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Metze D, Popp D, Schwab L, Keller NS, da Rocha UN, Richnow HH, Vogt C. Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer. FEMS Microbiol Ecol 2021; 97:6055686. [PMID: 33378450 DOI: 10.1093/femsec/fiaa261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.
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Affiliation(s)
- Dennis Metze
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany.,Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Althanstraße 14, Austria
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Laura Schwab
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Nina-Sophie Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
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Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV, Vishwanatha JK. Comparative analysis of racial differences in breast tumor microbiome. Sci Rep 2020; 10:14116. [PMID: 32839514 PMCID: PMC7445256 DOI: 10.1038/s41598-020-71102-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Studies have demonstrated that environmental, host genetic, and socioeconomic factors influence the breast cancer prevalence landscape with a far-reaching influence on racial disparity to subtypes of breast cancer. To understand whether breast tissue harbors race-specific microbiota, we performed 16S rRNA gene-based sequencing of retrospective tumor and matched normal tissue adjacent to tumor (NAT) samples collected from Black non-Hispanic (BNH) and White non-Hispanic (WNH) women. Analysis of Triple Negative Breast cancer (TNBC) and Triple Positive Breast Cancer (TPBC) tissues for microbiota composition revealed significant differences in relative abundance of specific taxa at both phylum and genus levels between WNH and BNH women cohorts. Our main findings are that microbial diversity as measured by Shannon index was significantly lower in BNH TNBC tumor tissue as compared to matched NAT zone. In contrast, the WNH cohort had an inverse pattern for the Shannon index, when TNBC tumor tissue was compared to the matched NAT. Unweighted Principle Coordinates Analysis (PCoA) revealed a distinct clustering of tumor and NAT microbiota in both BNH and WNH cohorts.
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Affiliation(s)
- Srikantha Thyagarajan
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Yan Zhang
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Santosh Thapa
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Michael S Allen
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Nicole Phillips
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Pankaj Chaudhary
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | | | - Jamboor K Vishwanatha
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
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Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:310-319. [PMID: 30550857 PMCID: PMC6364046 DOI: 10.1016/j.gpb.2018.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 11/23/2022]
Abstract
We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
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Farrugia DN, Elbourne LDH, Mabbutt BC, Paulsen IT. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res 2015; 43:4547-57. [PMID: 25883135 PMCID: PMC4482086 DOI: 10.1093/nar/gkv337] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5′ end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature.
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Affiliation(s)
- Daniel N Farrugia
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam D H Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Bridget C Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Hegemann JD, Zimmermann M, Zhu S, Klug D, Marahiel MA. Lasso peptides from proteobacteria: Genome mining employing heterologous expression and mass spectrometry. Biopolymers 2013; 100:527-42. [DOI: 10.1002/bip.22326] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 05/31/2013] [Accepted: 06/05/2013] [Indexed: 01/26/2023]
Affiliation(s)
| | | | | | | | - Mohamed A. Marahiel
- Department of Chemistry; Philipps-University Marburg, Hans-Meerwein-Strasse 4 and LOEWE-Center for Synthetic Microbiology; Marburg D-35032 Germany
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Santiago-Rodriguez TM, Toranzos GA, Bayman P, Massey SE, Cano RJ. Sociomicrobiome of wood decay in a tropical rain forest: unraveling complexity. SPRINGERPLUS 2013; 2:435. [PMID: 24052931 PMCID: PMC3776085 DOI: 10.1186/2193-1801-2-435] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/15/2013] [Indexed: 11/25/2022]
Abstract
Given that microbial interactions in nature are very complex, we propose that quorum-sensing, as well as quorum-quenching, phenazine and secondary metabolite production, resistance and toxin-antitoxin systems within a microbial community should all comprise the battery of processes involving the study of what we would define as the “sociomicrobiome”. In the present study the genes/molecules, subsystems and taxonomic breakup of the mentioned processes were identified in decaying tropical wood from the El Yunque rainforest in Puerto Rico, and soil using a shotgun metagenomic approach. The rapid decomposition of wood and litter in tropical regions suggests that processes in these settings are governed by unexplored microbes with the potential of being further studied and exploited for various purposes. Both ecosystems were characterized by the presence of specific genes/molecules, subsystems and microbes associated with the mentioned processes, although the average abundances for specific processes differed. Of the sociomicrobiomes studied, that from El Yunque was found to be the most complex. The approach considered in the present study could also be applied to study the sociomicrobiome of other ecosystems.
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Menchaca AC, Visi DK, Strey OF, Teel PD, Kalinowski K, Allen MS, Williamson PC. Preliminary assessment of microbiome changes following blood-feeding and survivorship in the Amblyomma americanum nymph-to-adult transition using semiconductor sequencing. PLoS One 2013; 8:e67129. [PMID: 23826210 PMCID: PMC3691118 DOI: 10.1371/journal.pone.0067129] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/14/2013] [Indexed: 11/28/2022] Open
Abstract
The physiology of ticks supports a diverse community of non-pathogenic and pathogenic organisms. This study aims to initially characterize the microbial community present within colony-reared Amblyomma americanum using PCR of the variable region 5 of the 16S rRNA gene followed by semiconductor sequencing and classification of sequence data using the Ribosomal Database Project and MG-RAST analysis tools. Comparison of amplicon library datasets revealed changes in the microbiomes in newly engorged nymphs, newly-molted adults, and aged adults, as well as ticks exposed to different environmental conditions. These preliminary data support the concept that microbe survivorship and diversity are partially dependent upon environmental variables and the sequence of blood feeding, molting, and aging. The maintenance and/or emergence of pathogens in ticks may be dependent in part on temporal changes in the microbial community of the tick microbiome.
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Affiliation(s)
- Arturo C. Menchaca
- Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas
| | - David K. Visi
- Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas
- Department of Biological Sciences, University of North Texas, Denton, Texas
| | - Otto F. Strey
- Department of Entomology, Texas AgriLife Research, Texas A&M University, College Station, Texas
| | - Pete D. Teel
- Department of Entomology, Texas AgriLife Research, Texas A&M University, College Station, Texas
| | - Kevin Kalinowski
- Center for Learning and Development, University of North Texas Health Science Center, Fort Worth, Texas
| | - Michael S. Allen
- Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas
- Department of Biological Sciences, University of North Texas, Denton, Texas
- * E-mail:
| | - Phillip C. Williamson
- Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas
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Geng J, Chiu CH, Tang P, Chen Y, Shieh HR, Hu S, Chen YYM. Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms. PLoS One 2012; 7:e34769. [PMID: 22529932 PMCID: PMC3329508 DOI: 10.1371/journal.pone.0034769] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/05/2012] [Indexed: 01/13/2023] Open
Abstract
Streptococcus parasanguinis, a primary colonizer of the tooth surface, is also an opportunistic pathogen for subacute endocarditis. The complete genome of strain FW213 was determined using the traditional shotgun sequencing approach and further refined by the transcriptomes of cells in early exponential and early stationary growth phases in this study. The transcriptomes also discovered 10 transcripts encoding known hypothetical proteins, one pseudogene, five transcripts matched to the Rfam and additional 87 putative small RNAs within the intergenic regions defined by the GLIMMER analysis. The genome contains five acquired genomic islands (GIs) encoding proteins which potentially contribute to the overall pathogenic capacity and fitness of this microbe. The differential expression of the GIs and various open reading frames outside the GIs at the two growth phases suggested that FW213 possess a range of mechanisms to avoid host immune clearance, to colonize host tissues, to survive within oral biofilms and to overcome various environmental insults. Furthermore, the comparative genome analysis of five S. parasanguinis strains indicates that albeit S. parasanguinis strains are highly conserved, variations in the genome content exist. These variations may reflect differences in pathogenic potential between the strains.
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Affiliation(s)
- Jianing Geng
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Molecular Infectious Disease Research Center, Chang Gung Children's Hospital, Tao-Yuan, Taiwan
- Graduate Institute of Basic Medical Sciences, Chang Gung University, Tao-Yuan, Taiwan
| | - Petrus Tang
- Graduate Institute of Basic Medical Sciences, Chang Gung University, Tao-Yuan, Taiwan
- Bioinformatics Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Yaping Chen
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hui-Ru Shieh
- Graduate Institute of Basic Medical Sciences, Chang Gung University, Tao-Yuan, Taiwan
- Department of Microbiology and Immunology, Chang Gung University, Tao-Yuan, Taiwan
| | - Songnian Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yi-Ywan M. Chen
- Graduate Institute of Basic Medical Sciences, Chang Gung University, Tao-Yuan, Taiwan
- Department of Microbiology and Immunology, Chang Gung University, Tao-Yuan, Taiwan
- * E-mail:
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A new esterase EstD2 isolated from plant rhizosphere soil metagenome. Appl Microbiol Biotechnol 2010; 88:1125-34. [DOI: 10.1007/s00253-010-2729-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 06/08/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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