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Antony Dass M, Sherman CDH, van Oorschot RAH, Hartman D, Carter G, Durdle A. A preliminary study on detecting human DNA in aquatic environments: Potential of eDNA in forensics. Forensic Sci Int Genet 2024; 74:103155. [PMID: 39383603 DOI: 10.1016/j.fsigen.2024.103155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 09/27/2024] [Accepted: 10/04/2024] [Indexed: 10/11/2024]
Abstract
Human environmental DNA (eDNA) application have not been fully applied or adequately considered in the fields of eDNA and forensics. Nonetheless, this technique holds great potential as a complementary tool for detecting human DNA in aquatic environments, particularly in cases involving crimes connect to such environments. However, the detectability or stability of eDNA can vary depending on several factors. Therefore, this preliminary study investigates the detection and degradation rates of human eDNA, as well as the recovery of nuclear short tandem repeat (STR) profiles and mitochondrial DNA (mtDNA) sequencing, using water samples from both saltwater and freshwater sources. To conduct the experiment, whole human blood was spiked into the water samples. Water samples were then filtered using a 5 µm pore size filter, and samples were collected at various time intervals up to 23 days. A human specific qPCR assay targeting HV1 region of human mtDNA was used to detect human eDNA. Results demonstrated that human eDNA remains detectable for up to 36 hours in freshwater samples and up 84 hours in saltwater samples. The limit of detection (LOD) of human eDNA, (205 copies/µl), was achieved after 60 hours in freshwater and 180 hours in saltwater samples. Partial STR profiles could be recovered up to 24 hours for freshwater and saltwater. Results from mtDNA sequencing indicate that full mtDNA profiles could be recovered from freshwater samples up to 48 hours and remained detectable up to 72 hours in saltwater. Overall, the findings of this study underscore the importance of considering and incorporating human eDNA analysis as a valuable tool in forensic practice. By harnessing the power of eDNA, law enforcement agencies can enhance their investigation capabilities, improve the accuracy of forensic reconstructions, and ultimately contribute to the resolution of cases involving aquatic environments. Further research and validation are needed to optimize and expand the utilization of eDNA techniques in forensic investigations.
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Affiliation(s)
- Marie Antony Dass
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong 3220, Australia.
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong 3220, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod 3085, Australia; School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora 3086, Australia
| | - Dadna Hartman
- Victorian Institute of Forensic Medicine, 65 Kavanagh Street, Southbank 3006, Australia; Department of Forensic Medicine, Monash University, 65 Kavanagh Street Southbank, Melbourne, Victoria 3006, Australia
| | - Gemma Carter
- Victorian Institute of Forensic Medicine, 65 Kavanagh Street, Southbank 3006, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong 3220, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod 3085, Australia
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2
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Wang S, Tian R, Bi Y, Meng F, Zhang R, Wang C, Wang D, Liu L, Zhang B. A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems. CHEMOSPHERE 2024; 359:142264. [PMID: 38714248 DOI: 10.1016/j.chemosphere.2024.142264] [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: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/09/2024]
Abstract
Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.
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Affiliation(s)
- Shaopo Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Ruimin Tian
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yanmeng Bi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Fansheng Meng
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Rui Zhang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Chenchen Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Dong Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Lingjie Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China.
| | - Bo Zhang
- Tianjin Eco-City Water Investment and Construction Co. Ltd, Hexu Road 276, Tianjin, 300467, China
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3
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Zhang J, Huang L, Wang Y. Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170162. [PMID: 38244634 DOI: 10.1016/j.scitotenv.2024.170162] [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: 10/12/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.
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Affiliation(s)
- Jianmin Zhang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, First Ring Road 24#, Chengdu 610065, People's Republic of China.
| | - Lei Huang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, First Ring Road 24#, Chengdu 610065, People's Republic of China.
| | - Yurong Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, First Ring Road 24#, Chengdu 610065, People's Republic of China.
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4
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Paris ER, Arandia-Gorostidi N, Klempay B, Bowman JS, Pontefract A, Elbon CE, Glass JB, Ingall ED, Doran PT, Som SM, Schmidt BE, Dekas AE. Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity. SCIENCE ADVANCES 2023; 9:eadj3594. [PMID: 38134283 PMCID: PMC10745694 DOI: 10.1126/sciadv.adj3594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the 0.409-aw brine (an MgCl2-dominated site) despite the presence of cell-like structures. Extrapolating our data, we predict an aw limit for detectable anabolic activity of 0.540, which is beyond the currently accepted limit of life based on cell division. This work demonstrates the utility of single-cell, metabolism-based techniques for detecting active life and expands the potential habitable space on Earth and beyond.
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Affiliation(s)
- Emily R. Paris
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | | | - Benjamin Klempay
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, USA
| | - Jeff S. Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, USA
| | | | - Claire E. Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ellery D. Ingall
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Peter T. Doran
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sanjoy M. Som
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Britney E. Schmidt
- Departments of Astronomy and Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Anne E. Dekas
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
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Kheiri R, Mehrshad M, Pourbabaee AA, Ventosa A, Amoozegar MA. Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation. Sci Rep 2023; 13:374. [PMID: 36611086 PMCID: PMC9825399 DOI: 10.1038/s41598-023-27429-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023] Open
Abstract
Lake Urmia located in Iran is a hypersaline environment with a salinity of about 27% (w/v). Metagenomic analyses of water samples collected from six locations in the lake exhibited a microbial community dominated by representatives of the family Haloferacaceae (69.8%), mainly those affiliated to only two genera, Haloquadratum (59.3%) and Halonotius (9.1%). Similar to other hypersaline lakes, the bacterial community was dominated by Salinibacter ruber (23.3%). Genomic variation analysis by inspecting single nucleotide variations (SNVs) and insertions/deletions (INDELs) exhibited a high level of SNVs and insertions, most likely through transformation for abundant taxa in the Lake Urmia community. We suggest that the extreme conditions of Lake Urmia and specifically its high ionic concentrations could potentially increase the SNVs and insertions, which can consequently hamper the assembly and genome reconstruction from metagenomic reads of Lake Urmia.
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Affiliation(s)
- Roohollah Kheiri
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Ahmad Ali Pourbabaee
- Department of Soil Science, Agriculture Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012, Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran.
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Riva V, Patania G, Riva F, Vergani L, Crotti E, Mapelli F. Acinetobacter baylyi Strain BD413 Can Acquire an Antibiotic Resistance Gene by Natural Transformation on Lettuce Phylloplane and Enter the Endosphere. Antibiotics (Basel) 2022; 11:1231. [PMID: 36140010 PMCID: PMC9495178 DOI: 10.3390/antibiotics11091231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
Antibiotic resistance spread must be considered in a holistic framework which comprises the agri-food ecosystems, where plants can be considered a bridge connecting water and soil habitats with the human microbiome. However, the study of horizontal gene transfer events within the plant microbiome is still overlooked. Here, the environmental strain Acinetobacter baylyi BD413 was used to study the acquisition of extracellular DNA (exDNA) carrying an antibiotic resistance gene (ARG) on lettuce phylloplane, performing experiments at conditions (i.e., plasmid quantities) mimicking those that can be found in a water reuse scenario. Moreover, we assessed how the presence of a surfactant, a co-formulant widely used in agriculture, affected exDNA entry in bacteria and plant tissues, besides the penetration and survival of bacteria into the leaf endosphere. Natural transformation frequency in planta was comparable to that occurring under optimal conditions (i.e., temperature, nutrient provision, and absence of microbial competitors), representing an entrance pathway of ARGs into an epiphytic bacterium able to penetrate the endosphere of a leafy vegetable. The presence of the surfactant determined a higher presence of culturable transformant cells in the leaf tissues but did not significantly increase exDNA entry in A. baylyi BD413 cells and lettuce leaves. More research on HGT (Horizontal Gene Transfer) mechanisms in planta should be performed to obtain experimental data on produce safety in terms of antibiotic resistance.
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Affiliation(s)
| | | | | | | | | | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, 20133 Milan, Italy
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7
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Ye M, Zhang Z, Sun M, Shi Y. Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome. IMETA 2022; 1:e34. [PMID: 38868707 PMCID: PMC10989830 DOI: 10.1002/imt2.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environment from the ribosome enzyme lysis, therein acting as the historical genetic information archive of the microbiome. As a consequence, both eDNA and iDNA can shed light on the functional gene variety and the corresponding microbial activity. In addition, eDNA is a ubiquitous composition of the cell membrane, which exerts a great impact on the resistance of outer stress from environmental pollutants, such as heavy metals, antibiotics, pesticides, and so on. This study focuses on the environmental dynamics and the ecological functions of the eDNA and iDNA from the perspectives of environmental behavior, genetic information transmission, resistance to the environmental contaminants, and so on. By reviewing the status quo and the future vista of the e/iDNAs research, this article sheds light on exploring the ecological functioning of the e/iDNAs in the environmental microbiome.
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Affiliation(s)
- Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
| | - Zhongyun Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
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8
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Palomba E, Chiaiese P, Termolino P, Paparo R, Filippone E, Mazzoleni S, Chiusano ML. Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111436. [PMID: 35684209 PMCID: PMC9183124 DOI: 10.3390/plants11111436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.
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Affiliation(s)
- Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Rosa Paparo
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Edgardo Filippone
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
- Correspondence: ; Tel.: +39-81-2539492
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9
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Scheffer G, Hubert CRJ, Enning DR, Lahme S, Mand J, de Rezende JR. Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir. Microorganisms 2021; 9:2266. [PMID: 34835392 PMCID: PMC8621343 DOI: 10.3390/microorganisms9112266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022] Open
Abstract
Oil reservoirs can represent extreme environments for microbial life due to low water availability, high salinity, high pressure and naturally occurring radionuclides. This study investigated the microbiome of saline formation water samples from a Gulf of Mexico oil reservoir. Metagenomic analysis and associated anaerobic enrichment cultures enabled investigations into metabolic potential for microbial activity and persistence in this environment given its high salinity (4.5%) and low nutrient availability. Preliminary 16S rRNA gene amplicon sequencing revealed very low microbial diversity. Accordingly, deep shotgun sequencing resulted in nine metagenome-assembled genomes (MAGs), including members of novel lineages QPJE01 (genus level) within the Halanaerobiaceae, and BM520 (family level) within the Bacteroidales. Genomes of the nine organisms included respiratory pathways such as nitrate reduction (in Arhodomonas, Flexistipes, Geotoga and Marinobacter MAGs) and thiosulfate reduction (in Arhodomonas, Flexistipes and Geotoga MAGs). Genomic evidence for adaptation to high salinity, withstanding radioactivity, and metal acquisition was also observed in different MAGs, possibly explaining their occurrence in this extreme habitat. Other metabolic features included the potential for quorum sensing and biofilm formation, and genes for forming endospores in some cases. Understanding the microbiomes of deep biosphere environments sheds light on the capabilities of uncultivated subsurface microorganisms and their potential roles in subsurface settings, including during oil recovery operations.
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Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
| | - Dennis R. Enning
- Faculty of Life Sciences and Technology, Berlin University of Applied Sciences and Technology, D-13347 Berlin, Germany;
| | - Sven Lahme
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
- Exxon Mobil Upstream Research Company, Spring, TX 77389, USA;
| | - Jaspreet Mand
- Exxon Mobil Upstream Research Company, Spring, TX 77389, USA;
| | - Júlia R. de Rezende
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
- The Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AS, UK
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10
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Huby TJC, Clark DR, McKew BA, McGenity TJ. Extremely halophilic archaeal communities are resilient to short-term entombment in halite. Environ Microbiol 2021; 23:3370-3383. [PMID: 31919959 PMCID: PMC8359394 DOI: 10.1111/1462-2920.14913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite-entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory-grown halite over 21 weeks, using high-throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite-entombed communities. These results show that halite-entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long-term successional dynamics in this environment.
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Affiliation(s)
- Tom J. C. Huby
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Dave R. Clark
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Boyd A. McKew
- School of Life SciencesUniversity of EssexColchesterEssexUK
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11
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Klempay B, Arandia-Gorostidi N, Dekas AE, Bartlett DH, Carr CE, Doran PT, Dutta A, Erazo N, Fisher LA, Glass JB, Pontefract A, Som SM, Wilson JM, Schmidt BE, Bowman JS. Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds. Environ Microbiol 2021; 23:3825-3839. [PMID: 33621409 DOI: 10.1111/1462-2920.15440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 01/02/2023]
Abstract
Concurrent osmotic and chaotropic stress make MgCl2 -rich brines extremely inhospitable environments. Understanding the limits of life in these brines is essential to the search for extraterrestrial life on contemporary and relict ocean worlds, like Mars, which could host similar environments. We sequenced environmental 16S rRNA genes and quantified microbial activity across a broad range of salinity and chaotropicity at a Mars-analogue salt harvesting facility in Southern California, where seawater is evaporated in a series of ponds ranging from kosmotropic NaCl brines to highly chaotropic MgCl2 brines. Within NaCl brines, we observed a proliferation of specialized halophilic Euryarchaeota, which corresponded closely with the dominant taxa found in salterns around the world. These communities were characterized by very slow growth rates and high biomass accumulation. As salinity and chaotropicity increased, we found that the MgCl2 -rich brines eventually exceeded the limits of microbial activity. We found evidence that exogenous genetic material is preserved in these chaotropic brines, producing an unexpected increase in diversity in the presumably sterile MgCl2 -saturated brines. Because of their high potential for biomarker preservation, chaotropic brines could therefore serve as repositories of genetic biomarkers from nearby environments (both on Earth and beyond) making them prime targets for future life-detection missions.
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Affiliation(s)
- Benjamin Klempay
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | | | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Douglas H Bartlett
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Christopher E Carr
- Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Earth and Atmospheric Studies, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Peter T Doran
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Avishek Dutta
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Natalia Erazo
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Luke A Fisher
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Studies, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Sanjoy M Som
- Blue Marble Space Institute of Science, Seattle, WA, 98154, USA
| | - Jesse M Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Britney E Schmidt
- School of Earth and Atmospheric Studies, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
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Fisher LA, Pontefract A, Som S, Carr CE, Klempay B, Schmidt B, Bowman J, Bartlett DH. Current state of athalassohaline deep‐sea hypersaline anoxic basin research—recommendations for future work and relevance to astrobiology. Environ Microbiol 2021; 23:3360-3369. [DOI: 10.1111/1462-2920.15414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/06/2023]
Affiliation(s)
- Luke A. Fisher
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego La Jolla CA 92093‐0202 USA
| | | | - Sanjoy Som
- Blue Marble Space Institute of Science Seattle WA 98104 USA
| | - Christopher E. Carr
- Daniel Guggenheim School of Aerospace Engineering Georgia Institute of Technology Atlanta GA 30332 USA
- Earth and Atmospheric Sciences Georgia Institute of Technology Atlanta GA 30332 USA
| | - Benjamin Klempay
- Integrative Oceanography Division, Scripps Institution of Oceanography University of California San Diego La Jolla CA 92093‐0218 USA
| | - Britney Schmidt
- Earth and Atmospheric Sciences Georgia Institute of Technology Atlanta GA 30332 USA
| | - Jeff Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography University of California San Diego La Jolla CA 92093‐0218 USA
- Center for Microbiome Innovation University of California San Diego La Jolla CA 92093‐0218 USA
| | - Douglas H. Bartlett
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego La Jolla CA 92093‐0202 USA
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13
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Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin. PLoS One 2020; 15:e0231676. [PMID: 32315331 PMCID: PMC7173876 DOI: 10.1371/journal.pone.0231676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/28/2020] [Indexed: 11/21/2022] Open
Abstract
In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments.
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14
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Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun Biol 2020; 3:169. [PMID: 32265485 PMCID: PMC7138834 DOI: 10.1038/s42003-020-0899-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress. Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.
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15
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Du XP, Cai ZH, Zuo P, Meng FX, Zhu JM, Zhou J. Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom. Microorganisms 2020; 8:microorganisms8010107. [PMID: 31940944 PMCID: PMC7023004 DOI: 10.3390/microorganisms8010107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 01/02/2023] Open
Abstract
Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.
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Affiliation(s)
- Xiao-Peng Du
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhong-Hua Cai
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ping Zuo
- The School of Geography and Ocean Science, Nanjing University, Nanjing 210000, China;
| | - Fan-Xu Meng
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310000, China
| | - Jian-Ming Zhu
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Zhou
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Correspondence:
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16
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Yang B, Qin C, Hu X, Xia K, Lu C, Gudda FO, Ma Z, Gao Y. Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system. ENVIRONMENT INTERNATIONAL 2019; 132:105087. [PMID: 31430607 DOI: 10.1016/j.envint.2019.105087] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 05/25/2023]
Abstract
The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.
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Affiliation(s)
- Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Kang Xia
- School of Plant and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China.
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McGonigle JM, Bernau JA, Bowen BB, Brazelton WJ. Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats. mSphere 2019; 4:e00378-19. [PMID: 31462415 PMCID: PMC6714890 DOI: 10.1128/msphere.00378-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.
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Affiliation(s)
- Julia M McGonigle
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Jeremiah A Bernau
- Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - Brenda B Bowen
- Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - William J Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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18
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Zeaiter Z, Marasco R, Booth JM, Prosdocimi EM, Mapelli F, Callegari M, Fusi M, Michoud G, Molinari F, Daffonchio D, Borin S, Crotti E. Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery. Front Microbiol 2019; 10:1304. [PMID: 31244812 PMCID: PMC6581673 DOI: 10.3389/fmicb.2019.01304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/27/2019] [Indexed: 12/03/2022] Open
Abstract
The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl2-saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis. The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.
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Affiliation(s)
- Zahraa Zeaiter
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Ramona Marasco
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jenny M. Booth
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Erica M. Prosdocimi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Francesca Mapelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Matteo Callegari
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francesco Molinari
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
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19
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Environmental DNA for improved detection and environmental surveillance of schistosomiasis. Proc Natl Acad Sci U S A 2019; 116:8931-8940. [PMID: 30975758 DOI: 10.1073/pnas.1815046116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Schistosomiasis is a water-based, infectious disease with high morbidity and significant economic burdens affecting >250 million people globally. Disease control has, with notable success, for decades focused on drug treatment of infected human populations, but a recent paradigm shift now entails moving from control to elimination. To achieve this ambitious goal, more sensitive diagnostic tools are needed to monitor progress toward transmission interruption in the environment, especially in low-intensity infection areas. We report on the development of an environmental DNA (eDNA)-based tool to efficiently detect DNA traces of the parasite Schistosoma mansoni directly in the aquatic environment, where the nonhuman part of the parasite life cycle occurs. This is a report of the successful detection of S. mansoni in freshwater samples by using aquatic eDNA. True eDNA was detected in as few as 10 cercariae per liter of water in laboratory experiments. The field applicability of the method was tested at known transmission sites in Kenya, where comparison of schistosome detection by conventional snail surveys (snail collection and cercariae shedding) with eDNA (water samples) showed 71% agreement between the methods. The eDNA method furthermore detected schistosome presence at two additional sites where snail shedding failed, demonstrating a higher sensitivity of eDNA sampling. We conclude that eDNA provides a promising tool to substantially improve the environmental surveillance of S. mansoni Given the proper method and guideline development, eDNA could become an essential future component of the schistosomiasis control tool box needed to achieve the goal of elimination.
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Gong Z, Liang Y, Wang M, Jiang Y, Yang Q, Xia J, Zhou X, You S, Gao C, Wang J, He J, Shao H, McMinn A. Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica. Front Microbiol 2018; 9:2981. [PMID: 30559737 PMCID: PMC6287040 DOI: 10.3389/fmicb.2018.02981] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022] Open
Abstract
A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.
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Affiliation(s)
- Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Qingwei Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Xia
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Siyuan You
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jian Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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21
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Nagler M, Insam H, Pietramellara G, Ascher-Jenull J. Extracellular DNA in natural environments: features, relevance and applications. Appl Microbiol Biotechnol 2018; 102:6343-6356. [PMID: 29858957 PMCID: PMC6061472 DOI: 10.1007/s00253-018-9120-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/13/2023]
Abstract
Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
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Affiliation(s)
- Magdalena Nagler
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria.
| | - Heribert Insam
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
| | - Giacomo Pietramellara
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - Judith Ascher-Jenull
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
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22
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Merlino G, Barozzi A, Michoud G, Ngugi DK, Daffonchio D. Microbial ecology of deep-sea hypersaline anoxic basins. FEMS Microbiol Ecol 2018; 94:4995905. [DOI: 10.1093/femsec/fiy085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/09/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Giuseppe Merlino
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Alan Barozzi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - David Kamanda Ngugi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
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23
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Zeaiter Z, Mapelli F, Crotti E, Borin S. Methods for the genetic manipulation of marine bacteria. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Salter I. Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation. PLoS One 2018; 13:e0192409. [PMID: 29474423 PMCID: PMC5825020 DOI: 10.1371/journal.pone.0192409] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/22/2018] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA), a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs). Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP) demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR) model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs.
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Affiliation(s)
- Ian Salter
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d’Océanographie Microbienne (LOMIC) Observatoire Océanologique, Banyuls/mer, France
- Faroe Marine Research Institute, Torshavn, Faroe Islands
- * E-mail:
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25
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Wang DN, Liu L, Qiu ZG, Shen ZQ, Guo X, Yang D, Li J, Liu WL, Jin M, Li JW. A new adsorption-elution technique for the concentration of aquatic extracellular antibiotic resistance genes from large volumes of water. WATER RESEARCH 2016; 92:188-198. [PMID: 26854607 DOI: 10.1016/j.watres.2016.01.035] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/30/2015] [Accepted: 01/17/2016] [Indexed: 06/05/2023]
Abstract
Extracellular antibiotic resistance genes (eARGs) that help in the transmission and spread of antibiotic-resistant bacteria are emerging environmental contaminants in water, and there is therefore a growing need to assess environmental levels and associated risks of eARGs. However, as they are present in low amounts, it is difficult to detect eARGs in water directly with PCR techniques. Here, we prepared a new type of nucleic acid adsorption particle (NAAP) with high capacity and developed an optimal adsorption-elution method to concentrate eARGs from large volumes of water. With this technique, we were able to achieve an eARG recovery rate of above 95% from 10 L of water samples. Moreover, combining this new method with quantitative real-time PCR (qPCR), the sensitivity of the eARG detection was 10(4) times that of single qPCR, with the detection limit lowered to 100 gene copies (GCs)/L. Our analyses showed that the eARG load, virus load and certain water characteristics such as pH, chemical oxygen demand (CODMn), and turbidity affected the eARGs recovery rate. However, high eARGs recovery rates always remained within the standard limits for natural surface water quality, while eARG levels in water were lower than the detection limits of single qPCR assays. The recovery rates were not affected by water temperature and heterotrophic plate counts (HPC). The eARGs whatever located in the plasmids or the short-length linear DNAs can be recovered from the water. Furthermore, the recovery rate was high even in the presence of high concentrations of plasmids in different natural water (Haihe river, well water, raw water for drinking water, Jinhe river, Tuanbo lake and the Yunqiao reservoir). By this technology, eARGs concentrations were found ranging from (2.70 ± 0.73) × 10(2) to (4.58 ± 0.47) × 10(4) GCs/L for the extracellular ampicillin resistance gene and (5.43 ± 0.41) × 10(2) to (2.14 ± 0.23) × 10(4) GCs/L for the extracellular gentamicin resistance gene in natural water for the first time, respectively. All these findings suggest that NAAPs have great potential for the monitoring of eARGs pollution in water.
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Affiliation(s)
- Da-Ning Wang
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Lu Liu
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Zhi-Gang Qiu
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Zhi-Qiang Shen
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Xuan Guo
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Dong Yang
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Jing Li
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Wei-Li Liu
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Min Jin
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China.
| | - Jun-Wen Li
- Department of Environment and Health, Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China.
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26
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Gales G, Tsesmetzis N, Neria I, Alazard D, Coulon S, Lomans BP, Morin D, Ollivier B, Borgomano J, Joulian C. Preservation of ancestral Cretaceous microflora recovered from a hypersaline oil reservoir. Sci Rep 2016; 6:22960. [PMID: 26965360 PMCID: PMC4786803 DOI: 10.1038/srep22960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/19/2016] [Indexed: 11/16/2022] Open
Abstract
Microbiology of a hypersaline oil reservoir located in Central Africa was investigated with molecular and culture methods applied to preserved core samples. Here we show that the community structure was partially acquired during sedimentation, as many prokaryotic 16S rRNA gene sequences retrieved from the extracted DNA are phylogenetically related to actual Archaea inhabiting surface evaporitic environments, similar to the Cretaceous sediment paleoenvironment. Results are discussed in term of microorganisms and/or DNA preservation in such hypersaline and Mg-rich solutions. High salt concentrations together with anaerobic conditions could have preserved microbial/molecular diversity originating from the ancient sediment basin wherein organic matter was deposited.
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Affiliation(s)
- Grégoire Gales
- Aix-Marseille Université, CEREGE, Centre St Charles, Case 67, 3 Place Victor Hugo, 13331 Marseille, France.,Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, Texas 77082, USA
| | - Isabel Neria
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Didier Alazard
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Stéphanie Coulon
- BRGM, Unité BioGéochimie Environnementale, 3 Avenue Claude Guillemin, BP 36009, 45060 ORLEANS cedex 2, France
| | - Bart P Lomans
- Emerging Technologies - Subsurface, Projects &Technologies, Shell Global Solutions International B.V., Kessler Park 1, 2288 GS Rijswijk, The Netherlands
| | - Dominique Morin
- BRGM, Unité BioGéochimie Environnementale, 3 Avenue Claude Guillemin, BP 36009, 45060 ORLEANS cedex 2, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Jean Borgomano
- Aix-Marseille Université, CEREGE, Centre St Charles, Case 67, 3 Place Victor Hugo, 13331 Marseille, France
| | - Catherine Joulian
- BRGM, Unité BioGéochimie Environnementale, 3 Avenue Claude Guillemin, BP 36009, 45060 ORLEANS cedex 2, France
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Brandes M, Albach DC, Vogt JC, Mayland-Quellhorst E, Mendieta-Leiva G, Golubic S, Palinska KA. Supratidal Extremophiles--Cyanobacterial Diversity in the Rock Pools of the Croatian Adria. MICROBIAL ECOLOGY 2015; 70:876-888. [PMID: 26048370 DOI: 10.1007/s00248-015-0637-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 05/29/2015] [Indexed: 06/04/2023]
Abstract
Hardly any molecular studies have been done on euendoliths of marine coastal environments, especially along the supratidal ranges of carbonate coasts. In our study, we provide a comparative sequence analysis using 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene combined with extensive microscopy of the endolithic community from rock pools of the Croatian Adria. Molecular diversity indices and richness estimates showed high level of diversity, particularly in high-salinity samples. The most common cyanobacteria belong to the order Pleurocapsales, similar to observations on limestone coasts in other parts of the world. Using single-cell amplification sequences of Hormathonema spp., Hyella caespitosa, and Kyrtuthrix dalmatica was for the first time introduced to the public GenBank.Microscopic investigations did not show qualitative variances in diversity among sites with different salinity but clear differences in prevalent organisms from similar environments suggesting that most of them are adapted to inhabit extreme, marine endolithic habitats and that similar species inhabit geographically separated but ecologically similar environments. This is a remarkable concordance rather seldom seen in molecular community studies in support of the hypothesis that endolithic ecosystems are seeded from a global meta-community.The relative diversity of the community is greater than those described from harsh endolithic habitats of cold and hot deserts. The maximum likelihood phylogenetic tree consisting of 166 operational taxonomic units (OTUs) at 96 % sequence similarity revealed 11 distinct clusters. Three clusters contained only epilithic or endolithic taxa, and five clusters contained mixed epilithic and endolithic taxa. Organisms clustered according to their taxonomic affiliations and not to their preferences to salt concentrations.
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Affiliation(s)
- Maria Brandes
- IBU, Plants Biodiversity and Evolution, CvO University of Oldenburg, D-26111, Oldenburg, Germany
| | - Dirk C Albach
- IBU, Plants Biodiversity and Evolution, CvO University of Oldenburg, D-26111, Oldenburg, Germany
| | - Janina C Vogt
- IBU, Plants Biodiversity and Evolution, CvO University of Oldenburg, D-26111, Oldenburg, Germany
| | - Eike Mayland-Quellhorst
- IBU, Plants Biodiversity and Evolution, CvO University of Oldenburg, D-26111, Oldenburg, Germany
| | - Glenda Mendieta-Leiva
- IBU, Functional Ecology of Plants, University of Oldenburg, D-26111, Oldenburg, Germany
| | - Stjepko Golubic
- Biological Science Center, Boston University, 5 Cummington Street, Boston, MA, 02215, USA
| | - Katarzyna A Palinska
- IBU, Plants Biodiversity and Evolution, CvO University of Oldenburg, D-26111, Oldenburg, Germany.
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28
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Antunes A, Alam I, Simões MF, Daniels C, Ferreira AJS, Siam R, El-Dorry H, Bajic VB. First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:304-9. [PMID: 26529193 PMCID: PMC4678784 DOI: 10.1016/j.gpb.2015.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/09/2015] [Accepted: 06/29/2015] [Indexed: 12/11/2022]
Abstract
The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies.
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Affiliation(s)
- André Antunes
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Intikhab Alam
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Marta Filipa Simões
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Camille Daniels
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Ari J S Ferreira
- Biology Department, American University in Cairo, New Cairo 11835, Egypt
| | - Rania Siam
- Biology Department, American University in Cairo, New Cairo 11835, Egypt
| | - Hamza El-Dorry
- Biology Department, American University in Cairo, New Cairo 11835, Egypt
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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29
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Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea). PLoS One 2015; 10:e0140766. [PMID: 26485717 PMCID: PMC4613831 DOI: 10.1371/journal.pone.0140766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 09/30/2015] [Indexed: 02/05/2023] Open
Abstract
In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.
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30
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Bernhard JM, Kormas K, Pachiadaki MG, Rocke E, Beaudoin DJ, Morrison C, Visscher PT, Cobban A, Starczak VR, Edgcomb VP. Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments. Front Microbiol 2014; 5:605. [PMID: 25452749 PMCID: PMC4233946 DOI: 10.3389/fmicb.2014.00605] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/24/2014] [Indexed: 11/24/2022] Open
Abstract
Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L’ Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.
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Affiliation(s)
- Joan M Bernhard
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly Volos, Greece
| | - Maria G Pachiadaki
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Emma Rocke
- Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong
| | - David J Beaudoin
- Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Colin Morrison
- Biology Department, University of Nevada Reno Reno, NV, USA
| | - Pieter T Visscher
- Department of Marine Sciences, University of Connecticut Groton, CT, USA
| | - Alec Cobban
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Victoria R Starczak
- Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
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31
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Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring. Extremophiles 2014; 19:1-15. [DOI: 10.1007/s00792-014-0703-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/532687] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The advent of molecular tools in microbial ecology paved the way to exploit the diversity of microbes in extreme environments. Here, we review these tools as applied in one of the most polyextreme habitats known on our planet, namely, deep hypersaline anoxic basins (DHABs), located at ca. 3000–3500 m depth in the Eastern Mediterranean Sea. Molecular gene signatures amplified from environmental DHAB samples identified a high degree of genetic novelty, as well as distinct communities in the DHABs. Canonical correspondence analyses provided strong evidence that salinity, ion composition, and anoxia were the strongest selection factors shaping protistan community structures, largely preventing cross-colonization among the individual basins. Thus, each investigated basin represents a unique habitat (“isolated islands of evolution”), making DHABs ideal model sites to test evolutionary hypotheses. Fluorescence in situ hybridization assays using specifically designed probes revealed that the obtained genetic signatures indeed originated from indigenous polyextremophiles. Electron microscopy imaging revealed unknown ciliates densely covered with prokaryote ectosymbionts, which may enable adaptations of eukaryotes to DHAB conditions. The research reviewed here significantly advanced our knowledge on polyextremophile eukaryotes, which are excellent models for a number of biological research areas, including ecology, diversity, biotechnology, evolutionary research, physiology, and astrobiology.
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Charvet S, Vincent WF, Lovejoy C. Effects of light and prey availability on Arctic freshwater protist communities examined by high-throughput DNA and RNA sequencing. FEMS Microbiol Ecol 2014; 88:550-64. [DOI: 10.1111/1574-6941.12324] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/22/2014] [Accepted: 03/06/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sophie Charvet
- Département de Biologie; Université Laval; Québec QC Canada
- Québec-Océan and Institut de Biologie Intégrative et des Systèmes (IBIS); Québec QC Canada
- Centre d'études nordiques (CEN); Québec QC Canada
| | - Warwick F. Vincent
- Département de Biologie; Université Laval; Québec QC Canada
- Centre d'études nordiques (CEN); Québec QC Canada
| | - Connie Lovejoy
- Département de Biologie; Université Laval; Québec QC Canada
- Québec-Océan and Institut de Biologie Intégrative et des Systèmes (IBIS); Québec QC Canada
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34
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Gulliver DM, Lowry GV, Gregory KB. CO2concentration and pH alters subsurface microbial ecology at reservoir temperature and pressure. RSC Adv 2014. [DOI: 10.1039/c4ra02139h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular ecology techniques are utilized to determine the impact of CO2concentrations on microbial communities under reservoir temperature and pressure simulating geological carbon sequestration.
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Affiliation(s)
- Djuna M. Gulliver
- Office of Research & Development
- National Energy Technology Laboratory
- Pittsburgh, USA
- Department of Civil and Environmental Engineering
- Carnegie Mellon University
| | - Gregory V. Lowry
- Office of Research & Development
- National Energy Technology Laboratory
- Pittsburgh, USA
- Department of Civil and Environmental Engineering
- Carnegie Mellon University
| | - Kelvin B. Gregory
- Office of Research & Development
- National Energy Technology Laboratory
- Pittsburgh, USA
- Department of Civil and Environmental Engineering
- Carnegie Mellon University
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Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. Environmental conditions influence eDNA persistence in aquatic systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:1819-27. [PMID: 24422450 DOI: 10.1021/es404734p] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.
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Affiliation(s)
- Matthew A Barnes
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame , Notre Dame, Indiana 46556, United States
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Wang Y, Lee OO, Yang JK, Li TG, Qian PY. Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea. PeerJ 2013; 1:e69. [PMID: 23646288 PMCID: PMC3642703 DOI: 10.7717/peerj.69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/26/2013] [Indexed: 11/20/2022] Open
Abstract
The Multiple Displacement Amplification (MDA) protocol is reported to introduce different artifacts into DNA samples with impurities. In this study, we report an artifactual effect of MDA with sediment DNA samples from a deep-sea brine basin in the Red Sea. In the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads over sizes of 50 to 220 bp. Gene fragments translocated from neighboring gene regions were identified in these reads. Occasionally, the translocation occurred between the gene fragments from different species. Reads containing these gene fragments could form a strong stem-loop structure. More than 60% of the artifactual reads could fit the structural models. MDA amplification is probably responsible for the massive generation of the artifactual reads with the secondary structure in the metagenomes. Possible sources of the translocations and structures are discussed.
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Affiliation(s)
- Yong Wang
- Division of Life Science, Hong Kong University of Science and Technology , Hong Kong SAR , China
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37
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Terrado R, Scarcella K, Thaler M, Vincent WF, Lovejoy C. Small phytoplankton in Arctic seas: vulnerability to climate change. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/14888386.2012.704839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Oren A. Life in Magnesium- and Calcium-Rich Hypersaline Environments: Salt Stress by Chaotropic Ions. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Charvet S, Vincent WF, Comeau A, Lovejoy C. Pyrosequencing analysis of the protist communities in a High Arctic meromictic lake: DNA preservation and change. Front Microbiol 2012; 3:422. [PMID: 23267353 PMCID: PMC3526917 DOI: 10.3389/fmicb.2012.00422] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/24/2012] [Indexed: 11/30/2022] Open
Abstract
High Arctic meromictic lakes are extreme environments characterized by cold temperatures, low nutrient inputs from their polar desert catchments and prolonged periods of low irradiance and darkness. These lakes are permanently stratified with an oxygenated freshwater layer (mixolimnion) overlying a saline, anoxic water column (monimolimnion). The physical and chemical properties of the deepest known lake of this type in the circumpolar Arctic, Lake A, on the far northern coast of Ellesmere Island, Canada, have been studied over the last 15 years, but little is known about the lake’s biological communities. We applied high-throughput sequencing of the V4 region of the 18S ribosomal RNA gene to investigate the protist communities down the water column at three sampling times: under the ice at the end of winter in 2008, during an unusual period of warming and ice-out the same year, and again under the ice in mid-summer 2009. Sequences of many protist taxa occurred throughout the water column at all sampling times, including in the deep anoxic layer where growth is highly unlikely. Furthermore, there were sequences for taxonomic groups including diatoms and marine taxa, which have never been observed in Lake A by microscopic analysis. However, the sequences of other taxa such as ciliates, chrysophytes, Cercozoa, and Telonema varied with depth, between years and during the transition to ice-free conditions. These seasonally active taxa in the surface waters of the lake are thus sensitive to depth and change with time. DNA from these taxa is superimposed upon background DNA from multiple internal and external sources that is preserved in the deep, cold, largely anoxic water column.
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Affiliation(s)
- Sophie Charvet
- Département de Biologie, Université Laval, Québec QC, Canada ; Québec-Océan, Québec QC, Canada
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Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters. Sci Rep 2012; 2:604. [PMID: 22930670 PMCID: PMC3428602 DOI: 10.1038/srep00604] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/09/2012] [Indexed: 11/25/2022] Open
Abstract
Meromictic lakes are useful biogeochemical models because of their stratified chemical gradients and separation of redox reactions down the water column. Perennially ice-covered meromictic lakes are particularly stable, with long term constancy in their density profiles. Here we sampled Lake A, a deep meromictic lake at latitude 83°N in High Arctic Canada. Sampling was before (May) and after (August) an unusual ice-out event during the warm 2008 summer. We determined the bacterial and archaeal community composition by high-throughput 16S rRNA gene tag-pyrosequencing. Both prokaryote communities were stratified by depth and the Bacteria differed between dates, indicating locally driven selection processes. We matched taxa to known taxon-specific biogeochemical functions and found a close correspondence between the depth of functional specialists and chemical gradients. These results indicate a rich microbial diversity despite the extreme location, with pronounced vertical structure in taxonomic and potential functional composition, and with community shifts during ice-out.
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Savichtcheva O, Debroas D, Kurmayer R, Villar C, Jenny JP, Arnaud F, Perga ME, Domaizon I. Quantitative PCR enumeration of total/toxic Planktothrix rubescens and total cyanobacteria in preserved DNA isolated from lake sediments. Appl Environ Microbiol 2011; 77:8744-53. [PMID: 21984244 PMCID: PMC3233095 DOI: 10.1128/aem.06106-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/29/2011] [Indexed: 11/20/2022] Open
Abstract
The variability of spatial distribution and the determinism of cyanobacterial blooms, as well as their impact at the lake scale, are still not understood, partly due to the lack of long-term climatic and environmental monitoring data. The paucity of these data can be alleviated by the use of proxy data from high-resolution sampling of sediments. Coupling paleolimnological and molecular tools and using biomarkers such as preserved DNA are promising approaches, although they have not been performed often enough so far. In our study, a quantitative PCR (qPCR) technique was applied to enumerate total cyanobacterial and total and toxic Planktothrix communities in preserved DNA derived from sediments of three lakes located in the French Alps (Lake Geneva, Lake Bourget, and Lake Annecy), containing a wide range of cyanobacterial species. Preserved DNA from lake sediments was analyzed to assess its quality, quantity, and integrity, with further application for qPCR. We applied the qPCR assay to enumerate the total cyanobacterial community, and multiplex qPCR assays were applied to quantify total and microcystin-producing Planktothrix populations in a single reaction tube. These methods were optimized, calibrated, and applied to sediment samples, and the specificity and reproducibility of qPCR enumeration were tested. Accurate estimation of potential inhibition within sediment samples was performed to assess the sensitivity of such enumeration by qPCR. Some precautions needed for interpreting qPCR results in the context of paleolimnological approaches are discussed. We concluded that the qPCR assay can be used successfully for the analysis of lake sediments when DNA is well preserved in order to assess the presence and dominance of cyanobacterial and Planktothrix communities.
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Affiliation(s)
- Olga Savichtcheva
- INRA-UMR 42 CARRTEL, Centre Alpin de Recherche sur les Réseaux Trophiques des Ecosystèmes Limniques, 74203 Thonon-les-Bains Cedex, France
| | - Didier Debroas
- Université Blaise Pascal Clermont, UMR CNRS 6023, Laboratoire Microorganismes: Génome & Environnement, 24 Av. des Landais, BP 80026, 63171 Aubière Cedex, France
| | - Rainer Kurmayer
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Clement Villar
- INRA-UMR 42 CARRTEL, Centre Alpin de Recherche sur les Réseaux Trophiques des Ecosystèmes Limniques, 74203 Thonon-les-Bains Cedex, France
| | - Jean Philippe Jenny
- CNRS Université de Savoie, UMR 5204, EDYTEM, 73379 Le Bourget du Lac, France
| | - Fabien Arnaud
- CNRS Université de Savoie, UMR 5204, EDYTEM, 73379 Le Bourget du Lac, France
| | - Marie Elodie Perga
- INRA-UMR 42 CARRTEL, Centre Alpin de Recherche sur les Réseaux Trophiques des Ecosystèmes Limniques, 74203 Thonon-les-Bains Cedex, France
| | - Isabelle Domaizon
- INRA-UMR 42 CARRTEL, Centre Alpin de Recherche sur les Réseaux Trophiques des Ecosystèmes Limniques, 74203 Thonon-les-Bains Cedex, France
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Antunes A, Ngugi DK, Stingl U. Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:416-433. [PMID: 23761304 DOI: 10.1111/j.1758-2229.2011.00264.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Red Sea harbours approximately 25 deep-sea anoxic brine pools. They constitute extremely unique and complex habitats with the conjugation of several extreme physicochemical parameters rendering them some of the most inhospitable environments on Earth. After 50 years of research mostly driven by chemists, geophysicists and geologists, the microbiology of the brines has been receiving increased interest in the last decade. Recent molecular and cultivation-based studies have provided us with a first glimpse on the enormous biodiversity of the local microbial communities, the identification of several new taxonomic groups, and the isolation of novel extremophiles that thrive in these environments. This review presents a general overview of these unusual biotopes and compares them with other similar environments in the Mediterranean Sea and the Gulf of Mexico, with a focus on their microbial ecology.
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Affiliation(s)
- André Antunes
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Rhodes ME, Spear JR, Oren A, House CH. Differences in lateral gene transfer in hypersaline versus thermal environments. BMC Evol Biol 2011; 11:199. [PMID: 21740576 PMCID: PMC3236060 DOI: 10.1186/1471-2148-11-199] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 07/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. RESULTS We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. CONCLUSIONS Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.
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Affiliation(s)
- Matthew E Rhodes
- Penn State Astrobiology Research Center and Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA.
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