1
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Lukhwareni R, Nomngongo PN, Nibamureke UMC, Moila K, Sekete NW, Ndamane GT, Njom HA, Sithole L, Rudolph M, Ngobese NZ. The assessment of Oreochromis mossambicus muscle tissue and the yield performance of Solanum tuberosum in a small-scale sandponics system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2025:10.1007/s11356-025-36495-0. [PMID: 40366580 DOI: 10.1007/s11356-025-36495-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Accepted: 05/01/2025] [Indexed: 05/15/2025]
Abstract
Aquaponics, integrating hydroponics and aquaculture in a circular system, offers a promising approach to addressing food and nutrition security while promoting water conservation in South Africa. This technology is a sustainable means of food production that minimizes environmental waste by simultaneously cultivating plants and rearing fish. This study aimed to evaluate the histology of muscle tissue in Mozambique tilapia (Oreochromis mossambicus) and the performance of Irish potato (Solanum tuberosum) in a small-scale sandponics system. Two potato cultivars (Moonlight and Taurus) were planted in a system linked to a 1000-L water tank containing 25 sexually mature Mozambique tilapia from January to June 2023. Fish histology and potato yield performance were assessed to gauge the efficiency of the system and to generate baseline data for future studies. Results showed that tuber production in the sandponics system was comparable to field conditions, with the Moonlight cultivar yielding the heaviest tubers (293-307 g per plant) with a short-oval shape, demonstrating its superior adaptability to this system. Taurus yielded lighter tubers (139-168 g per plant) that were either round or short oval depending on the grow beds used for production. Fish histological analysis revealed a higher prevalence of muscle tissue alterations in the control group compared to the experimental group. However, both groups displayed a similar condition factor (p < 0.05), indicating good overall health. Despite the promising results, the significantly high levels (p < 0.05) of metal accumulation (As, Cu, Mn, and Zn) in the fish were observed, raising concerns about their suitability for human consumption. This study demonstrates that sandponics systems can effectively support potato production with fish maintaining good general health. However, further investigation is needed to mitigate metal accumulation to ensure the safety of fish for consumption.
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Affiliation(s)
- Refilwe Lukhwareni
- Department of Zoology, University of Johannesburg, PO BOX 524, Johannesburg, 2006, South Africa.
| | - Philiswa Nosizo Nomngongo
- Department of Chemical Sciences, Faculty of Science, University of Johannesburg, PO BOX 524, Johannesburg, 2006, South Africa
| | - Uwineza Marie Clementine Nibamureke
- Department of Biological Sciences, Faculty of Science, Engineering & Agriculture, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
| | - Kgaohelo Moila
- Department of Zoology, University of Johannesburg, PO BOX 524, Johannesburg, 2006, South Africa
| | | | - Godfrey Tshokolo Ndamane
- Centre for Ecological Intelligence, Department of Electrical and Electronic Engineering, Faculty of Engineering and Build Environment, University of Johannesburg, Johannesburg, South Africa
| | - Henry Akum Njom
- Agricultural Research Council, Private Bag X1251, Potchefstroom, 2531, South Africa
| | - Lucky Sithole
- Department of Agriculture and Rural Development, Pietermaritzburg, 3245, South Africa
| | - Michael Rudolph
- Centre for Ecological Intelligence, Department of Electrical and Electronic Engineering, Faculty of Engineering and Build Environment, University of Johannesburg, Johannesburg, South Africa
| | - Nomali Ziphorah Ngobese
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X6001, Potchefstroom, South Africa
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2
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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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Chahed A, Nesler A, Esmaeel Q, Barka EA, Perazzolli M. The Amount of the Rare Sugar Tagatose on Tomato Leaves Decreases after Spray Application under Greenhouse Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:2781. [PMID: 36297805 PMCID: PMC9607558 DOI: 10.3390/plants11202781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Tagatose is a rare sugar that suppresses plant diseases, such as late blight of tomato, caused by Phytophthora infestans. Tagatose can be metabolized by some microorganisms and no information is available on its persistence on tomato leaves. The aim of this study was to assess the persistence of tagatose on tomato leaves under commercial greenhouse conditions. The amount of tagatose on tomato leaves and the inhibitory activity against P. infestans decreased seven days after spray application in the absence of rain wash-off. Potential tagatose-degrading bacteria were isolated from tomato leaves, and they belonged to Acinetobacter sp., Bacillus sp., Comamonas sp., Enterobacter sp., Methylobacterium sp., Microbacterium sp., Pantoea sp., Plantibacter sp., Pseudomonas sp., Ralstonia sp., Rhodococcus sp., Sphingobium sp., and Sphingomonas sp. Thus, indigenous phyllosphere microorganisms could partially metabolize tagatose laid on plant leaves after spray application, reducing the persistence of this fungal inhibitor on tomato leaves.
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Affiliation(s)
- Abdessalem Chahed
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
- Bi-PA nv, Technologielaan 7, 1840 Londerzeel, Belgium
- Induced Resistance and Plant Bioprotection, USC INRAE 1488, University of Reims, UFR Sciences, CEDEX 02, 51687 Reims, France
| | - Andrea Nesler
- Bi-PA nv, Technologielaan 7, 1840 Londerzeel, Belgium
| | - Qassim Esmaeel
- Induced Resistance and Plant Bioprotection, USC INRAE 1488, University of Reims, UFR Sciences, CEDEX 02, 51687 Reims, France
| | - Essaid Ait Barka
- Induced Resistance and Plant Bioprotection, USC INRAE 1488, University of Reims, UFR Sciences, CEDEX 02, 51687 Reims, France
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy
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Plant growth-promoting characteristics of halotolerant endophytic bacteria isolated from Sporobolus specatus (Vahr) Kunth and Cyperus laevigatus L. of Ethiopian rift valley lakes. Arch Microbiol 2022; 204:403. [PMID: 35723754 DOI: 10.1007/s00203-022-03021-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/25/2022] [Indexed: 11/02/2022]
Abstract
Understanding plant microbes' intimate relationship and search for beneficial microbes is a sustainable alternative to improve plant growth and yield under a wide range of biotic and abiotic stress conditions. More than 20% of the total global agricultural land is affected by salinity. High salinity challenges crop plants by affecting several metabolic pathways and decreasing plant growth and yield. Unlike chemical fertilizers and pesticides, endophytic microbes offer an eco-friendly approach to increasing crop yield via various metabolites during salinity stress. The objective of this study was to isolate and characterize endophytic halotolerant bacterial isolates from haloalkaliphytes, investigate their plant growth-promoting (PGP) properties and tolerance for various stress conditions. Sporobolus specatus (Vahr) Kunth and Cyperus laevigatus L. grass samples were collected from the shores of two Ethiopian soda lakes (Lakes Abijata, and Chitu, respectively). A total of 167 halotolerant endophytic bacterial isolates, that clustered into 21 ARDRA (Amplified ribosomal DNA restriction analysis) groups, affiliated to members of 11 bacterial genera, namely Halomonas, Agrobacterium, Exiguobacterium, Jonesia, Stenotrophomonas, Pseudomonas, Alishewanella, Kosakonia, Bacillus, Paracoccus and Pannonibacter, were identified based on 16S rRNA sequencing. Most of the strains were able to produce IAA (indole-3-acetic acid) and hydrogen cyanide, grow on a nitrogen-free medium and solubilize phosphate. In vitro tolerance tests reveal that isolates were tolerant to: 5.0-15% NaCl, up to 40% PEG 6000, temperatures up to 50 °C, and pH 5-11. These characteristics of the isolates indicate their potential PGP application under various plant stress conditions.
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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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Zhang D, Zhu Z, Li Y, Li X, Guan Z, Zheng J. Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium. mSystems 2021; 6:e0038321. [PMID: 34282940 PMCID: PMC8407118 DOI: 10.1128/msystems.00383-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022] Open
Abstract
Although the strategies used by bacteria to adapt to specific environmental conditions are widely reported, fewer studies have addressed how microbes with a cosmopolitan distribution can survive in diverse ecosystems. Exiguobacterium is a versatile genus whose members are commonly found in various habitats. To better understand the mechanisms underlying the universality of Exiguobacterium, we collected 105 strains from diverse environments and performed large-scale metabolic and adaptive ability tests. We found that most Exiguobacterium members have the capacity to survive under wide ranges of temperature, salinity, and pH. According to phylogenetic and average nucleotide identity analyses, we identified 27 putative species and classified two genetic groups: groups I and II. Comparative genomic analysis revealed that the Exiguobacterium members utilize a variety of complex polysaccharides and proteins to support survival in diverse environments and also employ a number of chaperonins and transporters for this purpose. We observed that the group I species can be found in more diverse terrestrial environments and have a larger genome size than the group II species. Our analyses revealed that the expansion of transporter families drove genomic expansion in group I strains, and we identified 25 transporter families, many of which are involved in the transport of important substrates and resistance to environmental stresses and are enriched in group I strains. This study provides important insights into both the overall general genetic basis for the cosmopolitan distribution of a bacterial genus and the evolutionary and adaptive strategies of Exiguobacterium. IMPORTANCE The wide distribution characteristics of Exiguobacterium make it a valuable model for studying the adaptive strategies of bacteria that can survive in multiple habitats. In this study, we reveal that members of the Exiguobacterium genus have a cosmopolitan distribution and share an extensive adaptability that enables them to survive in various environments. The capacities shared by Exiguobacterium members, such as their diverse means of polysaccharide utilization and environmental-stress resistance, provide an important basis for their cosmopolitan distribution. Furthermore, the selective expansion of transporter families has been a main driving force for genomic evolution in Exiguobacterium. Our findings improve our understanding of the adaptive and evolutionary mechanisms of cosmopolitan bacteria and the vital genomic traits that can facilitate niche adaptation.
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Affiliation(s)
- Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhaolu Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ziyu Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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7
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Liu F, Li Y, He W, Wang W, Zheng J, Zhang D. Exiguobacterium algae sp. nov. and Exiguobacterium qingdaonense sp. nov., two novel moderately halotolerant bacteria isolated from the coastal algae. Antonie van Leeuwenhoek 2021; 114:1399-1406. [PMID: 34251527 DOI: 10.1007/s10482-021-01594-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/16/2021] [Indexed: 10/20/2022]
Abstract
Two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial strains, S126T and S82T, were isolated from coastal algae of China. Strains S126T and S82T are halotolerant and could grow in the presence of 0-13% NaCl and 0-14% NaCl, respectively. The two strains shared 98.9% 16S rRNA gene sequence similarity with each other and 93.4-99.8% similarity with type strains of Exiguobacterium species. The major fatty acids (> 10%) of strains S126T and S82T were iso-C17:0, iso-C13:0, anteiso-C13:0 and iso-C15:0. The predominant quinones of strains S126T and S82T were MK-7 and MK-8. The polar lipid profiles of strain S126T and S82T contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell-wall peptidoglycans of both strains S126T and S82T were of the A3α L-Lys-Gly type. The average nucleotide identity (ANI) and average nucleotide index (AAI) between strains S126T and S82T and type strains of Exiguobacterium species were all below the thresholds to discriminate bacterial species, indicating that they constitute two novel species in the genus Exiguobacterium. Based on polyphasic taxonomy characterization and genomic aspects, the names Exiguobacterium algae sp. nov. and Exiguobacterium qingdaonense sp. nov. are proposed for the two novel species, with type strains being S126T (= CGMCC 1.17116T = KCTC 43079 T) and S82T (= CGMCC 1.17115T = KCTC 43078T), respectively.
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Affiliation(s)
- Fangming Liu
- First Institute of Oceanography (FIO), Ministry of Natural Resources (MNR) of China, Qingdao, 266061, China
| | - Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenxuan He
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqi Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266237, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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8
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Chahed A, Lazazzara V, Moretto M, Nesler A, Corneo PE, Barka EA, Pertot I, Puopolo G, Perazzolli M. The Differential Growth Inhibition of Phytophthora spp. Caused by the Rare Sugar Tagatose Is Associated With Species-Specific Metabolic and Transcriptional Changes. Front Microbiol 2021; 12:711545. [PMID: 34305881 PMCID: PMC8292896 DOI: 10.3389/fmicb.2021.711545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/16/2021] [Indexed: 12/03/2022] Open
Abstract
Tagatose is a rare sugar with no negative impacts on human health and selective inhibitory effects on plant-associated microorganisms. Tagatose inhibited mycelial growth and negatively affected mitochondrial processes in Phytophthora infestans, but not in Phytophthora cinnamomi. The aim of this study was to elucidate metabolic changes and transcriptional reprogramming activated by P. infestans and P. cinnamomi in response to tagatose, in order to clarify the differential inhibitory mechanisms of tagatose and the species-specific reactions to this rare sugar. Phytophthora infestans and P. cinnamomi activated distinct metabolic and transcriptional changes in response to the rare sugar. Tagatose negatively affected mycelial growth, sugar content and amino acid content in P. infestans with a severe transcriptional reprogramming that included the downregulation of genes involved in transport, sugar metabolism, signal transduction, and growth-related process. Conversely, tagatose incubation upregulated genes related to transport, energy metabolism, sugar metabolism and oxidative stress in P. cinnamomi with no negative effects on mycelial growth, sugar content and amino acid content. Differential inhibitory effects of tagatose on Phytophthora spp. were associated with an attempted reaction of P. infestans, which was not sufficient to attenuate the negative impacts of the rare sugar and with an efficient response of P. cinnamomi with the reprogramming of multiple metabolic processes, such as genes related to glucose transport, pentose metabolism, tricarboxylic acid cycle, reactive oxygen species detoxification, mitochondrial and alternative respiration processes. Knowledge on the differential response of Phytophthora spp. to tagatose represent a step forward in the understanding functional roles of rare sugars.
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Affiliation(s)
- Abdessalem Chahed
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Bi-PA nv, Londerzeel, Belgium.,Department of Induced Resistance and Plant Bioprotection, University of Reims, Reims, France
| | - Valentina Lazazzara
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Andrea Nesler
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Bi-PA nv, Londerzeel, Belgium
| | - Paola Elisa Corneo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Essaid Ait Barka
- Department of Induced Resistance and Plant Bioprotection, University of Reims, Reims, France
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Gerardo Puopolo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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10
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Chahed A, Nesler A, Navazio L, Baldan B, Busato I, Ait Barka E, Pertot I, Puopolo G, Perazzolli M. The Rare Sugar Tagatose Differentially Inhibits the Growth of Phytophthora infestans and Phytophthora cinnamomi by Interfering With Mitochondrial Processes. Front Microbiol 2020; 11:128. [PMID: 32117150 PMCID: PMC7015900 DOI: 10.3389/fmicb.2020.00128] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/20/2020] [Indexed: 12/18/2022] Open
Abstract
Rare sugars are monosaccharides with limited availability in nature and their biological functions are largely unknown. Among them, tagatose was developed as a low-calorie sweetener and showed beneficial effects on human health. Tagatose is metabolized by only certain microbial taxa and inhibits the growth of important crop pathogens (e.g., Phytophthora infestans), but its mode of action and the microbial responses are unknown. The aim of this study was to understand the tagatose mode of action against Phytophthora spp., with the final aim of developing new plant protection products. Tagatose inhibited P. infestans growth in vitro and caused severe ultrastructural alterations, with the formation of circular and concentric mitochondrial cristae. Decreased ATP content and reduced oxygen consumption rate (OCR) were found in tagatose-incubated P. infestans as compared to the control, with the consequent accumulation of reactive oxygen species (ROS) and induction of genes related to apoptosis and oxidative stress response. On the other hand, tagatose did not, or only slightly, affect the growth, cellular ultrastructure and mitochondrial processes in Phytophthora cinnamomi, indicating a species-specific response to this rare sugar. The mode of action of tagatose against P. infestans was mainly based on the inhibition of mitochondrial processes and this rare sugar seems to be a promising active substance for the further development of eco-friendly fungicides, thanks to its anti-nutritional properties on some phytopathogens and low risk for human health.
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Affiliation(s)
- Abdessalem Chahed
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Biological Products for Agriculture (Bi-PA), Londerzeel, Belgium.,Department of Plant Induced Resistance and Bioprotection, University of Reims Champagne-Ardenne, Reims, France
| | - Andrea Nesler
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Biological Products for Agriculture (Bi-PA), Londerzeel, Belgium
| | - Lorella Navazio
- Department of Biology, University of Padua, Padua, Italy.,Botanical Garden, University of Padua, Padua, Italy
| | - Barbara Baldan
- Department of Biology, University of Padua, Padua, Italy.,Botanical Garden, University of Padua, Padua, Italy
| | - Isabella Busato
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Department of Biology, University of Padua, Padua, Italy
| | - Essaid Ait Barka
- Department of Plant Induced Resistance and Bioprotection, University of Reims Champagne-Ardenne, Reims, France
| | - Ilaria Pertot
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
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11
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Ecological impact of a rare sugar on grapevine phyllosphere microbial communities. Microbiol Res 2019; 232:126387. [PMID: 31790975 DOI: 10.1016/j.micres.2019.126387] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 01/14/2023]
Abstract
Plants host a complex microbiota inside or outside their tissues, and phyllosphere microorganisms can be influenced by environmental, nutritional and agronomic factors. Rare sugars are defined as monosaccharides with limited availability in nature and they are metabolised by only few certain microbial taxa. Among rare sugars, tagatose (TAG) is a low-calories sweetener that stimulates and inhibits beneficial and pathogenic bacteria in the human gut microbiota, respectively. Based on this differential effect on human-associated microorganisms, we investigated the effect of TAG treatments on the grapevine phyllosphere microorganisms to evaluate whether it can engineer the microbiota and modify the ratio between beneficial and pathogenic plant-associated microorganisms. TAG treatments changed the structure of the leaf microbiota and they successfully reduced leaf infections of downy mildew (caused by Plasmopara viticola) and powdery mildew (caused by Erysiphe necator) under field conditions. TAG increased the relative abundance of indigenous beneficial microorganisms, such as some potential biocontrol agents, which could partially contribute to disease control. The taxonomic composition of fungal and bacterial leaf populations differed according to grapevine locations, therefore TAG effects on the microbial structure were influenced by the composition of the originally residing microbiota. TAG is a promising biopesticide that could shift the balance of pathogenic and beneficial plant-associated microorganisms, suggesting selective nutritional/anti-nutritional properties for some specific taxa. More specifically, TAG displayed possible plant prebiotic effects on the phyllosphere microbiota and this mechanism of action could represent a novel strategy that can be further developed for sustainable plant protection.
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12
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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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13
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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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14
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Rao Y, Qian Y, Tao Y, She X, Li Y, Che Z, Li H, Liu L. Influence of oxygen exposure on fermentation process and sensory qualities of Sichuan pickle (paocai). RSC Adv 2019; 9:38520-38530. [PMID: 35540217 PMCID: PMC9075915 DOI: 10.1039/c9ra05994f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
The physicochemical and microbial changes, volatile profile, texture and appearance were investigated in three groups of Sichuan pickles differing in oxygen exposure during a 64 day fermentation process.
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Affiliation(s)
- Yu Rao
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
| | - Yang Qian
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
- Department of Wine and Food Engineering
| | - Yufei Tao
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
| | - Xiao She
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
| | - Yalin Li
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
| | - Zhenming Che
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
| | - Hehe Li
- Beijing Key Laboratory of Flavor Chemistry
- Beijing Technology and Business University (BTBU)
- Beijing 100048
- China
| | - Lei Liu
- School of Food Science and Bioengineering
- Xihua University
- Chengdu 610039
- China
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15
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Draft Genome Sequence of Exiguobacterium sp. HVEsp1, a Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent in the Okinawa Trough. GENOME ANNOUNCEMENTS 2017; 5:5/17/e00253-17. [PMID: 28450519 PMCID: PMC5408117 DOI: 10.1128/genomea.00253-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report here the draft genome sequence of Exiguobacterium sp. HVEsp1, a thermophilic bacterium isolated from a deep-sea hydrothermal vent. The estimated genome size of this strain is 2,838,499 bp with a G+C content of 48.2%. The genome sequence data provide valuable information that will facilitate studies on the adaptation mechanisms of bacteria living in deep-sea hydrothermal vents.
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16
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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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17
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Brandes J, Kuhajek JM, Goodwin E, Wood SA. Molecular Characterisation and Co-cultivation of Bacterial Biofilm Communities Associated with the Mat-Forming Diatom Didymosphenia geminata. MICROBIAL ECOLOGY 2016; 72:514-525. [PMID: 27412380 DOI: 10.1007/s00248-016-0816-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Didymosphenia geminata (Lyngbye) M. Schmidt is a stalked freshwater diatom that is expanding its range globally. In some rivers, D. geminata forms thick and expansive polysaccharide-dominated mats. Like other stalked diatoms, D. geminata cells attach to the substratum with a pad of adhesive extracellular polymeric substance. Research on D. geminata and other diatoms suggests that bacterial biofilm composition may contribute to successful attachment. The aim of this study was to investigate the composition and role of bacterial biofilm communities in D. geminata attachment and survival. Bacterial biofilms were collected at four sites in the main stem of a river (containing D. geminata) and in four tributaries (free of D. geminata). Samples were characterised using automated rRNA intergenic spacer analysis and high-throughput sequencing (HTS). Mat-associated bacteria were isolated and their effect on the early establishment of D. geminata cells assessed using co-culturing experiments. ARISA and HTS data showed differences in bacterial communities between samples with and without D. geminata at two of the four sites. Samples with D. geminata had a higher relative abundance of Sphingobacteria (p < 0.01) and variability in community composition was reduced. Analysis of the 76 bacteria isolated from the mat revealed 12 different strains representing 8 genera. Co-culturing of a Carnobacterium sp. with D. geminata reduced survival (p < 0.001) and attachment (p < 0.001) of D. geminata. Attachment was enhanced by Micrococcus sp. and Pseudomonas sp. (p < 0.001 and p < 0.01, respectively). These data provide evidence that bacteria play a role in the initial attachment and on-going survival of D. geminata, and may partly explain observed distribution patterns.
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Affiliation(s)
- Josephin Brandes
- Cawthron Institute, Private Bag 2, Nelson, 7001, New Zealand
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | | | - Eric Goodwin
- Cawthron Institute, Private Bag 2, Nelson, 7001, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson, 7001, New Zealand.
- Environmental Research Institute, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand.
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18
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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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19
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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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20
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Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor. GENOME ANNOUNCEMENTS 2013; 1:1/6/e01059-13. [PMID: 24356831 PMCID: PMC3868855 DOI: 10.1128/genomea.01059-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a G+C content of 47.24%, and it may provide useful information about plant-microbe interactions and the genetic basis for the tolerance of the strain to various environmental stresses.
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21
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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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22
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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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23
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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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24
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Rebollar EA, Avitia M, Eguiarte LE, González-González A, Mora L, Bonilla-Rosso G, Souza V. Water-sediment niche differentiation in ancient marine lineages of Exiguobacterium endemic to the Cuatro Cienegas Basin. Environ Microbiol 2012; 14:2323-33. [PMID: 22639906 DOI: 10.1111/j.1462-2920.2012.02784.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The evolutionary history and ecological differentiation of the genus Exiguobacterium was characterized within natural communities from the Cuatro Cienegas Basin, Mexico. Exiguobacterium comprises both halophilic and alkaliphilic bacteria that are abundant among the aquatic systems of the Cuatro Cienegas Basin. We obtained complete sequences of the 16srRNA gene and partial sequences of four housekeeping genes (citC, rpoB, recA and hsp70) in 183 Exiguobacterium isolates retrieved from distinct aquatic systems. We defined three main phylogroups that are closely related to marine and thermophilic species of the genus. These phylogroups were neither specific to a given aquatic system nor to a particular salinity. Phylogenetic reconstruction indicated the presence of several small clusters within the phylogroups. These clusters consisted of isolates predominantly retrieved from sediment or water. Unifrac and AdaptML analyses confirmed this observation, pointing towards a clear pattern of differentiation linked to either sediment or water habitats. Our results are in line with the concept that niche differentiation is one of the main factors shaping prokaryotic populations and leading to evolutionary divergence.
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Affiliation(s)
- Eria A Rebollar
- Laboratorio de Evolución Molecular y Experimental, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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