1
|
Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
Collapse
|
2
|
Valdez S, de la Vega FV, Pairazaman O, Castellanos R, Esparza M. Hyperthermophile diversity microbes in the Calientes geothermal field, Tacna, Peru. Braz J Microbiol 2023; 54:2927-2937. [PMID: 37801222 PMCID: PMC10689642 DOI: 10.1007/s42770-023-01117-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 08/23/2023] [Indexed: 10/07/2023] Open
Abstract
Hyperthermophile microorganisms have been discovered worldwide, and several studies regarding biodiversity and the potential biotechnological applications have been reported. In this work, we describe for the first time the diversity of hyperthermophile communities in the Calientes Geothermal Field (CGF) located 4400 m above sea level in Tacna Region, Perú. Three hot springs were monitored and showed a temperature around 84 to 88 °C, for the microbiome analyzed was taken by sampling of sediment and water (pH 7.3-7.6). The hyperthermophile diversity was determined by PCR, DGGE, and DNA sequencing. The sediments analyzed showed a greater diversity than water samples. Sediments showed a more abundant population of bacteria than archaea, with the presence of at least 9 and 5 phylotypes, respectively. Most interestingly, in some taxa of bacteria (Bacillus) and archaea (Haloarcula and Halalkalicoccus), any of operational taxonomic units (OTUs) have not been observed before in hyperthermophile environments. Our results provide insight in the hyperthermophile diversity and reveal the possibility to develop new biotechnological applications based on the kind of environments.
Collapse
Affiliation(s)
- Silvia Valdez
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional Jorge Basadre Grohmann, Tacna, Perú
| | - Fabián Veliz de la Vega
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaiso-Chile Av. Brasil 2085, Valparaíso, Chile.
| | - Omar Pairazaman
- Laboratorio Regional de Salud Pública (Diresa), Cajamarca, Perú
| | - Roberto Castellanos
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional Jorge Basadre Grohmann, Tacna, Perú
| | - Mario Esparza
- Universidad Privada Antenor Orrego, Facultad de Medicina Humana, Laboratorio de Genética, Reproducción y Biología Molecular, Trujillo, Perú
| |
Collapse
|
3
|
Krawczyk A, Gosiewski T, Zapała B, Kowalska-Duplaga K, Salamon D. Alterations in intestinal Archaea composition in pediatric patients with Crohn's disease based on next-generation sequencing - a pilot study. Gut Microbes 2023; 15:2276806. [PMID: 37955638 PMCID: PMC10653639 DOI: 10.1080/19490976.2023.2276806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Intestinal dysbiosis can lead to the induction of systemic immune-mediated inflammatory diseases, such as Crohn's disease Although archaea are part of the commensal microbiota, they are still one of the least studied microorganisms. The aim of our study was the standardization of the optimal conditions and primers for sequencing of the gut archaeome using Next Generation Sequencing, and evaluation of the differences between the composition of archaea in patients and healthy volunteers, as well as analysis of the changes that occur in the archaeome of patients depending on disease activity. Newly diagnosed patients were characterized by similar archeal profiles at every taxonomic level as in healthy individuals (the dominance of Methanobacteria at the class level, and Methanobrevibacter at the genus level). In turn, in patients previously diagnosed with Crohn's disease (both in active and remission phase), an increased prevalence of Thermoplasmata, Thermoprotei, Halobacteria (at the class level), and Halococcus, Methanospaera or Picrophilus (at the genus level) were observed. Furthermore, we have found a significant correlation between the patient's parameters and the individual class or species of Archaea. Our study confirms changes in archaeal composition in pediatric patients with Crohn's disease, however, only in long-standing disease. At the beginning of the disease, the archeal profile is similar to that of healthy people. However, in the chronic form of the disease, significant differences in the composition of archaeome begin to appear. It seems that some archaea may be a good indicator of the chronicity and activity of Crohn's disease.
Collapse
Affiliation(s)
- A. Krawczyk
- Department of Molecular Medical Microbiology, Division of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - T. Gosiewski
- Department of Molecular Medical Microbiology, Division of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - B. Zapała
- Department of Pharmaceutical Microbiology, Jagiellonian University Medical College, Krakow, Poland
- Jagiellonian University Hospital in Krakow, Krakow, Poland
| | - K. Kowalska-Duplaga
- Department of Pediatrics, Gastroenterology and Nutrition,Jagiellonian University Medical College, Krakow, Poland
| | - D. Salamon
- Department of Molecular Medical Microbiology, Division of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| |
Collapse
|
4
|
Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
Collapse
Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
| |
Collapse
|
5
|
Ban Q, Zhang L, Li J. Correlating bacterial and archaeal community with efficiency of a coking wastewater treatment plant employing anaerobic-anoxic-oxic process in coal industry. CHEMOSPHERE 2022; 286:131724. [PMID: 34388873 DOI: 10.1016/j.chemosphere.2021.131724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Coking wastewater (CWW) contains various complex pollutants, and biological treatment processes are frequently applied in the coking wastewater treatment plants (CWWTPs). The present work is to evaluate the contaminants removal of a full-scale CWWTP with an anaerobic-anoxic-oxic process (A/A/O), to reveal function of bacterial and archaeal community involved in different bioreactors, and to clarify the relationship between the performance and microbial community. Illumina Miseq sequencing of bacteria showed that β-proteobacteria dominated in three bioreactors with relative abundance of 60.2%~81.7%. 75.2% of sequences were assigned to Petrobacter in the bioreactor A1, while Thiobacillus dominated in A2 and O with relative abundance of 31.8% and 38.7%, respectively. Illumina Miseq sequencing of archaea revealed a high diversity of methanogens existed in A1 and A2 activated sludge. Moreover, Halostagnicola was the dominant archaea in A1 and A2 activated sludge with relative abundance of 41.8% and 66.5%, respectively. Function predicted analysis explored that function of bacteria was similar to that of archaea but the relative abundance differed from each other. A putative biodegradation model of CWW treatment in A/A/O process indicated that A1 and A2 activated sludge mainly reduced carbohydrate, protein, TN, phenol and cyanide, as well as methane production. Bacteria in the bioreactor O were responsible for aerobic biotransformation of residual carbohydrates, refractory organics and nitrification. The redundancy analysis (RDA) further revealed that removal of COD, TN, and NO3--N, phenol and cyanides were highly correlated with some anaerobic bacteria and archaea, whereas the transformation of NH4+-N was positively correlated with some aerobic bacteria.
Collapse
Affiliation(s)
- Qiaoying Ban
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, PR China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China
| | - Liguo Zhang
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, PR China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
| |
Collapse
|
6
|
Kashif M, Majeed MI, Nawaz H, Rashid N, Abubakar M, Ahmad S, Ali S, Hyat H, Bashir S, Batool F, Akbar S, Anwar MA. Surface-enhanced Raman spectroscopy for identification of food processing bacteria. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 261:119989. [PMID: 34087771 DOI: 10.1016/j.saa.2021.119989] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Food processing bacteria play important role in providing flavors, ingredients and other beneficial characteristics to the food but at the same time some bacteria are responsible for food spoilage. Therefore, quick and reliable identification of these food processing bacteria is very necessary for the differentiation between different species which may help in the development of more useful food processing methodologies. In this study, analysis of different bacterial species (Lactobacillus fermentum, Fructobacillus fructosus, Pediococcus pentosaceus and Halalkalicoccus jeotgali) was performed with our in-house developed Ag NPs-based surface-enhanced Raman spectroscopy (SERS) method. The SERS spectral data was analyzed by multivariate data analysis techniques including principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). Bacterial species were differentiated on the basis of SERS spectral features and potential of SERS was compared with the Raman spectroscopy (RS). SERS along with PCA and PLS-DA was found to be an efficient technique for identification and differentiation of food processing bacterial species. Differentiation with accuracy of 99.5% and sensitivity of 99.7% was depicted by PLS-DA model using leave one out cross validation.
Collapse
Affiliation(s)
- Muhammad Kashif
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan.
| | - Nosheen Rashid
- Department of Physics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Hamza Hyat
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saba Bashir
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| |
Collapse
|
7
|
Song NE, Kim NJ, Kim YH, Baik SH. Probiotic Properties of Lactic Acid Bacteria with High Conjugated Linoleic Acid Converting Activity Isolated from Jeot-Gal, High-Salt Fermented Seafood. Microorganisms 2021; 9:2247. [PMID: 34835374 PMCID: PMC8625341 DOI: 10.3390/microorganisms9112247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Conjugated linoleic acid (CLA) isomers are potent health-promoting fatty acids. This study evaluated the probiotic properties of 10 strains of high CLA-producing lactic acid bacteria (LAB) isolated from Jeot-gal, a high-salt, fermented seafood. Two isolates, Lactiplantibacillus plantarum JBCC105683 and Lactiplantibacillus pentosus JBCC105676, produced the largest amounts of CLA (748.8 and 726.9 μg/mL, respectively). Five isolates, L. plantarum JBCC105675, L. pentosus JBCC105676, L. pentosus JBCC105674, L. plantarum JBCC105683, and Lactiplantibacillus paraplantarum JBCC105655 synthesized more cis-9, trans-11-CLA than trans-10, cis-12-CLA (approximately 80:20 ratio). All the strains survived severe artificial acidic environments and showed antimicrobial activity and strong adhesion capability to Caco-2 cells as compared to the commercial strain Lactocaseibacillus rhamnosus GG. Among them, Pediococcus acidilactici JBCC105117, L. paraplantarum JBCC105655, and L. plantarum JBCC105683 strongly stimulated the immunological regulatory gene PMK-1 and the host defense antimicrobial peptide gene clec-60 in Caenorhabditis elegans. Moreover, three strains showed a significant induction of tumor necrosis factor-α, interleukin (IL)-1β, IL-6, IL-12, and IL-10 production in RAW 264.7 macrophages, indicating that they were promising candidates for probiotics with high CLA-converting activity. Our results indicate that the newly isolated CLA-producing LAB might be useful as a functional probiotic with beneficial health effects that modulate the immune system.
Collapse
Affiliation(s)
- Nho-Eul Song
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Korea; (N.-E.S.); (N.-J.K.)
| | - Na-Jeong Kim
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Korea; (N.-E.S.); (N.-J.K.)
| | - Young-Hun Kim
- Department of Animal Science and Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - Sang-Ho Baik
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Korea; (N.-E.S.); (N.-J.K.)
| |
Collapse
|
8
|
Lavefve L, Cureau N, Rodhouse L, Marasini D, Walker LM, Ashley D, Lee S, Gadonna‐Widehem P, Anton PM, Carbonero F. Microbiota profiles and dynamics in fermented plant‐based products and preliminary assessment of their in vitro gut microbiota modulation. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Laura Lavefve
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Natacha Cureau
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Lindsey Rodhouse
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Daya Marasini
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Laura M. Walker
- Department of Biology Washington University in Saint‐Louis St Louis MO USA
| | - Danielle Ashley
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Sun‐Ok Lee
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Pascale Gadonna‐Widehem
- Transformations & Agroresources, ULR7519 Institut Polytechnique UniLaSalle, Universite d’Artois Beauvais France
| | - Pauline M. Anton
- Transformations & Agroresources, ULR7519 Institut Polytechnique UniLaSalle, Universite d’Artois Beauvais France
| | - Franck Carbonero
- Department of Food Science University of Arkansas Fayetteville AR USA
- Department of Nutrition and Exercise Physiology Elson Floyd School of Medicine Washington State University‐Spokane Spokane WA USA
| |
Collapse
|
9
|
Sorokin DY, Messina E, Smedile F, La Cono V, Hallsworth JE, Yakimov MM. Carbohydrate‐dependent sulfur respiration in halo(alkali)philic archaea. Environ Microbiol 2021; 23:3789-3808. [DOI: 10.1111/1462-2920.15421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences Moscow Russia
- Department of Biotechnology Delft University of Technology Delft The Netherlands
| | - Enzo Messina
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Francesco Smedile
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Violetta La Cono
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland BT9 5DL UK
| | - Michail M. Yakimov
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| |
Collapse
|
10
|
Ghauri K, Ali H, Munawar N, Ghauri MA, Anwar MA. Glycoside hydrolase family 68 gene of halophilic archaeon Halalkalicoccus jeotgali B3T codes for an inulosucrase enzyme. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1813726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Komal Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Nayla Munawar
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
- Department of Chemistry, College of Sciences, United Arab Emirates University, Al-Ain, UAE
| | - Muhammad Afzal Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| |
Collapse
|
11
|
Ghauri K, Ali H, Munawar N, Ghauri MA, Anwar MA. Glycoside hydrolase family 68 gene of halophilic archaeon Halalkalicoccus jeotgali B3T codes for an inulosucrase enzyme. BIOCATAL BIOTRANSFOR 2020. [DOI: https://doi.org/10.1080/10242422.2020.1813726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Komal Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Nayla Munawar
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
- Department of Chemistry, College of Sciences, United Arab Emirates University, Al-Ain, UAE
| | - Muhammad Afzal Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| |
Collapse
|
12
|
Relative abundance of halophilic archaea and bacteria in diverse salt-fermented fish products. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108688] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
13
|
Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics. Appl Environ Microbiol 2019; 85:AEM.02935-18. [PMID: 30658981 DOI: 10.1128/aem.02935-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
The canonical pathway for sucrose metabolism in haloarchaea utilizes a modified Embden-Meyerhof-Parnas pathway (EMP), in which ketohexokinase and 1-phosphofructokinase phosphorylate fructose released from sucrose hydrolysis. However, our survey of haloarchaeal genomes determined that ketohexokinase and 1-phosphofructokinase genes were not present in all species known to utilize fructose and sucrose, thereby indicating that alternative mechanisms exist for fructose metabolism. A fructokinase gene was identified in the majority of fructose- and sucrose-utilizing species, whereas only a small number possessed a ketohexokinase gene. Analysis of a range of hypersaline metagenomes revealed that haloarchaeal fructokinase genes were far more abundant (37 times) than haloarchaeal ketohexokinase genes. We used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase) and identified changes in protein abundance that relate to growth on sucrose. Proteins inferred to be involved in sucrose metabolism included fructokinase, a carbohydrate primary transporter, a putative sucrose hydrolase, and two uncharacterized carbohydrate-related proteins encoded in the same gene cluster as fructokinase and the transporter. Homologs of these proteins were present in the genomes of all haloarchaea that use sugars for growth. Enzymes involved in the semiphosphorylative Entner-Doudoroff pathway also had higher abundances in sucrose-grown H. litchfieldiae cells, consistent with this pathway functioning in the catabolism of the glucose moiety of sucrose. The study revises the current understanding of fundamental pathways for sugar utilization in haloarchaea and proposes alternatives to the modified EMP pathway used by haloarchaea for sucrose and fructose utilization.IMPORTANCE Our ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When genomic or metagenomic data are used, metabolic capacity is inferred from genetic potential. Here, we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase occurs only in a small proportion of haloarchaeal genomes and is underrepresented in metagenomes. Instead, fructokinase genes are present in the majority of genomes/metagenomes. In addition to genomic and metagenomic analyses, we used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase but lacks ketohexokinase) and identified changes in protein abundance that related to growth on sucrose. In this way, we identified novel proteins implicated in sucrose metabolism in haloarchaea, comprising a transporter and various catabolic enzymes (including proteins that are annotated as hypothetical).
Collapse
|
14
|
Chen S, Xu Y, Sun S, Chen F, Liu J. Halalkalicoccus subterraneus sp. nov., an extremely halophilic archaeon isolated from a subterranean halite deposit. Antonie van Leeuwenhoek 2019; 112:1067-1075. [PMID: 30707397 DOI: 10.1007/s10482-019-01241-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/22/2019] [Indexed: 11/29/2022]
Abstract
An extremely halophilic archaeon, designated strain GSM28T, was isolated from a subterranean halite deposit in a Yunnan salt mine, China. Cells of the strain were observed to be cocci, non-motile and Gram-variable, and to require at least 15% (w/v) NaCl for growth (optimum 20%). Growth was found to occur in the ranges of 20-45 °C (optimum 42 °C) and pH 6.0-8.5 (optimum 7.5). Cells did not lyse in distilled water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain belongs to the genus Halalkalicoccus and shows 99.1% similarities with its close phylogenetic relative Halalkalicoccus paucihalophilus DSM 24557T. Genomic ANI analysis showed that the DNA-DNA relatedness between strain GSM28T and the closely related species Hac. paucihalophilus DSM 24557T and Halalkalicoccus jeotgali B3T was 83.7% and 83.1%, respectively. The major polar lipids were determined to be phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl-glucosyl-glycerol diether-1 and two unidentified glycolipids. The DNA G + C content was determined to be 61.8 mol %. On the basis of physiological, biochemical tests and phylogenetic differentiations, strain GSM28T is concluded to represent a novel species in the genus Halalkalicoccus, for which the name Halalkalicoccus subterraneus sp. nov. is proposed. The type strain is GSM28T (= CGMCC 1.16344T = NBRC 113432T).
Collapse
Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China. .,College of Life Sciences, Honghe University, No. 1 Xuefu Road, Mengzi, 661100, Yunnan, People's Republic of China.
| | - Yao Xu
- College of Life Sciences, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Siqi Sun
- College of Life Sciences, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Feilong Chen
- College of Life Sciences, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Jingwen Liu
- College of Life Sciences, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| |
Collapse
|
15
|
Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. MICROBIOLOGY-SGM 2017; 163:623-645. [PMID: 28548036 DOI: 10.1099/mic.0.000463] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.
Collapse
Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Siroosi
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| |
Collapse
|
16
|
Nkamga VD, Henrissat B, Drancourt M. Archaea: Essential inhabitants of the human digestive microbiota. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2016.11.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
17
|
Williams TJ, Allen M, Tschitschko B, Cavicchioli R. Glycerol metabolism of haloarchaea. Environ Microbiol 2016; 19:864-877. [PMID: 27768817 DOI: 10.1111/1462-2920.13580] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.
Collapse
Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Michelle Allen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| |
Collapse
|
18
|
Song HS, Cha IT, Rhee JK, Yim KJ, Kim AY, Choi JS, Baek SJ, Seo MJ, Park SJ, Nam YD, Roh SW. Halostella salina gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt. Int J Syst Evol Microbiol 2016; 66:2740-2746. [PMID: 27118259 DOI: 10.1099/ijsem.0.001118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon designated strain CBA1114T was isolated from solar salt in the Republic of Korea. Strain CBA1114T, cells of which were coccoid and Gram-stain-negative, grew in the presence of 15-30 % (w/v) NaCl (optimum, 20 %) and at 20-50 °C (optimum, 40 °C) and pH 7.0-9.0 (optimum, pH 8.0). Strain CBA1114T required Mg2+ for growth. Strain CBA1114T had three 16S rRNA genes, rrnA, rrnB and rrnC; levels of similarity between the sequences were 99.7-99.9 %. The 16S rRNA gene sequence of strain CBA1114T showed 91.7 % similarity to that of Haloterrigena thermotolerans PR5T. In multilocus sequence analysis (MLSA), five housekeeping genes, atpB, EF-2, radA, rpoB' and secY, were found to be closely related to those of the members of the genera Halorientalis(89.7 % similarity of the atpB gene sequence), Halomicroarcula(91.9 %, EF-2), Haloterrigena(85.4 %, radA), Natronoarchaeum(89.2 %, rpoB') and Natrinema(75.7 %, secY). A phylogenetic tree generated from the results of MLSA of the five housekeeping genes showed that strain CBA1114T was closely related to species of the genus Halorientalis in the family Halobacteriaceae. The major polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and unidentified lipids. The G+C content of the genomic DNA of strain CBA1114T was 68.1 mol%. According to the results of phylogenetic, phenotypic and chemotaxonomic analyses, we designate strain CBA1114T (=JCM 30111T=KCTC 4206T) as the type strain of Halostella salina gen. nov., sp. nov., a novel species of a new genus within the family Halobacteriaceae.
Collapse
Affiliation(s)
- Hye Seon Song
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, South Korea
| | - In-Tae Cha
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Division of Bioengineering, Incheon National University, Incheon 22012, South Korea
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, South Korea
| | - Kyung June Yim
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea
| | - Ah Yoon Kim
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea
| | - Jong-Soon Choi
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Su Jeong Baek
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon 22012, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju 63243, South Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam 13539, South Korea
| | - Seong Woon Roh
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea
| |
Collapse
|
19
|
Aurell E, Innocenti N, Zhou HJ. The bulk and the tail of minimal absent words in genome sequences. Phys Biol 2016; 13:026004. [PMID: 27043075 DOI: 10.1088/1478-3975/13/2/026004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the concept of a core of a MAW, which are sequences present in the genome and closest to a given MAW. We show that in E. faecalis, E. coli and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs. We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.
Collapse
Affiliation(s)
- Erik Aurell
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden. Department of Information and Computer Science, Aalto University, FI-02150 Espoo, Finland
| | | | | |
Collapse
|
20
|
Ross AA, Neufeld JD. Microbial biogeography of a university campus. MICROBIOME 2015; 3:66. [PMID: 26620848 PMCID: PMC4666157 DOI: 10.1186/s40168-015-0135-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/17/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Microorganisms are distributed on surfaces within homes, workplaces, and schools, with the potential to impact human health and disease. University campuses represent a unique opportunity to explore the distribution of microorganisms within built environments because of high human population densities, throughput, and variable building usage. For example, the main campus of the University of Waterloo spans four square kilometres, hosts over 40,000 individuals daily, and is comprised of a variety of buildings, including lecture halls, gyms, restaurants, residences, and a daycare. RESULTS Representative left and right entrance door handles from each of the 65 buildings at the University of Waterloo were swabbed at three time points during an academic term in order to determine if microbial community assemblages coincided with building usage and whether these communities are stable temporally. Across all door handles, the dominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, which comprised 89.0 % of all reads. A total of 713 genera were observed, 16 of which constituted a minimum of 1 % of the 2,458,094 classified and rarefied reads. Archaea were found in low abundance (~0.03 %) but were present on 42.8 % of the door handles on 96 % of buildings across all time points, indicating that they are ubiquitous at very low levels on door handle surfaces. Although inter-handle variability was high, several individual building entrances harbored distinct microbial communities that were consistent over time. The presence of visible environmental debris on a subset of handles was associated with distinct microbial communities (beta diversity), increased richness (alpha diversity), and higher biomass (adenosine 5'-triphosphate; ATP). CONCLUSIONS This study demonstrates highly variable microbial communities associated with frequently contacted door handles on a university campus. Nonetheless, the data also revealed several building-specific and temporally stable bacterial and archaeal community patterns, with a potential impact of accumulated debris, a possible result of low human throughput, on detected microbial communities.
Collapse
Affiliation(s)
- Ashley A Ross
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
| |
Collapse
|
21
|
Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes. Sci Rep 2015; 5:16425. [PMID: 26553382 PMCID: PMC4639753 DOI: 10.1038/srep16425] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/12/2015] [Indexed: 12/27/2022] Open
Abstract
Flamingoes (Phoenicopterus spp.) whose plumage displays elegant colors, inhabit warm regions close to the ocean throughout the world. The pink or reddish color of their plumage originates from carotenoids ingested from carotenoid-abundant food sources, since flamingoes are unable to synthesize these compounds de novo. In this study, viable red-colored archaeal strains classified as extremely halophilic archaea (i.e., haloarchaea) and belonging to the genera Halococcus and Halogeometricum were isolated from the plumage of flamingoes in captivity. Detailed analysis for haloarchaeal community structure in flamingo feathers based on metagenomic data identified several haloarchaeal genera and unclassified sequences of the class Halobacteria at the genus level. Carotenoid pigment analyses showed that a bacterioruberin precursor carotenoid in haloarchaea was identical to one of the pigments found in flamingo plumage. To the best of our knowledge, this is the first report of viable extremophilic archaea in avian plumage, thus contributing to our understanding of the ecology of haloarchaea. The potential influence of haloarchaea as an environmental factor determining avian plumage coloration should be investigated in further studies.
Collapse
|
22
|
Henriet O, Fourmentin J, Delincé B, Mahillon J. Exploring the diversity of extremely halophilic archaea in food-grade salts. Int J Food Microbiol 2014; 191:36-44. [DOI: 10.1016/j.ijfoodmicro.2014.08.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/07/2014] [Accepted: 08/13/2014] [Indexed: 10/24/2022]
|
23
|
Liu BB, Zhao WY, Chu X, Hozzein WN, Prabhu DM, Wadaan MAM, Tang SK, Zhang LL, Li WJ. Haladaptatus pallidirubidus sp. nov., a halophilic archaeon isolated from saline soil samples in Yunnan and Xinjiang, China. Antonie van Leeuwenhoek 2014; 106:901-10. [PMID: 25190334 DOI: 10.1007/s10482-014-0259-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Two extremely halophilic archaea, designated YIM 90917 and YIM 93656(T), were isolated from saline soils in Yunnan province and Lup nur region in Xinjiang province, western China, respectively. Colonies of the two strains were observed to be pink-pigmented. The cells were found to be Gram-stain negative, coccoid and non-motile. The organisms were found to be aerobic and could grow in an NaCl range of 6-35 % (optimum 18 %), temperatures ranging from 25 to 50 °C (optimum 37-42 °C), pH range from 6.0-8.5 (optimum pH 7.0-7.5) and Mg(2+) range from 0 to 1.5 M (optimum 0.5-1.0 M); Mg(2+) was not necessary for growth. Cells were not observed to lyse in distilled water. Strains YIM 90917 and YIM 93656(T) showed the highest 16S rRNA gene sequence similarities to Haladaptatus cibarius JCM 15962(T) (97.6 and 97.9 %, respectively). In addition, the DNA-DNA hybridizations of strains YIM 90917 and YIM 93656(T) with type strains H. cibarius JCM 15962(T), Haladaptatus litoreus JCM 15771(T) and Haladaptatus paucihalophilus JCM 13897(T) were 37.2 and 38.2 %, 36.6 and 39.0 % and 27.9 and 27.7 %, respectively. The DNA G+C contents of strains YIM 90917 and YIM 93656(T) were determined to be 56.0 and 57.4 mol%. The major polar lipids of the two strains were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and other four unidentified glycolipids. On the basis of physiological, chemotaxonomic data and phylogenetic analysis, the strains YIM 90917 and YIM 93656(T) can be classified as a novel species of the genus Haladaptatus, for which the name Haladaptatus pallidirubidus sp. nov. is proposed. The type strain is YIM 93656(T) (=JCM 17504(T) = CCTCC AB2010454(T)).
Collapse
Affiliation(s)
- Bing-Bing Liu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Halolamina rubra sp. nov., a haloarchaeon isolated from non-purified solar salt. Antonie van Leeuwenhoek 2014; 105:907-14. [PMID: 24633912 DOI: 10.1007/s10482-014-0145-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
Two Gram-stain negative, rod-shaped and motile extreme halophiles, designated CBA1107(T) and CBA1108, were isolated from non-purified solar salt. Based on the phylogenetic analysis, strains CBA1107(T) and CBA1108 were shown to belong to the genus Halolamina, with similarities for the 16S rRNA gene sequences between strains CBA1107(T) and Halolamina pelagica TBN21(T) , Halolamina salina WSY15-H3(T) and Halolamina salifodinae WSY15-H1(T) of 98.3, 97.6 and 97.3 %, respectively; the similarities for the rpoB' gene sequences between the same strains were 96.0, 95.3 and 94.6 %, respectively. The colonies of both strains were observed to be red pigmented on growth medium. Strain CBA1107(T) was observed to grow at 20-50 °C, in the presence of 15-30 % NaCl, at pH 6.0-9.0, and with 0.005-0.5 M Mg(2+). The cells of both strains lysed in distilled water. The DNA-DNA hybridization experiments showed that strain CBA1107(T) shared 97 % relatedness with CBA1108 and <50 % relatedness with H. pelagica JCM 16809(T), H. salina JCM 18549(T) and H. salifodinae JCM 18548(T). The genomic DNA G+C content of strain CBA1107(T) was determined to be 65.1 mol%. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and glycolipids including sulfated mannosyl glucosyl diether and mannosyl glucosyl diether. Based on the polyphasic taxonomic analyses, the strains are considered to represent a new taxon for which the name Halolamina rubra sp. nov. is proposed, with the type strain CBA1107(T) (=CECT 8421(T) =JCM 19436(T)).
Collapse
|
25
|
Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood. Antonie van Leeuwenhoek 2014; 105:603-12. [PMID: 24442192 DOI: 10.1007/s10482-014-0115-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
A novel, red-pigmented, pleomorphic and short rod-shaped haloarchaeon, designated B8(T), was isolated from a salt-fermented seafood. Strain B8(T) was found to be able to grow at 20-45 °C, in the presence of 15-30 % (w/v) NaCl and at pH 7.0-9.0. The optimum requirements were found to be a temperature range of 35-40 °C, pH 8.0 and the presence of 25 % NaCl. The cells of strain B8(T) were observed to be Gram-staining negative and lysed in distilled water. Anaerobic growth did not occur in the presence of nitrate, L-arginine, dimethyl sulfoxide or trimethylamine N-oxide. The catalase and oxidase activities were found to be positive and nitrate was reduced in aerobic conditions. Tween 20, 40 and 80 were found to be hydrolyzed, whereas casein, gelatin and starch were not hydrolyzed. Indole or H2S was not formed and urease activity was not detected. A phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B8(T) is most closely related to members of the genus Halorubrum in the family Halobacteriaceae. Strain B8(T) was found to have three 16S rRNA genes, rrnA, rrnB and rrnC; similarities between the 16S rRNA gene sequences are 99.0-99.8 %. Strain B8(T) shared 99.0 % 16S rRNA gene sequence similarity with Halorubrum (Hrr.) lipolyticum JCM 13559(T) and Hrr. saccharovorum DSM 1137(T), 98.8 % with Hrr. kocurii JCM 14978(T), 98.3 % with Hrr. lacusprofundi DSM 5036(T), 98.0 % with Hrr. arcis JCM 13916(T), 97.7 % with Hrr. aidingense JCM 13560(T) and 97.0 % with Hrr. aquaticum JCM 14031(T), as well as 93.7-96.5 % with other type strains in the genus Halorubrum. The RNA polymerase subunit B' gene sequence similarity of strain B8(T) with Hrr. kocurii JCM 14978(T) is 97.2 % and lower with other members of the genus Halorubrum. DNA-DNA hybridization experiments showed that strain B8(T) shared equal or lower than 50 % relatedness with reference species in the genus Halorubrum. The genomic DNA G+C content of strain B8(T) was determined to be 64.6 mol%. The major isoprenoid quinone of strain B8(T) was identified as menaquinone-8 and the major polar lipids as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and an unidentified phospholipid. Based on this polyphasic taxonomic study, strain B8(T) is considered to represent a new species in the genus Halorubrum, for which the name Hrr. halophilum sp. nov. is proposed. The type strain is B8(T) (=JCM 18963(T) = CECT 8278(T)).
Collapse
|
26
|
Cui HL, Qiu XX. Salinarubrum litoreum gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from Chinese marine solar salterns. Antonie van Leeuwenhoek 2013; 105:135-41. [DOI: 10.1007/s10482-013-0061-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/17/2013] [Indexed: 10/26/2022]
|
27
|
Minegishi H, Shimane Y, Echigo A, Ohta Y, Hatada Y, Kamekura M, Maruyama T, Usami R. Thermophilic and halophilic β-agarase from a halophilic archaeon Halococcus sp. 197A. Extremophiles 2013; 17:931-9. [PMID: 23949137 PMCID: PMC3824881 DOI: 10.1007/s00792-013-0575-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/30/2013] [Indexed: 11/28/2022]
Abstract
An agar-degrading archaeon Halococcus sp. 197A was isolated from a solar salt sample. The agarase was purified by hydrophobic column chromatography using a column of TOYOPEARL Phenyl-650 M. The molecular mass of the purified enzyme, designated as Aga-HC, was ~55 kDa on both SDS-PAGE and gel-filtration chromatography. Aga-HC released degradation products in the order of neoagarohexose, neoagarotetraose and small quantity of neoagarobiose, indicating that Aga-HC was a β-type agarase. Aga-HC showed a salt requirement for both stability and activity, being active from 0.3 M NaCl, with maximal activity at 3.5 M NaCl. KCl supported similar activities as NaCl up to 3.5 M, and LiCl up to 2.5 M. These monovalent salts could not be substituted by 3.5 M divalent cations, CaCl2 or MgCl2. The optimal pH was 6.0. Aga-HC was thermophilic, with optimum temperature of 70 °C. Aga-HC retained approximately 90 % of the initial activity after incubation for 1 hour at 65-80 °C, and retained 50 % activity after 1 hour at 95 °C. In the presence of additional 10 mM CaCl2, approximately 17 % remaining activity was detected after 30 min at 100 °C. This is the first report on agarase purified from Archaea.
Collapse
Affiliation(s)
- Hiroaki Minegishi
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe, Saitama, 350-8585, Japan,
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Liu BB, Tang SK, Cui HL, Zhang YG, Li L, Zhang YM, Zhang LL, Li WJ. Halopelagius fulvigenes sp. nov., a halophilic archaeon isolated from a lake. Int J Syst Evol Microbiol 2013; 63:2192-2196. [DOI: 10.1099/ijs.0.045773-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, designated YIM 94188T and YIM 94189, were isolated from Qijiaojing lake in Xinjiang province, north-west China and subjected to taxonomic characterization using a polyphasic approach. The cells of the two strains were coccoid, non-motile and Gram-stain-negative. Colonies were pink–white-pigmented and aerobic. Growth occurred at 10–30 % (w/v) NaCl, 20–55 °C and pH 6.0–8.0 (optimum: 20–25 % NaCl, 37–42 °C, pH 6.5–7.0). Magnesium was necessary for growth in the range of 0.2–1.2 M. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the two strains belonged to the genus
Halopelagius
showing 98.5 % sequence similarity to the closest phylogenetic neighbour,
Halopelagius inordinatus
RO5-2T. In addition, the DNA–DNA hybridization values of strains YIM 94188T and YIM 94189 to
Halopelagius inordinatus
RO5-2T were 35.7 % and 37.7 %, respectively. Polar lipid analyses revealed that the two strains contained phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The DNA G+C contents of strains YIM 94188T and YIM 94189 were 66.3 mol% and 64.6 mol%, respectively. On the basis of physiological and chemotaxonomic data, and phylogenetic analysis, strains YIM 94188T and YIM 94189 were classified as representing a novel species in the genus
Halopelagius
. The name Halopelagius fulvigenes sp. nov. is proposed, with YIM 94188T ( = CCTCC AB 2010456T = JCM 17506T) as the type strain.
Collapse
Affiliation(s)
- Bing-Bing Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Shu-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 650091, PR China
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Yuan-Ming Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Li-Li Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Tarim University, Alar 843300, PR China
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, 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 650091, PR China
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| |
Collapse
|
29
|
Jung JY, Lee SH, Lee HJ, Jeon CO. Microbial succession and metabolite changes during fermentation of saeu-jeot: traditional Korean salted seafood. Food Microbiol 2013; 34:360-8. [PMID: 23541203 DOI: 10.1016/j.fm.2013.01.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 01/02/2013] [Accepted: 01/16/2013] [Indexed: 01/13/2023]
Abstract
Saeu-jeot is made by the fermentation of highly salted [approximately 25% (w/v)] shrimp in Korea. Saeu-jeot samples were prepared in triplicate and their cell number, bacterial community, and metabolites were monitored periodically for 183 days. Quantitative PCR showed that bacterial populations were much more abundant than archaeal populations during the entire saeu-jeot fermentation period, which suggested that bacterial populations, not archaeal populations, might be primarily responsible for saeu-jeot fermentation. Pyrosequencing analysis revealed that Proteobacteria were dramatically replaced with halophilic Firmicutes as the fermentation progressed and members of Pseudoalteromonas, Staphylococcus, Salimicrobium, and Alkalibacillus were sequentially dominant and, eventually, Halanaerobium predominated after 66 days of fermentation. Halophilic archaeal genera, Halorubrum, Halolamina, Halobacterium, Haloarcula, and Haloplanus belonging to Euryarchaeota, were dominant, but their communities were relatively constant over the entire fermentation period. Metabolite analysis using a (1)H NMR spectroscopy showed that the amount of metabolites including amino acids, glycerol, and nitrogen compounds rapidly increased during the early fermentation stage, but their levels were relatively constant or they decreased after approximately 49 days of fermentation. A statistical analysis based on bacterial communities and metabolites demonstrated that members of Halanaerobium might be responsible for the production of acetate, butyrate, and methylamines after 66 days of fermentation, which could be considered as a potential indicator to decide the appropriate seafood fermentation time. This study will provide insights into the microbial succession and metabolites of fermented seafood and allow for a greater understanding of the relationships between the microbial community and metabolites in seafood fermentation.
Collapse
Affiliation(s)
- Ji Young Jung
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | | | | | | |
Collapse
|
30
|
Liu BB, Tang SK, Zhang YG, Lu XH, Li L, Cheng J, Zhang YM, Zhang LL, Li WJ. Halalkalicoccus paucihalophilus sp. nov., a halophilic archaeon from Lop Nur region in Xinjiang, northwest of China. Antonie van Leeuwenhoek 2013; 103:1007-14. [PMID: 23338603 DOI: 10.1007/s10482-013-9880-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 01/10/2013] [Indexed: 11/28/2022]
Abstract
Two extremely halophilic archaea, designated YIM 93701(T) and YIM 93664, were isolated from Lop Nur region in Xinjiang Province, northwest of China. The cells of the two strains were observed to be cocci, non-motile and Gram-negative. The organisms were determined to be aerobic and required at least 6 % NaCl for growth (optimum 20-25 % and maximum 35 %). Growth was found to occur in the ranges of 16-50 °C (optimum 37 °C) and pH 6.0-8.5 (optimum 6.5-7.5). Cells did not lyse in distilled water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belongs to the genus Halalkalicoccus and possessed 99.3 and 99.5 % similarities with their closest phylogenetic relative Halalkalicoccus tibetensis JCM 11890(T). Major polar lipids of the two strains were determined to be phosphatidylglycerol(PG),phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS) and three unidentified glycolipids. The DNA G+C contents were determined to be 60.0-60.4 mol%. The DNA hybridization between the two strains was 92.0 %. In addition, the hybridizations of both strains to H. tibetensis were 49 and 52 %, respectively, and to Halalkalicoccus jeotali were 38 and 33 %, respectively. On the basis of physiological, biochemical tests and phylogenetic differentiations, strains YIM 93701(T) and YIM 93664 were classified as the same species which represent a novel species in the genus Halalkalicoccus, for which the name Halalkalicoccus paucihalophilus sp. nov. is proposed. The type strain is YIM 93701(T) (=JCM 17505(T) = CCTCC 2012803(T)).
Collapse
Affiliation(s)
- Bing-Bing Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Ürűmqi, People's Republic of China
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Arakawa T, Tokunaga H, Ishibashi M, Tokunaga M. Halophilic Properties and their Manipulation and Application. Extremophiles 2012. [DOI: 10.1002/9781118394144.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
32
|
Syutkin AS, Pyatibratov MG, Beznosov SN, Fedorov OV. Various mechanisms of flagella helicity formation in haloarchaea. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712050153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
33
|
Bengtson P, Bastviken D, Oberg G. Possible roles of reactive chlorine II: assessing biotic chlorination as a way for organisms to handle oxygen stress. Environ Microbiol 2012; 15:991-1000. [PMID: 22712445 DOI: 10.1111/j.1462-2920.2012.02807.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Natural formation of organically bound chlorine is extensive in many environments. The enzymes associated with the formation of chlorinated organic matter are produced by a large variety of organisms. Little is known about the ecological role of the process, the key question being: why do microorganisms promote chlorination of organic matter? In a recent paper we discuss whether organic matter chlorination may be a result of antagonistic interactions among microorganisms. In the present paper we evaluate whether extracellular microbial formation of reactive chlorine may be used as a defence against oxygen stress, and we discuss whether this process is likely to contribute to the formation of chlorinated organic matter. Our analysis suggests that periodic exposure to elevated concentrations of reactive oxygen species is a common denominator among the multitude of organisms that are able to enzymatically catalyse formation of reactive chlorine. There is also some evidence suggesting that the production of such enzymes in algae and bacteria is induced by oxygen stress. The relative contribution from this process to the extensive formation of chlorinated organic matter in natural environments remains to be empirically assessed.
Collapse
Affiliation(s)
- Per Bengtson
- Department of Biology - Microbial Ecology, Lund University, The Ecology Building, Lund SE-223 62, Sweden
| | | | | |
Collapse
|
34
|
Cui HL, Yang X, Mou YZ. Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria. Extremophiles 2011; 15:625-31. [PMID: 21901373 DOI: 10.1007/s00792-011-0393-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 08/22/2011] [Indexed: 11/29/2022]
Abstract
Halophilic archaeal strains R26(T) and R22 were isolated from the brown alga Laminaria produced at Dalian, Liaoning Province, China. Cells from the two strains were pleomorphic rods and Gram negative, and colonies were red pigmented. Strains R26(T) and R22 were able to grow at 20-50°C (optimum 37°C) in 1.4-5.1 M NaCl (optimum 3.1-4.3 M) at pH 5.5-9.5 (optimum pH 8.0-8.5) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimum NaCl concentration required to prevent cell lysis was 8% (w/v) for strain R26(T) and 12% (w/v) for strain R22. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phosphatidylglycerol sulfate; glycolipids were not detected. Phylogenetic analyses based on 16S rRNA genes and rpoB' genes revealed that strains R26(T) and R22 formed a distinct clade with the closest relative, Natronoarchaeum mannanilyticum. The DNA G+C content of strains R26(T) and R22 was 65.8 and 66.4 mol%, respectively. The DNA-DNA hybridization value between strains R26(T) and R22 was 89%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the strains R26(T) and R22 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Salinarchaeum laminariae gen. nov., sp. nov. is proposed. The type strain is R26(T) (type strain R26(T) = CGMCC 1.10590(T) = JCM 17267(T), reference strain R22 = CGMCC 1.10589).
Collapse
Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Jingkou District, Zhenjiang, People's Republic of China.
| | | | | |
Collapse
|
35
|
Inoue K, Itoh T, Ohkuma M, Kogure K. Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium. Int J Syst Evol Microbiol 2011; 61:942-946. [DOI: 10.1099/ijs.0.020677-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0–8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data support the placement of isolate KeC-11T in a novel species in a new genus within the family Halobacteriaceae, for which the name Halomarina oriensis gen. nov., sp. nov. is proposed; the type strain is KeC-11T ( = JCM 16495T = KCTC 4074T).
Collapse
Affiliation(s)
- Kentaro Inoue
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuhiro Kogure
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
| |
Collapse
|
36
|
Bowers KJ, Wiegel J. Temperature and pH optima of extremely halophilic archaea: a mini-review. Extremophiles 2011; 15:119-28. [DOI: 10.1007/s00792-010-0347-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 12/08/2010] [Indexed: 11/25/2022]
|
37
|
Cui HL, Gao X, Yang X, Xu XW. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 2010; 14:493-9. [PMID: 20824294 DOI: 10.1007/s00792-010-0329-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/25/2010] [Indexed: 11/24/2022]
Abstract
Two halophilic archaeal strains TBN4(T) and TBN5 were isolated from Taibei marine solar saltern in Jiangsu, China. Both strains showed light red-pigmented colonies and their cells were rod, motile and Gram-stain-negative. They were able to grow at 25-50°C (optimum 37°C), at 1.4-4.3 M NaCl (optimum 2.1 M NaCl), at 0-1.0 M MgCl(2) (optimum 0.005 M MgCl(2)) and at pH 6.0-9.0 (optimum pH 7.0). Their cells lyse in distilled water and minimal NaCl concentration to prevent cell lysis is 8% (w/v). The major polar lipids of the two strains were PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester), PGS (phosphatidylglycerol sulfate) and five glycolipids chromatographically identical to S-TGD-1 (sulfated galactosyl mannosyl glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), TGD-1 (galactosyl mannosyl glucosyl diether), DGD-1 (mannosyl glucosyl diether) and DGD-2 (an unknown diglycosyl diether). Phylogenetic analysis revealed that TBN4(T) and strain TBN5 formed a distinct clade with genus Haladaptatus (showing 90.0-90.9% 16S rRNA gene similarities). The DNA G + C content of strain TBN4(T) and strain TBN5 are 66.1 and 65.4 mol%, respectively. The DNA-DNA hybridization value between strain TBN4(T) and strain TBN5 was 94.3%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain TBN4(T) and strain TBN5 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halorussus rarus gen. nov., sp. nov. is proposed. The type strain is TBN4(T) (=CGMCC 1.10122(T) = JCM 16429(T)).
Collapse
Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
| | | | | | | |
Collapse
|
38
|
Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon. J Bacteriol 2010; 192:4528-9. [PMID: 20601480 DOI: 10.1128/jb.00663-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halalkalicoccus jeotgali B3(T), isolated from salt-fermented seafood from South Korea, is an extremely halophilic archaeon belonging to the family Halobacteriaceae. Here, we present the complete genome sequence of the type strain H. jeotgali B3(T) (3,698,650 bp, with a G+C content of 62.5%), which consists of one chromosome and six plasmids. This is the first complete genome sequence of the Halalkalicoccus species.
Collapse
|
39
|
Oren A. Industrial and environmental applications of halophilic microorganisms. ENVIRONMENTAL TECHNOLOGY 2010; 31:825-834. [PMID: 20662374 DOI: 10.1080/09593330903370026] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In comparison with the thermophilic and the alkaliphilic extremophiles, halophilic microorganisms have as yet found relatively few biotechnological applications. Halophiles are involved in centuries-old processes such as the manufacturing of solar salt from seawater and the production of traditional fermented foods. Two biotechnological processes involving halophiles are highly successful: the production of beta-carotene by the green alga Dunaliella and the production of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid), used as a stabilizer for enzymes and now also applied in cosmetic products, from moderately halophilic bacteria. The potential use of bacteriorhodopsin, the retinal protein proton pump of Halobacterium, in optoelectronic devices and photochemical processes is being explored, and may well lead to commercial applications in the near future. Demand for salt-tolerant enzymes in current manufacturing or related processes is limited. Other possible uses of halophilic microorganisms such as treatment of saline and hypersaline wastewaters, and the production of exopolysaccharides, poly-beta-hydroxyalkanoate bioplastics and biofuel are being investigated, but no large-scale applications have yet been reported.
Collapse
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
| |
Collapse
|
40
|
Kim MS, Roh SW, Bae JW. Halomonas jeotgali sp. nov., a new moderate halophilic bacterium isolated from a traditional fermented seafood. J Microbiol 2010; 48:404-10. [DOI: 10.1007/s12275-010-0032-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 03/09/2010] [Indexed: 11/28/2022]
|
41
|
Jung MJ, Roh SW, Kim MS, Bae JW. Lentibacillus jeotgali sp. nov., a halophilic bacterium isolated from traditional Korean fermented seafood. Int J Syst Evol Microbiol 2010; 60:1017-1022. [DOI: 10.1099/ijs.0.013565-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-positive, non-motile, endospore-forming and moderately halophilic bacterium, strain GrbiT, was isolated from a traditional Korean fermented seafood. The organism grew optimally in the presence of 10–15 % NaCl, at 37 °C and pH 8.0. The peptidoglycan of the cell wall consisted of meso-diaminopimelic acid, and the predominant menaquinone was MK-7. The major fatty acids of strain GrbiT were iso-C16 : 0 (36.4 %), anteiso-C15 : 0 (30.3 %) and iso-C14 : 0 (18.2 %). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content was 42.5 mol%. Strain GrbiT was most closely related to the type strain Lentibacillus kapialis JCM 12580T, with which it shared 97.5 % 16S rRNA gene sequence similarity. The DNA–DNA hybridization value between strains GrbiT and L. kapialis JCM 12580T was 8 %. Based on phenotypic, genotypic and phylogenetic data, strain GrbiT should be classified as a novel species within the genus Lentibacillus, for which the name Lentibacillus jeotgali sp. nov. is proposed. The type strain is GrbiT (=KCTC 13300T=JCM 15795T).
Collapse
Affiliation(s)
- Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Seong Woon Roh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| |
Collapse
|
42
|
Jung M, Chang YH, Kim W. A real-time PCR assay for detection and quantification ofLactococcus garvieae. J Appl Microbiol 2010; 108:1694-701. [DOI: 10.1111/j.1365-2672.2009.04568.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
43
|
Oxley APA, Lanfranconi MP, Würdemann D, Ott S, Schreiber S, McGenity TJ, Timmis KN, Nogales B. Halophilic archaea in the human intestinal mucosa. Environ Microbiol 2010; 12:2398-410. [PMID: 20438582 DOI: 10.1111/j.1462-2920.2010.02212.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The human gastrointestinal tract microbiota, despite its key roles in health and disease, remains a diverse, variable and poorly understood entity. Current surveys reveal a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea. In an analysis of the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease we found 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae (haloarchaea), including novel phylotypes. As the human colon is not considered a salty environment and haloarchaea are described as extreme halophiles, we evaluated and further discarded the possibility that these sequences originated from pre-colonoscopy saline lavage solutions. Furthermore, aerobic enrichment cultures prepared from a patient biopsy at low salinity (2.5% NaCl) yielded haloarchaeal sequence types. Microscopic observation after fluorescence in situ hybridization provided evidence of the presence of viable archaeal cells in these cultures. These results prove the survival of haloarchaea in the digestive system and suggest that they may be members of the mucosal microbiota, even if present in low numbers in comparison with methanogenic archaea. Investigation of a potential physiological basis of this association may lead to new insights into gastrointestinal health and disease.
Collapse
Affiliation(s)
- Andrew P A Oxley
- Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Application of quantitative real-time PCR for enumeration of total bacterial, archaeal, and yeast populations in kimchi. J Microbiol 2010; 47:682-5. [PMID: 20127459 DOI: 10.1007/s12275-009-0297-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 10/26/2009] [Indexed: 12/22/2022]
Abstract
Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45 x 10(6) which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.
Collapse
|
45
|
Roh SW, Lee ML, Bae JW. Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus. Int J Syst Evol Microbiol 2009; 60:1187-1190. [PMID: 19667394 DOI: 10.1099/ijs.0.013037-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, extremely halophilic archaeon, D43(T), was isolated from traditional salt-fermented seafood in Korea. The cells were Gram-negative-staining and motile. The strain grew at 15-50 degrees C, 10-30 % (w/v) NaCl and pH 6.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D43(T) is affiliated with the family Halobacteriaceae in the domain Archaea and had 95.5 % 16S rRNA gene sequence similarity with Haladaptatus paucihalophilus DX253(T). The sequence from strain D43(T) formed a clade with those from Hap. paucihalophilus regardless of which tree-generating algorithm was used. DNA-DNA hybridization experiments showed 25.8 % relatedness between the isolate and Hap. paucihalophilus KCTC 4006(T). Major lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two unidentified glycolipids. The DNA G+C content of the isolate was 56.5 mol%. On the basis of this polyphasic taxonomic study, strain D43(T) represents a novel species in the genus Haladaptatus, for which the name Haladaptatus cibarius sp. nov. is proposed. The type strain is D43(T) (=DSM 19505(T) =JCM 15962(T)).
Collapse
Affiliation(s)
- Seong Woon Roh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Myung-Lip Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| |
Collapse
|
46
|
Roh SW, Nam YD, Chang HW, Kim KH, Sung Y, Kim MS, Oh HM, Bae JW. Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food. Int J Syst Evol Microbiol 2009; 59:2359-63. [DOI: 10.1099/ijs.0.008243-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
47
|
Roh SW, Kim KH, Nam YD, Chang HW, Park EJ, Bae JW. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME JOURNAL 2009; 4:1-16. [PMID: 19587773 DOI: 10.1038/ismej.2009.83] [Citation(s) in RCA: 183] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Little is known about the archaeal diversity of fermented seafood; most of the earlier studies of fermented food have focused on lactic acid bacteria (LAB) in the fermentation process. In this study, the archaeal and bacterial diversity in seven kinds of fermented seafood were culture-independently examined using barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) methods. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers, using different primers for Archaea or Bacteria. Because PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results were compared with the results of the barcoded pyrosequencing analysis. A total of 13 372 sequences were retrieved from 15 898 pyrosequencing reads and were analyzed to evaluate the diversity of the archaeal and bacterial populations in seafood. The most predominant types of archaea and bacteria identified in the samples included extremely halophilic archaea related to the family Halobacteriaceae; various uncultured mesophilic Crenarchaeota, including Crenarchaeota Group I.1 (CG I.1a and CG I.1b), Marine Benthic Group B (MBG-B), and Miscellaneous Crenarchaeotic Group (MCG); and LAB affiliated with genus Lactobacillus and Weissella. Interestingly, numerous uncultured mesophilic Crenarchaeota groups were as ubiquitous in the fermented seafood as in terrestrial and aquatic niches; the existence of these Crenarchaeota groups has not been reported in any fermented food. These results indicate that the archaeal populations in the fermented seafood analyzed are diverse and include the halophilic and mesophilic groups, and that barcoded pyrosequencing is a promising and cost-effective method for analyzing microbial diversity compared with conventional approaches.
Collapse
Affiliation(s)
- Seong Woon Roh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | | | | | | | | | | |
Collapse
|
48
|
Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays. Int J Food Microbiol 2009; 130:140-6. [DOI: 10.1016/j.ijfoodmicro.2009.01.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/07/2009] [Accepted: 01/09/2009] [Indexed: 11/21/2022]
|