple Lake of Guizhou Province, China. The DNA G+C content of the strain HF60T was 55.0 %. The predominant isoprenoid quinones were identified as MK-7 (56.4 %) and MK-8 (35.7 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophosphoglycolipid. The major fatty acids were anteiso-C13 : 0, iso-C15 : 0, C16 : 0 and iso-C13 : 0. The strain had cell wall peptidoglycan type A3α l-Lys-Gly. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain HF60T belonged to the genus Exiguobacterium and was most closely related to Exiguobacterium sibiricum JCM 13490T (97.2 % 16S rRNA gene sequence similarity), followed by Exiguobacterium undae DSM 14481T (97.1 %), Exiguobacterium antarcticum DSM 14480T (96.9 %) and Exiguobacterium aurantiacum NBRC 14763T (94.5 %). The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness indicated that strain HF60T can be considered to represent a novel species of the genus Exiguobacterium, for which the name Exiguobacterium flavidum sp. nov. is proposed, The type strain is HF60T (=MCCC 1H00336T=KCTC 33987T).
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Affiliation(s)
- Xue Meng
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Qi Chang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Liu-Yan Zhou
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China.,State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
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Hotaling S, Foley ME, Zeglin LH, Finn DS, Tronstad LM, Giersch JJ, Muhlfeld CC, Weisrock DW. Microbial assemblages reflect environmental heterogeneity in alpine streams. GLOBAL CHANGE BIOLOGY 2019; 25:2576-2590. [PMID: 31077498 DOI: 10.1111/gcb.14683] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/01/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasingly homogeneous. Much attention has been devoted to macroinvertebrate diversity in alpine headwaters, yet to fully understand the breadth of climate change threats, a more thorough accounting of microbial diversity is needed. We characterized microbial diversity (specifically Bacteria and Archaea) of 13 streams in two disjunct Rocky Mountain subranges through 16S rRNA gene sequencing. Our study encompassed the spectrum of alpine stream sources (glaciers, snowfields, subterranean ice, and groundwater) and three microhabitats (ice, biofilms, and streamwater). We observed no difference in regional (γ) diversity between subranges but substantial differences in diversity among (β) stream types and microhabitats. Within-stream (α) diversity was highest in groundwater-fed springs, lowest in glacier-fed streams, and positively correlated with water temperature for both streamwater and biofilm assemblages. We identified an underappreciated alpine stream type-the icy seep-that are fed by subterranean ice, exhibit cold temperatures (summer mean <2°C), moderate bed stability, and relatively high conductivity. Icy seeps will likely be important for combatting biodiversity losses as they contain similar microbial assemblages to streams fed by surface ice yet may be buffered against climate change by insulating debris cover. Our results show that the patterns of microbial diversity support an ominous trend for alpine stream biodiversity; as meltwater sources decline, stream communities will become more diverse locally, but regional diversity will be lost. Icy seeps, however, represent a source of optimism for the future of biodiversity in these imperiled ecosystems.
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Affiliation(s)
- Scott Hotaling
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Mary E Foley
- Department of Biology, University of Kentucky, Lexington, Kentucky
- Biology Department, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Lydia H Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Debra S Finn
- Department of Biology, Missouri State University, Springfield, Missouri
| | - Lusha M Tronstad
- Wyoming Natural Diversity Database, University of Wyoming, Laramie, Wyoming
| | - J Joseph Giersch
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana
| | - Clint C Muhlfeld
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana
- Flathead Lake Biological Station, The University of Montana, Polson, Montana
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, Kentucky
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Singh VK, Mishra A, Jha B. 3-Benzyl-Hexahydro-Pyrrolo[1,2-a]Pyrazine-1,4-Dione Extracted From Exiguobacterium indicum Showed Anti-biofilm Activity Against Pseudomonas aeruginosa by Attenuating Quorum Sensing. Front Microbiol 2019; 10:1269. [PMID: 31231348 PMCID: PMC6568026 DOI: 10.3389/fmicb.2019.01269] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 05/22/2019] [Indexed: 11/13/2022] Open
Abstract
Bacterial cell-to-cell communication promotes biofilm formation and can potentially lead to multidrug resistance development. Quorum sensing inhibition (QSI) is an effective and widely employed strategy against biofilm formation. The extract from Exiguobacterium indicum SJ16, a gram-positive bacterium, isolated from the rhizosphere of Cyperus laevigatus showed significant anti-quorum sensing activity (about 99%) against the reference Chromobacterium violaceum CV026 strain without exerting any antibacterial effect. The potentially active QSI compound identified in the SJ16 extract was 3-Benzyl-hexahydro-pyrrolo[1, 2-a]pyrazine-1,4-dione. The SJ16 extract containing this active compound showed significant anti-quorum sensing activity against a model quorum sensing bacterium strain Pseudomonas aeruginosa PAO1 and a clinical isolate P. aeruginosa PAH by preventing biofilm formation without attenuating the cell growth within the biofilm. More specifically, the SJ16 extract changed the topography and architecture of the biofilm, thus preventing bacterial adherence and further development of the biofilm. Furthermore, it decreased virulence factors (rhamnolipid and pyocyanin), the bacterial motility, as well as the elastase, and protease activities in P. aeruginosa. Microarray analysis revealed the differential expression of quorum sensing regulatory genes. Based on these results, we herein propose a hypothetical model, characterizing the role of this QSI agent in the transcriptional regulation of quorum sensing in P. aeruginosa PAO1, demonstrating that this compound has significant drug-development potential. Further research is required to delineate its possible applications in therapeutics in the context of biofilm forming bacterial infections.
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Affiliation(s)
- Vijay K Singh
- Division of Biotechnology and Phycology, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Avinash Mishra
- Division of Biotechnology and Phycology, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Bhavanath Jha
- Division of Biotechnology and Phycology, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
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Aburto C, Castillo C, Cornejo F, Arenas-Salinas M, Vásquez C, Guerrero C, Arenas F, Illanes A, Vera C. β-Galactosidase from Exiguobacterium acetylicum: Cloning, expression, purification and characterization. BIORESOURCE TECHNOLOGY 2019; 277:211-215. [PMID: 30639092 DOI: 10.1016/j.biortech.2019.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
The main goal of this work was to evaluate the performance of β-galactosidase from Exiguobacterium acetylicum MF03 in both hydrolysis and transgalactosylation reactions from different substrates. The enzyme gene was expressed in Escherichia coli BL21 (DE3), sequenced, and subjected to bioinformatic and kinetic assessment. Results showed that the enzyme was able to hydrolyze lactulose and o-nitrophenyl-β-d-galactopyranoside, but unable to hydrolyze lactose, o-nitrophenyl-β-d-glucopyranoside, butyl- and pentyl-β-d-galactosides. This unique and novel substrate specificity converts the E. acetylicum MF03 β-galactosidase into an ideal catalyst for the formulation of an enzymatic kit for lactulose quantification in thermally processed milk. This is because costly steps to eliminate glucose (resulting from hydrolysis of lactose when a customary β-galactosidase is used) can be avoided.
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Affiliation(s)
- Carla Aburto
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile
| | - Carlos Castillo
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Fabián Cornejo
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Mauricio Arenas-Salinas
- Center of Bioinformatic and Molecular Simulation, Faculty of Engineering, Universidad de Talca (UTALCA), Talca, Chile
| | - Claudio Vásquez
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Cecilia Guerrero
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile
| | - Felipe Arenas
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Andrés Illanes
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile
| | - Carlos Vera
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile (USACH), Santiago, Chile.
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21
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White RA, Soles SA, Gavelis G, Gosselin E, Slater GF, Lim DSS, Leander B, Suttle CA. The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges. Front Microbiol 2019; 9:3189. [PMID: 30671032 PMCID: PMC6331483 DOI: 10.3389/fmicb.2018.03189] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 12/10/2018] [Indexed: 11/25/2022] Open
Abstract
Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake microbialites. Strain RW2 could also contribute to microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., microbialites/microbial mats), and a blueprint model for diverse metabolic processes.
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Affiliation(s)
- Richard Allen White
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Sarah A Soles
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Greg Gavelis
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Emma Gosselin
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Greg F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Darlene S S Lim
- Bay Area Environmental Institute, Petaluma, CA, United States.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Brian Leander
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
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Dias LM, Folador ARC, Oliveira AM, Ramos RTJ, Silva A, Baraúna RA. Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome. Genome Biol Evol 2018; 10:731-741. [PMID: 29438502 PMCID: PMC5833320 DOI: 10.1093/gbe/evy029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth's cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was >90%. Three genomic islands were identified in the E. antarcticum B7 genome. These islands contained genes involved in flagella biosynthesis and chemotaxis, as well as enzymes for carotenoid biosynthesis. Clustering of cold shock proteins by Ka/Ks ratio suggests the occurrence of a positive selection over these genes. Neighbor-joining clustering of complete genomes showed that the E. sibiricum was the most closely related to E. antarcticum. A total of 92 genes were shared between Exiguobacterium and Psychrobacter. A reduction in the genomic content of E. antarcticum B7 was observed. It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. In our study, eight genomes of Exiguobacterium and Psychrobacter were compared and analysed. Psychrobacter showed higher genomic plasticity and E. antarcticum B7 presented a large decrease in genomic content without changing its ability to grow in cold environments.
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Affiliation(s)
- Larissa M Dias
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Amanda M Oliveira
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rommel T J Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
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Shamshuddin Z, Kirse C, Briesen H, Doble M. Mathematical modelling of AHL production in Exiguobacterium MPO strain. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Remonsellez F, Castro-Severyn J, Pardo-Esté C, Aguilar P, Fortt J, Salinas C, Barahona S, León J, Fuentes B, Areche C, Hernández KL, Aguayo D, Saavedra CP. Characterization and Salt Response in Recurrent Halotolerant Exiguobacterium sp. SH31 Isolated From Sediments of Salar de Huasco, Chilean Altiplano. Front Microbiol 2018; 9:2228. [PMID: 30294311 PMCID: PMC6158405 DOI: 10.3389/fmicb.2018.02228] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/31/2018] [Indexed: 12/22/2022] Open
Abstract
Poly-extremophiles microorganisms have the capacity to inhabit hostile environments and can survive several adverse conditions that include as variations in temperature, pH, and salinity, high levels UV light and atmospheric pressure, and even the presence of toxic compounds and the formation of reactive oxygen species (ROS). A halotolerant Exiguobacterium strain was isolated from Salar de Huasco (Chilean Altiplano), a well-known shallow lake area with variable salinity levels, little human intervention, and extreme environmental conditions, which makes it ideal for the study of resistant mechanisms and the evolution of adaptations. This bacterial genus has not been extensively studied, although its cosmopolitan location indicates that it has high levels of plasticity and adaptive capacity. However, to date, there are no studies regarding the tolerance and resistance to salinity and osmotic pressure. We set out to characterize the Exiguobacterium sp. SH31 strain and describe its phenotypical and genotypical response to osmotic stress. In this context, as a first step to characterize the response to the SH31 strain to salinity and to establish the bases for a molecular study, we proposed to compare its response under three salt conditions (0, 25, and 50 g/l NaCl). Using different physiology, genomic, and transcriptomic approaches, we determined that the bacterium is able to grow properly in a NaCl concentration of up to 50 g/l; however, the best growth rate was observed at 25 g/l. Although the presence of flagella is not affected by salinity, motility was diminished at 25 g/l NaCl and abolished at 50 g/l. Biofilm formation was induced proportionally with increases in salinity, which was expected. These phenotypic results correlated with the expression of related genes: fliG and fliS Motility); opuBA and putP (transport); glnA, proC, gltA, and gbsA (compatible solutes); ywqC, bdlA, luxS y pgaC (biofilm and stress response); and therefore, we conclude that this strain effectively modifies gene expression and physiology in a differential manner when faced with different concentrations of NaCl and these modifications aid survival.
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Affiliation(s)
- Francisco Remonsellez
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Jonathan Fortt
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Cesar Salinas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Sergio Barahona
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Joice León
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Bárbara Fuentes
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Klaudia L. Hernández
- Centro de Investigación Marina Quintay, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities. Appl Environ Microbiol 2018; 84:AEM.02755-17. [PMID: 29330184 PMCID: PMC5812945 DOI: 10.1128/aem.02755-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/18/2022] Open
Abstract
Extreme habitats are not only limited to natural environments, but also exist in manmade systems, for instance, household appliances such as dishwashers. Limiting factors, such as high temperatures, high and low pHs, high NaCl concentrations, presence of detergents, and shear force from water during washing cycles, define microbial survival in this extreme system. Fungal and bacterial diversity in biofilms isolated from rubber seals of 24 different household dishwashers was investigated using next-generation sequencing. Bacterial genera such as Pseudomonas, Escherichia, and Acinetobacter, known to include opportunistic pathogens, were represented in most samples. The most frequently encountered fungal genera in these samples belonged to Candida, Cryptococcus, and Rhodotorula, also known to include opportunistic pathogenic representatives. This study showed how specific conditions of the dishwashers impact the abundance of microbial groups and investigated the interkingdom and intrakingdom interactions that shape these biofilms. The age, usage frequency, and hardness of incoming tap water of dishwashers had significant impact on bacterial and fungal community compositions. Representatives of Candida spp. were found at the highest prevalence (100%) in all dishwashers and are assumed to be one of the first colonizers in recently purchased dishwashers. Pairwise correlations in tested microbiomes showed that certain bacterial groups cooccur, as did the fungal groups. In mixed bacterial-fungal biofilms, early adhesion, contact, and interactions were vital in the process of biofilm formation, where mixed complexes of bacteria and fungi could provide a preliminary biogenic structure for the establishment of these biofilms. IMPORTANCE Worldwide demand for household appliances, such as dishwashers and washing machines, is increasing, as is the number of immunocompromised individuals. The harsh conditions in household dishwashers should prevent the growth of most microorganisms. However, our research shows that persisting polyextremotolerant groups of microorganisms in household appliances are well established under these unfavorable conditions and supported by the biofilm mode of growth. The significance of our research is in identifying the microbial composition of biofilms formed on dishwasher rubber seals, how diverse abiotic conditions affect microbiota, and which key microbial members were represented in early colonization and contamination of dishwashers, as these appliances can present a source of domestic cross-contamination that leads to broader medical impacts.
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Rafiq M, Hayat M, Anesio AM, Jamil SUU, Hassan N, Shah AA, Hasan F. Recovery of metallo-tolerant and antibiotic resistant psychrophilic bacteria from Siachen glacier, Pakistan. PLoS One 2017; 12:e0178180. [PMID: 28746396 PMCID: PMC5528264 DOI: 10.1371/journal.pone.0178180] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/09/2017] [Indexed: 11/18/2022] Open
Abstract
Cultureable bacterial diversity of previously unexplored Siachen glacier, Pakistan, was studied. Out of 50 isolates 33 (66%) were Gram negative and 17 (34%) Gram positive. About half of the isolates were pigment producers and were able to grow at 4-37°C. 16S rRNA gene sequences revealed Gram negative bacteria dominated by Proteobacteria (especially γ-proteobacteria and β-proteobacteria) and Flavobacteria. The genus Pseudomonas (51.51%, 17) was dominant among γ- proteobacteria. β-proteobacteria constituted 4 (12.12%) Alcaligenes and 4 (12.12%) Janthinobacterium strains. Among Gram positive bacteria, phylum Actinobacteria, Rhodococcus (23.52%, 4) and Arthrobacter (23.52%, 4) were the dominating genra. Other bacteria belonged to Phylum Firmicutes with representative genus Carnobacterium (11.76%, 2) and 4 isolates represented 4 genera Bacillus, Lysinibacillus, Staphylococcus and Planomicrobium. Most of the Gram negative bacteria were moderate halophiles, while most of the Gram positives were extreme halophiles and were able to grow up to 6.12 M of NaCl. More than 2/3 of the isolates showed antimicrobial activity against multidrug resistant S. aureus, E. coli, Klebsiella pneumonia, Enterococcus faecium, Candida albicans, Aspergillus flavus and Aspergillus fumigatus and ATCC strains. Gram positive bacteria (94.11%) were more resistant to heavy metals as compared to Gram negative (78.79%) and showed maximum tolerance against iron and least tolerance against mercury.
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Affiliation(s)
- Muhammad Rafiq
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Muhammad Hayat
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Alexandre M. Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Syed Umair Ullah Jamil
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Earth and Environmental Sciences, Bahria University, Islamabad, Pakistan
| | - Noor Hassan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Cong M, Jiang Q, Xu X, Huang L, Su Y, Yan Q. The complete genome sequence of Exiguobacterium arabatum W-01 reveals potential probiotic functions. Microbiologyopen 2017; 6. [PMID: 28589562 PMCID: PMC5635162 DOI: 10.1002/mbo3.496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 12/27/2022] Open
Abstract
Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W‐01, a gram‐positive and orange‐pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole‐genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843.98 bp and a mean GC content of 48.11%, accounting for 89.27% of the genome. Among these ORFs, 2,884 (93.5%) genes were classified into Clusters of Orthologous Groups (COG) families comprising 21 functional categories, and 1,650 ORFs were classified into 83 functional Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 27 rRNA operons and 68 tRNAs were identified, with all 20 amino acids represented. In addition, 91 genomic islands, 68 potential prophages, and 33 tandem repeats, but no clustered regularly interspaced short palindromic repeats (CRISPRs), were found. No resistance genes and only one virulence gene were identified. Among the 150 secreted proteins of E. arabatum W‐01, a variety of transport system substrate‐binding proteins, enzymes, and biosynthetic proteins, which play important roles in the uptake and metabolism of nutrients, were found. Two adherence‐related protein genes and 31 flagellum‐related protein genes were also identified. Taken together, these results indicate potential probiotic functions for E. arabatum W‐01.
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Affiliation(s)
- Meinan Cong
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Qingling Jiang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Xiaojin Xu
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Yongquan Su
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China.,College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China
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Kasana RC, Pandey CB. Exiguobacterium: an overview of a versatile genus with potential in industry and agriculture. Crit Rev Biotechnol 2017; 38:141-156. [DOI: 10.1080/07388551.2017.1312273] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - C. B. Pandey
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
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Mora Collazos A, Bravo Montaño E. Aislamiento de microorganismos electrogénicos con potencial para reducir cromo hexavalente. ACTA BIOLÓGICA COLOMBIANA 2017. [DOI: 10.15446/abc.v22n1.57189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Se realizó el aislamiento de microorganismos cultivables a partir de la biopelícula formada sobre el ánodo de una celda de combustible microbiana puesta en operación durante 30 días; los microorganismos aislados fueron evaluados en su capacidad de producir energía en celdas de combustible microbianas y de reducir el cromo hexavalente, Cr (VI). Se aislaron cinco microorganismos, los cuales fueron caracterizados mediante análisis del gen del ARNr 16S, el cual ubicó a los microorganismos en cuatro géneros bacterianos: Exiguobacterium (CrMFC1), Acinetobacter (CrMFC2), Aeromonas (CrMFC3 y CrMFC5), y Serratia (CrMFC4). Todas las cepas aisladas mostraron actividad electrogénica y capacidad para reducir cromo hexavalente; la cepa de Acinetobacter CrMFC2 mostró el mejor desempeño electroquímico al registrar una densidad de potencia máxima de 18,61 mW/m2; las demás cepas mostraron valores de densidad de potencia máxima entre 4,6 mW/m2 y 7.1 mW/m2. Las cepas de Aeromonas CrMFC5 y Exiguobacterium CrMFC1 mostraron las mejores tasas de reducción de cromo al ser capaces de reducir el 100% del Cr (VI) en menos de 24 horas, destacándose la cepa de Aeromonas CrMFC5 la cual redujo el 100 % de Cr (VI) en 10 horas; las demás cepas redujeron el 100 % del contaminante al cabo de 28 a 30 horas. Los microorganismos aislados en este estudio son escasamente conocidos por su capacidad electrogénica y de reducir el Cr (VI); no obstante, se muestran promisorios para su utilización en sistemas mixtos que involucren la producción de energía acoplada a sistema de biorremediación de aguas contaminadas con cromo.
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30
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Park JH, Chon HT. Characterization of cadmium biosorption by Exiguobacterium sp. isolated from farmland soil near Cu-Pb-Zn mine. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:11814-11822. [PMID: 26951224 DOI: 10.1007/s11356-016-6335-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
Bacteria have the ability to bind heavy metals on their cell wall. Biosorption is a passive and energy-independent mechanism to adsorb heavy metals. The efficiency of heavy metal biosorption can vary depending on several factors such as the growth phase of bacteria, solution pH, and existence of competitive heavy metals. In this study, Exiguobacterium sp. isolated from farmland soil near a mine site were used, and optimal conditions for Cd biosorption in solution were investigated. As bacterial growth progressed, Cd biosorption increased, which is attributed to changes in the structure and composition of the cell wall during bacterial growth. The biosorption process was rapid and was completed within 30 min. Cadmium biosorption was highest at pH 7 due to the dissociation of hydrogen ions and the increase of negative charges with increasing pH. In the mixed metal solution of Cd, Pb, and Zn, the amount of biosorption was in the order of Pb>Cd>Zn while in a single metal solution, the order was Cd≥Pb>Zn. The maximum adsorption capacity for Cd by the isolated bacteria was 15.6 mg/g biomass, which was calculated from the Langmuir isotherm model. Different adsorption efficiencies under various environmental conditions indicate that, to control metal mobility, the conditions for biosorption should be optimized before applying bacteria. The results showed that the isolated bacteria can be used to immobilize metals in metal-contaminated wastewater.
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Affiliation(s)
- Jin Hee Park
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon, 34132, Republic of Korea.
| | - Hyo-Taek Chon
- Department of Energy Resources Engineering, Seoul National University, Seoul, 08826, Republic of Korea
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31
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Mathur A, Kumari J, Parashar A, T. L, Chandrasekaran N, Mukherjee A. Decreased Phototoxic Effects of TiO₂ Nanoparticles in Consortium of Bacterial Isolates from Domestic Waste Water. PLoS One 2015; 10:e0141301. [PMID: 26496250 PMCID: PMC4619802 DOI: 10.1371/journal.pone.0141301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022] Open
Abstract
This study is aimed to explore the toxicity of TiO2 nanoparticles at low concentrations (0.25, 0.50 & 1.00 μg/ml); on five bacterial isolates and their consortium in waste water medium both in dark and UVA conditions. To critically examine the toxic effects of nanoparticles and the response mechanism(s) offered by microbes, several aspects were monitored viz. cell viability, ROS generation, SOD activity, membrane permeability, EPS release and biofilm formation. A dose and time dependent loss in viability was observed for treated isolates and the consortium. At the highest dose, after 24h, oxidative stress was examined which conclusively showed more ROS generation & cell permeability and less SOD activity in single isolates as compared to the consortium. As a defense mechanism, EPS release was enhanced in case of the consortium against the single isolates, and was observed to be dose dependent. Similar results were noticed for biofilm formation, which substantially increased at highest dose of nanoparticle exposure. Concluding, the consortium showed more resistance against the toxic effects of the TiO2 nanoparticles compared to the individual isolates.
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Affiliation(s)
- Ankita Mathur
- Centre for Nanobiotechnology, VIT University, Vellore, India
| | - Jyoti Kumari
- Centre for Nanobiotechnology, VIT University, Vellore, India
| | | | - Lavanya T.
- Centre for Nanobiotechnology, VIT University, Vellore, India
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32
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Draft Genome Sequence of Exiguobacterium sp. Strain BMC-KP, an Environmental Isolate from Bryn Mawr, Pennsylvania. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01164-15. [PMID: 26450734 PMCID: PMC4599093 DOI: 10.1128/genomea.01164-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Exiguobacterium sp. strain BMC-KP was isolated as part of a student environmental sampling project at Bryn Mawr College, PA. Sequencing of bacterial DNA assembled a 3.32-Mb draft genome. Analysis suggests the presence of genes for tolerance to cold and toxic metals, broad carbohydrate metabolism, and genes derived from phage.
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Yadav AN, Sachan SG, Verma P, Kaushik R, Saxena AK. Cold active hydrolytic enzymes production by psychrotrophic Bacilli isolated from three sub-glacial lakes of NW Indian Himalayas. J Basic Microbiol 2015; 56:294-307. [PMID: 26933936 DOI: 10.1002/jobm.201500230] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/29/2015] [Indexed: 11/08/2022]
Abstract
The diversity of culturable, cold-active enzymes producing Bacilli was investigated from three sub-glacial lakes of north western Indian Himalayas. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes Alu I, Msp I, and Hae III led to the clustering of 136 Bacilli into 26, 23, and 22 clusters at 75% similarity index from Chandratal Lake, Dashair Lake, and Pangong Lake, respectively. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 35 Bacilli that could be grouped in seven families viz.: Bacillaceae (48%), Staphylococcaceae (14%), Bacillales incertae sedis (13%), Planococcaceae (12%), Paenibacillaceae (9%), Sporolactobacillaceae (3%), and Carnobacteriaceae (1%), which included twelve different genera Bacillus, Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus, and Virgibacillus. Based on their optimal temperature for growth, 35 Bacilli were grouped as psychrophilic (11 strains), psychrotrophic (17 strains), or psychrotolerant (7 strains), respectively. The representative isolates from each cluster were screened for cold-active enzyme activities. Amylase, β-glucosidase, pectinase, and protease activities at 4 °C were detected in more than 80% of the strains while approximately 40, 31, 23, 14, 11, and 9% of strains possessed cellulase, xylanase, β-galactosidase, laccase, chitinase, and lipase activity, respectively. Among 35 Bacilli, Bacillus amyloliquefaciens, Bacillus marisflavi, Exiguobacterium indicum, Paenibacillus terrae, Pontibacillus sp., Sporosarcina globispora, and Sporosarcina psychrophila were efficient producers of different cold-active enzymes. These cold-adapted Bacilli could play an important role in industrial and agricultural processes.
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Affiliation(s)
- Ajar Nath Yadav
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India.,Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India
| | | | - Priyanka Verma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
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34
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Fang L, Chen L, Liu Y, Tao W, Zhang Z, Liu H, Tang Y. Planktonic and sedimentary bacterial diversity of Lake Sayram in summer. Microbiologyopen 2015; 4:814-25. [PMID: 26242906 PMCID: PMC4618613 DOI: 10.1002/mbo3.281] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/23/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Lake Sayram is an ancient cold water lake locating at a mountain basin in Xinjiang, China. The lake water is brackish, alkaline, unpolluted, and abundant in SO4(2-) and Mg(2+). The lacustrine ecosystem of Lake Sayram has been intensely investigated. However, profiles of the microbial communities in the lake remain largely unknown. In this study, taxonomic compositions of the planktonic and sedimentary bacterial communities in Lake Sayram were investigated using 16S rRNA metagenomics. The lacustrine bacterial communities were generally structured by environmental conditions, including the hydrological and physicochemical parameters. Proteobacteria was the dominating phylum. In the lake water, the genera Acinetobacter and Ilumatobacter held an absolute predominance, implying their metabolic significance. In the bottom sediment, biogeochemically significant bacteria and thermophilic or acidothermophilic extremophiles were recovered. In contrast to the planktonic bacteria, an appreciable portion of the sedimentary bacteria could not be classified into any known taxonomic unit, indicating the largely unknown bacteriosphere hiding in the bottom sediment of Lake Sayram.
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Affiliation(s)
- Lei Fang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Lei Chen
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China.,School of Life Sciences, Liaoning Normal University, Dalian, 116029, China
| | - Yuan Liu
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Wei Tao
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Zhongzhe Zhang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Haiying Liu
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Yong Tang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
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35
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Draft Genome Sequence of Thermophilic Exiguobacterium sp. Strain JLM-2, Isolated from Deep-Sea Ferromanganese Nodules. GENOME ANNOUNCEMENTS 2015. [PMID: 26205856 PMCID: PMC4513150 DOI: 10.1128/genomea.00794-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Exiguobacterium sp. strain JLM-2 is a thermophilic bacterium isolated from deep-sea ferromanganese (FeMn) nodules. The estimated genome of this strain is 2.9 Mb, with a G+C content of 48.32%. It has a novel circular 15,570-bp plasmid. The draft genome sequence may provide useful information about Mn-microbe interactions and the genetic basis for tolerance to environment stresses.
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36
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Venkatachalam S, Gowdaman V, Prabagaran SR. Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal. MICROBIAL ECOLOGY 2015; 69:472-91. [PMID: 25204748 DOI: 10.1007/s00248-014-0476-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/28/2014] [Indexed: 05/18/2023]
Abstract
Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.
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Affiliation(s)
- Siddarthan Venkatachalam
- Molecular Microbiology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
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37
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Dastager SG, Mawlankar R, Sonalkar VV, Thorat MN, Mual P, Verma A, Krishnamurthi S, Tang SK, Li WJ. Exiguobacterium enclense sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2015; 65:1611-1616. [PMID: 25716950 DOI: 10.1099/ijs.0.000149] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterium, designated strain NIO-1109(T), was isolated from a marine sediment sample from Chorao Island, Goa, India. Phenotypic and chemotaxonomic characteristics and data from phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109(T) was related to the genus Exiguobacterium . Strain NIO-1109(T) exhibited >98.0% 16S rRNA gene sequence similarity with respect to Exiguobacterium indicum HHS 31(T) (99.5%) and Exiguobacterium acetylicum NCIMB 9889(T) (99.1%); the type strains of other species showed <98% similarity. Levels of DNA-DNA relatedness between strain NIO-1109(T) and E. acetylicum DSM 20416(T) and E. indicum LMG 23471(T) were less than 70% (33.0 ± 2.0 and 37 ± 3.2%, respectively). Strain NIO-1109(T) also differed from these two closely related species in a number of phenotypic traits. Based on phenotypic, chemotaxonomic and phylogenetic data, strain NIO-1109(T) is considered to represent a novel species of the genus Exiguobacterium , for which the name Exiguobacterium enclense sp. nov. is proposed. The type strain is NIO-1109(T) ( =NCIM 5457(T) =DSM 25128(T) = CCTCC AB 2011124(T)).
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Affiliation(s)
- Syed G Dastager
- NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India
| | - Rahul Mawlankar
- NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India
| | - Vidya V Sonalkar
- NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India
| | - Meghana N Thorat
- NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India
| | - Poonam Mual
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh-160036, India
| | - Ashish Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh-160036, India
| | - Shan-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
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38
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Culturable diversity and functional annotation of psychrotrophic bacteria from cold desert of Leh Ladakh (India). World J Microbiol Biotechnol 2014; 31:95-108. [DOI: 10.1007/s11274-014-1768-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022]
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39
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Draft Genome Sequence of Haloalkaliphilic Exiguobacterium sp. Strain AB2 from Manleluag Ophiolitic Spring, Philippines. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00840-14. [PMID: 25125654 PMCID: PMC4132630 DOI: 10.1128/genomea.00840-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exiguobacterium sp. AB2 is a haloalkaliphilic bacterium isolated from a hyperalkaline spring in Manleluag, Pangasinan, Philippines. Sequencing of bacterial DNA assembled a 2.85 MB draft genome. Analysis suggests the presence of genes for tolerance to stresses such as elevated pH and salt concentrations and toxic metals.
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40
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Nonaka K, Yoon KS, Ogo S. Biochemical characterization of psychrophilic Mn-superoxide dismutase from newly isolated Exiguobacterium sp. OS-77. Extremophiles 2014; 18:363-73. [PMID: 24414928 DOI: 10.1007/s00792-013-0621-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/29/2013] [Indexed: 02/01/2023]
Abstract
Many types of superoxide dismutases have been purified and characterized from various bacteria, however, a psychrophilic Mn-superoxide dismutase (MnSOD) has not yet been reported. Here, we describe the purification and the biochemical characterization of the psychrophilic MnSOD from Exiguobacterium sp. strain OS-77 (EgMnSOD). According to 16S rRNA sequence analysis, a newly isolated bacterium strain OS-77 belongs to the genus Exiguobacterium. The optimum growth temperature of the strain OS-77 is 20 °C. The EgMnSOD is a homodimer of 23.5 kDa polypeptides determined by SDS-PAGE and gel filtration analysis. UV-Vis spectrum and ICP-MS analysis clearly indicated that the homogeneously purified enzyme contains only a Mn ion as a metal cofactor. The optimal reaction pH and temperature of the enzyme were pH 9.0 and 5 °C, respectively. Notably, the purified EgMnSOD was thermostable up to 45 °C and retained 50% activity after 21.2 min at 60 °C. The differential scanning calorimetry also indicated that the EgMnSOD is thermostable, exhibiting two protein denaturation peaks at 65 and 84 °C. The statistical analysis of amino acid sequence and composition of the EgMnSOD suggests that the enzyme retains psychrophilic characteristics.
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Affiliation(s)
- Kyoshiro Nonaka
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
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41
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Draft Genome Sequence of Exiguobacterium pavilionensis Strain RW-2, with Wide Thermal, Salinity, and pH Tolerance, Isolated from Modern Freshwater Microbialites. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00597-13. [PMID: 23929485 PMCID: PMC3738901 DOI: 10.1128/genomea.00597-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Exiguobacterium pavilionensis strain RW-2, isolated from a cold thrombolytic microbialite. The isolate grows at temperatures from 4 to 50°C, at pH levels from 5 to 11, and in media without added NaCl or KCl or with 7% added NaCl.
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42
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Reddy GSN, Manasa BP, Singh SK, Shivaji S. Paenisporosarcina
indica sp. nov., a psychrophilic bacterium from a glacier, and reclassification of
Sporosarcina antarctica
Yu et al., 2008 as
Paenisporosarcina
antarctica comb. nov. and emended description of the genus
Paenisporosarcina. Int J Syst Evol Microbiol 2013; 63:2927-2933. [DOI: 10.1099/ijs.0.047514-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, spore-forming, rod-shaped bacterium, PN2T, was isolated from a soil sample collected near the Pindari glacier. It contained anteiso-C15 : 0, iso-C15 : 0 and C16 : 1ω7c alcohol as the predominant fatty acids, MK-7 as the major menaquinone and A4α type (l-Lys–d-Glu) peptidoglycan. Based on these characteristics, strain PN2T was assigned to the genus
Paenisporosarcina
. Phylogenetic analysis based on 16S rRNA gene sequence placed strain PN2T within the genus
Paenisporosarcina
and showed a sequence similarity of 98.5–99.0 % with members of this genus.
Paenisporosarcina macmurdoensis
CMS 21wT,
Paenisporosarcina quisquiliarum
SK 55T and
Sporosarcina antarctica
N-05T were identified as the most closely related species with 16S rRNA gene sequence similarities of 98.6 %, 99.0 % and 98.4 %, respectively. The values for DNA–DNA relatedness between strain PN2T and
P. macmurdoensis
,
P. quisquiliarum
and
S. antarctica
were below the 70 % threshold value (32.0 %, 42.0 % and 38.0 % respectively). In addition, strain PN2T exhibited a number of phenotypic differences from
P. macmurdoensis
,
P. quisquiliarum
and
S. antarctica
. Based on the cumulative differences, strain PN2T was identified as representing a novel species and the name
Paenisporosarcina
indica sp. nov. was proposed. The type strain of
Paenisporosarcina
indica sp. nov. is PN2T (LMG 23933T = JCM 15114T). Furthermore, based on the morphological and chemotaxonomic characteristics, the species
Sporosarcina antarctica
was reclassified as a species of the genus
Paenisporosarcina
and renamed
Paenisporosarcina
antarctica comb. nov. In addition, an emended description of the genus
Paenisporosarcina
is presented.
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Affiliation(s)
- G. S. N. Reddy
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
| | - B. Poorna Manasa
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
| | - Sanjay K. Singh
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
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Mohan Kulshreshtha N, Kumar R, Begum Z, Shivaji S, Kumar A. Exiguobacterium alkaliphilum sp. nov. isolated from alkaline wastewater drained sludge of a beverage factory. Int J Syst Evol Microbiol 2013; 63:4374-4379. [PMID: 23838447 DOI: 10.1099/ijs.0.039123-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, alkaliphilic, Gram-stain-positive, rod-shaped bacterium, designated strain 12/1(T), isolated from alkaline wastewater drained sludge of a beverage industry facility located near New Delhi, India, was subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain 12/1(T) belonged to the genus Exiguobacterium and was most closely related to Exiguobacterium aurantiacum DSM 6208(T) (99.46 %), E. aquaticum IMTB-3094(T) (99.18 %), E. mexicanum 8N(T) (99.06 %), E. profundum 10C(T) (98.17 %), E. aestuarii TF-16(T) (98.1 %) and E. marinum TF-80(T) (98.03 %). The DNA G+C content of strain 12/1(T) was 55.6 mol%, major respiratory isoprenoid quinone was MK-7, major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine and the cell-wall peptidoglycan was of the A3α l-Lys-Gly type, characteristics consistent with its affiliation to the genus Exiguobacterium. Strain 12/1(T) showed levels of DNA-DNA hybridization of less than 70 % with the closely related species of the genus Exiguobacterium. Overall, the phenotypic, chemotaxonomic and phylogenetic data presented in this study suggest that strain 12/1(T) represents a novel species of the genus Exiguobacterium, for which the name Exiguobacterium alkaliphilum sp. nov. is proposed. The type strain is 12/1(T) ( = CCM 8459(T) = DSM 21148(T)).
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Affiliation(s)
| | - Rita Kumar
- Institute of Genomics and Integrative Biology, Mall Road, New Delhi 110007, India
| | - Zareena Begum
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - S Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Anil Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Zhu W, Lan Y, Lou X, Han N, Ran T, Xu L, Xu D, Wang WW. Isolation of proteorhodopsin-bearing bacterium JL-3 from fresh water and characterization of the proteorhodopsin. FEMS Microbiol Lett 2013; 344:10-7. [PMID: 23551202 DOI: 10.1111/1574-6968.12144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/26/2013] [Accepted: 03/29/2013] [Indexed: 11/30/2022] Open
Abstract
Proteorhodopsins (PRs), light-driven proton pumps, constitute the largest family of the microbial rhodopsins. PRs are widely distributed in the oceanic environment and freshwater, but no bacteria with PRs have been isolated from freshwater so far. To facilitate isolation of the bacteria with PR genes, we constructed a vector system that can be used to clone potential PR genes and render color changes when overexpressed in Escherichia coli. Using this method, we successfully isolated a strain with PR gene from freshwater and identified it as Exiguobacterium sp. JL-3. The full length PR gene was then cloned using the SEFA PCR method. Protein sequence alignment showed that JL-3_PR shares high sequence identity (84-89%) with the PRs from Exiguobacterium strains, but low sequence identity (< 38%) with other PRs. Surprisingly, we could not detect any proton-pumping activity in the native JL-3 cells and protoplasts, but the recombinant JL-3_PR do pump protons when overexpressed in E. coli. Sequence analysis further revealed that the PRs from Exiguobacterium had an unusual lysine as the proton donor instead of the typical acidic residue. These data suggest that JL-3_PR is a sensory PR rather than a proton pump.
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Affiliation(s)
- Wenjun Zhu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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45
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Singh NK, Raichand R, Kaur I, Kaur C, Pareek S, Mayilraj S. Exiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas. Antonie van Leeuwenhoek 2012; 103:789-96. [PMID: 23229437 DOI: 10.1007/s10482-012-9861-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 11/26/2012] [Indexed: 10/27/2022]
Abstract
The taxonomic position of an orange coloured bacterium, strain K22-26(T) isolated from a soil sample was studied using a polyphasic approach. The organism had phenotypic and chemotaxonomic properties consistent with its allocation into the genus Exiguobacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain K22-26(T) belongs to the genus Exiguobacterium and was related to Exiguobacterium aurantiacum DSM 6208(T) (99.0 %) Exiguobacterium mexicanum DSM 16483(T) (98.6 %), Exiguobacterium aquaticum (98.6 %), Exiguobacterium aestuarii DSM 16306(T) (98.1 %), Exiguobacterium profundum DSM 17289(T) (98.1 %) and Exiguobacterium marinum DSM 16483(T) (97.9 %), whereas sequence similarity values with respect to other Exiguobacterium species with validly published names were between 92.5-94.0 %. The major polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major menaquinone was determined to be MK-7 (83 %) whereas MK-8 (11 %) and MK-6 (6 %) occur in smaller amounts. The peptidoglycan of the strain was found to contain L-lysine as the diagnostic diamino acid. The major fatty acids detected were iso C13:0 (11.2 %), anteiso C13:0 (15.4 %), iso C15:0 (13.2 %) and iso C17:0 (16.1 %). However, analysis of the DNA-DNA relatedness confirmed that strain K22-26(T) belongs to a novel species. The G + C content of the strain K22-26(T) was determined to be 50.1 mol %. The novel strain was distinguished from closely related type species of the genus Exiguobacterium using DNA-DNA relatedness and phenotypic data. Based on these differences, the strain K22-26(T) should be classified as a novel species of the genus Exiguobacterium, for which the name Exiguobacterium himgiriensis sp. nov. strain K22-26(T) (= MTCC 7628(T) = JCM 14260(T)) is proposed.
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Affiliation(s)
- Nitin Kumar Singh
- A Constituent Laboratory of Council of Scientific and Industrial Research (CSIR), Chandigarh, India
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46
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Raichand R, Pareek S, Singh NK, Mayilraj S. Exiguobacterium aquaticum sp. nov., a member of the genus Exiguobacterium. Int J Syst Evol Microbiol 2011; 62:2150-2155. [PMID: 22058319 DOI: 10.1099/ijs.0.035790-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, motile, short rod-shaped, orange pigmented bacterium, designated strain IMTB-3094(T), was isolated from a water sample collected from Tikkar Tal Lake, Haryana, and subjected to detailed polyphasic taxonomic analysis. Strain IMTB-3094(T) possessed most of the phenotypic and chemotaxonomic properties of the genus Exiguobacterium and, based on 16S rRNA gene sequence analysis, was assigned to this genus. Strain IMTB-3094(T) exhibited the highest 16S rRNA gene sequence similarity to Exiguobacterium mexicanum MTCC 7759(T) (99.5 %) followed by Exiguobacterium aurantiacum MTCC 6414(T) (99.1 %), Exiguobacterium aestuarii MTCC 7750(T) (98.0 %), Exiguobacterium profundum MTCC 10851(T) (98.0 %) and Exiguobacterium marinum MTCC 7751(T) (98.0 %). The G+C content of the genomic DNA of strain IMTB-3094(T) was 53.2 mol% and a DNA-DNA relatedness study confirmed that it represents a novel species. The major fatty acids of strain IMTB-3094(T) were iso-C(17 : 0) (16.1 %), anteiso-C(13 : 0) (19.0 %), iso-C(13 : 0) (11.9 %), iso-C(15 : 0) (9.8 %) and iso-C(17 : 1) (12.7 %). The predominant quinones were MK-7 (55.0 %) and MK-6 (26.0 %) with minor amounts of MK-8 (12.0 %). Based on phenotypic, chemotaxonomic and phylogenetic analyses, strain IMTB-3094(T) represents a novel species of the genus Exiguobacterium, for which the name Exiguobacterium aquaticum sp. nov. is proposed. The type strain is IMTB-3094(T) (= MTCC 10958(T) = JCM 17977(T)).
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Affiliation(s)
- Revti Raichand
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Siddhika Pareek
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
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Bacterial diversity of soil in the vicinity of Pindari glacier, Himalayan mountain ranges, India, using culturable bacteria and soil 16S rRNA gene clones. Extremophiles 2011; 15:1-22. [PMID: 21061031 DOI: 10.1007/s00792-010-0333-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/22/2010] [Indexed: 10/18/2022]
Abstract
Three 16S rRNA gene clone libraries (P1L, P4L and P8L) were constructed using three soil samples (P1S, P4S and P8S) collected near Pindari glacier, Himalayas. The three libraries yielded a total of 703 clones. Actinobacteria, Firmicutes and Proteobacteria were common to the three libraries. In addition to the above P1L and P8L shared the phyla Acidobacteria, Bacteroidetes, Gemmatimonadetes and Planctomycetes. Phyla Chlamydiae, Chlorobi, Chloroflexi, Dictyoglomi, Fibrobacteres, Nitrospirae, Verrucomicrobia, candidate division SPAM and candidate TM7s TM7a phylum were present only in P1L. Rarefaction analysis indicated that the bacterial diversity in P4S and P8S soil samples was representative of the sample. Principal component analysis (PCA) revealed that P1S and P8S were different from P4S soil sample. PCA also indicated that arsenic content, pH, Cr and altitude influence the observed differences in the percentage of specific OTUs in the three 16S rRNA gene clone libraries. The observed bacterial diversity was similar to that observed for other Himalayan and non-polar cold habitats. A total of 40 strains of bacteria were isolated from the above three soil samples and based on the morphology 20 bacterial strains were selected for further characterization. The 20 bacteria belonged to 12 different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase and urease activities were detected in majority of the strains but lipase and protease activities were not detected. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.
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Cerritos R, Eguiarte LE, Avitia M, Siefert J, Travisano M, Rodríguez-Verdugo A, Souza V. Diversity of culturable thermo-resistant aquatic bacteria along an environmental gradient in Cuatro Ciénegas, Coahuila, México. Antonie van Leeuwenhoek 2010; 99:303-18. [PMID: 20711674 DOI: 10.1007/s10482-010-9490-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
Abstract
At the desert oasis of Cuatro Ciénegas in Coahuila, México, more than 300 oligotrophic pools can be found and a large number of endemic species of plants and animals. The most divergent taxa of diatoms, snail and fishes are located in the Churince hydrological system, where we analyzed the local diversification of cultivable Firmicutes and Actinobacteria. The Churince hydrological system is surrounded by gypsum dunes and has a strong gradient for salinity, temperature, pH and dissolved oxygen. In August 2003, surface water samples were taken in 10 sites along the Churince system together with the respective environmental measurements. 417 thermo-resistant bacteria were isolated and DNA was extracted to obtain their BOX-PCR fingerprints, revealing 55 different patterns. In order to identify similarities and differences in the diversity of the various sampling sites, an Ordination Analysis was applied using Principal Component Analysis. This analysis showed that conductivity is the environmental factor that explains the distribution of most of the microbial diversity. Phylogenetic reconstruction from their 16S rRNA sequences was performed for a sample of 150 isolates. Only 17 sequences had a 100% match in the Gene Bank (NCBI), representing 10 well known cosmopolitan taxa. The rest of the sequences cluster in 22 clades for Firmicutes and another 22 clades for Actinobacteria, supporting the idea of high diversity and differentiation for this site.
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Affiliation(s)
- René Cerritos
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico Exterior, Mexico, DF, Mexico
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49
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The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 2009; 13:541-55. [DOI: 10.1007/s00792-009-0243-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Accepted: 03/30/2009] [Indexed: 10/20/2022]
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50
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Rodrigues DF, da C Jesus E, Ayala-Del-Río HL, Pellizari VH, Gilichinsky D, Sepulveda-Torres L, Tiedje JM. Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. ISME JOURNAL 2009; 3:658-65. [PMID: 19322243 DOI: 10.1038/ismej.2009.25] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genera Exiguobacterium and Psychrobacter have been frequently detected in and isolated from polar permafrost and ice. These two genera have members that can grow at temperatures as low as -5 and -10 degrees C, respectively. We used quantitative PCR (Q-PCR) to quantify members of these genera in 54 soil or sediment samples from polar, temperate and tropical environments to determine to what extent they are selected by cold environments. These results were further analyzed by multiple linear regression to identify the most relevant environmental factors corresponding to their distribution. Exiguobacterium was detected in all three climatic zones at similar densities, but was patchier in the temperate and tropical samples. Psychrobacter was present in almost all polar samples, was at highest densities in Antarctica sediment samples, but was in very low densities and infrequently detected in temperate and tropical soils. Clone libraries, specific for the 16S rRNA gene for each genus, were constructed from a sample from each climatic region. The clone libraries were analyzed for alpha and beta diversities, as well as for variation in population structure by using analysis of molecular variance. Results confirm that both genera were found in all three climatic zones; however, Psychrobacter populations seemed to be much more diverse than Exiguobacterium in all three climatic zones. Furthermore, Psychrobacter populations from Antarctica are different from those in Michigan and Puerto Rico, which are similar to each other.
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Affiliation(s)
- Debora F Rodrigues
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
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