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Du Z, Behrens SF. Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities. PLoS One 2024; 19:e0299930. [PMID: 38452018 PMCID: PMC10919606 DOI: 10.1371/journal.pone.0299930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/17/2024] [Indexed: 03/09/2024] Open
Abstract
Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.
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Affiliation(s)
- Zhe Du
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing, China
- The BioTechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, United States of America
| | - Sebastian F. Behrens
- The BioTechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, United States of America
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota Twin Cities, Minneapolis, Minnesota, United States of America
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2
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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Development of a Real-Time Quantitative PCR Assay for the Specific Detection of Bacillus velezensis and Its Application in the Study of Colonization Ability. Microorganisms 2022; 10:microorganisms10061216. [PMID: 35744733 PMCID: PMC9230654 DOI: 10.3390/microorganisms10061216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 12/18/2022] Open
Abstract
Bacillus velezensis is a widely used biocontrol agent closely related to B. amyloliquefaciens, and the two species cannot be distinguished by universal primers that are currently available. The study aimed to establish a rapid, specific detection approach for B. velezensis. Many unique gene sequences of B. velezensis were selected through whole genome sequence alignment of B. velezensis strains and were used to design a series of forward and reverse primers, which were then screened by PCR and qPCR using different Bacillus samples as templates. The colonization ability of B. velezensis ZF2 in different soils and different soil environmental conditions was measured by qPCR and a 10-fold dilution plating assay. A specific primer pair targeting the sequence of the D3N19_RS13500 gene of B. velezensis ZF2 was screened and could successfully distinguish B. velezensis from B. amyloliquefaciens. A rapid specific real-time qPCR detection system for B. velezensis was established. B. velezensis ZF2 had a very strong colonization ability in desert soil, and the optimal soil pH was 7-8. Moreover, the colonization ability of strain ZF2 was significantly enhanced when organic matter from different nitrogen sources was added to the substrate. This study will provide assistance for rapid specificity detection and biocontrol application of B. velezensis strains.
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Korsa G, Masi C, Konwarh R, Tafesse M. Harnessing the potential use of cellulolytic Klebsiella oxytoca (M21WG) and Klebsiella sp. (Z6WG) isolated from the guts of termites (Isoptera). ANN MICROBIOL 2022. [DOI: 10.1186/s13213-021-01662-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
For many years, denim-heavy quality cotton twill colored with indigo colors and with a well-worn/faded look has held a lot of appeal. Machine damage, drainage system blockage, and other issues come with the conventional usage of pumice stones for “stone-washing” denims. In view of the abovementioned information, a range of works has been done to investigate the economic prospects of bacterial cellulase enzymes for use in industrial processes, including biopolishing in the textile sector. Ethiopia has excellent termite diversity to isolate bacterial gut-associated cellulose enzymes for biostoning applications. The main purpose of this study was, therfore, to decipher how to isolate and characterize cellulase enzymes from termite (Isoptera) gut bacteria with the intention of employing it for biostoning of textiles.
Purpose
To use cellulolytic enzymes of Klebsiella oxytoca (M21WG) and Klebsiella sp. (Z6WG) isolated from termite guts in biostoning of textiles and improving garment quality.
Methods
Cellulase enzyme-producing bacteria were isolated and screened from the guts of worker termites sampled from Meki and Zeway termite mounds in the Central Rift Valley region of Ethiopia. Bacterial screening, biochemical, morphological, and 16S rRNA sequence identification techniques were employed to characterize the bacterial strains. In addition, the production, optimization, and purification of the associated cellulase enzymes were employed, and the potential application of the enzymes for biostoning of a textile was demonstrated.
Result
The isolated M21WG was found to be 99% identical to the Klebsiella oxytoca (MT104573.1) strain, while the isolated Z6WG showed 97.3% identity to the Klebsiella sp. strain (MN629242.1). At an ideal pH of 7, a temperature of 37 °C, a 72-h incubation time, and a substrate concentration of 1.5% carboxymethylcellulose sodium, the maximum activity of the crude cellulase extract from these bacteria was assessed. These bacteria produced cellulase enzymes that were moderately efficient. Consequently, it was determined that the cellulase enzymes were effective for biostoning of denim cloth.
Conclusion
It was determined that Klebsiella oxytoca (M21WG) and Klebsiella sp. (Z6WG) could be used as a doorway to better understand harnessing the use of these cellulase-producing bacteria from termite (Isoptera) guts. In this study, it was also attempted to assess the effectiveness of the two bacterial isolates in biostoning in anticipation of their potential application in the textile realm.
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Liu Y, Hu Z, Deng Y, Shang L, Gobler CJ, Tang YZ. Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates. HARMFUL ALGAE 2021; 109:102108. [PMID: 34815026 DOI: 10.1016/j.hal.2021.102108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Dinoflagellates are an ecologically important group of protists in aquatic environment and have evolved many unusual and enigmatic genomic features such as immense genome sizes, high repeated genes, and a large portion of hydroxymethyluracil in DNA. Although previous studies have observed positive correlations between the large subunit (LSU) rRNA gene copy number and genome size of a variety of eukaryotic organisms (e.g. higher plants and animals), or between cell volume and LSU rRNA gene copy number, and/or between genome size and cell size, which suggests a possible co-evolution among these three features in different lineages of life, it remains an open question regarding the relationships among these three parameters in dinoflagellates. For the first time, we estimated the copy numbers of the LSU rRNA gene, the genome sizes, and cell volumes within a broad range of dinoflagellates (covering 15 species of 11 genera) using single-cell qPCR-based assay (determining LSU rRNA gene copy number), FlowCAM (cell volume measurement), and ultraviolet spectrophotometry (genome size estimation). The measured copy number of LSU rRNA gene ranged from 398 ± 184 (Prorocentrum minimum) to 152,078 ± 33,555 copies•cell-1 (Alexandrium pacificum), while the genome size and the cell volume ranged from 5.6 ± 0.2 (Karlodinium veneficum) to 853 ± 19.9 pg•cell-1 (Pseliodinium pirum), and from 1,070 ± 225 (Kar. veneficum) to 168,474 ± 124,180 μm3 (Ps. pirum), respectively. Together with the three parameters measured in literature, there are significant positive linear correlations between LSU rRNA gene copy numbers and genome sizes, cell volumes and LSU rRNA gene copy numbers, and between genome sizes and cell volumes via comparisons of multi-model regression analyses, suggesting a dependence of genome size and rRNA gene copy number on the cell volumes of dinoflagellates. Validation of the measurement methods was conducted via comparisons between reported data in the literature and that predicted using the linear equations we obtained, and between genome size measured by flow cytometry (FCM) and ultraviolet spectrophotometry (Nanodrop). These results provide insightful understandings of dinoflagellate evolution in terms of the relationships among genomes, gene copy number, and cell volume, and of rRNA gene-based studies in intra-populational and intra-individual genetic diversity, taxonomy, and diversity assessment in the environment of dinoflagellates. The results also provide a dataset useful for reads calibration in environmental metabarcoding studies of dinoflagellates and selection of candidate species for whole genome sequencing.
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Affiliation(s)
- Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790, USA
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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6
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Olonade I, van Zyl LJ, Trindade M. Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring. Microorganisms 2021; 9:2043. [PMID: 34683373 PMCID: PMC8537503 DOI: 10.3390/microorganisms9102043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/29/2022] Open
Abstract
Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Here, we report the identification of a prophage (Smhb1) that infects Salinivibrio kushneri BNH isolated from a Namib Desert salt pan (playa). Analysis of the genome revealed that it showed the greatest similarity to P2-like phages that infect Vibrio species and showed no relation to any of the previously described Salinivibrio-infecting phages. Despite being distantly related to these Vibrio infecting phages and sharing the same modular gene arrangement as seen in most P2-like viruses, the nucleotide identity to its closest relatives suggest that, for now, Smhb1 is the lone member of the Peduovirus genus Playavirus. Although host range testing was not extensive and no secondary host could be identified for Smhb1, genomic evidence suggests that the phage is capable of infecting other Salinivibrio species, including Salinivibrio proteolyticus DV isolated from the same playa. Taken together, the analysis presented here demonstrates how adaptable the P2 phage model can be.
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Affiliation(s)
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, Cape Town 7535, South Africa; (I.O.); (M.T.)
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7
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Masi C, Gemechu G, Tafesse M. Isolation, screening, characterization, and identification of alkaline protease-producing bacteria from leather industry effluent. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01631-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
A wide variety of bacterial species produces protease enzyme, and the application of the same enzyme has been manipulated precisely and used in various biotechnological areas including industrial and environmental sectors. The main aim of this research study was to isolate, screen, and identify alkaline protease-producing bacteria that were sampled from leather industry effluent present in the outer skirts of Addis Ababa, Ethiopia.
Purpose
To isolate and characterize the alkaline protease-producing bacteria from leather industrial effluents.
Methods
Samples are collected from Modji leather industrial effluents and stored in the microbiology lab. After isolated bacteria from effluent using serial dilution and followed by isolated protease-producing bacteria using skim milk agar media. After studying primary and secondary screening using zonal inhibition methods to select potential protease-producing bacteria using skim milk agar media. Finally, to identify the potential bacteria using biochemical methods, bacterial biomass, protease activity, and gene sequencing (16S rRNA) method to finalize the best alkaline protease producing bacteria identified.
Results
First twenty-eight different bacterial colonies were isolated initially from the leather industry effluent sample situated at the Modjo town of Ethiopia. The isolated bacteria were screened using the primary and secondary screening method with skim milk agar medium. At the primary level, we selected three isolates namely ML5(14 mm), ML12(18 mm), and MS12 (15 mm), showing the highest zone of proteolysis as a result of casein degradation on the agar plates were selected and subjected to primary screening. Further secondary screening confirmed that the zone of inhibition methods ML5 (14.00±0.75 mm), ML12 (19.50±0.66 mm), and MS12 (15.00±1.32 mm) has efficient proteolytic activity and can be considered as effective protease producer. The three isolates were then subjected to morphological and biochemical tests to identify probably bacterial species, and all the three bacterial isolates were found out to be of Bacillus species. The shake flask method was carried out to identify the most potent one having greater biomass production capabilities and protease activity. ML12 isolated from leather effluent waste showed the highest protease activity (19 U/ml), high biomass production, and the same was subjected to molecular identification using 16s sequencing and a phylogenetic tree was constructed to identify the closest neighbor. The isolate ML12 (Bacillus cereus strain -MN629232.1) is 97.87% homologous to Bacillus cereus strain (KY995152.1) and 97.86% homologous to Bacillus cereus strain (MK968813.1).
Conclusions
This study has exposed that from twenty-eight different bacterial samples isolated from leather industry effluent; further primary and secondary screening methods were selected three potential alkaline protease strains. Finally, based on its biochemical identification, biomass, and protease activity, ML12 (Bacillus cereus strains) is the best strain identified. The alkaline protease has the significant feature of housing potent bacterial species for producing protease of commercial value.
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8
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Pankoke H, Maus I, Loh G, Hüser A, Seifert J, Tilker A, Hark S, Sczyrba A, Pelzer S, Kleinbölting J. Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota. FEMS Microbiol Lett 2021; 368:fnz033. [PMID: 30915459 PMCID: PMC8112482 DOI: 10.1093/femsle/fnz033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
16S rRNA gene amplicon sequencing is a state of the art technology to analyze bacterial communities via microbiome profiling. Choosing an appropriate DNA extraction protocol is crucial for characterizing the microbial community and can be challenging, especially when preliminary knowledge about the sample matrix is scarce. The aim of the present study was to evaluate seven commercial DNA extraction kits suitable for 16S rRNA gene amplicon sequencing of the bacterial community of the chicken cecum, taking into account different criteria such as high technical reproducibility, high bacterial diversity and easy handling. The DNA extraction kits differed strongly with respect to extractable DNA quantity, DNA quality, technical reproducibility and bacterial diversity determined after 16S rRNA gene amplicon sequencing and subsequent bioinformatic and biostatistical data processing. While some of the DNA extraction protocols under-represented specific bacterial community members, the removal of PCR inhibitors supported technical reproducibility and subsequently enhanced the recovered bacterial diversity from the chicken cecum community. In conclusion, the removal of PCR inhibitors from the sample matrix seemed to be one of the main drivers for a consistent representation of the bacterial community even of low abundant taxa in chicken cecum samples.
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Affiliation(s)
- Helga Pankoke
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Irena Maus
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Gunnar Loh
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Andrea Hüser
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6–10, 70599 Stuttgart, Germany
| | - Alexandra Tilker
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Sarah Hark
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Alexander Sczyrba
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Stefan Pelzer
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
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9
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Park JH, Lemons AR, Roseman J, Green BJ, Cox-Ganser JM. Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors. MICROBIOME 2021; 9:15. [PMID: 33472703 PMCID: PMC7819239 DOI: 10.1186/s40168-020-00954-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/06/2020] [Indexed: 05/10/2023]
Abstract
Characterizing indoor microbial communities using molecular methods provides insight into bacterial assemblages present in environments that can influence occupants' health. We conducted an environmental assessment as part of an epidemiologic study of 50 elementary schools in a large city in the northeastern USA. We vacuumed dust from the edges of the floor in 500 classrooms accounting for 499 processed dust aliquots for 16S Illumina MiSeq sequencing to characterize bacterial assemblages. DNA sequences were organized into operational taxonomic units (OTUs) and identified using a database derived from the National Center for Biotechnology Information. Bacterial diversity and ecological analyses were performed at the genus level. We identified 29 phyla, 57 classes, 148 orders, 320 families, 1193 genera, and 2045 species in 3073 OTUs. The number of genera per school ranged from 470 to 705. The phylum Proteobacteria was richest of all while Firmicutes was most abundant. The most abundant order included Lactobacillales, Spirulinales, and Clostridiales. Halospirulina was the most abundant genus, which has never been reported from any school studies before. Gram-negative bacteria were more abundant and richer (relative abundance = 0.53; 1632 OTUs) than gram-positive bacteria (0.47; 1441). Outdoor environment-associated genera were identified in greater abundance in the classrooms, in contrast to homes where human-associated bacteria are typically more abundant. Effects of school location, degree of water damage, building condition, number of students, air temperature and humidity, floor material, and classroom's floor level on the bacterial richness or community composition were statistically significant but subtle, indicating relative stability of classroom microbiome from environmental stress. Our study indicates that classroom floor dust had a characteristic bacterial community that is different from typical house dust represented by more gram-positive and human-associated bacteria. Health implications of exposure to the microbiomes in classroom floor dust may be different from those in homes for school staff and students. Video abstract.
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Affiliation(s)
- Ju-Hyeong Park
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA.
| | - Angela R Lemons
- Health Effect Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Jerry Roseman
- Philadelphia Federation of Teachers Health & Welfare Fund & Union, Philadelphia, PA, USA
| | - Brett J Green
- Health Effect Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Jean M Cox-Ganser
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
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10
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Pérez-Cobas AE, Gomez-Valero L, Buchrieser C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 2020; 6:mgen000409. [PMID: 32706331 PMCID: PMC7641418 DOI: 10.1099/mgen.0.000409] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
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11
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Saad OS, Lin X, Ng TY, Li L, Ang P, Lin S. Genome Size, rDNA Copy, and qPCR Assays for Symbiodiniaceae. Front Microbiol 2020; 11:847. [PMID: 32528423 PMCID: PMC7264167 DOI: 10.3389/fmicb.2020.00847] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/08/2020] [Indexed: 11/29/2022] Open
Abstract
Symbiodiniaceae community structure in corals is crucial for understanding the plasticity of different holobionts under environmental stress. While this relies on molecular analyses, accuracy of molecular quantification, as influenced by DNA extraction efficiency and rDNA copy number variations in particular, has rarely been systematically investigated. Here, we report the development of a set of genus-specific qPCR assays. First, a protocol for efficient DNA isolation and accurate measurements of genome size and rDNA copy number was established. Second, seven newly designed genus-specific ITS2 primer sets were validated using computational and empirical analyses and qPCR assays were developed. We find that while the genome size ranges between 1.75 ± 0.21 and 4.5 ± 0.96 Gbp, rDNA copy number shows over 10-fold variation among Symbiodiniaceae species. Our protocol produced standard curves with high efficiencies (89.8–99.3%; R2 ≥ 0.999) and tight Cq values over different PCR conditions, illustrating high specificity and sensitivity of the qPCR assays. Tested on mock communities of mixed culture species, our qPCR results agreed well with microscopic counts and facilitated calibration of metabarcoding data. To test the applicability of our protocol for field samples, we analyzed three different Hong Kong coral samples. Six Symbiodiniaceae genera were detected in Acropora valida, Oulastrea crispata, and Platygyra acuta, with Breviolum, Effrenium, Fugacium, and Gerakladium sp. being reported for the first time. Our results suggest that aggressively disrupting cells to ensure thorough cell lysis, estimating cell loss and DNA loss, and validating qPCR assays are critical for success. The number of species examined here is limited, but the primers are potentially applicable to most species in respective genera, and the protocol and the approach to develop it provide a base and template toward a standardized procedure for quantitatively characterizing Symbiodiniaceae communities in corals.
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Affiliation(s)
- Osama S Saad
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Tsz Yan Ng
- Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Put Ang
- Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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12
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Alarcón Elvira F, Pardío Sedas VT, Martínez Herrera D, Quintana Castro R, Oliart Ros RM, López Hernández K, Flores Primo A, Ramírez Elvira K. Comparative Survival and the Cold-Induced Gene Expression of Pathogenic and Nonpathogenic Vibrio Parahaemolyticus from Tropical Eastern Oysters during Cold Storage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17061836. [PMID: 32178325 PMCID: PMC7143714 DOI: 10.3390/ijerph17061836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 02/01/2023]
Abstract
Expression of the regulatory stress rpoS gene controls the transcription of cspA genes, which are involved in survival and adaptation to low temperatures. The purpose of this study was to assess the growth kinetics of naturally occurring V. parahaemolyticus in shellstock oysters and in vitro and the cold-shock-induced expression of the rpoS and cspA gene response in vitro during postharvest refrigeration. Naturally contaminated eastern oysters (Crassostrea virginica) and pathogenic (Vp-tdh) and nonpathogenic (Vp-tlh) isolates were stored at 7 ± 1 °C for 168 h and 216 h, respectively. The regulatory stress (rpos) and cold-shock (cspA) gene expressions were determined by reverse transcription PCR. At 24 h, the (Vp-tdh) strain grew faster (p < 0.05) than the (Vp-tlh) strain in oysters (λ = 0.33, 0.39, respectively) and in vitro (λ = 0.89, 37.65, respectively), indicating a better adaptation to cold shock for the (Vp-tdh) strain in live oysters and in vitro. At 24 h, the (Vp-tdh) strain rpoS and cspA gene expressions were upregulated by 1.9 and 2.3-fold, respectively, but the (Vp-tlh) strain rpoS and cspA gene expressions were repressed and upregulated by -0.024 and 1.9-fold, respectively. The V. parahaemolyticus strains that were isolated from tropical oysters have adaptive expression changes to survive and grow at 7 °C, according to their virulence.
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Affiliation(s)
- Francisco Alarcón Elvira
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Av. Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, Veracruz, Ver. CP 91710, Mexico; (F.A.E.); (D.M.H.); (K.L.H.); (A.F.P.); (K.R.E.)
| | - Violeta T. Pardío Sedas
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Av. Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, Veracruz, Ver. CP 91710, Mexico; (F.A.E.); (D.M.H.); (K.L.H.); (A.F.P.); (K.R.E.)
- Correspondence: ; Tel.: +52-229-9342075 (ext. 24125); Fax: +52-229-9342075 (ext. 24104)
| | - David Martínez Herrera
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Av. Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, Veracruz, Ver. CP 91710, Mexico; (F.A.E.); (D.M.H.); (K.L.H.); (A.F.P.); (K.R.E.)
| | - Rodolfo Quintana Castro
- Facultad de Bioanálisis, Universidad Veracruzana, Calle Iturbide s/n, Col. Centro, Veracruz, Ver. CP 91700, Mexico;
| | - Rosa María Oliart Ros
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Av. Miguel A. de Quevedo 2779, Veracruz, Ver. 91897, Mexico;
| | - Karla López Hernández
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Av. Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, Veracruz, Ver. CP 91710, Mexico; (F.A.E.); (D.M.H.); (K.L.H.); (A.F.P.); (K.R.E.)
| | - Argel Flores Primo
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Av. Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, Veracruz, Ver. CP 91710, Mexico; (F.A.E.); (D.M.H.); (K.L.H.); (A.F.P.); (K.R.E.)
| | - Karen Ramírez Elvira
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Av. Miguel Ángel de Quevedo s/n esq. Yáñez, Col. Unidad Veracruzana, Veracruz, Ver. CP 91710, Mexico; (F.A.E.); (D.M.H.); (K.L.H.); (A.F.P.); (K.R.E.)
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13
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Zhou JL, Xu J, Jiao AG, Yang L, Chen J, Callac P, Liu Y, Wang SX. Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom. Front Microbiol 2019; 10:2686. [PMID: 31803173 PMCID: PMC6877668 DOI: 10.3389/fmicb.2019.02686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/05/2019] [Indexed: 11/16/2022] Open
Abstract
The polymerase chain reaction (PCR) is widely used in modern biology and medicine. However, PCR artifacts can complicate the interpretation of PCR-based results. The internal transcribed spacer (ITS) region of the ribosomal RNA gene cluster is the consensus fungal barcode marker and suspected PCR artifacts have been reported in many studies, especially for the analyses of environmental fungal samples. At present, the patterns of PCR artifacts in the whole fungal ITS region (ITS1+5.8S+ITS2) are not known. In this study, we analyzed the error rates of PCR at three template complexity levels using the divergent copies of ITS from the mushroom Agaricus subrufescens. Our results showed that PCR using the Phusion® High-Fidelity DNA Polymerase has a per nucleotide error rate of about 4 × 10–6 per replication. Among the detected mutations, transitions were much more frequent than transversions, insertions, and deletions. When divergent alleles were mixed as templates in the same reaction, a significant proportion (∼30%) of recombinant molecules were detected. The in vitro mixed-template results were comparable to those obtained from using the genomic DNA of the original mushroom specimen as template. Our results indicate that caution should be in place when interpreting ITS sequences from individual fungal specimens, especially those containing divergent ITS copies. Similar results could also happen to PCR-based analyses of other multicopy DNA fragments as well as single-copy DNA sequences with divergent alleles in diploid organisms.
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Affiliation(s)
- Jun-Liang Zhou
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China.,International Exchange and Cooperation Department, Kunming University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - An-Guo Jiao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Li Yang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Jie Chen
- Instituto de Ecología, Veracruz, Mexico
| | | | - Yu Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Shou-Xian Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
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14
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Comparison of Six Commercial Meat Starter Cultures for the Fermentation of Yellow Mealworm ( Tenebrio molitor) Paste. Microorganisms 2019; 7:microorganisms7110540. [PMID: 31717367 PMCID: PMC6920846 DOI: 10.3390/microorganisms7110540] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
In this study, six commercial meat starters, each consisting of a pure strain of a lactic acid-fermenting bacterium (including Lactococcus lactis, Lactobacillus curvatus, L. farciminis, L. plantarum, L. sakei, and Pediococcus acidilactici), were tested for their ability to ferment a paste produced from the yellow mealworm (Tenebrio molitor). During fermentation, microbial counts, pH, and the bacterial community composition were determined. In addition, UPLC-MS was applied to monitor the consumption of glucose and the production of glutamic (Glu) and aspartic (Asp) acid. All tested starters were able to ferment the mealworm paste, judged by a pH reduction from 6.68 to 4.60–4.95 within 72 h. Illumina amplicon sequencing showed that all starters were able to colonize the substrate efficiently. Moreover, the introduction of the starter cultures led to the disappearance of Bacillus and Clostridium species, which were the dominant microorganisms in un-inoculated samples. Of the six cultures tested, Lactobacillus farciminis was most promising as its application resulted in the largest increase (±25 mg/100 g of paste) in the content of free glutamic and aspartic acid. These amino acids are responsible for the appreciated umami flavour in fermented food products and might stimulate the acceptance of insects and their consumption.
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15
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Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria. Sci Rep 2019; 9:4822. [PMID: 30886210 PMCID: PMC6423039 DOI: 10.1038/s41598-019-41195-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/26/2019] [Indexed: 12/19/2022] Open
Abstract
Obesity and inactivity are major risk factors of feline diabetes mellitus (FDM) and human type II diabetes mellitus (T2DM). In recent years, changes in the gut microbiota have been suggested as a contributing factor to T2DM. Whether the gut microbiota (GM) composition plays a role in FDM remains unknown. The aim of the current study was firstly a cross-sectional comparison of the GM of diabetic cats, to that of lean, and of obese/overweight non-diabetic cats of a similar age. Specifically, fecal samples from 82 privately-owned cats from Denmark and Switzerland were sequenced using 16S rRNA gene amplicon metabarcoding. Secondly dietary intervention data was generated, by obtaining additional samples from a subset of cats after placing them on a high-protein diet for four weeks. The GM diversity of diabetic cats was lower than that of lean cats in the cross-sectional study, and lower compared to lean and to overweight/obese cats after diet intervention. Diabetic cats also exhibited fewer Anaerotruncus, Dialister, and unknown Ruminococcaceae than lean cats. Serum fructosamine levels correlated negatively with Prevotellaceae abundance and positively with Enterobacteriaceae abundance. In summary the intestinal microbiota of diabetic cats was characterized by decreased GM diversity and loss of butyrate producing bacterial genera.
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16
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Peruzy M, Murru N, Yu Z, Cnockaert M, Joossens M, Proroga Y, Houf K. Determination of the microbiological contamination in minced pork by culture dependent and 16S amplicon sequencing analysis. Int J Food Microbiol 2019; 290:27-35. [DOI: 10.1016/j.ijfoodmicro.2018.09.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/14/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022]
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17
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Baldrian P. The known and the unknown in soil microbial ecology. FEMS Microbiol Ecol 2019; 95:5281230. [DOI: 10.1093/femsec/fiz005] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/08/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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18
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Jones CE, Maddox A, Hurley D, Barkovskii AL. Persistence of bacterial pathogens, antibiotic resistance genes, and enterococci in tidal creek tributaries. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 240:875-883. [PMID: 29787978 DOI: 10.1016/j.envpol.2018.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Intertidal creeks form the primary hydrologic link between estuaries and land-based activities on barrier islands. Fecal indicators Enterococcus spp. (Entero1), pathogens Shigella spp. (ipaH), Salmonella spp. (invA), E. coli of EHEC/EPEC groups (eaeA), E. coli of EAEC, EIEC, and UPEC groups (set1B), E. coli of STEC group (stx1); and tetracycline resistance genes (tet(B), tet(C), tet(D), tet(E), tet(K), tet(Q), tet(W), and tet(X); TRG) were detected in the headwater of Oakdale Creek (Sapelo Island, GA) receiving runoffs from Hog Hammock village. Excavation of drainage ditches around the village caused a high increase in the incidence of the above determinants. Water samples were collected from the headwater, transferred to diffusion chambers, submersed in the headwater, saltmarsh, and mouth of the creek; and the determinants were monitored for 3 winter months. With some exceptions, their persistence decreased in order headwater > saltmarsh > mouth. Genes associated with Enterococcus spp. were the most persistent at all the sites, following in the headwater with determinants for Salmonella spp. and E. coli of EAEC, EIEC, and UPEC groups. In the mouth, the most persistent gene was eaeA indicating EHEC, EPEC, and STEC. Tet(B) and tet(C) persisted the longest in headwater and saltmarsh. No TRG persisted after 11 days in the mouth. Most determinants revealed correlations with temperature and pH, and inverse correlations with dissolved oxygen. Decay rates of the above determinants varied in the range of -0.02 to -0.81/day, and were up to 40 folds higher in the saltmarsh and mouth than in the headwater. Our data demonstrated that water parameters could to some extent predict a general trend in the fate of virulence and antibiotic resistance determinants in tidal creek tributaries but strongly suggested that their persistence in these tributaries cannot be predicted from that of enterococci, or extrapolated from one biological contaminant to another.
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Affiliation(s)
- Chance E Jones
- Department of Biological and Environmental Sciences, Georgia College & State University, 221 North Wilkinson St., PO Box 081, Milledgeville, GA 31061, USA.
| | - Anthony Maddox
- Department of Biological and Environmental Sciences, Georgia College & State University, 221 North Wilkinson St., PO Box 081, Milledgeville, GA 31061, USA.
| | - Dorset Hurley
- Sapelo Island National Estuarine Research Reserve, P.O. Box 15, Sapelo Island, GA 31327, USA.
| | - Andrei L Barkovskii
- Department of Biological and Environmental Sciences, Georgia College & State University, 221 North Wilkinson St., PO Box 081, Milledgeville, GA 31061, USA.
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19
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Piñol J, Senar MA, Symondson WOC. The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative. Mol Ecol 2018; 28:407-419. [PMID: 29939447 DOI: 10.1111/mec.14776] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022]
Abstract
DNA metabarcoding is a technique used to survey biodiversity in many ecological settings, but there are doubts about whether it can provide quantitative results, that is, the proportions of each species in the mixture as opposed to a species list. While there are several experimental studies that report quantitative metabarcoding results, there are a similar number that fail to do so. Here, we provide the rationale to understand under what circumstances the technique can be quantitative. In essence, we simulate a mixture of DNA of S species with a defined initial abundance distribution. In the simulated PCR, each species increases its concentration following a certain amplification efficiency. The final DNA concentration will reflect the initial one when the efficiency is similar for all species; otherwise, the initial and final DNA concentrations would be poorly related. Although there are many known factors that modulate amplification efficiency, we focused on the number of primer-template mismatches, arguably the most important one. We used 15 common primers pairs targeting the mitochondrial COI region and the mitogenomes of ca. 1,200 insect species. The results showed that some primers pairs produced quantitative results under most circumstances, whereas some other primers failed to do so. In conclusion, depending on the primer pair used in the PCR amplification and on the characteristics of the mixture analysed (i.e., high species richness, low evenness), DNA metabarcoding can provide a quantitative estimate of the relative abundances of different species.
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Affiliation(s)
- Josep Piñol
- Universitat Autònoma Barcelona, Cerdanyola del Vallès, Spain.,CREAF, Cerdanyola del Vallès, Spain
| | - Miquel A Senar
- Universitat Autònoma Barcelona, Cerdanyola del Vallès, Spain
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20
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Subirats J, Timoner X, Sànchez-Melsió A, Balcázar JL, Acuña V, Sabater S, Borrego CM. Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities. WATER RESEARCH 2018; 138:77-85. [PMID: 29573631 DOI: 10.1016/j.watres.2018.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/01/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Wastewater effluents increase the nutrient load of receiving streams while introducing a myriad of anthropogenic chemical pollutants that challenge the resident aquatic (micro)biota. Disentangling the effects of both kind of stressors and their potential interaction on the dissemination of antibiotic resistance genes in bacterial communities requires highly controlled manipulative experiments. In this work, we investigated the effects of a combined regime of nutrients (at low, medium and high concentrations) and a mixture of emerging contaminants (ciprofloxacin, erythromycin, sulfamethoxazole, diclofenac, and methylparaben) on the bacterial composition, abundance and antibiotic resistance profile of biofilms grown in artificial streams. In particular, we investigated the effect of this combined stress on genes encoding resistance to ciprofloxacin (qnrS), erythromycin (ermB), sulfamethoxazole (sul1 and sul2) as well as the class 1 integron-integrase gene (intI1). Only genes conferring resistance to sulfonamides (sul1 and sul2) and intI1 gene were detected in all treatments during the study period. Besides, bacterial communities exposed to emerging contaminants showed higher copy numbers of sul1 and intI1 genes than those not exposed, whereas nutrient amendments did not affect their abundance. However, bacterial communities exposed to both emerging contaminants and a high nutrient concentration (1, 25 and 1 mg L-1 of phosphate, nitrate and ammonium, respectively) showed the highest increase on the abundance of sul1 and intI1 genes thus suggesting a factors synergistic effect of both stressors. Since none of the treatments caused a significant change on the composition of bacterial communities, the enrichment of sul1 and intI1 genes within the community was caused by their dissemination under the combined pressure exerted by nutrients and emerging contaminants. To the best of our knowledge, this is the first study demonstrating the contribution of nutrients on the maintenance and spread of antibiotic resistance genes in streambed biofilms under controlled conditions. Our results also highlight that nutrients could enhance the effect of emerging contaminants on the dissemination of antibiotic resistance.
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Affiliation(s)
- Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| | - Xisca Timoner
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; GRECO, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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21
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Pan Z, Li L, Shen Z, Chen Y, Li M. Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing. J Food Prot 2018; 81:1022-1029. [PMID: 29761724 DOI: 10.4315/0362-028x.jfp-17-498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The microbial communities in air- and vacuum-packed crisp grass carp ( Ctenopharyngodon idella C. et V.) fillets have not been characterized during chilled storage. High-throughput sequencing of bacterial 16S rRNA has now revealed that the bacterial community in fresh fillets is diverse and distinct from that in spoiled samples. The predominant phylum was Proteobacteria, and 66 genera were identified. In fresh fillets, the most abundant genera were Acinetobacter (53.3%), Wautersiella (6.3%), unclassified Alcaligenaceae (4.4%), Stenotrophomonas (3.8%), unclassified Enterobacteriaceae (3.8%), and Enhydrobacter (3.6%). These genera diminished during chilled storage and sometimes disappeared. At the end of storage, Aeromonas and Pseudomonas were the most abundant. Similar results were obtained by PCR-denaturing gradient gel electrophoresis. These data provide detailed insight into the evolving bacterial communities in air- and vacuum-packed crisp grass carp fillets during storage, revealing Aeromonas and Pseudomonas as major spoilage organisms. These data may be useful for improvement of crisp grass carp quality and shelf life during chilled storage.
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Affiliation(s)
- Ziqiang Pan
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Lin Li
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Zhihua Shen
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Yan Chen
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Mei Li
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
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22
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Lemons AR, Lindsley WG, Green BJ. Collection and Extraction of Occupational Air Samples for Analysis of Fungal DNA. J Vis Exp 2018. [PMID: 29782003 DOI: 10.3791/56730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several limitations that have resulted in the exclusion of many species. Advances in the field over the last two decades have led occupational health researchers to turn to molecular-based approaches for identifying fungal hazards. These methods have resulted in the detection of many species within indoor and occupational environments that have not been detected using traditional methods. This protocol details an approach for determining fungal diversity within air samples through genomic DNA extraction, amplification, sequencing, and taxonomic identification of fungal internal transcribed spacer (ITS) regions. ITS sequencing results in the detection of many fungal species that are either not detected or difficult to identify to species level using culture or microscopy. While these methods do not provide quantitative measures of fungal burden, they offer a new approach to hazard identification and can be used to determine overall species richness and diversity within an occupational environment.
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Affiliation(s)
- Angela R Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention;
| | - William G Lindsley
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention
| | - Brett J Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention
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23
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Wang S, Lin Y, Gifford S, Eveleth R, Cassar N. Linking patterns of net community production and marine microbial community structure in the western North Atlantic. THE ISME JOURNAL 2018; 12:2582-2595. [PMID: 29934639 PMCID: PMC6193967 DOI: 10.1038/s41396-018-0163-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/03/2018] [Accepted: 05/11/2018] [Indexed: 11/09/2022]
Abstract
Marine net community production (NCP) tracks uptake of carbon by plankton communities and its potential transport to depth. Relationships between marine microbial community composition and NCP currently remain unclear despite their importance for assessing how different taxa impact carbon export. We conducted 16 and 18S rRNA gene (rDNA) sequencing on samples collected across the Western North Atlantic in parallel with high-resolution O2/Ar-derived NCP measurements. Using an internal standard technique to estimate in-situ prokaryotic and eukaryotic rDNA abundances per liter, we employed statistical approaches to relate patterns of microbial diversity to NCP. Taxonomic abundances calculated using internal standards provided valuable context to traditional relative abundance metrics. A bloom in the Mid-Atlantic Bight featured high eukaryote abundances with low eukaryotic diversity and was associated with the harmful algal bloom-forming Aureococcus anophagefferens, phagotrophic algae, heterotrophic flagellates, and particle-associated bacteria. These results show that coastal Aureococcus blooms host a distinct community associated with regionally significant peaks in NCP. Meanwhile, weak relationships between taxonomy and NCP in less-productive waters suggest that productivity across much of this region is not linked to specific microplankton taxa.
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Affiliation(s)
- Seaver Wang
- Division of Earth and Ocean Sciences, Duke University, Durham, USA
| | - Yajuan Lin
- Division of Earth and Ocean Sciences, Duke University, Durham, USA
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France
| | - Scott Gifford
- Department of Marine Sciences, the University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Rachel Eveleth
- Division of Earth and Ocean Sciences, Duke University, Durham, USA
- Department of Environmental Sciences, University of Virginia, Virginia, USA
| | - Nicolas Cassar
- Division of Earth and Ocean Sciences, Duke University, Durham, USA.
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France.
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24
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Gomri MA, Rico-Díaz A, Escuder-Rodríguez JJ, El Moulouk Khaldi T, González-Siso MI, Kharroub K. Production and Characterization of an Extracellular Acid Protease from Thermophilic Brevibacillus sp. OA30 Isolated from an Algerian Hot Spring. Microorganisms 2018; 6:E31. [PMID: 29649122 PMCID: PMC6027330 DOI: 10.3390/microorganisms6020031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/18/2022] Open
Abstract
Proteases have numerous biotechnological applications and the bioprospection for newly-thermostable proteases from the great biodiversity of thermophilic microorganisms inhabiting hot environments, such as geothermal sources, aims to discover more effective enzymes for processes at higher temperatures. We report in this paper the production and the characterization of a purified acid protease from strain OA30, a moderate thermophilic bacterium isolated from an Algerian hot spring. Phenotypic and genotypic study of strain OA30 was followed by the production of the extracellular protease in a physiologically-optimized medium. Strain OA30 showed multiple extracellular proteolytic enzymes and protease 32-F38 was purified by chromatographic methods and its biochemical characteristics were studied. Strain OA30 was affiliated with Brevibacillus thermoruber species. Protease 32-F38 had an estimated molecular weight of 64.6 kDa and was optimally active at 50 °C. It showed a great thermostability after 240 min and its optimum pH was 6.0. Protease 32-F38 was highly stable in the presence of different detergents and solvents and was inhibited by metalloprotease inhibitors. The results of this work suggest that protease 32-F38 might have interesting biotechnological applications.
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Affiliation(s)
- Mohamed Amine Gomri
- Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Route de Ain El Bey, 25000 Constantine, Algérie; (M.A.G.); (K.K.)
| | - Agustín Rico-Díaz
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain; (A.R.-D.); (J.-J.E.-R.)
| | - Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain; (A.R.-D.); (J.-J.E.-R.)
| | - Tedj El Moulouk Khaldi
- Laboratoire Alimentation, Nutrition et Santé (ALNUTS), Institut de la Nutrition, de l’Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Route de Ain El Bey, 25000 Constantine, Algérie;
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain; (A.R.-D.); (J.-J.E.-R.)
| | - Karima Kharroub
- Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Route de Ain El Bey, 25000 Constantine, Algérie; (M.A.G.); (K.K.)
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Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
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Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
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Guerrero LD, Vikram S, Makhalanyane TP, Cowan DA. Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems. Environ Microbiol 2017; 19:3755-3767. [PMID: 28752953 DOI: 10.1111/1462-2920.13877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022]
Abstract
Microorganisms able to synthesize rhodopsins have the capacity to translocate ions through their membranes, using solar energy to generate a proton motive force. Rhodopsins are the most abundant phototrophic proteins in oceanic surface waters and are key constituents in marine bacterial ecology. However, it remains unclear how rhodopsins are used in most microorganisms. Despite their abundance in marine and fresh-water systems, the presence of functional rhodopsin systems in edaphic habitats has never been reported. Here, we show the presence of several new putative H+ , Na+ and Cl+ pumping rhodopsins identified by metagenomic analysis of Antarctic desert hypolithic communities. Reconstruction of two Proteobacteria genomes harboring xanthorhodopsin-like proteins and one Bacteroidetes genome with a Na-pumping-like rhodopsin indicated that these bacteria were aerobic heterotrophs possessing the apparent capacity for the functional expression of rhodopsins. The existence of these protein systems in hypolithic bacteria expands the known role of rhodopsins to include terrestrial environments and suggests a possible predominant function as heterotrophic energy supply proteins, a feasible microbial adaptation to the harsh conditions prevalent in Antarctic edaphic systems.
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Affiliation(s)
- Leandro D Guerrero
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Centre of Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
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Lemons AR, Hogan MB, Gault RA, Holland K, Sobek E, Olsen-Wilson KA, Park Y, Park JH, Gu JK, Kashon ML, Green BJ. Microbial rRNA sequencing analysis of evaporative cooler indoor environments located in the Great Basin Desert region of the United States. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:101-110. [PMID: 28091681 PMCID: PMC5450635 DOI: 10.1039/c6em00413j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recent studies conducted in the Great Basin Desert region of the United States have shown that skin test reactivity to fungal and dust mite allergens are increased in children with asthma or allergy living in homes with evaporative coolers (EC). The objective of this study was to determine if the increased humidity previously reported in EC homes leads to varying microbial populations compared to homes with air conditioners (AC). Children with physician-diagnosed allergic rhinitis living in EC or AC environments were recruited into the study. Air samples were collected from the child's bedroom for genomic DNA extraction and metagenomic analysis of bacteria and fungi using the Illumina MiSeq sequencing platform. The analysis of bacterial populations revealed no major differences between EC and AC sampling environments. The fungal populations observed in EC homes differed from AC homes. The most prevalent species discovered in AC environments belonged to the genera Cryptococcus (20%) and Aspergillus (20%). In contrast, the most common fungi identified in EC homes belonged to the order Pleosporales and included Alternaria alternata (32%) and Phoma spp. (22%). The variations in fungal populations provide preliminary evidence of the microbial burden children may be exposed to within EC environments in this region.
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Affiliation(s)
- Angela R Lemons
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, WV 26505, USA.
| | - Mary Beth Hogan
- Department of Pediatrics, Pediatrics Center, University of Nevada School of Medicine, Las Vegas, NV, USA
| | - Ruth A Gault
- Department of Microbiology and Immunology, Center for Molecular Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Kathleen Holland
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Kimberly A Olsen-Wilson
- Department of Pediatrics, Center for Molecular Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Yeonmi Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ju-Hyeong Park
- Field Studies Branch, Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ja Kook Gu
- Biostatistics and Epidemiology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Michael L Kashon
- Biostatistics and Epidemiology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Brett J Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, WV 26505, USA.
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28
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Jumpponen A, Johnson LC. Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulations—a case study from tallgrass prairie. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
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29
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Torzilli AP, Sikaroodi M, Chalkley D, Gillevet PM. A comparison of fungal communities from four salt marsh plants using automated ribosomal intergenic spacer analysis (ARISA). Mycologia 2017. [DOI: 10.1080/15572536.2006.11832641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Albert P. Torzilli
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia 22030
| | - Masoumeh Sikaroodi
- Department of Environmental Science and Policy, George Mason University, Manassas, Virginia 20110
| | - David Chalkley
- American Type Culture Collection, 10801 University Boulevard, Manassas, Virginia 20110-2209
| | - Patrick M. Gillevet
- Department of Environmental Science and Policy, George Mason University, Manassas, Virginia 20110
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Takahashi H, Saito R, Miya S, Tanaka Y, Miyamura N, Kuda T, Kimura B. Development of quantitative real-time PCR for detection and enumeration of Enterobacteriaceae. Int J Food Microbiol 2017; 246:92-97. [PMID: 28270336 DOI: 10.1016/j.ijfoodmicro.2016.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 10/20/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022]
Abstract
The family Enterobacteriaceae, members of which are widely distributed in the environment, includes many important human pathogens. In this study, a rapid real-time PCR method targeting rplP, coding for L16 protein, a component of the ribosome large subunit, was developed for enumerating Enterobacteriaceae strains, and its efficiency was evaluated using naturally contaminated food products. The rplP-targeted real-time PCR amplified Enterobacteriaceae species with Ct values of 14.0-22.8, whereas the Ct values for non-Enterobacteriaceae species were >30, indicating the specificity of this method for the Enterobacteriaceae. Using a calibration curve of Ct=-3.025 (log CFU/g)+37.35, which was calculated from individual plots of the cell numbers in different concentrations of 5 Enterobacteriaceae species, the rplP-targeted real-time PCR was applied to 51 food samples. A <1log difference between the real-time PCR and culture methods was obtained in a majority of the food samples (81.8%), with good correlation (r2=0.8285). This study demonstrated that the rplP-targeted real-time PCR method could detect and enumerate Enterobacteriaceae species in foods rapidly and accurately, and therefore, it can be used for the microbiological risk analysis of foods.
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Affiliation(s)
- Hajime Takahashi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan.
| | - Rumi Saito
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Satoko Miya
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Yuichiro Tanaka
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Natsumi Miyamura
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Takashi Kuda
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Bon Kimura
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
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31
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Filippidou S, Wunderlin T, Junier T, Jeanneret N, Dorador C, Molina V, Johnson DR, Junier P. A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes. Front Microbiol 2016; 7:1707. [PMID: 27857706 PMCID: PMC5094177 DOI: 10.3389/fmicb.2016.01707] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.
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Affiliation(s)
- Sevasti Filippidou
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, University of NeuchâtelNeuchâtel, Switzerland; Vital-IT group, Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Nicole Jeanneret
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, CeBiB, University of ChileSantiago, Chile
| | - Veronica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas. Universidad de Playa Ancha Valparaíso, Chile
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
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Okazaki Y, Nakano SI. Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan). ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:780-788. [PMID: 27402328 DOI: 10.1111/1758-2229.12439] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/20/2016] [Indexed: 05/03/2023]
Abstract
In freshwater microbial ecology, extensive studies are attempting to characterize the vast majority of uncultivated bacterioplankton taxa. However, these studies mainly focus on the epilimnion and little is known regarding the bacterioplankton inhabiting the hypolimnion of deep holomictic lakes, despite its biogeochemical importance. In this study, we investigated the bacterioplankton community composition in a deep freshwater lake with a fully oxygenated hypolimnion (Lake Biwa, Japan) using high-throughput 16S rRNA gene amplicon sequencing. Sampling at a pelagic site over 15 months throughout the water column revealed that the community composition in the hypolimnion was significantly different from that in the epilimnion. The bacterial community in the hypolimnion was composed of groups dominating in the whole water layer (e.g., bacI-A1 and acI-B1) and groups that were hypolimnion habitat specialists. Among the hypolimnion specialists, members of Chloroflexi and Planctomycetes were highly represented (e.g., CL500-11, CL500-15 and CL500-37), followed by members of Acidobacteria, Chlorobi and nitrifiers (e.g., Ca. Nitrosoarchaeum, Nitrosospira and Nitrospira). This study identified the number of previously understudied taxa dominating the deep aerobic freshwater habitat, suggesting that the biogeochemical cycling there is driven by the microbial community that are different from that in the epilimnion.
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Affiliation(s)
- Yusuke Okazaki
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, 520-2113, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, 520-2113, Japan
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33
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Wu W, Chen Y, Faisal S, Khan A, Chen Z, Ling Z, Liu P, Li X. Improving methane production in cow dung and corn straw co-fermentation systems via enhanced degradation of cellulose by cabbage addition. Sci Rep 2016; 6:33628. [PMID: 27641709 PMCID: PMC5027527 DOI: 10.1038/srep33628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/31/2016] [Indexed: 01/19/2023] Open
Abstract
The effects of cabbage waste (CW) addition on methane production in cow dung and corn straw co-fermentation systems were investigated. Four experimental groups, each containing 55 g of substrate, were set up as follows: 100% cow dung (C); 36% cabbage and 64% cow dung (CC); 36% straw and 64% cow dung (SC); and 18% cabbage, 18% straw, and 64% cow dung (CSC). After seven days of fermentation, the maximum methane yield was 134 mL in the CSC group, which was 2.81-fold, 1.78-fold, and 1340-fold higher than that obtained in the CC, SC, and C groups, respectively. CW treatment of the CSC group enhanced cellulase activity and enriched culturable cellulose-degrading bacterial strains. Miseq sequencing data revealed that the predominant phylum in the CSC group was Bacteroidetes, which contains most of the cellulose-degrading bacteria. Our results suggested that CW treatment elevated cellulose degradation and promoted methane production.
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Affiliation(s)
- Wenyang Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Yong Chen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Shah Faisal
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Aman Khan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Zhengjun Chen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Zhenmin Ling
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Pu Liu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
| | - Xiangkai Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, P.R. China
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Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon. Sci Rep 2016; 6:32165. [PMID: 27577787 PMCID: PMC5006002 DOI: 10.1038/srep32165] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/28/2016] [Indexed: 12/04/2022] Open
Abstract
The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies.
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Alexander J, Knopp G, Dötsch A, Wieland A, Schwartz T. Ozone treatment of conditioned wastewater selects antibiotic resistance genes, opportunistic bacteria, and induce strong population shifts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 559:103-112. [PMID: 27058129 DOI: 10.1016/j.scitotenv.2016.03.154] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
An ozone treatment system was investigated to analyze its impact on clinically relevant antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). A concentration of 0.9±0.1g ozone per 1g DOC was used to treat conventional clarified wastewater. PCR, qPCR analyses, Illumina 16S Amplicon Sequencing, and PCR-DGGE revealed diverse patterns of resistances and susceptibilities of opportunistic bacteria and accumulations of some ARGs after ozone treatment. Molecular marker genes for enterococci indicated a high susceptibility to ozone. Although they were reduced by almost 99%, they were still present in the bacterial population after ozone treatment. In contrast to this, Pseudomonas aeruginosa displayed only minor changes in abundance after ozone treatment. This indicated different mechanisms of microorganisms to cope with the bactericidal effects of ozone. The investigated ARGs demonstrated an even more diverse pattern. After ozone treatment, the erythromycin resistance gene (ermB) was reduced by 2 orders of magnitude, but simultaneously, the abundance of two other clinically relevant ARGs increased within the surviving wastewater population (vanA, blaVIM). PCR-DGGE analysis and 16S-Amplicon-Sequencing confirmed a selection-like process in combination with a substantial diversity loss within the vital wastewater population after ozone treatment. Especially the PCR-DGGE results demonstrated the survival of GC-rich bacteria after ozone treatment.
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Affiliation(s)
- Johannes Alexander
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Gregor Knopp
- Technische Universität Darmstadt, Institute IWAR, Wastewater Technology, Franziska-Braun-Straße 7, 64287, Darmstadt, Germany
| | - Andreas Dötsch
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Arne Wieland
- Xylem Services GmbH, Boschstraße 4 - 14, 32051, Herford, Germany
| | - Thomas Schwartz
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021, Karlsruhe, Germany.
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Pessi IS, Maalouf PDC, Laughinghouse HD, Baurain D, Wilmotte A. On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats. JOURNAL OF PHYCOLOGY 2016; 52:356-68. [PMID: 27273529 DOI: 10.1111/jpy.12399] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/31/2016] [Indexed: 05/12/2023]
Abstract
The study of Antarctic cyanobacterial diversity has been mostly limited to morphological identification and traditional molecular techniques. High-throughput sequencing (HTS) allows a much better understanding of microbial distribution in the environment, but its application is hampered by several methodological and analytical challenges. In this work, we explored the use of HTS as a tool for the study of cyanobacterial diversity in Antarctic aquatic mats. Our results highlight the importance of using artificial communities to validate the parameters of the bioinformatics procedure used to analyze natural communities, since pipeline-dependent biases had a strong effect on the observed community structures. Analysis of microbial mats from five Antarctic lakes and an aquatic biofilm from the Sub-Antarctic showed that HTS is a valuable tool for the assessment of cyanobacterial diversity. The majority of the operational taxonomic units retrieved were related to filamentous taxa such as Leptolyngbya and Phormidium, which are common genera in Antarctic lacustrine microbial mats. However, other phylotypes related to different taxa such as Geitlerinema, Pseudanabaena, Synechococcus, Chamaesiphon, Calothrix, and Coleodesmium were also found. Results revealed a much higher diversity than what had been reported using traditional methods and also highlighted remarkable differences between the cyanobacterial communities of the studied lakes. The aquatic biofilm from the Sub-Antarctic had a distinct cyanobacterial community from the Antarctic lakes, which in turn displayed a salinity-dependent community structure at the phylotype level.
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Affiliation(s)
- Igor Stelmach Pessi
- Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Pedro De Carvalho Maalouf
- Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Haywood Dail Laughinghouse
- Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Denis Baurain
- Eukaryotic Phylogenomics, Department of Life Sciences/PhytoSYSTEMS, University of Liège, Chemin de la Vallée 4, B22, Quartier Vallée 1, Sart-Tilman, 4000, Liège, Belgium
| | - Annick Wilmotte
- Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
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Numberger D, Herlemann DPR, Jürgens K, Dehnhardt G, Schulz-Vogt H. Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina). Microbiologyopen 2016; 5:782-792. [PMID: 27734626 PMCID: PMC5061715 DOI: 10.1002/mbo3.369] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 01/12/2023] Open
Abstract
The gut microbiota has many beneficial effects on host metabolism and health, and its composition is determined by numerous factors. It is also assumed that there was a co‐evolution of mammals and the bacteria inhabiting their gut. Current knowledge of the mammalian gut microbiota mainly derives from studies on humans and terrestrial animals, whereas those on marine mammals are sparse. However, they could provide additional information on influencing factors, such as the role of diet and co‐evolution with the host. In this study, we investigated and compared the bacterial diversity in the feces of five male harbor seals (Phoca vitulina). Because this small population included two half‐brother pairs, each sharing a common father, it allowed an evaluation of the impact of host relatedness or genetic similarity on the gut microbial community. Fresh feces obtained from the seals by an enema were analyzed by fluorescence in situ hybridization and amplicon sequencing of 16S rRNA genes. The results showed that the bacterial communities in the seals' feces mainly consisted of the phyla Firmicutes (19–43%), Bacteroidetes (22–36%), Fusobacteria (18–32%), and Proteobacteria (5–17%) . Twenty‐one bacterial members present in the fecal samples of the five seals contributed an average relative abundance of 93.7 + 8.7% of the total fecal microbial community. Contrary to all expectations based on previous studies a comparison of the fecal community between individual seals showed a higher similarity between unrelated than related individuals.
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Affiliation(s)
- Daniela Numberger
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany. .,University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany.
| | - Daniel P R Herlemann
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany.,University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany
| | - Guido Dehnhardt
- University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany.,Marine Science Center, Am Yachthafen 3a, Rostock, D-18119, Germany
| | - Heide Schulz-Vogt
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany.,University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany
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Jung JY, Lee HJ, Chun BH, Jeon CO. Effects of Temperature on Bacterial Communities and Metabolites during Fermentation of Myeolchi-Aekjeot, a Traditional Korean Fermented Anchovy Sauce. PLoS One 2016; 11:e0151351. [PMID: 26977596 PMCID: PMC4792383 DOI: 10.1371/journal.pone.0151351] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/27/2016] [Indexed: 11/18/2022] Open
Abstract
Myeolchi-aekjeot (MA) in Korea is produced outdoors without temperature controls, which is a major obstacle to produce commercial MA products with uniform quality. To investigate the effects of temperature on MA fermentation, pH, bacterial abundance and community, and metabolites were monitored during fermentation at 15°C, 20°C, 25°C, and 30°C. Initial pH values were approximately 6.0, and pH values increased after approximately 42 days, with faster increases at higher temperatures. Bacterial abundances increased rapidly in all MA samples after quick initial decreases during early fermentation and then they again steadily decreased after reaching their maxima, which were significantly greater at higher temperatures. Bacterial community analysis revealed that Proteobacteria and Tenericutes were predominant in all initial MA samples, but they were rapidly displaced by Firmicutes as fermentation progressed. Photobacterium and Mycoplasma belonging to Proteobacteria and Tenericutes, respectively, which may include potentially pathogenic strains, were dominant in initial MA, but decreased with the growth of Chromohalobacter, which occurred faster at higher temperatures--they were dominant until 273 and 100 days at 15°C and 20°C, respectively, but not detected after 30 days at 25°C and 30°C. Chromohalobacter also decreased with the appearance of subsequent genera belonging to Firmicutes in all MA samples. Tetragenococcus, halophilic lactic acid bacteria, appeared predominantly at 20°C, 25°C, and 30°C; they were most abundant at 30°C, but not detected at 15°C. Alkalibacillus and Lentibacillus appeared as dominant genera with the decrease of Tetragenococcus at 25°C and 30°C, but only Lentibacillus was dominant at 15°C and 20°C. Metabolite analysis showed that amino acids related to tastes were major metabolites and their concentrations were relatively higher at high temperatures. This study suggests that high temperatures (approximately 30°C) may be appropriate in MA fermentation, in the light of faster disappearance of potentially pathogenic genera, higher amino acids, growth of Tetragenococcus, and faster fermentation.
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Affiliation(s)
- Ji Young Jung
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyo Jung Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
- * E-mail:
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Fang L, Zhou Z, Ren L, Shi F, Can M, Chai S, Meng Q. Ruminal Bacterial Diversity of Yaks (Bos Grunniens) Fed by Grazing or Indoor Regime on the Tibetan Plateau by Analysis of165 rRNAGene Libraries. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Le Roux JJ, Mavengere NR, Ellis AG. The structure of legume-rhizobium interaction networks and their response to tree invasions. AOB PLANTS 2016; 8:plw038. [PMID: 27255514 PMCID: PMC4940501 DOI: 10.1093/aobpla/plw038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/07/2016] [Indexed: 05/09/2023]
Abstract
Establishing mutualistic interactions in novel environments is important for the successful establishment of some non-native plant species. These associations may, in turn, impact native species interaction networks as non-natives become dominant in their new environments. Using phylogenetic and ecological interaction network approaches we provide the first report of the structure of belowground legume-rhizobium interaction networks and how they change along a gradient of invasion (uninvaded, semi invaded and heavily invaded sites) by Australian Acacia species in South Africa's Cape Floristic Region. We found that native and invasive legumes interact with distinct rhizobial lineages, most likely due to phylogenetic uniqueness of native and invasive host plants. Moreover, legume-rhizobium interaction networks are not nested, but significantly modular with high levels of specialization possibly as a result of legume-rhizobium co-evolution. Although network topology remained constant across the invasion gradient, composition of bacterial communities associated with native legumes changed dramatically as acacias increasingly dominated the landscape. In stark contrast to aboveground interaction networks (e.g. pollination and seed dispersal) we show that invasive legumes do not infiltrate existing native legume-rhizobium networks but rather form novel modules. This absence of mutualist overlap between native and invasive legumes suggests the importance of co-invading rhizobium-acacia species complexes for Acacia invasion success, and argues against a ubiquitous role for the formation and evolutionary refinement of novel interactions.
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Affiliation(s)
- Johannes J Le Roux
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
| | - Natasha R Mavengere
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
| | - Allan G Ellis
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
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Yund PO, Tilburg CE, McCartney MA. Across-shelf distribution of blue mussel larvae in the northern Gulf of Maine: consequences for population connectivity and a species range boundary. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150513. [PMID: 27018654 PMCID: PMC4807459 DOI: 10.1098/rsos.150513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/03/2015] [Indexed: 05/05/2023]
Abstract
Studies of population connectivity have largely focused on along-shelf, as opposed to across-shelf, processes. We hypothesized that a discontinuity in across-shelf mixing caused by the divergence of the Eastern Maine Coastal Current (EMCC) from shore acts as an ecological barrier to the supply of mussel larvae to the coast. Existing data on the relative abundance of two congeneric blue mussels, Mytilus edulis and M. trossulus, were analysed to quantify the association of M. trossulus with the colder temperature signal of the EMCC and generate larval distribution predictions. We then sampled the across-shelf distribution of larvae along two transects during 2011. Larvae were identified using restriction digests of PCR amplicons from the mitochondrial 16S rDNA. Mytilus edulis larvae were consistently abundant on either the inshore and offshore transect ends, but not homogeneously distributed across the shelf, while M. trossulus larvae were less common throughout the study area. The divergence of the EMCC from shore appears to create a break in the connectivity of M. edulis populations by isolating those inshore of the EMCC from upstream larval sources. Across-shelf transport processes can thus produce connectivity patterns that would not be predicted solely on the basis of along-shelf processes.
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Affiliation(s)
- Philip O. Yund
- The Downeast Institute, Beals, ME 04611, USA
- Author for correspondence: Philip O. Yund e-mail:
| | - Charles E. Tilburg
- Department of Marine Sciences, University of New England, Biddeford, ME 04005, USA
| | - Michael A. McCartney
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28409, USA
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Lazzaro A, Hilfiker D, Zeyer J. Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects. Front Microbiol 2015; 6:1330. [PMID: 26635785 PMCID: PMC4660872 DOI: 10.3389/fmicb.2015.01330] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/12/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. However, little is known on the combined impact of such factors on microbial community structure. We assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930-2519 m a.s.l.) over 14 months. Samples were taken during all four seasons, even under the winter snowpack and at snowmelt. Microbial community structures and abundances were investigated using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR (qPCR) of the 16S and 18S rRNA genes. Illumina sequencing was performed to identify key bacterial groups in selected samples. We found that the soil properties varied significantly with the seasons and along the elevational gradient. For example, concentrations of soluble nutrients (e.g., [Formula: see text], [Formula: see text], [Formula: see text]) significantly increased in October but decreased drastically under the winter snowpack. At all times, the alpine meadows showed higher soluble nutrient concentrations than the glacier forefield. Microbial community structures at the different sites were strongly affected by seasonal variations. Under winter snowpack, bacterial communities were dominated by ubiquitous groups (i.e., beta-Proteobacteria, which made up to 25.7% of the total reads in the glacier forefield). In the snow-free seasons, other groups (i.e., Cyanobacteria) became more abundant (from 1% under winter snow in the glacier forefield samples to 8.1% in summer). In summary, elevation had a significant effect on soil properties, whereas season influenced soil properties as well as microbial community structure. Vegetation had a minor impact on microbial communities. At every elevation analyzed, bacterial, and fungal community structures exhibited a pronounced annual cycle.
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Affiliation(s)
- Anna Lazzaro
- Environmental Microbiology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich Zurich, Switzerland
| | - Daniela Hilfiker
- Environmental Microbiology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich Zurich, Switzerland
| | - Josef Zeyer
- Environmental Microbiology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich Zurich, Switzerland
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Alsalah D, Al-Jassim N, Timraz K, Hong PY. Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:12391-411. [PMID: 26445052 PMCID: PMC4626975 DOI: 10.3390/ijerph121012391] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 11/16/2022]
Abstract
This study examines the groundwater quality in wells situated near agricultural fields in Saudi Arabia. Fruits (e.g., tomato and green pepper) irrigated with groundwater were also assessed for the occurrence of opportunistic pathogens to determine if food safety was compromised by the groundwater. The amount of total nitrogen in most of the groundwater samples exceeded the 15 mg/L permissible limit for agricultural irrigation. Fecal coliforms in densities > 12 MPN/100 mL were detected in three of the groundwater wells that were in close proximity to a chicken farm. These findings, coupled with qPCR-based fecal source tracking, show that groundwater in wells D and E, which were nearest to the chicken farm, had compromised quality. Anthropogenic contamination resulted in a shift in the predominant bacterial phyla within the groundwater microbial communities. For example, there was an elevated presence of Proteobacteria and Cyanobacteria in wells D and E but a lower overall microbial richness in the groundwater perturbed by anthropogenic contamination. In the remaining wells, the genus Acinetobacter was detected at high relative abundance ranging from 1.5% to 48% of the total groundwater microbial community. However, culture-based analysis did not recover any antibiotic-resistant bacteria or opportunistic pathogens from these groundwater samples. In contrast, opportunistic pathogenic Enterococcus faecalis and Pseudomonas aeruginosa were isolated from the fruits irrigated with the groundwater from wells B and F. Although the groundwater was compromised, quantitative microbial risk assessment suggests that the annual risk incurred from accidental consumption of E. faecalis on these fruits was within the acceptable limit of 10−4. However, the annual risk arising from P. aeruginosa was 9.55 × 10−4, slightly above the acceptable limit. Our findings highlight that the groundwater quality at this agricultural site in western Saudi Arabia is not pristine and that better agricultural management practices are needed alongside groundwater treatment strategies to improve food safety.
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Affiliation(s)
- Dhafer Alsalah
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Nada Al-Jassim
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Kenda Timraz
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Syst Appl Microbiol 2015; 38:330-9. [DOI: 10.1016/j.syapm.2015.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 01/06/2023]
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Rettedal EA, Brözel VS. Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H 218 O. Microbiologyopen 2015; 4:208-219. [PMID: 25650291 PMCID: PMC4398504 DOI: 10.1002/mbo3.230] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 11/08/2014] [Accepted: 11/17/2014] [Indexed: 11/10/2022] Open
Abstract
Current limitations in culture-based methods have lead to a reliance on culture-independent approaches, based principally on the comparative analysis of primary semantides such as ribosomal gene sequences. DNA can be remarkably stable in some environments, so its presence does not indicate live bacteria, but extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of active cells. Stable isotope probing (SIP) involves the incorporation of heavy isotopes into newly synthesized nucleic acids, and can be used to separate newly synthesized from existing DNA or rRNA. H218 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. The aim of our work was to compare soil bacterial community composition as revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented with H218 O and after 38 days the DNA and RNA were co-extracted. Heavy nucleic acids were separated out by CsCl and CsTFA density centrifugation. The 16S rRNA gene pools were characterized by DGGE and pyrosequencing, and the sequence results analyzed using mothur. The majority of DNA (~60%) and RNA (~75%) from the microcosms incubated with H218 O were labeled by the isotope. The analysis indicated that total and active members of the same type of nucleic acid represented similar community structures, which suggested that most dominant OTUs in the total nucleic acid extracts contained active members. It also supported that H218 O was an effective universal label for SIP for both DNA and RNA. DNA and RNA-derived diversity was dissimilar. RNA from this soil more comprehensively recovered bacterial richness than DNA because the most abundant OTUs were less numerous in RNA than DNA-derived community data, and dominant OTU pools didn't mask rare OTUs as much in RNA.
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Affiliation(s)
- Elizabeth A Rettedal
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, South Dakota, 57007
| | - Volker S Brözel
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, South Dakota, 57007
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, 0004, South Africa
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Piasecka A, Bernstein R, Ollevier F, Meersman F, Souffreau C, Bilad RM, Cottenie K, Vanysacker L, Denis C, Vankelecom I. Study of biofilms on PVDF membranes after chemical cleaning by sodium hypochlorite. Sep Purif Technol 2015. [DOI: 10.1016/j.seppur.2014.12.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, high-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools-such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization-have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.
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Affiliation(s)
- Zackary I Johnson
- Marine Laboratory (Nicholas School of the Environment) and Department of Biology, Duke University, Beaufort, North Carolina 28516;
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Lee CK, Kim B, Kang YM, Lee HY, Hwang CE, Ahn MJ, Seo WT, Cho KM. Microbial Diversity in the Enrichment Cultures from the Fermented Beverage of Plant Extract Using Ribosomal RNA Sequence Analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.7845/kjm.2014.4034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Stevens D, Cornmell R, Taylor D, Grimshaw SG, Riazanskaia S, Arnold DS, Fernstad SJ, Smith AM, Heaney LM, Reynolds JC, Thomas CLP, Harker M. Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles. FEMS Microbiol Ecol 2014; 91:1-11. [DOI: 10.1093/femsec/fiu018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Shi YW, Zhang X, Lou K. Analysis of endophytic bacterial community composition by 16S rDNA clone library in Achnatherum inebrians. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714060174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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