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Khan NF, Ahmed SS, Abdulraheem MI, Reshi ZA, Wahab A, Abdi G. Deciphering mycobiota and its functional dynamics in root hairs of Rhododendron campanulatum D. Don through Next-gen sequencing. Sci Rep 2024; 14:10294. [PMID: 38704448 PMCID: PMC11069570 DOI: 10.1038/s41598-024-61120-4] [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: 01/20/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024] Open
Abstract
The Himalayas provide unique opportunities for the extension of shrubs beyond the upper limit of the tree. However, little is known about the limitation of the biotic factors belowground of shrub growth at these cruising altitudes. To fill this gap, the present study deals with the documentation of root-associated microbiota with their predicted functional profiles and interactions in the host Rhododendron campanulatum, a krummholz species. While processing 12 root samples of R. campanulatum from the sites using Omics we could identify 134 root-associated fungal species belonging to 104 genera, 74 families, 39 orders, 17 classes, and 5 phyla. The root-associated microbiota members of Ascomycota were unambiguously dominant followed by Basidiomycota. Using FUNGuild, we reported that symbiotroph and pathotroph as abundant trophic modes. Furthermore, FUNGuild revealed the dominant prevalence of the saptroptroph guild followed by plant pathogens and wood saprotrophs. Alpha diversity was significantly different at the sites. The heatmap dendrogram showed the correlation between various soil nutrients and some fungal species. The study paves the way for a more in-depth exploration of unidentified root fungal symbionts, their interactions and their probable functional roles, which may serve as an important factor for the growth and conservation of these high-altitude ericaceous plants.
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Affiliation(s)
- Nafeesa Farooq Khan
- Biological Invasion Lab, Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India.
| | - Sheikh Sajad Ahmed
- Biological Invasion Lab, Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | - Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou, 450002, China
| | - Zafar Ahmad Reshi
- Biological Invasion Lab, Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | - Abdul Wahab
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gul Research Institute, Persian Gulf University, Bushehr, 75169, Iran.
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2
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Miao X, Wang E, Zhou Y, Zhan Y, Yan N, Chen C, Li Q. Effect of ginsenosides on microbial community and enzyme activity in continuous cropping soil of ginseng. Front Microbiol 2023; 14:1060282. [PMID: 37213491 PMCID: PMC10196390 DOI: 10.3389/fmicb.2023.1060282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/07/2023] [Indexed: 05/23/2023] Open
Abstract
Root exudates contain plant metabolites secreted by the roots into the soil, such as ginsenosides secreted by the ginseng root. However, little is known about ginseng root exudate and its impact on the chemical and microbial properties of soil. In this study, the effect of increasing concentrations of ginsenosides on the chemical and microbial properties of soil was tested. Chemical analysis and high-throughput sequencing techniques were used to evaluate the soil chemical properties and microbial characteristics following exogenous application of 0.1 mg·L-1, 1 mg·L-1, and 10 mg·L-1 ginsenosides. Ginsenosides application significantly altered soil enzyme activities; SOM-dominated physicochemical properties were significantly reduced which altered the composition and structure of the soil microbial community. In particular, treatment with 10 mg∙L-1 ginsenosides significantly increased the relative abundance of pathogenic fungi such as Fusarium, Gibberella and Neocosmospora. These findings indicate that ginsenosides in root exudates are important factors that may lead to increased deterioration of soil during ginseng cultivation and provided new research direction for the subsequent study on the mechanism of interaction between ginsenosides and soil microbial communities.
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Affiliation(s)
| | | | | | | | | | | | - Qiong Li
- *Correspondence: Qiong Li, ; Changbao Chen,
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3
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Fokt H, Unni R, Repnik U, Schmitz RA, Bramkamp M, Baines JF, Unterweger D. Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice. Arch Microbiol 2022; 204:546. [PMID: 35939214 PMCID: PMC9360105 DOI: 10.1007/s00203-022-03148-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022]
Abstract
Two bacterial strains, KH365_2T and KH569_7, were isolated from the cecum contents of wild-derived house mice. The strains were characterized as Gram-negative, rod-shaped, strictly anaerobic, and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both strains were most closely related to Bacteroides uniformis ATCC 8492T. Whole genome sequences of KH365_2T and KH569_7 strains have a DNA G + C content of 46.02% and 46.03% mol, respectively. Most morphological and biochemical characteristics did not differ between the newly isolated strains and classified Bacteroides strains. However, the average nucleotide identity (ANI) and dDNA-DNA hybridization (dDDH) values clearly distinguished the two strains from described members of the genus Bacteroides. Here, we present the phylogeny, morphology, and physiology of a novel species of the genus Bacteroides and propose the name Bacteroides muris sp. nov., with KH365_2T (DSM 114231T = CCUG 76277T) as type strain.
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Affiliation(s)
- Hanna Fokt
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Rahul Unni
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
- Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Urska Repnik
- Central Microscopy Facility, Kiel University, 24118, Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Marc Bramkamp
- Central Microscopy Facility, Kiel University, 24118, Kiel, Germany
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
- Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany.
| | - Daniel Unterweger
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
- Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany.
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4
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Ameur H, Cantatore V, Filannino P, Cavoski I, Nikoloudaki O, Gobbetti M, Di Cagno R. Date Seeds Flour Used as Value-Added Ingredient for Wheat Sourdough Bread: An Example of Sustainable Bio-Recycling. Front Microbiol 2022; 13:873432. [PMID: 35516437 PMCID: PMC9062590 DOI: 10.3389/fmicb.2022.873432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Our study proposed date seeds flour (DSF) as an innovative ingredient for sourdough bread production through sustainable bio-recycling. We isolated autochthonous lactic acid bacteria and yeasts from DSF and DSF-derived doughs to build up a reservoir of strains from which to select starters ensuring rapid adaptation and high ecological fitness. The screening based on pro-technological criteria led to the formulation of a mixed starter consisting of Leuconostoc mesenteroides, Lactiplantibacillus plantarum, and Saccharomyces cerevisiae strains, which allowed obtaining a mature type I sourdough after consecutive refreshments, in which an aliquot of the durum wheat flour (DWF) was replaced by DSF. The resulting DSF sourdough and bread underwent an integrated characterization. Sourdough biotechnology was confirmed as a suitable procedure to improve some functional and sensory properties of DWF/DSF mixture formulation. The radical scavenging activity increased due to the consistent release of free phenolics. Perceived bitterness and astringency were considerably diminished, likely because of tannin degradation.
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Affiliation(s)
- Hana Ameur
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Vincenzo Cantatore
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
- *Correspondence: Pasquale Filannino,
| | - Ivana Cavoski
- CIHEAM-MAIB, Mediterranean Agronomic Institute of Bari, Valenzano, Bari, Italy
| | - Olga Nikoloudaki
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
- Raffaella Di Cagno,
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5
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Clarification of the Taxonomic Position of Paramecium caudatum Micronucleus Symbionts. Curr Microbiol 2021; 78:4098-4102. [PMID: 34636935 DOI: 10.1007/s00284-021-02667-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Bacteria of genus Holospora (order Holosporales, class Alphaproteobacteria) are obligate intranuclear symbionts of ciliates Paramecium spp. with strict host species and nuclear (macronucleus or micronucleus) specificity. However, three species under study Holospora undulata, Holospora elegans and 'Holospora recta' occupy the same ecological niche-micronucleus of Paramecium caudatum and demonstrate some differences in morphology of infectious form. The genetic diversity of holosporas by rrs and rpoB sequence analysis was determined. Phylogenetic and phylogenomic analysis of Holospora spp., as well as some phenotypic features indicate that there is no distinctive difference supporting studied micronuclear endosymbionts as distinct species. Therefore, Holospora elegans and 'Holospora recta' should be considered subspecies of Holospora undulata (ex Haffkine 1890) Gromov and Ossipov 1981, which was described first. Thus, we confirmed the evolutionary aspects of the development of symbiotic relationships: holosporas have a strict specificity to the host species and the type of nucleus.
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6
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Mixotrophic bacteria for environmental detoxification of contaminated waste and wastewater. Appl Microbiol Biotechnol 2021; 105:6627-6648. [PMID: 34468802 DOI: 10.1007/s00253-021-11514-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
Mixotrophic bacteria provide a desirable alternative to the use of classical heterotrophic or chemolithoautotrophic bacteria in environmental technology, particularly under limiting nutrients conditions. Their bi-modal ability of adapting to inorganic or organic carbon feed and sulfur, nitrogen, or even heavy metal stress conditions are attractive features to achieve efficient bacterial activity and favorable operation conditions for the environmental detoxification or remediation of contaminated waste and wastewater. This review provides an overview on the state of the art and summarizes the metabolic traits of the most promising and emerging non-model mixotrophic bacteria for the environmental detoxification of contaminated wastewater and waste containing excess amounts of limiting nutrients. Although mixotrophic bacteria usually function with low organic carbon sources, the unusual capabilities of mixotrophic electroactive exoelectrogens and electrotrophs in bioelectrochemical systems and in microbial electrosynthesis for accelerating simultaneous metabolism of inorganic or organic C and N, S or heavy metals are reviewed. The identification of the mixotrophic properties of electroactive bacteria and their capability to drive mono- or bidirectional electron transfer processes are highly exciting and promising aspects. These aspects provide an appealing potential for unearthing new mixotrophic exoelectrogens and electrotrophs, and thus inspire the next generation of microbial electrochemical technology and mixotrophic bacterial metabolic engineering. KEY POINTS: • Mixotrophic bacteria efficiently and simultaneously remove C and N, S or heavy metals. • Exoelectrogens and electrotrophs accelerate metabolism of C and N, S or heavy metals. • New mixotrophic exoelectrogens and electrotrophs should be discovered and exploited.
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7
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Pontonio E, Arora K, Dingeo C, Carafa I, Celano G, Scarpino V, Genot B, Gobbetti M, Di Cagno R. Commercial Organic Versus Conventional Whole Rye and Wheat Flours for Making Sourdough Bread: Safety, Nutritional, and Sensory Implications. Front Microbiol 2021; 12:674413. [PMID: 34322100 PMCID: PMC8312275 DOI: 10.3389/fmicb.2021.674413] [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: 03/01/2021] [Accepted: 06/10/2021] [Indexed: 01/04/2023] Open
Abstract
Organic farming is gaining a broad recognition as sustainable system, and consumer demand for organic products has increased dramatically in the recent past. Whether organic agriculture delivers overall advantages over conventional agriculture is, however, contentious. Here, the safety, nutritional, and sensory implications of using commercial organic rye, soft, and durum wheat flours rather than conventional-made sourdough bread have been investigated. Culture-dependent and culture-independent approaches were used to explore the microbial architecture of flours and to study their dynamics during sourdough propagation. Besides biochemical features, the main nutritional (amino acid content, asparagine level, and antioxidant activity) characteristics of sourdoughs were investigated, and their effect on the structural, nutritional, and sensory profiles of breads assessed. Overall, the organic farming system led to flours characterized by lower content of asparagine and cell density of Enterobacteriaceae while showing higher concentration of total free amino acids. Differences of the flours mirrored those of sourdoughs and breads. The use of sourdough fermentation guaranteed a further improvement of the flour characteristics; however, a microbial and sensory profile simplification as well as a slight decrease of the biochemical parameters was observed between breads with sourdough after one-cycle fermentation and 10 days of propagation.
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Affiliation(s)
- Erica Pontonio
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Kashika Arora
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Cinzia Dingeo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Carafa
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Giuseppe Celano
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Valentina Scarpino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | | | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
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8
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Richarte V, Sánchez-Mora C, Corrales M, Fadeuilhe C, Vilar-Ribó L, Arribas L, Garcia E, Rosales-Ortiz SK, Arias-Vasquez A, Soler-Artigas M, Ribasés M, Ramos-Quiroga JA. Gut microbiota signature in treatment-naïve attention-deficit/hyperactivity disorder. Transl Psychiatry 2021; 11:382. [PMID: 34238926 PMCID: PMC8266901 DOI: 10.1038/s41398-021-01504-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Compelling evidence supports alterations in gut microbial diversity, bacterial composition, and/or relative abundance of several bacterial taxa in attention-deficit/hyperactivity disorder (ADHD). However, findings for ADHD are inconsistent among studies, and specific gut microbiome signatures for the disorder remain unknown. Given that previous studies have mainly focused on the pediatric form of the disorder and involved small sample sizes, we conducted the largest study to date to compare the gastrointestinal microbiome composition in 100 medication-naïve adults with ADHD and 100 sex-matched healthy controls. We found evidence that ADHD subjects have differences in the relative abundance of several microbial taxa. At the family level, our data support a lower relative abundance of Gracilibacteraceae and higher levels of Selenomonadaceae and Veillonellaceae in adults with ADHD. In addition, the ADHD group showed higher levels of Dialister and Megamonas and lower abundance of Anaerotaenia and Gracilibacter at the genus level. All four selected genera explained 15% of the variance of ADHD, and this microbial signature achieved an overall sensitivity of 74% and a specificity of 71% for distinguishing between ADHD patients and healthy controls. We also tested whether the selected genera correlate with age, body mass index (BMI), or scores of the ADHD rating scale but found no evidence of correlation between genera relative abundance and any of the selected traits. These results are in line with recent studies supporting gut microbiome alterations in neurodevelopment disorders, but further studies are needed to elucidate the role of the gut microbiota on the ADHD across the lifespan and its contribution to the persistence of the disorder from childhood to adulthood.
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Grants
- PI15/01789,PI16/01505,PI17/00289,PI18/01788,PI19/00721,PI19/01224,PI20/00041 Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)
- PI15/01789,PI16/01505,PI17/00289,PI18/01788,PI19/00721,PI19/01224,PI20/00041 Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)
- PI15/01789,PI16/01505,PI17/00289,PI18/01788,PI19/00721,PI19/01224,PI20/00041 Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)
- PI15/01789,PI16/01505,PI17/00289,PI18/01788,PI19/00721,PI19/01224,PI20/00041 Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)
- H2020/2014-2020 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)
- H2020/2014-2020 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)
- H2020/2014-2020 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)
- 092330/31 EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)
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Affiliation(s)
- Vanesa Richarte
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Sánchez-Mora
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Montserrat Corrales
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Christian Fadeuilhe
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Laura Vilar-Ribó
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Lorena Arribas
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Estela Garcia
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Silvia Karina Rosales-Ortiz
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Alejandro Arias-Vasquez
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - María Soler-Artigas
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Department of Genetics, Microbiology & Statistics, University of Barcelona, Barcelona, Spain
| | - Marta Ribasés
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain.
- Department of Genetics, Microbiology & Statistics, University of Barcelona, Barcelona, Spain.
| | - Josep Antoni Ramos-Quiroga
- Department of Psychiatry, Mental Health and Addictions, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain.
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain.
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9
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Progress, Challenges, and Perspectives of Bioleaching for Recovering Heavy Metals from Mine Tailings. ADSORPT SCI TECHNOL 2021. [DOI: 10.1155/2021/9941979] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The accumulation of mine tailings on Earth is a serious environmental challenge. The importance for the recovery of heavy metals, together with the economic benefits of precious and base metals, is a strong incentive to develop sustainable methods to recover metals from tailings. Currently, researchers are attempting to improve the efficiency of metal recovery from tailings using bioleaching, a more sustainable method compared to traditional methods. In this work, the research status of using biological leaching technologies to recover heavy metals from tailings was reviewed. Furthermore, CiteSpace 5.7.R2 was used to visually analyze the keywords of relevant studies on biological leaching of tailings to intuitively establish the current research hotspots. We found that current research has made recent progress on influencing factors and microbial genetic data, and innovations have also been made regarding the improvement of the rate of metal leaching by biological leaching combined with other technologies. This is of great significance for the development of bioleaching technologies and industrial production of heavy metals in tailings. Finally, challenges and opportunities for bioleaching provide directions for further research by the scientific community.
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10
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Ge Y, Zhang G, Yang J, Lai XH, Jin D, Lu S, Pu J, Huang Y, Luo X, Zheng H, Zhang X, Xu J. Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 33881983 DOI: 10.1099/ijsem.0.004772] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Four unknown strains, characterized as Gram-stain-negative, strictly anaerobic, non-motile and rod-shaped, were isolated from fresh faeces of healthy humans in PR China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two clusters. Cluster I (strains HF-5141T and HF-106) was most closely related to Bacteroides xylanisolvens XB1AT (98.0-98.3 % similarity) and Bacteroides ovatus ATCC 8483T (97.3-97.5 %), whereas cluster II (strains HF-5287T and HF-5300) exhibited a similarity range of 96.8-97.0 % to Bacteroides finegoldii JCM 13345T, 96.7-96.9 % to Bacteroides faecis MAJ27T and 96.4-96.5 % to Bacteroides xylanisolvens XB1AT. The DNA G+C contents of type strains HF-5141T and HF-5287T were 41.5 and 42.6 mol%, respectively. These strains had anteiso-C15 : 0 as the major cellular fatty acid, MK-9 and MK-11 as the predominant respiratory quinones, and phosphatidylethanolamine, aminophospholipids and phospholipids as major polar lipids, which is typical for members of the genus Bacteroides. However, the average nucleotide identity and digital DNA-DNA hybridization values, accompanied by different phenotypic and biochemical characteristics, distinguished them from their corresponding closest relatives as well as from other recognized members of the genus Bacteroides. Therefore, strains HF-5141T and HF-5287T represent two novel species in the genus Bacteroides, for which the names Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov. are proposed, with HF-5141T (=CGMCC 1.16787T=GDMCC 1.1591T=JCM 33480T) and HF-5287T (=CGMCC 1.16724T=GDMCC 1.1590T=JCM 33481T) as type strains.
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Affiliation(s)
- Yajun Ge
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xuelian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
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11
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Zhou X, Xuan D, Hu S, Du J, Pu J, Jin D, Zhao F, Yin F, Cui X, Huang Y, Wang G, Wu Q, Lu G, Niu L. Pelistega ratti sp. nov. from Rattus norvegicus of Hainan island. Int J Syst Evol Microbiol 2021; 71. [PMID: 33688803 DOI: 10.1099/ijsem.0.004733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (NLN63T and NLN82) of Gram-stain-negative, oxidase- and catalase-positive, bacilli-shaped organisms were isolated from the faecal samples of two separate Rattus norvegicus in Baisha county of Hainan Province, Southern PR China. Phylogenetic analysis based on the near full-length 16S rRNA sequences revealed that strain NLN63T belongs to the genus Pelistega, having maximum similarity to Pelistega suis CCUG 64465T (97.1 %), Pelistega europaea CCUG 39967T (96.2 %) and Pelistega indica DSM 27484T (96.2 %), respectively. The phylogenomic tree built on 553 core genes from genomes of 20 species in the genus Pelistega and other adjacent genera further confirmed that strains NLN63T and NLN82 form a distinct subline and exhibit specific phylogenetic affinity with P. europaea CCUG 39967T. In digital DNA-DNA hybridization analyses, strain NLN63T showed low estimated DNA reassociation values (21.4-22.6 %) with the type strains of the species in the genus Pelistega. The DNA G+C contents of strains NLN63T and NLN82 were 37.3 and 37.1 mol%, respectively. Strain NLN63T had a unique MALDI-TOF MS profile, contained Q-8 as the major quinone and C16 : 0, summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c or both) and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c or both) as the dominant fatty acids. Based upon these polyphasic characterization data obtained from the present study, a novel species of the genus Pelistega, Pelistega ratti sp. nov., is proposed with NLN63T (=GDMCC 1.1697T=JCM 33788T) as the type strain.
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Affiliation(s)
- Xiaojun Zhou
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Clinical laboratory department of Hainan General Hospital, Haikou, 570311, PR China
| | - Duanduan Xuan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China
| | - Shoukui Hu
- Peking University shougang hospital, Beijing, 100144, PR China
| | - Jiang Du
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Fan Zhao
- Peking University shougang hospital, Beijing, 100144, PR China
| | - Feifei Yin
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Xiuji Cui
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Yi Huang
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Gaoyu Wang
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Qiang Wu
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Gang Lu
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Lina Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China
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12
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The Gut Microbiota and Its Relevance to Peripheral Lymphocyte Subpopulations and Cytokines in Patients with Rheumatoid Arthritis. J Immunol Res 2021; 2021:6665563. [PMID: 33506059 PMCID: PMC7810541 DOI: 10.1155/2021/6665563] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022] Open
Abstract
Growing experimental and clinical evidence suggests that a chronic inflammatory response induced by gut microbiome critically contribute to the development of rheumatoid arthritis (RA). Previous studies demonstrated the disturbance of lymphocyte subpopulations in RA patients. The purpose of this study was to explore the characteristics of gut microbiome and the associations between bacterium and lymphocyte subpopulations as well as cytokines in patients with RA. Fecal samples from 205 RA patients and 199 healthy controls (HCs) were collected for bacterial DNA extraction and 16S ribosomal RNA (rRNA) gene sequencing. The levels of peripheral lymphocyte subpopulation such as T, B, CD4+T, CD8+T, NK, T helper 1 (Th1), Th2, Th17, and regulatory T cells (Tregs) of these subjects were detected by flow cytometry combined with standard absolute counting beads. The serum levels of cytokines interleukin-2 (IL-2), IL-4, IL-6, IL-10, IL-17, tumour necrosis factor-α (TNF-α), and interferon-γ (INF-γ) were tested by flow cytometric bead array (CBA). Alpha and beta diversity of gut microbiome were explored by bioinformatics analysis. Spearman rank correlation test was used to explore the relationships between gut microbiome and lymphocyte subsets as well as serum cytokines. The diversity and relative abundance of intestinal microbiota in patients with RA were significantly different from those in HCs. Detailly, the abundant of phylum Proteobacteria in RA patients was more than that in HCs, while Firmicutes was less than in HCs. There was increased relative abundance of genus Clostridium_XlVa as well as genus Blautia, more abundance of Ruminococcus2 in patients with lower levels of T, B, CD4+T, and Tregs. In addition, the relative abundances of Pelagibacterium, Oxalobacter, ClostridiumXlVb, and ClostridiumXVIII were correlated with cytokines. Gut microbiome of RA patients was clearly different from that of HCs. Abnormal bacteria communities are associated with the altered levels of lymphocyte subpopulation and cytokines, which might be one of the pathogenesis of RA.
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13
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Dingeo C, Difonzo G, Paradiso VM, Rizzello CG, Pontonio E. Teff Type-I Sourdough to Produce Gluten-Free Muffin. Microorganisms 2020; 8:microorganisms8081149. [PMID: 32751312 PMCID: PMC7466135 DOI: 10.3390/microorganisms8081149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
The increasing number of persons following a gluten-free (GF) diet and the need for healthy and natural products are forcing researchers and industries to provide gluten-free products with high nutritional value. Here, a biotechnological approach combining the use of teff flour and type-I sourdough has been proposed to produce GF muffins with nutritional benefits. Teff-sourdough was prepared and propagated following the traditional daily refreshment procedure until the biochemical stability was achieved. The sourdough, dominated by Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Saccharomyces cerevisiae strains, was used to produce muffins at three different levels (up to 15%, wt/wt) of fortification, achieving several positive effects on the nutritional properties of the products. The use of teff flour led to high content of fiber (>3 g/100 g) and proteins (>6 g/100 g) in muffins achieving the nutritional requirements for the healthy claims "source of fiber" and "rich in protein". Thanks to their metabolic traits, sourdough lactic acid bacteria caused the increase of the total free amino acids (TFAA, up to 1000 mg/kg, final concentration) and phytic acid decrease (50% lower than control), which positively affect the nutritional properties of the products. Besides, high in vitro protein digestibility (IVPD, 79%) and low starch hydrolysis rate (HI, 52%) characterized the fortified muffins. Muffins also presented high in vitro antioxidant (56%) and mold-inhibitory activities, potentially contributing to an extended shelf-life of the products.
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Affiliation(s)
- Cinzia Dingeo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (C.D.); (G.D.); (C.G.R.)
| | - Graziana Difonzo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (C.D.); (G.D.); (C.G.R.)
| | - Vito Michele Paradiso
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Carlo Giuseppe Rizzello
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (C.D.); (G.D.); (C.G.R.)
| | - Erica Pontonio
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (C.D.); (G.D.); (C.G.R.)
- Correspondence: ; Tel.: +39-080-5442950
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14
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Vardanyan N, Sevoyan G, Navasardyan T, Vardanyan A. Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium. ENVIRONMENTAL TECHNOLOGY 2019; 40:3467-3472. [PMID: 29781399 DOI: 10.1080/09593330.2018.1478454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.
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Affiliation(s)
- Narine Vardanyan
- Department of Microbiology, SPC "Armbiotechnology" of the National Academy of Sciences of Armenia , Yerevan , Armenia
| | - Garegin Sevoyan
- Department of Chemical, Biological and Environmental Technologies, Armenian National Polytechnic University , Yerevan , Armenia
| | | | - Arevik Vardanyan
- Department of Microbiology, SPC "Armbiotechnology" of the National Academy of Sciences of Armenia , Yerevan , Armenia
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15
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Effects of Conventional Flotation Frothers on the Population of Mesophilic Microorganisms in Different Cultures. Processes (Basel) 2019. [DOI: 10.3390/pr7100653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bioleaching is an environment-friendly and low-investment process for the extraction of metals from flotation concentrate. Surfactants such as collectors and frothers are widely used in the flotation process. These chemical reagents may have inhibitory effects on the activity of microorganisms through a bioleaching process; however, there is no report indicating influences of reagents on the activity of microorganisms in the mixed culture which is mostly used in the industry. In this investigation, influences of typical flotation frothers (methyl isobutyl carbinol and pine oil) in different concentrations (0.01, 0.10, and 1.00 g/L) were examined on activates of bacteria in the mesophilic mixed culture (Acidithiobacillus ferrooxidans, Leptospirillum ferrooxidans, and Acidithiobacillus thiooxidans). For comparison purposes, experiments were repeated by pure cultures of Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans in the same conditions. Results indicated that increasing the dosage of frothers has a negative correlation with bacteria activities while the mixed culture showed a lower sensitivity to the toxicity of these frothers in comparison with examined pure cultures. Outcomes showed the toxicity of Pine oil is lower than methyl isobutyl carbinol (MIBC). These results can be used for designing flotation separation procedures and to produce cleaner products for bio extraction of metals.
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16
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Fecal microbiota in patients with ankylosing spondylitis: Correlation with dietary factors and disease activity. Clin Chim Acta 2019; 497:189-196. [PMID: 31377126 DOI: 10.1016/j.cca.2019.07.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/02/2019] [Accepted: 07/31/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND We investigated the characterization of the gut microbiome in Chinese patients with ankylosing spondylitis (AS) and healthy controls (HCs) and to explore the association ofbacteria communities with dietary factors and disease activity. METHODS 16S ribosomal RNA gene sequencing was performed on fecal DNA isolated from stool samples in consecutive cross-sectional cohorts. Alpha and beta diversities were assessed using QIIME, and comparisons were performed using one-way ANOVA, Student's t-test, and SKN multiple range comparisons to examine differences between groups and a correlation network analysis was performed. RESULTS We investigated 207 samples from 103 AS patients and 104 HCs. Alpha diversity was not significant difference in AS compared with HCs. For the community structure, Bacteroidetes was the most represented class. Megamonas, Dorea, and Blautia were significantly greater in AS than in HCs, whereas the abundance of Lachnospira, Ruminococcus, and Clostridium_XlVb was significantly lower in AS than in HCs. In addition, Specific gut microbiome was significantly correlated with disease activity and dietary factors. CONCLUSIONS Our results suggest that the human gut microbiome of AS patients was clearly different from that of HCs and bacteria communities are associated with dietary factors and disease activity.
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17
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Abstract
In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.
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18
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Novel solid-state fermentation of bee-collected pollen emulating the natural fermentation process of bee bread. Food Microbiol 2019; 82:218-230. [PMID: 31027777 DOI: 10.1016/j.fm.2019.02.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 01/31/2019] [Accepted: 02/12/2019] [Indexed: 01/29/2023]
Abstract
Structure of lactic acid bacteria biota in ivy flowers, fresh bee-collected pollen (BCP), hive-stored bee bread, and honeybee gastrointestinal tract was investigated. Although a large microbial diversity characterized flowers and fresh BCP, most of lactic acid bacteria species disappeared throughout the bee bread maturation, giving way to Lactobacillus kunkeei and Fructobacillus fructosus to dominate long stored bee bread and honeybee crop. Adaptation of lactic acid bacteria was mainly related to species-specific, and, more in deep, to strain-specific features. Bee bread preservation seemed related to bacteria metabolites, produced especially by some L. kunkeei strains, which likely gave to lactic acid bacteria the capacity to outcompete other microbial groups. A protocol to ferment BCP was successfully set up, which included the mixed inoculum of selected L. kunkeei strains and Hanseniaspora uvarum AN8Y27B, almost emulating the spontaneous fermentation of bee bread. The strict relationship between lactic acid bacteria and yeasts during bee bread maturation was highlighted. The use of the selected starters increased the digestibility and bioavailability of nutrients and bioactive compounds naturally occurring in BCP. Our biotechnological protocol ensured a product microbiologically stable and safe. Conversely, raw BCP was more exposed to the uncontrolled growth of yeasts, moulds, and other bacterial groups.
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19
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De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M. Use of autochthonous mesophilic lactic acid bacteria as starter cultures for making Pecorino Crotonese cheese: Effect on compositional, microbiological and biochemical attributes. Food Res Int 2018; 116:1344-1356. [PMID: 30716924 DOI: 10.1016/j.foodres.2018.10.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 10/07/2018] [Indexed: 11/16/2022]
Abstract
The use of selected autochthonous mesophilic lactic acid bacteria as starter cultures was investigated according to the traditional protocol for making Pecorino Crotonose (PC). Leuconostoc mesenteroides subsp. mesenteroides 2A, Lactobacillus casei 23C and Lactobacillus plantarum 18C (Autochthonous Starter, AS1) and Leuc. mesenteroides subsp. mesenteroides 2A, and L. casei 25D and 16A (AS2) were isolated and identified from aged ewes' milk PC cheeses, selected based on several enzymatic activities, and used as starter cultures. As shown by the in vitro kinetic of acidification, selected starter cultures had suitable capabilities to acidify. The manufacture of PC cheeses was carried out at an industrial plant scale. A control cheese (CC) was also made, using commercial starters consisting of mesophilic and thermophilic species. Ripening lasted 105 days at 10 °C. A poly-phasic approach was used to compare cheeses during manufacture and ripening, mainly based on pyrosequencing of the 16S rRNA targeting DNA, proteolysis and volatile component analyses. Compared to CC, both autochthonous starter cultures slightly affected the gross chemical composition of PC cheese. The cell density of thermophilic starters of CC progressively decreased throughout ripening. Plate count and RAPD-PCR showed that the cell number of autochthonous lactobacilli cultures of PC cheeses, made with AS1 and AS2, was almost constant throughout ripening and abundantly higher than that observed in CC. As shown by culture-independent analysis, the OTUs found during ripening varied depending on the manufacture with or without autochthonous starter cultures. The major chemical differences among cheeses were the concentration of free amino acids and the synthesis of some key volatile components (e.g., 2-methyl-1-propanol, 2-methyl-1-butanol, isobutyric, isovaleric, and isocaproic acids). Compared to CC, the use of AS1 positively affected the overall cheese quality.
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Affiliation(s)
- Ilaria De Pasquale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari 70126, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy.
| | - Solange Buchin
- Technologie et Analyses Laitières, INRA, Poligny UR 342, France
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari 70126, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
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20
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Pontonio E, Di Cagno R, Tarraf W, Filannino P, De Mastro G, Gobbetti M. Dynamic and Assembly of Epiphyte and Endophyte Lactic Acid Bacteria During the Life Cycle of Origanum vulgare L. Front Microbiol 2018; 9:1372. [PMID: 29997592 PMCID: PMC6029521 DOI: 10.3389/fmicb.2018.01372] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/06/2018] [Indexed: 12/02/2022] Open
Abstract
Origanum vulgare L. (oregano) was chosen as suitable model to investigate the ability of the endophyte-microbiome, especially that of lactic acid bacteria, to develop specific interactions with the plant, mediated by the essential oils (EOs). Combined culture-dependent and -independent approaches analyzed the bacterial dynamic and assembly of Origanum vulgare L. throughout the life cycle. Epiphyte bacteria were more abundant than the endophyte ones. The number of presumptive lactic acid bacteria increased throughout oregano life cycle, according to the plant organ. Diverse species of lactic acid bacteria populated the plant, but Lactobacillus plantarum stably dominated both epiphyte and endophyte populations. High-throughput DNA sequencing showed highest epiphyte bacterial diversity at early vegetative and full-flowering stages, with blooming signing the main microbial differentiation among plant organs. Proteobacteria, Actinobacteria and Bacteroidetes, and Firmicutes and Cyanobacteria at lower abundance were the main phyla. Various genera were detectable, but oregano harbored mainly Methylobacterium, Sphingomonas, Rhizobium and Aurantimonas throughout phenological stages. Firmicutes epiphyte and endophyte microbiotas were different, with a core microbiota consisting of Bacillus, Exiguobacterium, Streptococcus, Staphylococcus and Lactobacillus genera. Bacillus dominated throughout phenological stages. High-throughput DNA sequencing confirmed the dominance of L. plantarum within the epiphyte and endophyte populations of lactic acid bacteria. Yields of EOs varied among plant organs and throughout plant life cycle. L. plantarum strains were the most resistant to the total EOs (mainly thymol and carvacrol) as extracted from the plant. The positive correlation among endophyte lactic acid bacteria and the EOs content seems confirm the hypothesis that the colonization within plant niches may be regulated by mechanisms linked to the synthesis of the secondary metabolites.
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Affiliation(s)
- Erica Pontonio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Waed Tarraf
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Giuseppe De Mastro
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
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21
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Panyushkina AE, Tsaplina IA, Kondrat’eva TF, Belyi AV, Bulaev AG. Physiological and Morphological Characteristics of Acidophilic Bacteria Leptospirillum ferriphilum and Acidithiobacillus thiooxidans, Members of a Chemolithotrophic Microbial Consortium. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718030086] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Hart A, Cortés MP, Latorre M, Martinez S. Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium. PLoS One 2018; 13:e0195869. [PMID: 29742107 PMCID: PMC5942774 DOI: 10.1371/journal.pone.0195869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.
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Affiliation(s)
- Andrew Hart
- UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Macul, Santiago, Chile
- Universidad de O'Higgins, Instituto de Ciencias de la Ingeniería, Rancagua, Chile
- * E-mail: (ML); (SM)
| | - Servet Martinez
- Departamento de Ingeniería Matemática, UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
- * E-mail: (ML); (SM)
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Insights into Carbon Metabolism Provided by Fluorescence In Situ Hybridization-Secondary Ion Mass Spectrometry Imaging of an Autotrophic, Nitrate-Reducing, Fe(II)-Oxidizing Enrichment Culture. Appl Environ Microbiol 2018; 84:AEM.02166-17. [PMID: 29500258 DOI: 10.1128/aem.02166-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/20/2018] [Indexed: 01/03/2023] Open
Abstract
The enrichment culture KS is one of the few existing autotrophic, nitrate-reducing, Fe(II)-oxidizing cultures that can be continuously transferred without an organic carbon source. We used a combination of catalyzed amplification reporter deposition fluorescence in situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) to analyze community dynamics, single-cell activities, and interactions among the two most abundant microbial community members (i.e., Gallionellaceae sp. and Bradyrhizobium spp.) under autotrophic and heterotrophic growth conditions. CARD-FISH cell counts showed the dominance of the Fe(II) oxidizer Gallionellaceae sp. under autotrophic conditions as well as of Bradyrhizobium spp. under heterotrophic conditions. We used NanoSIMS to monitor the fate of 13C-labeled bicarbonate and acetate as well as 15N-labeled ammonium at the single-cell level for both taxa. Under autotrophic conditions, only the Gallionellaceae sp. was actively incorporating 13C-labeled bicarbonate and 15N-labeled ammonium. Interestingly, both Bradyrhizobium spp. and Gallionellaceae sp. became enriched in [13C]acetate and [15N]ammonium under heterotrophic conditions. Our experiments demonstrated that Gallionellaceae sp. was capable of assimilating [13C]acetate while Bradyrhizobium spp. were not able to fix CO2, although a metagenomics survey of culture KS recently revealed that Gallionellaceae sp. lacks genes for acetate uptake and that the Bradyrhizobium sp. carries the genetic potential to fix CO2 The study furthermore extends our understanding of the microbial reactions that interlink the nitrogen and Fe cycles in the environment.IMPORTANCE Microbial mechanisms by which Fe(II) is oxidized with nitrate as the terminal electron acceptor are generally referred to as "nitrate-dependent Fe(II) oxidation" (NDFO). NDFO has been demonstrated in laboratory cultures (such as the one studied in this work) and in a variety of marine and freshwater sediments. Recently, the importance of NDFO for the transport of sediment-derived Fe in aquatic ecosystems has been emphasized in a series of studies discussing the impact of NDFO for sedimentary nutrient cycling and redox dynamics in marine and freshwater environments. In this article, we report results from an isotope labeling study performed with the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS, which was first described by Straub et al. (1) about 20 years ago. Our current study builds on the recently published metagenome of culture KS (2).
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Nionelli L, Pontonio E, Gobbetti M, Rizzello CG. Use of hop extract as antifungal ingredient for bread making and selection of autochthonous resistant starters for sourdough fermentation. Int J Food Microbiol 2018; 266:173-182. [DOI: 10.1016/j.ijfoodmicro.2017.12.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 10/18/2022]
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25
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Integrating the microbiome as a resource in the forensics toolkit. Forensic Sci Int Genet 2017; 30:141-147. [DOI: 10.1016/j.fsigen.2017.06.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/26/2017] [Accepted: 06/24/2017] [Indexed: 11/19/2022]
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26
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Di Cagno R, Filannino P, Cavoski I, Lanera A, Mamdouh BM, Gobbetti M. Bioprocessing technology to exploit organic palm date ( Phoenix dactylifera L. cultivar Siwi) fruit as a functional dietary supplement. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.01.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Nuñez H, Moya-Beltrán A, Covarrubias PC, Issotta F, Cárdenas JP, González M, Atavales J, Acuña LG, Johnson DB, Quatrini R. Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon. Front Microbiol 2017; 8:30. [PMID: 28154559 PMCID: PMC5243848 DOI: 10.3389/fmicb.2017.00030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/05/2017] [Indexed: 11/13/2022] Open
Abstract
The acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model.
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Affiliation(s)
- Harold Nuñez
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | - Ana Moya-Beltrán
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
- Faculty of Biological Sciences, Andres Bello UniversitySantiago, Chile
| | | | - Francisco Issotta
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | | | - Mónica González
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | - Joaquín Atavales
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | - Lillian G. Acuña
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | | | - Raquel Quatrini
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
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Wang ZB, Li YQ, Lin JQ, Pang X, Liu XM, Liu BQ, Wang R, Zhang CJ, Wu Y, Lin JQ, Chen LX. The Two-Component System RsrS-RsrR Regulates the Tetrathionate Intermediate Pathway for Thiosulfate Oxidation in Acidithiobacillus caldus. Front Microbiol 2016; 7:1755. [PMID: 27857710 PMCID: PMC5093147 DOI: 10.3389/fmicb.2016.01755] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/19/2016] [Indexed: 01/10/2023] Open
Abstract
Acidithiobacillus caldus (A. caldus) is a common bioleaching bacterium that possesses a sophisticated and highly efficient inorganic sulfur compound metabolism network. Thiosulfate, a central intermediate in the sulfur metabolism network of A. caldus and other sulfur-oxidizing microorganisms, can be metabolized via the tetrathionate intermediate (S4I) pathway catalyzed by thiosulfate:quinol oxidoreductase (Tqo or DoxDA) and tetrathionate hydrolase (TetH). In A. caldus, there is an additional two-component system called RsrS-RsrR. Since rsrS and rsrR are arranged as an operon with doxDA and tetH in the genome, we suggest that the regulation of the S4I pathway may occur via the RsrS-RsrR system. To examine the regulatory role of the two-component system RsrS-RsrR on the S4I pathway, ΔrsrR and ΔrsrS strains were constructed in A. caldus using a newly developed markerless gene knockout method. Transcriptional analysis of the tetH cluster in the wild type and mutant strains revealed positive regulation of the S4I pathway by the RsrS-RsrR system. A 19 bp inverted repeat sequence (IRS, AACACCTGTTACACCTGTT) located upstream of the tetH promoter was identified as the binding site for RsrR by using electrophoretic mobility shift assays (EMSAs) in vitro and promoter-probe vectors in vivo. In addition, ΔrsrR, and ΔrsrS strains cultivated in K2S4O6-medium exhibited significant growth differences when compared with the wild type. Transcriptional analysis indicated that the absence of rsrS or rsrR had different effects on the expression of genes involved in sulfur metabolism and signaling systems. Finally, a model of tetrathionate sensing by RsrS, signal transduction via RsrR, and transcriptional activation of tetH-doxDA was proposed to provide insights toward the understanding of sulfur metabolism in A. caldus. This study also provided a powerful genetic tool for studies in A. caldus.
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Affiliation(s)
- Zhao-Bao Wang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Ya-Qing Li
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | | | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Yan Wu
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
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Di Cagno R, Filannino P, Vincentini O, Lanera A, Cavoski I, Gobbetti M. Exploitation of Leuconostoc mesenteroides strains to improve shelf life, rheological, sensory and functional features of prickly pear (Opuntia ficus-indica L.) fruit puree. Food Microbiol 2016; 59:176-89. [DOI: 10.1016/j.fm.2016.06.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/23/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022]
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Metabolism of Fructophilic Lactic Acid Bacteria Isolated from the Apis mellifera L. Bee Gut: Phenolic Acids as External Electron Acceptors. Appl Environ Microbiol 2016; 82:6899-6911. [PMID: 27637884 DOI: 10.1128/aem.02194-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/14/2016] [Indexed: 01/21/2023] Open
Abstract
Fructophilic lactic acid bacteria (FLAB) are strongly associated with the gastrointestinal tracts (GITs) of Apis mellifera L. worker bees due to the consumption of fructose as a major carbohydrate. Seventy-seven presumptive lactic acid bacteria (LAB) were isolated from GITs of healthy A. mellifera L. adults, which were collected from 5 different geographical locations of the Apulia region of Italy. Almost all of the isolates showed fructophilic tendencies: these isolates were identified as Lactobacillus kunkeei (69%) or Fructobacillus fructosus (31%). A high-throughput phenotypic microarray targeting 190 carbon sources was used to determine that 83 compounds were differentially consumed. Phenotyping grouped the strains into two clusters, reflecting growth performance. The utilization of phenolic acids, such as p-coumaric, caffeic, syringic, or gallic acids, as electron acceptors was investigated in fructose-based medium. Almost all FLAB strains showed tolerance to high phenolic acid concentrations. p-Coumaric acid and caffeic acid were consumed by all FLAB strains through reductases or decarboxylases. Syringic and gallic acids were partially metabolized. The data collected suggest that FLAB require external electron acceptors to regenerate NADH. The use of phenolic acids as external electron acceptors by the 4 FLAB showing the highest phenolic acid reductase activity was investigated in glucose-based medium supplemented with p-coumaric acid. Metabolic responses observed through a phenotypic microarray suggested that FLAB may use p-coumaric acid as an external electron acceptor, enhancing glucose dissimilation but less efficiently than other external acceptors such as fructose or pyruvic acid.IMPORTANCE Fructophilic lactic acid bacteria (FLAB) remain to be fully explored. This study intends to link unique biochemical features of FLAB with their habitat. The quite unique FLAB phenome within the group lactic acid bacteria (LAB) may have practical relevance in food fermentations. The FLAB phenome may have implications for the levels of hexose metabolism products in fermented foods, as well as food probiotication. Due to the harsh conditions of honeybees' GITs, these bacteria had to develop specific physiological and biochemical characteristics, such as tolerance to phenolic acids. The screening of FLAB strains based on metabolic pathways involving phenolic acids may allow the selection of starter cultures with both technological and functional beneficial attributes. Bioconversion of phenolic compounds may contribute to the aroma attributes and biofunctionality of fermented foods. Thus, the selection of FLAB strains as starter cultures with specific enzymatic activities involving phenolic acids may have a promising role in food fermentations.
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31
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Huang LN, Kuang JL, Shu WS. Microbial Ecology and Evolution in the Acid Mine Drainage Model System. Trends Microbiol 2016; 24:581-593. [PMID: 27050827 DOI: 10.1016/j.tim.2016.03.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/19/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill.
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Affiliation(s)
- Li-Nan Huang
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia-Liang Kuang
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China.
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32
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Microbial profiling of South African acid mine water samples using next generation sequencing platform. Appl Microbiol Biotechnol 2016; 100:6069-79. [DOI: 10.1007/s00253-016-7428-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 02/23/2016] [Accepted: 02/26/2016] [Indexed: 11/25/2022]
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Cordova LT, Long CP, Venkataramanan KP, Antoniewicz MR. Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium. Metab Eng 2015; 32:74-81. [PMID: 26391740 DOI: 10.1016/j.ymben.2015.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 08/26/2015] [Accepted: 09/11/2015] [Indexed: 02/07/2023]
Abstract
We have isolated a new extremely thermophilic fast-growing Geobacillus strain that can efficiently utilize xylose, glucose, mannose and galactose for cell growth. When grown aerobically at 72 °C, Geobacillus LC300 has a growth rate of 2.15 h(-1) on glucose and 1.52 h(-1) on xylose (doubling time less than 30 min). The corresponding specific glucose and xylose utilization rates are 5.55 g/g/h and 5.24 g/g/h, respectively. As such, Geobacillus LC300 grows 3-times faster than E. coli on glucose and xylose, and has a specific xylose utilization rate that is 3-times higher than the best metabolically engineered organism to date. To gain more insight into the metabolism of Geobacillus LC300 its genome was sequenced using PacBio's RS II single-molecule real-time (SMRT) sequencing platform and annotated using the RAST server. Based on the genome annotation and the measured biomass composition a core metabolic network model was constructed. To further demonstrate the biotechnological potential of this organism, Geobacillus LC300 was grown to high cell-densities in a fed-batch culture, where cells maintained a high xylose utilization rate under low dissolved oxygen concentrations. All of these characteristics make Geobacillus LC300 an attractive host for future metabolic engineering and biotechnology applications.
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Affiliation(s)
- Lauren T Cordova
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA
| | - Christopher P Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA
| | - Keerthi P Venkataramanan
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA.
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Multilocus Sequence Analysis of Clinical "Candidatus Neoehrlichia mikurensis" Strains from Europe. J Clin Microbiol 2015; 53:3126-32. [PMID: 26157152 DOI: 10.1128/jcm.00880-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/21/2015] [Indexed: 01/07/2023] Open
Abstract
"Candidatus Neoehrlichia mikurensis" is the tick-borne agent of neoehrlichiosis, an infectious disease that primarily affects immunocompromised patients. So far, the genetic variability of "Ca. Neoehrlichia" has been studied only by comparing 16S rRNA genes and groEL operon sequences. We describe the development and use of a multilocus sequence analysis (MLSA) protocol to characterize the genetic diversity of clinical "Ca. Neoehrlichia" strains in Europe and their relatedness to other species within the Anaplasmataceae family. Six genes were selected: ftsZ, clpB, gatB, lipA, groEL, and 16S rRNA. Each MLSA locus was amplified by real-time PCR, and the PCR products were sequenced. Phylogenetic trees of MLSA locus relatedness were constructed from aligned sequences. Blood samples from 12 patients with confirmed "Ca. Neoehrlichia" infection from Sweden (n = 9), the Czech Republic (n = 2), and Germany (n = 1) were analyzed with the MLSA protocol. Three of the Swedish strains exhibited identical lipA sequences, while the lipA sequences of the strains from the other nine patients were identical to each other. One of the Czech strains had one differing nucleotide in the clpB sequence from the sequences of the other 11 strains. All 12 strains had identical sequences for the genes 16S rRNA, ftsZ, gatB, and groEL. According to the MLSA, among the Anaplasmataceae, "Ca. Neoehrlichia" is most closely related to Ehrlichia ruminantium, less so to Anaplasma phagocytophilum, and least to Wolbachia endosymbionts. To conclude, three sequence types of infectious "Ca. Neoehrlichia" were identified: one in the west of Sweden, one in the Czech Republic, and one spread throughout Europe.
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Velvizhi G, Venkata Mohan S. Bioelectrogenic role of anoxic microbial anode in the treatment of chemical wastewater: microbial dynamics with bioelectro-characterization. WATER RESEARCH 2015; 70:52-63. [PMID: 25506763 DOI: 10.1016/j.watres.2014.11.002] [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: 07/04/2014] [Revised: 10/29/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
A membrane-less anoxic bioelectrochemical treatment (AxBET) system was evaluated to study the influence of bioelectrogenic activity during the treatment of chemical wastewater (CW). Increment in power generation was observed with increase in substrate loading (61-204 mW/m(2)) indicating the ability of anodic bacteria in BET system to utilize the complex chemicals as the sole carbon source. Derivative analysis of voltammograms depicted by positive and negative peak potentials which relate to the extracellular electron transport sites (EETs) that presumably play a significant role in electron transfer. These self-driven redox mediators varied with respect to the substrate load. The microbial population was dominated by anaerobic microorganisms which are commonly involved in effluent treatment plants during the initial phase of operation. A gradual shift in the microbial community was observed towards enrichment of electrogenically active bacteria belonging to phyla viz., Firmicutes and Proteobacteria after prolonged operation. Shannon Index and principal component analysis correlated with the microbial profile studies. The feasibility of self-driven bioremediation of chemical wastewater in an AxBET system demonstrated bioelectricity production along with multipollutant removal simultaneously.
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Affiliation(s)
- G Velvizhi
- Bioengineering and Environmental Sciences (BEES), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences (BEES), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India.
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Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 2015; 15:141-61. [PMID: 25722247 PMCID: PMC4361730 DOI: 10.1007/s10142-015-0433-4] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/18/2022]
Abstract
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.
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Affiliation(s)
- Miriam Land
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Loren Hauser
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996 USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996 USA
| | - Se-Ran Jun
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Intawat Nookaew
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Michael R. Leuze
- Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tae-Hyuk Ahn
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tatiana Karpinets
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, 2800 Denmark
| | - Guruprased Kora
- Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Trudy Wassenaar
- Molecular Microbiology and Genomics Consultants, Tannenstr 7, 55576 Zotzenheim, Germany
| | - Suresh Poudel
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - David W. Ussery
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996 USA
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, 2800 Denmark
- Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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37
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Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME JOURNAL 2014; 9:1579-92. [PMID: 25535937 PMCID: PMC4478699 DOI: 10.1038/ismej.2014.245] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/16/2014] [Indexed: 01/17/2023]
Abstract
The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.
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38
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Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform. Appl Microbiol Biotechnol 2014; 99:3233-42. [DOI: 10.1007/s00253-014-6213-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/22/2023]
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39
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Wu X, Liu L, Zhang Z, Deng F, Liu X. Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments. World J Microbiol Biotechnol 2014; 30:3197-209. [PMID: 25252934 DOI: 10.1007/s11274-014-1747-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/19/2014] [Indexed: 11/28/2022]
Abstract
To study the phylogenetic relationships and genetic heterogeneity of 21 Acidithiobacillus strains isolated from different environments, we amplified and sequenced the 16S-23S rRNA gene intergenic spacers (ITS) of all these strains. These sequence data, combined with related sequences available from GenBank, were divided into six phylogenetic groups by 16S rRNA gene and by 16S-23S rRNA gene sequence analysis. The results of phylogenetic analysis were consistent with those obtained by repetitive element PCR and arbitrarily primed PCR. In this research, the Acidithiobacillus ferrooxidans (A. ferrooxidans) strains were always separated into two groups in phylogenetic and cluster analyses. Genotypic analyses of the genes rusA, rusB, hip and iro suggest that these two groups may have different biochemical mechanisms for oxidizing ferrous iron. Strains in one A. ferrooxidans group were detected with rusA gene that encodes rusticyanin A which plays a very important role in the iron respiratory chain. The second A. ferrooxidans group was found to contain rusB gene which encode a homologous protein (RusB). The data suggested that ITS-based phylogeny is an effective tool to elucidate the relationships of Acidithiobacillus and that a different iron oxidation pathway may exist in different A. ferrooxidans groups.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Biobuilding, Lushan South Road 932, Yuelu District, Changsha, 410083, Hunan Province, People's Republic of China
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40
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Nuñez H, Loyola D, Cárdenas JP, Holmes DS, Johnson DB, Quatrini R. Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Res Microbiol 2014; 165:735-42. [PMID: 25176612 DOI: 10.1016/j.resmic.2014.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 11/30/2022]
Abstract
Phenotypic, metabolic and genetic properties of several Acidithiobacillus caldus strains indicate the existence of as yet undefined levels of variation within the species. Inspite of this, intraspecies genetic diversity has not yet been explored in detail. In this study, the design and implementation of a Multi Locus Sequence Typing (MLST) scheme for At. caldus is described. This represents the first MLST-based study applied to industrial isolates of the species. Seven informative and discriminant MLST markers were selected using a sequence-driven approach and a custom-designed bioinformatic pipeline. The allelic profiles of thirteen At. caldus strains from diverse geographical origins and industrial settings were derived using this scheme. MLST-based population structure analysis indicated only moderate amounts of genetic diversity within the set of strains, further supporting their current assignment to a single species. Also, no clear evidence for geographical isolation could be derived from this study. However, the prevalence of sequence type 1 in heap leaching industrial settings support the view that bioprocess conditions and dynamics may have a strong influence on At. caldus (microbial) microdiversity patterns. The MLST scheme presented herein is a valuable tool for the identification and classification of strains of At. caldus for either ecological or evolutionary studies and possibly also for industrial monitoring purposes.
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Affiliation(s)
| | - David Loyola
- National Center for Genomics, Proteomics and Bioinformatics of Chile, Santiago, Chile
| | - Juan Pablo Cárdenas
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile
| | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile
| | - D Barrie Johnson
- School of Biological Sciences, University of Wales, LL572UW Bangor, UK
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile.
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41
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Ozer EA, Allen JP, Hauser AR. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. BMC Genomics 2014; 15:737. [PMID: 25168460 PMCID: PMC4155085 DOI: 10.1186/1471-2164-15-737] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 08/22/2014] [Indexed: 12/11/2022] Open
Abstract
Background Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as “accessory genome”. Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed. Results We developed a bioinformatic method for identifying the accessory genome of P. aeruginosa. First, the core genome was determined based on sequence conserved among the completed genomes of twelve reference strains using Spine, a software program developed for this purpose. The core genome was 5.84 Mbp in size and contained 5,316 coding sequences. We then developed an in silico genome subtraction program named AGEnt to filter out core genomic sequences from P. aeruginosa whole genomes to identify accessory genomic sequences of these reference strains. This analysis determined that the accessory genome of P. aeruginosa ranged from 6.9-18.0% of the total genome, was enriched for genes associated with mobile elements, and was comprised of a majority of genes with unknown or unclear function. Using these genomes, we showed that AGEnt performed well compared to other publically available programs designed to detect accessory genomic elements. We then demonstrated the utility of the AGEnt program by applying it to the draft genomes of two previously unsequenced P. aeruginosa strains, PA99 and PA103. Conclusions The P. aeruginosa genome is rich in accessory genetic material. The AGEnt program accurately identified the accessory genomes of newly sequenced P. aeruginosa strains, even when draft genomes were used. As P. aeruginosa genomes become available at an increasingly rapid pace, this program will be useful in cataloging the expanding accessory genome of this bacterium and in discerning correlations between phenotype and accessory genome makeup. The combination of Spine and AGEnt should be useful in defining the accessory genomes of other bacterial species as well. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-737) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University, 645 North Michigan Avenue, Suite 900, Chicago, IL 60611, USA.
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42
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Wang Y, Yasuda T, Sharmin S, Kanao T, Kamimura K. Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan. Biosci Biotechnol Biochem 2014; 78:1274-82. [DOI: 10.1080/09168451.2014.915735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51 mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.
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Affiliation(s)
- Yang Wang
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Takashi Yasuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Sultana Sharmin
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Tadayoshi Kanao
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kazuo Kamimura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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43
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Limam RD, Chouari R, Mazéas L, Wu TD, Li T, Grossin-Debattista J, Guerquin-Kern JL, Saidi M, Landoulsi A, Sghir A, Bouchez T. Members of the uncultured bacterial candidate division WWE1 are implicated in anaerobic digestion of cellulose. Microbiologyopen 2014; 3:157-67. [PMID: 24497501 PMCID: PMC3996565 DOI: 10.1002/mbo3.144] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/21/2013] [Accepted: 10/28/2013] [Indexed: 11/16/2022] Open
Abstract
Clones of the WWE1 (Waste Water of Evry 1) candidate division were retrieved during the exploration of the bacterial diversity of an anaerobic mesophilic (35 ± 0.5°C) digester. In order to investigate the metabolic function of WWE1 members, a 16S rRNA gene-based stable isotope probing (SIP) method was used. Eighty-seven percent of 16S r rRNA gene sequences affiliated to WWE1 candidate division were retrieved in a clone library obtained after polymerase chain reaction (PCR) amplification of enriched DNA fraction from anaerobic municipal solid waste samples incubated with 13C-cellulose, at the end of the incubation (day 63) using a Pla46F-1390R primer pair. The design of a specific WWE1 probe associated with the fluorescence in situ hybridization (FISH) technique corroborated the abundant representation of WWE1 members in our 13C-cellulose incubations. Secondary ion mass spectrometry–in situ hybridization (SIMSISH) using an iodine-labeled oligonucleotide probe combined with high-resolution nanometer-scale SIMS (NanoSIMS) observation confirmed the isotopic enrichment of members of WWE1 candidate division. The 13C apparent isotopic composition of hybridized WWE1 cells reached the value of about 40% early during the cellulose degradation process, suggesting that these bacteria play a role either in an extracellular cellulose hydrolysis process and/or in the uptake fermentation products.
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Affiliation(s)
- Rim Driss Limam
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes CS 10030, F-92761, Antony Cedex, France; CEA/Genoscope CNS 2, rue Gaston Crémieux, Evry, 91000, France; University of Evry-Val d'Essonne, Evry, 91057, France; UR04CNSTN01 "Medical and Agricultural Applications of Nuclear Techniques", CNSTN, Sidi Thabet, Ariana, 2020, Tunisia; Faculté des Sciences de Bizerte, Laboratoire de Biochimie et Biologie Moléculaire, 03/UR/0902, Bizerte, Tunisia
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44
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Karwowska E, Andrzejewska-Morzuch D, Łebkowska M, Tabernacka A, Wojtkowska M, Telepko A, Konarzewska A. Bioleaching of metals from printed circuit boards supported with surfactant-producing bacteria. JOURNAL OF HAZARDOUS MATERIALS 2014; 264:203-210. [PMID: 24295772 DOI: 10.1016/j.jhazmat.2013.11.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 06/02/2023]
Abstract
This study has evaluated the possibility of bioleaching zinc, copper, lead, nickel, cadmium and chromium from printed circuit boards by applying a culture of sulphur-oxidising bacteria and a mixed culture of biosurfactant-producing bacteria and sulphur-oxidising bacteria. It was revealed that zinc was removed effectively both in a traditional solution acidified by a way of microbial oxidation of sulphur and when using a microbial culture containing sulphur-oxidising and biosurfactant-producing bacteria. The average process efficiency was 48% for Zn dissolution. Cadmium removal was similar in both media, with a highest metal release of 93%. For nickel and copper, a better effect was obtained in the acidic medium, with a process effectiveness of 48.5% and 53%, respectively. Chromium was the only metal that was removed more effectively in the bioleaching medium containing both sulphur-oxidising and biosurfactant-producing bacteria. Lead was removed from the printed circuit boards with very low effectiveness (below 0.5%). Aerating the culture medium with compressed air increased the release of all metals in the medium with sulphur and biosurfactant, and of Ni, Cu, Zn and Cr in the acidic medium. Increasing the temperature of the medium (to 37°C) had a more significant impact in the acidic environment than in the neutral environment.
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Affiliation(s)
- Ewa Karwowska
- Warsaw University of Technology, Faculty of Environmental Engineering, Biology Division, Nowowiejska 20, 00-653 Warsaw, Poland.
| | - Dorota Andrzejewska-Morzuch
- Warsaw University of Technology, Faculty of Environmental Engineering, Biology Division, Nowowiejska 20, 00-653 Warsaw, Poland
| | - Maria Łebkowska
- Warsaw University of Technology, Faculty of Environmental Engineering, Biology Division, Nowowiejska 20, 00-653 Warsaw, Poland
| | - Agnieszka Tabernacka
- Warsaw University of Technology, Faculty of Environmental Engineering, Biology Division, Nowowiejska 20, 00-653 Warsaw, Poland.
| | - Małgorzata Wojtkowska
- Warsaw University of Technology, Faculty of Environmental Engineering, Nowowiejska 20, 00-653 Warsaw, Poland
| | - Alicja Telepko
- Warsaw University of Technology, Faculty of Environmental Engineering, Nowowiejska 20, 00-653 Warsaw, Poland
| | - Agnieszka Konarzewska
- Warsaw University of Technology, Faculty of Environmental Engineering, Nowowiejska 20, 00-653 Warsaw, Poland
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45
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Liu YQ, Wang BJ, Zhou N, Liu SJ. Undibacterium terreum sp. nov., isolated from permafrost soil. Int J Syst Evol Microbiol 2013; 63:2296-2300. [DOI: 10.1099/ijs.0.043927-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain C3T was isolated from permafrost soil in Beijicun, Mohe County, Heilongjiang province, China. Cells of strain C3T were Gram-stain-negative rods, 0.3–0.4 µm in diameter and 1.0–2.6 µm in length. Strain C3T was strictly aerobic. Growth occurred at 15–37 °C but not at 4 or 42 °C, at pH 5.0–9.0 (optimum pH 6.0–7.0) and in the presence of 0–8 g NaCl l−1 (optimum 0–1 g l−1). The analysis of 16S rRNA gene sequences indicated that strain C3T was phylogenetically related to members of the genus
Undibacterium
, with similarities ranging from 94.7 to 96.5 %. Strain C3T contained ubiquinone 8 as the major respiratory quinone. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C17 : 0 cyclo, straight-chain C16 : 0, C12 : 0 and C10 : 0, unsaturated C18 : 1ω7c and hydroxylated fatty acids C10 : 0 3-OH and C12 : 0 2-OH. The polar lipids were mainly phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamines were putrescine and 2-hydroxyputrescine. The DNA G+C content was 57.4 mol% (determined from Tm
). Based on these results, it is concluded that strain C3T represents a novel species of the genus
Undibacterium
, for which the name Undibacterium terreum sp. nov. is proposed, with C3T ( = CGMCC 1.10998T = NBRC 108789T) representing the type strain.
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Affiliation(s)
- Yi-Qian Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
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46
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Hedrich S, Johnson DB. Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium. Int J Syst Evol Microbiol 2013; 63:4018-4025. [PMID: 23710060 DOI: 10.1099/ijs.0.049759-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twelve strains of iron-oxidizing acidithiobacilli isolated from acidic sites throughout the world, including some previously shown by multi-locus sequence analyses and DNA-DNA hybridization to comprise a distinct species, were characterized in terms of their physiologies. The bacteria were shown to be obligately chemolithotrophic, acidophilic and mesophilic, and grew in both oxic and anoxic environments, using ferrous iron, reduced sulfur or hydrogen as electron donors and oxygen or ferric iron as electron acceptors. Some of the strains grew at lower pH than those reported for the two recognized iron-oxidizing Acidithiobacillus species, Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans. Tolerance of transition metals and aluminium, and also specific rates of iron oxidation and reduction, were more similar to those of A. ferrooxidans (to which the strains are more closely related) than to A. ferrivorans. The name Acidithiobacillus ferridurans sp. nov. is proposed to accommodate the 12 strains, with the type strain being JCM 18981(T) ( = ATCC 33020(T)).
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Affiliation(s)
- Sabrina Hedrich
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - D Barrie Johnson
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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47
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Li L, Abu Al-Soud W, Bergmark L, Riber L, Hansen LH, Magid J, Sørensen SJ. Investigating the Diversity of Pseudomonas spp. in Soil Using Culture Dependent and Independent Techniques. Curr Microbiol 2013; 67:423-30. [DOI: 10.1007/s00284-013-0382-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/13/2013] [Indexed: 11/30/2022]
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Kuang JL, Huang LN, Chen LX, Hua ZS, Li SJ, Hu M, Li JT, Shu WS. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. THE ISME JOURNAL 2013; 7:1038-50. [PMID: 23178673 PMCID: PMC3635239 DOI: 10.1038/ismej.2012.139] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/01/2012] [Accepted: 10/01/2012] [Indexed: 11/17/2022]
Abstract
A wide array of microorganisms survive and thrive in extreme environments. However, we know little about the patterns of, and controls over, their large-scale ecological distribution. To this end, we have applied a bar-coded 16S rRNA pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (AMD) sites across Southeast China, revealing for the first time environmental variation as the major factor explaining community differences in these harsh environments. Our data showed that overall microbial diversity estimates, including phylogenetic diversity, phylotype richness and pairwise UniFrac distance, were largely correlated with pH conditions. Furthermore, multivariate regression tree analysis also identified solution pH as a strong predictor of relative lineage abundance. Betaproteobacteria, mostly affiliated with the 'Ferrovum' genus, were explicitly predominant in assemblages under moderate pH conditions, whereas Alphaproteobacteria, Euryarchaeota, Gammaproteobacteria and Nitrospira exhibited a strong adaptation to more acidic environments. Strikingly, such pH-dependent patterns could also be observed in a subsequent comprehensive analysis of the environmental distribution of acidophilic microorganisms based on 16S rRNA gene sequences previously retrieved from globally distributed AMD and associated environments, regardless of the long-distance isolation and the distinct substrate types. Collectively, our results suggest that microbial diversity patterns are better predicted by contemporary environmental variation rather than geographical distance in extreme AMD systems.
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Affiliation(s)
- Jia-Liang Kuang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Lin-Xing Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Sheng-Jin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Min Hu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin-Tian Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen-Sheng Shu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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Ghosh S, Moitra M, Woolverton CJ, Leff LG. Effects of remediation on the bacterial community of an acid mine drainage impacted stream. Can J Microbiol 2012; 58:1316-26. [DOI: 10.1139/w2012-110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.
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Affiliation(s)
- Suchismita Ghosh
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Moumita Moitra
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | | | - Laura G. Leff
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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50
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Baumdicker F, Hess WR, Pfaffelhuber P. The infinitely many genes model for the distributed genome of bacteria. Genome Biol Evol 2012; 4:443-56. [PMID: 22357598 PMCID: PMC3342869 DOI: 10.1093/gbe/evs016] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 1011 and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality.
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Affiliation(s)
- Franz Baumdicker
- University of Freiburg, Center for Biosystems Analysis, Habsburgerstrasse 49, Germany
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