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de la Haba RR, Arahal DR, Sánchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A. A long-awaited taxogenomic investigation of the family Halomonadaceae. Front Microbiol 2023; 14:1293707. [PMID: 38045027 PMCID: PMC10690426 DOI: 10.3389/fmicb.2023.1293707] [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: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 12/05/2023] Open
Abstract
The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - David R. Arahal
- Departament of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Liu J, Yu J, Si W, Ding G, Zhang S, Gong D, Bi J. Variations in bacterial diversity and community structure in the sediments of an alkaline lake in Inner Mongolia plateau, China. PeerJ 2023; 11:e15909. [PMID: 37637159 PMCID: PMC10448878 DOI: 10.7717/peerj.15909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos' desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = -0.924, p < 0.01; r = -0.800, p < 0.01; r = -0.933, p < 0.01) and salinity (r = -0.615, p < 0.05; r = -0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.
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Affiliation(s)
- Jumei Liu
- College of Chemistry and Environmental Engineering, Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jingli Yu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Wantong Si
- College of Chemistry and Environmental Engineering, Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences, Chongqing, China
| | - Ge Ding
- College of Chemistry and Environmental Engineering, Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Donghui Gong
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia Autonomous Region, China
| | - Jie Bi
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia Autonomous Region, China
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Biswas J, Jana SK, Mandal S. Biotechnological impacts of Halomonas: a promising cell factory for industrially relevant biomolecules. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36253947 DOI: 10.1080/02648725.2022.2131961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
Extremophiles are the most fascinating life forms for their special adaptations and ability to offer unique extremozymes or bioactive molecules. Halophiles, the natural inhabitants of hypersaline environments, are one among them. Halomonas are the common genus of halophilic bacteria. To support growth in unusual environments, Halomonas produces various hydrolytic enzymes, compatible solutes, biopolymers like extracellular polysaccharides (EPS) and polyhydroxy alkaloates (PHA), antibiotics, biosurfactants, pigments, etc. Many of such molecules are being produced in large-scale bioreactors for commercial use. However, the prospect of the remaining bioactive molecules with industrial relevance is far from their application. Furthermore, the genetic engineering of the respective gene clusters could open up a new path to bio-prospect these molecules by overproducing their products through heterologous expression. The present survey on Halomonas highlights their ecological diversity, application potential of the their various industrially relevant biomolecules and impact of these biomolecules on respective fields.
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Affiliation(s)
- Jhuma Biswas
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Santosh Kumar Jana
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
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Shang J, Xu L, Yang R, Zhao Y, Tang SK, Sun JQ. Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil, and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996. Syst Appl Microbiol 2022; 45:126351. [PMID: 35905572 DOI: 10.1016/j.syapm.2022.126351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 10/17/2022]
Abstract
Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7WT and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8-91.3% and 84.1-92.6%, respectively. The major polar lipids of M5N1S17T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C18:1ω6c and/or C18:1ω7c, C16:0, and C16:1ω7c and/or C16:1ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17T (= CGMCC 1.19023T = KCTC 92130T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443T clustered tightly with Halomonas desiderata FB2T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.
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Affiliation(s)
- Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rui Yang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yang Zhao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China.
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
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Fang S, Nan H, Lv D, You X, Chen J, Li C, Zhang J. Effects of sulfoxaflor on greenhouse vegetable soil N 2O emissions and its microbial driving mechanism. CHEMOSPHERE 2021; 267:129248. [PMID: 33321281 DOI: 10.1016/j.chemosphere.2020.129248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/29/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
The wide application of pesticides ensures the safety of food production, but it also has a serious impact on soil ecosystem. Although sulfoxaflor as a pesticide has great potential for application due to its excellent insecticidal activity and low crossresistance, little is known about its soil environmental safety risks. In this study, the effects of sulfoxaflor on N2O emissions and microorganisms in greenhouse vegetable soils were studied by indoor simulation culture experiments. Dynamic changes of soil main inorganic N and N2O emission rate were tested, and the abundance and community of total bacteria and microorganisms related to N cycle were analyzed. The results indicated that soil microorganisms rapidly degraded sulfoxaflor, and the N2O emissions rate and ammonium nitrogen (NH4+-N) content significantly increased, while nitrate nitrogen (NO3--N) content was significantly decreased. Sulfoxaflor significantly changed the abundance and community of total bacteria, nitrite reducing and nitrous oxide reducing bacteria, but had no significant effect on ammoxidation microorganisms. The N2O emission rate was positively correlated with gene abundance of denitrifying microorganisms. Under 65% soil maximum water holding capacity, sulfoxaflor may broke the dynamic balance of N2O production and consumption in the denitrification process, which caused a significant increase in N2O emission. Therefore, the application of sulfoxaflor had a certain effect on N cycling and utilization in greenhouse vegetable soil.
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Affiliation(s)
- Song Fang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Laboratory of Tobacco and Aromatic Plants Quality and Safety Risk Assessment, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Hai Nan
- Laboratory of Tobacco and Aromatic Plants Quality and Safety Risk Assessment, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Dongqing Lv
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiangwei You
- Laboratory of Tobacco and Aromatic Plants Quality and Safety Risk Assessment, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jianqiu Chen
- State Key Laboratory of Nutrition Resources Integrated Utilization, Kingenta Ecological Engineering Co., Ltd., Linshu, 276700, China
| | - Chengliang Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Jiguang Zhang
- Laboratory of Tobacco and Aromatic Plants Quality and Safety Risk Assessment, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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6
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Rahman Z, Thomas L. Chemical-Assisted Microbially Mediated Chromium (Cr) (VI) Reduction Under the Influence of Various Electron Donors, Redox Mediators, and Other Additives: An Outlook on Enhanced Cr(VI) Removal. Front Microbiol 2021; 11:619766. [PMID: 33584585 PMCID: PMC7875889 DOI: 10.3389/fmicb.2020.619766] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Chromium (Cr) (VI) is a well-known toxin to all types of biological organisms. Over the past few decades, many investigators have employed numerous bioprocesses to neutralize the toxic effects of Cr(VI). One of the main process for its treatment is bioreduction into Cr(III). Key to this process is the ability of microbial enzymes, which facilitate the transfer of electrons into the high valence state of the metal that acts as an electron acceptor. Many underlying previous efforts have stressed on the use of different external organic and inorganic substances as electron donors to promote Cr(VI) reduction process by different microorganisms. The use of various redox mediators enabled electron transport facility for extracellular Cr(VI) reduction and accelerated the reaction. Also, many chemicals have employed diverse roles to improve the Cr(VI) reduction process in different microorganisms. The application of aforementioned materials at the contaminated systems has offered a variety of influence on Cr(VI) bioremediation by altering microbial community structures and functions and redox environment. The collective insights suggest that the knowledge of appropriate implementation of suitable nutrients can strongly inspire the Cr(VI) reduction rate and efficiency. However, a comprehensive information on such substances and their roles and biochemical pathways in different microorganisms remains elusive. In this regard, our review sheds light on the contributions of various chemicals as electron donors, redox mediators, cofactors, etc., on microbial Cr(VI) reduction for enhanced treatment practices.
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Affiliation(s)
- Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
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Moopantakath J, Imchen M, Siddhardha B, Kumavath R. 16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140699. [PMID: 32679495 DOI: 10.1016/j.scitotenv.2020.140699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Madangchanok Imchen
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India.
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Antipov AN, Mordkovich NN, Khijniak TV, Okorokova NA, Veiko VP. Cloning of Nucleoside Phosphorylase Genes from the Extremophilic Bacterium Halomonas chromatireducens AGD 8-3 with the Construction of Recombinant Producer Strains of These Proteins and the Study of Their Enzymatic Properties. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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9
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Ren J, Wei C, Ma H, Dai M, Fan J, Liu Y, Wu Y, Han R. The Nitrogen-Removal Efficiency of a Novel High-Efficiency Salt-Tolerant Aerobic Denitrifier, Halomonas Alkaliphile HRL-9, Isolated from a Seawater Biofilter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16224451. [PMID: 31766146 PMCID: PMC6888400 DOI: 10.3390/ijerph16224451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022]
Abstract
Aerobic denitrification microbes have great potential to solve the problem of NO3--N accumulation in industrialized recirculating aquaculture systems (RASs). A novel salt-tolerant aerobic denitrifier was isolated from a marine recirculating aquaculture system (RAS) and identified as Halomonas alkaliphile HRL-9. Its aerobic denitrification performance in different dissolved oxygen concentrations, temperatures, and C/N ratios was studied. Investigations into nitrogen balance and nitrate reductase genes (napA and narG) were also carried out. The results showed that the optimal conditions for nitrate removal were temperature of 30 °C, a shaking speed of 150 rpm, and a C/N ratio of 10. For nitrate nitrogen (NO3--N) (initial concentration 101.8 mg·L-1), the sole nitrogen source of the growth of HRL-9, the maximum NO3--N removal efficiency reached 98.0% after 24 h and the maximum total nitrogen removal efficiency was 77.3% after 48 h. Nitrogen balance analysis showed that 21.7% of NO3--N was converted into intracellular nitrogen, 3.3% of NO3--N was converted into other nitrification products (i.e., nitrous nitrogen, ammonium nitrogen, and organic nitrogen), and 74.5% of NO3--N might be converted to gaseous products. The identification of functional genes confirmed the existence of the napA gene in strain HRL-9, but no narG gene was found. These results confirm that the aerobic denitrification strain, Halomonas alkaliphile HRL-9, which has excellent aerobic denitrification abilities, can also help us understand the microbiological mechanism and transformation pathway of aerobic denitrification in RASs.
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Affiliation(s)
- Jilong Ren
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Chenzheng Wei
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Hongjing Ma
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Mingyun Dai
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Jize Fan
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Ying Liu
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Yinghai Wu
- College of Marine and Civil Engineering, Dalian Ocean University, Dalian 116023, China;
- South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Rui Han
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Correspondence:
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10
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Reduction of hexavalent chromium by a moderately halophilic bacterium, Halomonas smyrnensis KS802 under saline environment. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-00037-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Lara P, Morett E, Juárez K. Acetate biostimulation as an effective treatment for cleaning up alkaline soil highly contaminated with Cr(VI). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25513-25521. [PMID: 27525740 DOI: 10.1007/s11356-016-7191-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Stimulation of microbial reduction of Cr(VI) to the less toxic and less soluble Cr(III) through electron donor addition has been regarded as a promising approach for the remediation of chromium-contaminated soil and groundwater sites. However, each site presents different challenges; local physicochemical characteristics and indigenous microbial communities influence the effectiveness of the biostimulation processes. Here, we show microcosm assays stimulation of microbial reduction of Cr(VI) in highly alkaline and saline soil samples from a long-term contaminated site in Guanajuato, Mexico. Acetate was effective promoting anaerobic microbial reduction of 15 mM of Cr(VI) in 25 days accompanied by an increase in pH from 9 to 10. Our analyses showed the presence of Halomonas, Herbaspirillum, Nesterenkonia/Arthrobacter, and Bacillus species in the soil sample collected. Moreover, from biostimulated soil samples, it was possible to isolate Halomonas spp. strains able to grow at 32 mM of Cr(VI). Additionally, we found that polluted groundwater has bacterial species different to those found in soil samples with the ability to resist and reduce chromate using acetate and yeast extract as electron donors.
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Affiliation(s)
- Paloma Lara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, 14610, México, Distrito Federal, Mexico
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
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Kalwasińska A, Felföldi T, Szabó A, Deja-Sikora E, Kosobucki P, Walczak M. Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland. Antonie van Leeuwenhoek 2017; 110:945-962. [PMID: 28382378 PMCID: PMC5486852 DOI: 10.1007/s10482-017-0866-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/28/2017] [Indexed: 11/30/2022]
Abstract
Soda lime is a by-product of the Solvay soda process for the production of sodium carbonate from limestone and sodium chloride. Due to a high salt concentration and alkaline pH, the lime is considered as a potential habitat of haloalkaliphilic and haloalkalitolerant microbial communities. This artificial and unique environment is nutrient-poor and devoid of vegetation, due in part to semi-arid, saline and alkaline conditions. Samples taken from the surface layer of the lime and from the depth of 2 m (both having pH ~11 and ECe up to 423 dS m−1) were investigated using culture-based (culturing on alkaline medium) and culture-independent microbiological approaches (microscopic analyses and pyrosequencing). A surprisingly diverse bacterial community was discovered in this highly saline, alkaline and nutrient-poor environment, with the bacterial phyla Proteobacteria (representing 52.8% of the total bacterial community) and Firmicutes (16.6%) showing dominance. Compared to the surface layer, higher bacterial abundance and diversity values were detected in the deep zone, where more stable environmental conditions may occur. The surface layer was dominated by members of the genera Phenylobacterium, Chelativorans and Skermanella, while in the interior layer the genus Fictibacillus was dominant. The culturable aerobic, haloalkaliphilic bacteria strains isolated in this study belonged mostly to the genus Bacillus and were closely related to the species Bacillus pseudofirmus, B. cereus, B. plakortidis, B. thuringensis and B. pumilus.
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Affiliation(s)
- Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland.
| | - Tamás Felföldi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Edyta Deja-Sikora
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - Przemysław Kosobucki
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland
| | - Maciej Walczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
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Draft Genome Sequence of "Halomonas chromatireducens" Strain AGD 8-3, a Haloalkaliphilic Chromate- and Selenite-Reducing Gammaproteobacterium. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00160-16. [PMID: 26988058 PMCID: PMC4796137 DOI: 10.1128/genomea.00160-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the complete genome sequence (3.97 Mb) of "Halomonas chromatireducens" AGD 8-3, a denitrifying bacterium capable of chromate and selenite reduction under extreme haloalkaline conditions. This strain was isolated from soda solonchak soils of the Kulunda steppe, Russian Federation.
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Aguirre-Garrido JF, Ramírez-Saad HC, Toro N, Martínez-Abarca F. Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island, Mexico. MICROBIAL ECOLOGY 2016; 71:68-77. [PMID: 26391805 DOI: 10.1007/s00248-015-0676-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Isabel Lake is a moderate saline soda crater lake located in Isabel Island in the eastern tropical Pacific coast of Mexico. Lake is mainly formed by rainfall and is strongly affected by evaporation and high input of nutrients derived from excretions of a large bird community inhabiting the island. So far, only the island macrobiota has been studied. The knowledge of the prokaryotic biota inhabiting the upper layers of this meromictic lake can give clues for the maintenance of this ecosystem. We assessed the diversity and composition of prokaryotic community in sediments and water of the lake by DGGE profiling, 16S rRNA gene amplicon pyrosequencing, and cultivation techniques. The bacterial community is largely dominated by halophilic and halotolerant microorganisms. Alpha diversity estimations reveal higher value in sediments than in water (P > 0.005). The lake water is dominated by γ-Proteobacteria belonging to four main families where Halomonadaceae presents the highest abundance. Aerobic, phototrophic, and halotolerant prokaryotes such as Cyanobacteria GPIIa, Halomonas, Alcanivorax, Idiomarina, and Cyclobacterium genera are commonly found. However, in sediment samples, Formosa, Muricauda, and Salegentibacter genera corresponding to Flavobacteriaceae family accounted for 15-20 % of the diversity. Heterotrophs like those involved in sulfur cycle, Desulfotignum, Desulfuromonas, Desulfofustis, and Desulfopila, appear to play an important role in sediments. Finally, a collection of aerobic halophilic bacterial isolates was created from these samples; members of the genus Halomonas were predominantly isolated from lake water. This study contributes to state the bacterial diversity present in this particular soda saline crater lake.
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Affiliation(s)
- José Félix Aguirre-Garrido
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Granada, Spain
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calz. del Hueso 1110, CP 14310, DF México, Mexico
| | - Hugo César Ramírez-Saad
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calz. del Hueso 1110, CP 14310, DF México, Mexico
| | - Nicolás Toro
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Granada, Spain
| | - Francisco Martínez-Abarca
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Granada, Spain.
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Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium. Appl Environ Microbiol 2015; 81:5511-8. [PMID: 26048926 PMCID: PMC4510161 DOI: 10.1128/aem.00853-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments.
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Zakharyuk AG, Kozyreva LP, Khijniak TV, Namsaraev BB, Shcherbakova VA. Desulfonatronum zhilinae sp. nov., a novel haloalkaliphilic sulfate-reducing bacterium from soda Lake Alginskoe, Trans-Baikal Region, Russia. Extremophiles 2015; 19:673-80. [DOI: 10.1007/s00792-015-0747-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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Mabrouk MEM, Arayes MA, Sabry SA. Hexavalent chromium reduction by chromate-resistant haloalkaliphilic Halomonas sp. M-Cr newly isolated from tannery effluent. BIOTECHNOL BIOTEC EQ 2014; 28:659-667. [PMID: 26740769 PMCID: PMC4684053 DOI: 10.1080/13102818.2014.937092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 02/12/2014] [Indexed: 10/25/2022] Open
Abstract
The current study aimed to isolate and characterize a chromate-resistant bacterium from tannery effluent, able to reduce Cr(VI) aerobically at high pH and salinity. Environmental contamination by hexavalent chromium, Cr(VI), presents a serious public health problem. Enrichment led to the isolation of 12 bacteria displaying different degrees of chromate reduction. Phenotypic characterization and phylogenetic analysis based on 16S rDNA sequence comparison indicated that the most potent strain belonged to the genus Halomonas. The new strain designated as Halomonas sp. M-Cr was able to reduce 82% of 50 mg L-1 Cr(VI) in 48 h, concomitant with discolouring of yellow colour of the medium and formation of white insoluble precipitate of Cr(III). It exhibited growth up to 3500 mg L-1 Cr(VI), 20% NaCl and showed strong Cr(VI) reduction under alkaline condition, pH 10. Scanning electron microscopy revealed precipitation of chromium hydroxide on bacterial cell surfaces, which showed characteristic peak of chromium in energy-dispersive X-ray analysis. Plackett-Burman design was used to evaluate the influence of related parameters for enhancing Cr(VI) reduction. Glucose, yeast extract and KH2PO 4 were confirmed as significant variables in the medium. Data suggest Halomonas sp. M-Cr as a promising candidate for bioremediation of Cr(VI) contaminated effluents particularly in saline and alkaline environments. Up to our knowledge, this is the first report on isolation of haloalkaliphilic Halomonas sp. from tannery effluent.
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Affiliation(s)
- Mona E M Mabrouk
- Botany Department, Faculty of Science, Damanhour University , Damanhour , Egypt
| | - Mervat A Arayes
- Botany Department, Faculty of Science, Damanhour University , Damanhour , Egypt
| | - Soraya A Sabry
- Botany and Microbiology Department, Faculty of Science, Alexandria University , Alexandria , Egypt
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Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014; 18:791-809. [PMID: 25156418 PMCID: PMC4158274 DOI: 10.1007/s00792-014-0670-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 01/26/2023]
Abstract
Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, RAS, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tom Berben
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Emily Denise Melton
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lex Overmars
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte D. Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerard Muyzer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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Kim KK, Lee JS, Stevens DA. Microbiology and epidemiology of Halomonas species. Future Microbiol 2014; 8:1559-73. [PMID: 24266356 DOI: 10.2217/fmb.13.108] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.
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Affiliation(s)
- Kwang Kyu Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Tugarova AV, Vetchinkina EP, Loshchinina EA, Shchelochkov AG, Nikitina VE, Kamnev AA. The ability of the rhizobacterium Azospirillum brasilense to reduce selenium(IV) to selenium(0). Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713030120] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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