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Llorenç-Vicedo A, Lluesma Gomez M, Zeising O, Kleiner T, Freitag J, Martinez-Hernandez F, Wilhelms F, Martinez-Garcia M. New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves. mSphere 2024; 9:e0007324. [PMID: 38666797 PMCID: PMC11237435 DOI: 10.1128/msphere.00073-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 05/30/2024] Open
Abstract
The signs of climate change are undeniable, and the impact of these changes on ecosystem function heavily depends on the response of microbes that underpin the food web. Antarctic ice shelf is a massive mass of floating ice that extends from the continent into the ocean, exerting a profound influence on global carbon cycles. Beneath Antarctic ice shelves, marine ice stores valuable genetic information, where marine microbial communities before the industrial revolution are archived. Here, in this proof-of-concept, by employing a combination of single-cell technologiesand metagenomics, we have been able to sequence frozen microbial DNA (≈300 years old) stored in the marine ice core B15 collected from the Filchnner-Ronne Ice Shelf. Metagenomic data indicated that Proteobacteria and Thaumarchaeota (e.g., Nitrosopumilus spp.), followed by Actinobacteria (e.g., Actinomarinales), were abundant. Remarkably, our data allow us to "travel to the past" and calibrate genomic and genetic evolutionary changes for ecologically relevant microbes and functions, such as Nitrosopumilus spp., preserved in the marine ice (≈300 years old) with those collected recently in seawater under an ice shelf (year 2017). The evolutionary divergence for the ammonia monooxygenase gene amoA involved in chemolithoautotrophy was about 0.88 amino acid and 2.8 nucleotide substitution rate per 100 sites in a century, while the accumulated rate of genomic SNPs was 2,467 per 1 Mb of genome and 100 years. Whether these evolutionary changes remained constant over the last 300 years or accelerated during post-industrial periods remains an open question that will be further elucidated. IMPORTANCE Several efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic ice shelves before the industrial revolution. This potentially allows us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core data sets across various periods and sites. Such a data set would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.
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Affiliation(s)
- Aitana Llorenç-Vicedo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Carretera San Vicente del Raspeig, Alicante, Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Carretera San Vicente del Raspeig, Alicante, Spain
| | - Ole Zeising
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Thomas Kleiner
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Johannes Freitag
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Francisco Martinez-Hernandez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
| | - Frank Wilhelms
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Carretera San Vicente del Raspeig, Alicante, Spain
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2
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Claveau L, Hudson N, Jeffrey P, Hassard F. To gate or not to gate: Revisiting drinking water microbial assessment through flow cytometry fingerprinting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169138. [PMID: 38070556 DOI: 10.1016/j.scitotenv.2023.169138] [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: 10/09/2023] [Revised: 11/20/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Flow cytometry has been utilized for over a decade as a rapid and reproducible approach to assessing microbial quality of drinking water. However, the need for specialized expertise in gating-a fundamental strategy for distinguishing cell populations-introduces the potential for human error and obstructs the standardization of methods. This work conducts a comprehensive analysis of various gating approaches applied to flow cytometric scatter plots, using a dataset spanning a year. A sensitivity analysis is carried out to examine the impact of different gating strategies on final cell count results. The findings show that dynamic gating, which requires user intervention, is essential for the analysis of highly variable raw waters and distributed water. In contrast, static gating proved suitable for more stable water sources, interstage sample locations, and water presenting a particularly low cell count. Our conclusions suggest that cell count analysis should be supplemented with fluorescence fingerprinting to gain a more complete understanding of the variability in microbial populations within drinking water supplies. Establishing dynamic baselines for each water type in FCM monitoring studies is essential for choosing the correct gating strategy. FCM fingerprinting offers a dynamic approach to quantify treatment processes, enabling options for much better monitoring and control. This study offers new insights into the vagaries of various flow cytometry gating strategies, thereby substantially contributing to best practices in the water industry. The findings foster more efficient and reliable water analysis, improving of standardizing methods in microbial water quality assessment using FCM.
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Affiliation(s)
- L Claveau
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - N Hudson
- South East Water, Rocfort Road, Snodland, Kent ME6 5AH, UK
| | - P Jeffrey
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - F Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK.
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3
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Shen L, Zhang Z, Wang R, Wu S, Wang Y, Fu S. Metatranscriptomic data mining together with microfluidic card uncovered the potential pathogens and seasonal RNA viral ecology in a drinking water source. J Appl Microbiol 2024; 135:lxad310. [PMID: 38130237 DOI: 10.1093/jambio/lxad310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
AIMS Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources. METHODS AND RESULTS We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus, and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV, and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens, including Acinetobacter johnsonii and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV, and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126, and 457 types of viruses were identified in spring, summer, autumn, and winter, respectively. The viromes were dominated by the Pisuviricota phylum, including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae, and Picobirnaviridae families. Further phylogenetic analyses of RNA (Ribonucleic Acid)-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens, including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified. CONCLUSIONS Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.
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Affiliation(s)
- Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Shuang Wu
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yongjie Wang
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai 200093, China
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
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4
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Mettler MK, Goemann HM, Mueller RC, Vanegas OA, Lopez G, Singh N, Venkateswaran K, Peyton BM. Development of Martian saline seep models and their implications for planetary protection. Biofilm 2023; 5:100127. [PMID: 37252227 PMCID: PMC10209689 DOI: 10.1016/j.bioflm.2023.100127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/04/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
While life on Mars has not been found, Earth-based microorganisms may contaminate the Red Planet during rover expeditions and human exploration. Due to the survival advantages conferred by the biofilm morphology to microorganisms, such as resistance to UV and osmotic stress, biofilms are particularly concerning from a planetary protection perspective. Modeling and data from the NASA Phoenix mission indicate that temporary liquid water might exist on Mars in the form of high salinity brines. These brines could provide colonization opportunities for terrestrial microorganisms brought by spacecraft or humans. To begin testing for potential establishment of microbes, results are presented from a simplified laboratory model of a Martian saline seep inoculated with sediment from Hailstone Basin, a terrestrial saline seep in Montana (USA). The seep was modeled as a sand-packed drip flow reactor at room temperature fed media with either 1 M MgSO4 or 1 M NaCl. Biofilms were established within the first sampling point of each experiment. Endpoint 16S rRNA gene community analysis showed significant selection of halophilic microorganisms by the media. Additionally, we detected 16S rRNA gene sequences highly similar to microorganisms previously detected in two spacecraft assembly cleanrooms. These experimental models provide an important foundation for identifying microbes that could hitch-hike on spacecraft and may be able to colonize Martian saline seeps. Future model optimization will be vital to informing cleanroom sterilization procedures.
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Affiliation(s)
- Madelyn K. Mettler
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Hannah M. Goemann
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- USDA Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | | | | | - Nitin Singh
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Brent M. Peyton
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
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Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis. mSystems 2023; 8:e0093122. [PMID: 36722950 PMCID: PMC9948707 DOI: 10.1128/msystems.00931-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their "one-to-many" correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics. IMPORTANCE There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult. In this study, we examined viral infection in abundant prokaryotes by monitoring the monthly dynamics of prokaryotic and viral communities at a eutrophic coastal site, Osaka Bay. We compared the community dynamics of viruses with those of their putative hosts based on genome-based in silico host prediction. We observed frequent cooccurrence among the predicted virus-host pairs, suggesting that viral infection is prevalent in abundant prokaryotes regardless of their taxa or temporal dynamics. This likely indicates that frequent lysis of the abundant prokaryotes via viral infection has a considerable contribution to the biogeochemical cycling and maintenance of prokaryotic community diversity.
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6
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Eissler Y, Castillo-Reyes A, Dorador C, Cornejo-D'Ottone M, Celis-Plá PSM, Aguilar P, Molina V. Virus-to-prokaryote ratio in the Salar de Huasco and different ecosystems of the Southern hemisphere and its relationship with physicochemical and biological parameters. Front Microbiol 2022; 13:938066. [PMID: 36060762 PMCID: PMC9434117 DOI: 10.3389/fmicb.2022.938066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
The virus-to-prokaryote ratio (VPR) has been used in many ecosystems to study the relationship between viruses and their hosts. While high VPR values indicate a high rate of prokaryotes' cell lysis, low values are interpreted as a decrease in or absence of viral activity. Salar de Huasco is a high-altitude wetland characterized by a rich microbial diversity associated with aquatic sites like springs, ponds, streams and a lagoon with variable physicochemical conditions. Samples from two ponds, Poza Rosada (PR) and Poza Verde (PV), were analyzed by epifluorescence microscopy to determine variability of viral and prokaryotic abundance and to calculate the VPR in a dry season. In addition, to put Salar de Huasco results into perspective, a compilation of research articles on viral and prokaryotic abundance, VPR, and metadata from various Southern hemisphere ecosystems was revised. The ecosystems were grouped into six categories: high-altitude wetlands, Pacific, Atlantic, Indian, and Southern Oceans and Antarctic lakes. Salar de Huasco ponds recorded similar VPR values (an average of 7.4 and 1.7 at PR and PV, respectively), ranging from 3.22 to 15.99 in PR. The VPR variability was associated with VA and chlorophyll a, when considering all data available for this ecosystem. In general, high-altitude wetlands recorded the highest VPR average (53.22 ± 95.09), followed by the Oceans, Southern (21.91 ± 25.72), Atlantic (19.57 ± 15.77) and Indian (13.43 ± 16.12), then Antarctic lakes (11.37 ± 15.82) and the Pacific Ocean (6.34 ± 3.79). Physicochemical variables, i.e., temperature, conductivity, nutrients (nitrate, ammonium, and phosphate) and chlorophyll a as a biological variable, were found to drive the VPR in the ecosystems analyzed. Thus, the viral activity in the Wetland followed similar trends of previous reports based on larger sets of metadata analyses. In total, this study highlights the importance of including viruses as a biological variable to study microbial temporal dynamics in wetlands considering their crucial role in the carbon budgets of these understudied ecosystems in the southern hemisphere.
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Affiliation(s)
- Yoanna Eissler
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- *Correspondence: Yoanna Eissler
| | - Alonso Castillo-Reyes
- Escuela de Biología Marina, Facultad de Ciencias del Mar y de Recursos Naturales, Universidad de Valparaíso, Viña del Mar, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Marcela Cornejo-D'Ottone
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Paula S. M. Celis-Plá
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar, Chile
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Polette Aguilar
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Verónica Molina
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile
- Verónica Molina
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Burford MA, Franklin H, Faggotter SJ, Chuang A, Hayton JB, Carroll AR. Effects of terrestrial dissolved organic matter on a bloom of the toxic cyanobacteria, Raphidiopsis raciborskii. HARMFUL ALGAE 2022; 117:102269. [PMID: 35944957 DOI: 10.1016/j.hal.2022.102269] [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: 02/24/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
The concentration of coloured terrestrial dissolved organic matter (tDOM) from vegetation appears to be increasing in lakes in some regions of the world, leading to the term brownification. The light attenuating effect of coloured tDOM on phytoplankton growth has been a major focus of attention, but the phytotoxic effects of tDOM, particularly on cyanobacterial blooms, are less well understood. This mesocosm study tested whether coloured tDOM, leached from the leaves of a Eucalyptus tree species, inhibited a naturally occurring bloom of the toxic cyanobacterium, Raphidiopsis raciborskii, in a reservoir over a 10 day period. The study found that tDOM leachate, measured as dissolved organic carbon (DOC), inhibited photosynthesis and growth of both R. raciborskii, as well as species present at lower densities, i.e. other cyanobacteria and diatoms. However, the effect was greater at higher tDOM input loads. The photosynthetic yield (Fv/Fm) of cyanobacteria decreased rapidly in treatments with 5.9 and 25 mg L-1 DOC addition, compared to the control (reservoir water with background DOC concentration of 6.85 ± 1.09 mg L-1). tDOM had no measurable effect in the 2 and 3.3 mg L-1 DOC addition treatments. By day 5, cell densities of cyanobacteria, including R. raciborskii, and diatoms, in treatments with 5.9 and 25 mg L-1 DOC addition were significantly lower than the control with no tDOM addition, and this effect continued throughout the experiment. This is despite the leachate addition increasing phosphate concentrations which counteracted the low background concentrations of phosphate. Light attenuation and dissolved oxygen (DO) levels were also affected by the tDOM addition, but were only significantly lower in the 25 mg L-1 DOC treatment compared with the control. DOC, dissolved organic nitrogen (DON) and dissolved organic phosphorus (DOP) concentrations all decreased in the tDOM addition treatments over the first 3 days, as the microbial cell densities increased. The components of the tDOM that decreased over time were determined by 1H NMR spectroscopy in the 25 mg L-1 DOC treatment. After 5 d, the relative concentrations of fatty acids, sugars and gallic acid decreased by around 60%, while concentrations of flavonoids and myo-inositol decreased by 45 and 35% respectively. This study suggests that phytotoxic compounds in tDOM can suppress cyanobacterial blooms, despite the increased nutrient inputs. This has implications for predicting the future likelihood of cyanobacterial blooms in lakes and reservoirs with climate-change driven changes in flow events, and other changes in the amount and types of vegetation cover. Revegetation of riparian zones, resulting in increased tDOM into waterways, may also be beneficial in reducing cyanobacterial blooms.
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Affiliation(s)
- M A Burford
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia; School of Environment and Science, Griffith University, Nathan, Queensland, Australia..
| | - H Franklin
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - S J Faggotter
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
| | - A Chuang
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - J B Hayton
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
| | - A R Carroll
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia.; Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
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8
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Liu L, Liang X, Li Z, Zhang M, Gao M. Detection of ATP in cancer cells with a label-free fluorescent aptasensor. Nanomedicine (Lond) 2022; 17:765-774. [PMID: 35642581 DOI: 10.2217/nnm-2021-0466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To develop a new detection technique for ATP in cancer cells using fluorescent biosensing. Materials & methods: This research presents a new label-free fluorescent aptasensor for ATP measurement that incorporates a DNA aptamer, SYBR Gold and single-walled carbon nanohorns. Results: The aptasensor showed selectivity toward ATP and a low limit of detection (37.6 nM). The linear detection range was 100-50,000 nM, and the fluorescence intensity and ATP concentration logarithm showed an excellent linear correlation (R2 = 0.9924). Conclusion: The developed aptasensor may be used to detect cellular ATP in cancer cells and could be employed for biological sample analysis. The benefits of the aptasensor, such as its simplicity, speed, cost-effectiveness, specificity and sensitivity, give it promising implications as a potentially adaptable sensing platform.
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Affiliation(s)
- Liying Liu
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xiuju Liang
- Department of Oncology, No. 960 Hospital, The People's Liberation Army, Jinan, 250031, China
| | - Zhaoming Li
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - MingZhi Zhang
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Ming Gao
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
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Maltseva M, Langlois MA. Flow Virometry for Characterizing the Size, Concentration, and Surface Antigens of Viruses. Curr Protoc 2022; 2:e368. [PMID: 35201679 DOI: 10.1002/cpz1.368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Application of flow cytometry principles for the analysis of viruses has been referred to as flow virometry (FVM). FVM is a multiparametric, high-throughput, and sensitive technique that allows viral particles to be detected, quantified, and characterized based on the biophysical properties of the virus and the expression of proteins on their surface. More specifically, by calibrating the flow cytometer with reference materials, it is possible to measure the concentration of intact viral particles in a sample, the abundance of a target antigen on the surface of the virus, and the relative diameter of the virus. Here, we describe a comprehensive overview of procedures used to stain, detect, and quantify viral and host-derived proteins located on the surface of retroviruses. These outlined techniques can be applied for the rapid phenotypic characterization of retroviruses, other enveloped viruses, and generally most viruses at the single-particle level through the direct staining of viruses collected from the supernatant of infected cells, without the need for enrichment or purification. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Virus production Basic Protocol 2: Instrument setup, standardization, and quality control for fluorescence quantification Basic Protocol 3: Flow virometry analysis Basic Protocol 4: Viral surface antigen staining and fluorescence quantification Support Protocol: Determination of the optimal antibody concentration for virus staining Basic Protocol 5: Gain configuration optimization.
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Affiliation(s)
- Mariam Maltseva
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,uOttawa Centre for Infection, Immunity and Inflammation, Ottawa, Ontario, Canada
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Bhat T, Cao A, Yin J. Virus-like Particles: Measures and Biological Functions. Viruses 2022; 14:383. [PMID: 35215979 PMCID: PMC8877645 DOI: 10.3390/v14020383] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases.
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Affiliation(s)
| | | | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA; (T.B.); (A.C.)
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White K, Yu JH, Eraclio G, Dal Bello F, Nauta A, Mahony J, van Sinderen D. Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods. MICROBIOME RESEARCH REPORTS 2022; 1:3. [PMID: 38089066 PMCID: PMC10714293 DOI: 10.20517/mrr.2021.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 02/19/2024]
Abstract
Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Jun-Hyeok Yu
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | | | | | - Arjen Nauta
- FrieslandCampina, Amersfoort 3800 BN, The Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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12
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Induction and Genomic Analysis of a Lysogenic Phage of Hafnia paralvei. Curr Microbiol 2022; 79:50. [PMID: 34982243 DOI: 10.1007/s00284-021-02698-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/25/2021] [Indexed: 11/03/2022]
Abstract
Hafnia paralvei is a bacterium that can cause zoonoses. No research has been reported on H. paralvei prophage. In this study, a Hafnia phage yong1 was induced from pathogenic H. paralvei LY-23 by mitomycin C. The phage showed a Myoviridae-like morphology having a hexagonal head of approximately 65 nm in diameter and a contractile tail of approximately 95 nm in length and 17 nm in width. Its genome was sequenced by using the Illumina Miseq platform. The complete genome of Hafnia phage yong1 is 43,329 bp with a G + C content of 47.65%. BLASTn analysis revealed that Hafnia phage yong1 had the highest sequence similarity with the predicted prophages of Enterobacter chengduensis strain WCHECl-C4 = WCHECh050004 recovered from a human blood sample and Escherichia coli strain L103-2 recovered from a goose farm in China. Hafnia phage yong1 contains a tRNA gene and 76 predicted open reading frames, 33 of which were annotated. Gene strings similar to the bacteriophage λ cro-cI-rexA-rexB operon conferring Imm and Rex to lysogenic cells were found in Hafnia phage yong1 genome. Hafnia phage yong1 is the first Myoviridae-like phage found to contain such contiguous genes. Hafnia phage yong1 formed an independent branch between two families, Chaseviridae and Drexlerviridae, in the Proteomic tree.
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Shamash M, Maurice CF. OnePetri: Accelerating Common Bacteriophage Petri Dish Assays with Computer Vision. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:224-231. [PMID: 36159886 PMCID: PMC9041512 DOI: 10.1089/phage.2021.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Introduction: Bacteriophage plaque enumeration is a critical step in a wide array of protocols. The current gold standard for plaque enumeration on Petri dishes is through manual counting. However, this approach is not only time-consuming and prone to human error but also limited to Petri dishes with countable number of plaques resulting in low throughput. Materials and Methods: We present OnePetri, a collection of trained machine learning models and open-source mobile application for the rapid enumeration of bacteriophage plaques on circular Petri dishes. Results: When compared against the current gold standard of manual counting, OnePetri was ∼30 × faster. Compared against other similar tools, OnePetri had lower relative error (∼13%) than Plaque Size Tool (PST) (∼86%) and CFU.AI (∼19%), while also having significantly reduced detection times over PST (1.7 × faster). Conclusions: The OnePetri application is a user-friendly platform that can rapidly enumerate phage plaques on circular Petri dishes with high precision and recall.
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Affiliation(s)
- Michael Shamash
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Corinne F. Maurice
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
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Nitrospina-like Bacteria Are Dominant Potential Mercury Methylators in Both the Oyashio and Kuroshio Regions of the Western North Pacific. Microbiol Spectr 2021; 9:e0083321. [PMID: 34494859 PMCID: PMC8557936 DOI: 10.1128/spectrum.00833-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Highly neurotoxic methylmercury (MeHg) accumulates in marine organisms, thereby negatively affecting human and environmental health. Recent studies have revealed that oceanic prokaryotes harboring the hgcAB gene pair are involved in Hg methylation. Presently, little is known about the distribution and phylogeny of these genes in distinct oceanic regions of the western North Pacific. In this study, we used metagenomics to survey the distribution of hgcAB genes in the seawater columns of the subarctic Oyashio region and the subtropical Kuroshio region. The hgcAB genes were detected in the MeHg-rich offshore mesopelagic layers of both the Oyashio region, which is a highly productive area in the western North Pacific, and the Kuroshio region, which has low productivity. Comparative analysis revealed that hgcAB genes belonging to the Nitrospina-like lineage were dominant in the MeHg-rich mesopelagic layers of both regions. These results indicate that Nitrospina-like bacteria are the dominant Hg methylators in the mesopelagic layers throughout the western North Pacific. IMPORTANCE MeHg is highly neurotoxic and accumulates in marine organisms. Thus, understanding MeHg production in seawater is critical for environmental and human health. Recent studies have shown that microorganisms harboring mercury-methylating genes (hgcA and hgcB) are involved in MeHg production in several marine environments. Knowing the distribution and phylogeny of hgcAB genes in seawater columns can facilitate assessment of microbial MeHg production in the ocean. We report that hgcAB genes affiliated with the microaerophilic Nitrospina lineage were detected in the MeHg-rich mesopelagic layers of two hydrologically distinct oceanic regions of the western North Pacific. This finding facilitates understanding of the microbial Hg methylation and accumulation in seawater columns of the western North Pacific.
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Turzynski V, Monsees I, Moraru C, Probst AJ. Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples. Viruses 2021; 13:2126. [PMID: 34834933 PMCID: PMC8622608 DOI: 10.3390/v13112126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.
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Affiliation(s)
- Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany;
| | - Alexander J. Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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16
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Bray RT, Jankowska K, Kulbat E, Łuczkiewicz A, Sokołowska A. Ultrafiltration Process in Disinfection and Advanced Treatment of Tertiary Treated Wastewater. MEMBRANES 2021; 11:membranes11030221. [PMID: 33804673 PMCID: PMC8003589 DOI: 10.3390/membranes11030221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/01/2021] [Accepted: 03/16/2021] [Indexed: 11/18/2022]
Abstract
The paper presents the results of research on the use of ultrafiltration, using membranes of 200 and 400 kDa separation, for disinfection of municipal treated wastewater. The research was conducted on a fractional technical scale using real municipal treated wastewater from two large wastewater treatment plants treating most of the wastewater over the one-million polycentric Gdańsk agglomeration (1.2 million inhabitants). UF 200 kDa and UF 400 kDa processes enabled further improvement of the physical and chemical parameters of treated wastewater. Total phosphorus (to below 0.2 mg/L–UF 200 kDa, 0.13 mg/L–UF 400 kDa) and turbid substances (to below 0.2 mg/L, both membranes) were removed in the highest degree. COD was reduced efficiently (to below 25.6 mgO2/L–UF 200 kDa, 26.8 mgO2/L–UF 400 kDa), while total nitrogen was removed to a small extent (to 7.12 mg/L–UF 200 kDa and 5.7 mg/L–UF 400 kDa. Based on the reduction of indicator bacteria; fecal coliforms including E. coli (FC) and fecal enterococci (FE) it was found that the ultrafiltration is an effective method of disinfection. Not much indicator bacterial were observed in the permeate after processes (UF 200 kDa; FC—5 CFU/L; FE—1 CFU/L and UF 400 kDa; FC—70 CFU/L; FE—10 CFU/L. However, microscopic analysis of prokaryotic cells and virus particles showed their presence after the application of both membrane types; TCN 3.0 × 102 cells/mL–UF 200 kDa, 5.0 × 103 cells/mL–UF 400 kDa, VP 1.0 × 105/mL. The presence of potentially pathogenic, highly infectious virus particles means that ultrafiltration cannot be considered a sufficient disinfection method for treated wastewater diverted for reuse or discharged from high load wastewater treatment plants to recreational areas. For full microbiological safety it would be advisable to apply an additional disinfection method (e.g., ozonation).
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17
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Heinrichs ME, De Corte D, Engelen B, Pan D. An Advanced Protocol for the Quantification of Marine Sediment Viruses via Flow Cytometry. Viruses 2021; 13:v13010102. [PMID: 33451082 PMCID: PMC7828538 DOI: 10.3390/v13010102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses are highly abundant, diverse, and active components of marine environments. Flow cytometry has helped to increase the understanding of their impact on shaping microbial communities and biogeochemical cycles in the pelagic zone. However, to date, flow cytometric quantification of sediment viruses is still hindered by interference from the sediment matrix. Here, we developed a protocol for the enumeration of marine sediment viruses by flow cytometry based on separation of viruses from sediment particles using a Nycodenz density gradient. Results indicated that there was sufficient removal of background interference to allow for flow cytometric quantification. Applying this new protocol to deep-sea and tidal-flat samples, viral abundances enumerated by flow cytometry correlated well (R2 = 0.899) with counts assessed by epifluorescence microscopy over several orders of magnitude from marine sediments of various compositions. Further optimization may be needed for sediments with low biomass or high organic content. Overall, the new protocol enables fast and accurate quantification of marine sediment viruses, and opens up the options for virus sorting, targeted viromics, and single-virus sequencing.
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Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany; (M.E.H.); (D.D.C.); (B.E.)
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany; (M.E.H.); (D.D.C.); (B.E.)
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany; (M.E.H.); (D.D.C.); (B.E.)
| | - Donald Pan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan
- Department of Ecology and Environmental Studies, The Water School, Florida Gulf Coast University, Fort Myers, FL 33913, USA
- Correspondence:
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18
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Lahrich S, Laghrib F, Farahi A, Bakasse M, Saqrane S, El Mhammedi MA. Review on the contamination of wastewater by COVID-19 virus: Impact and treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:142325. [PMID: 33182015 PMCID: PMC7481832 DOI: 10.1016/j.scitotenv.2020.142325] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 04/14/2023]
Abstract
Emerging viruses are a major public health problem. Most zoonotic pathogens originate in wildlife, including human immunodeficiency virus (HIV), influenza, Ebola, and coronavirus. Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a coronavirus called SARS-associated coronavirus (SARS-CoV). Viruses are charged colloidal particles that have the ability to adsorb on surfaces depending on pH. Their sorptive interaction with solid particles has important implications for their behavior in aquatic environments, soils, sewage sludge, and other solid materials and their removal or concentration by water treatment processes. Current state of knowledge on the potential of wastewater surveillance to understand the COVID-19 pandemic is reviewed. This study also identified wastewater irrigation systems with a higher risk of COVID-19 transmission. Emphasis was placed on methodologies for the detection and quantification of SARS-CoV-2 in wastewater.
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Affiliation(s)
- S Lahrich
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco
| | - F Laghrib
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco
| | - A Farahi
- Ibn Zohr University, Team of Catalysis and Environment, Faculty of Sciences, BP 8106 Cité Dakhla, Agadir, Morocco
| | - M Bakasse
- Chouaib Doukkali University, Faculty of Sciences, Laboratory of Organic Bioorganic Chemistry and Environment, El Jadida, Morocco
| | - S Saqrane
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco
| | - M A El Mhammedi
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco.
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19
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Vishwakarma A, Lal R, Ramya M. Aptamer-based approaches for the detection of waterborne pathogens. Int Microbiol 2021; 24:125-140. [PMID: 33404933 DOI: 10.1007/s10123-020-00154-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.
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Affiliation(s)
- Archana Vishwakarma
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Roshni Lal
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Mohandass Ramya
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India.
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20
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Ali P, Chen F, Hassan F, Sosa A, Khan S, Badshah M, Shah AA. Bacterial community characterization of Batura Glacier in the Karakoram Range of Pakistan. Int Microbiol 2021; 24:183-196. [PMID: 33404934 DOI: 10.1007/s10123-020-00153-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022]
Abstract
High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4-35 °C), pH (5-12), and salinity (1-6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.
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Affiliation(s)
- Pervaiz Ali
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.,Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Fariha Hassan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ana Sosa
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Samiullah Khan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Malik Badshah
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aamer Ali Shah
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Trombetta T, Vidussi F, Roques C, Scotti M, Mostajir B. Marine Microbial Food Web Networks During Phytoplankton Bloom and Non-bloom Periods: Warming Favors Smaller Organism Interactions and Intensifies Trophic Cascade. Front Microbiol 2020; 11:502336. [PMID: 33193116 PMCID: PMC7644461 DOI: 10.3389/fmicb.2020.502336] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/02/2020] [Indexed: 01/17/2023] Open
Abstract
Microbial food web organisms are at the base of the functioning of pelagic ecosystems and support the whole marine food web. They are very reactive to environmental changes and their interactions are modified in response to different productive periods such as phytoplankton bloom and non-bloom as well as contrasted climatic years. To study ecological associations, identify potential interactions between microorganisms and study the structure of the microbial food web in coastal waters, a weekly monitoring was carried out in the Thau Lagoon on the French Mediterranean coast. The monitoring lasted from winter to late spring during two contrasting climatic years, a typical Mediterranean (2015) and a year with an extreme warm winter (2016). Correlation networks comprising 110 groups/taxa/species were constructed to characterize potential possible interactions between the microorganisms during bloom and non-bloom periods. Complex correlation networks during the bloom and dominated by negative intraguild correlations and positive correlations of phytoplankton with bacteria. Such pattern can be interpreted as a dominance of competition and mutualism. In contrast, correlation networks during the non-bloom period were less complex and mostly dominated by tintinnids associations with bacteria mostly referring to potential feeding on bacteria, which suggests a shift of biomass transfer from phytoplankton-dominated food webs during bloom to more bacterioplankton-based food webs during non-bloom. Inter-annual climatic conditions significantly modified the structure of microbial food webs. The warmer year favored relationships among smaller group/taxa/species at the expense of large phytoplankton and ciliates, possibly due to an intensification of the trophic cascade with a potential shift in energy circulation through microbial food web. Our study compares a typical Mediterranean spring with another mimicking the prospected intensification of global warming; if such consideration holds true, the dominance of future coastal marine ecosystems will be shifted from the highly productive herbivorous food web to the less productive microbial food web.
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Affiliation(s)
- Thomas Trombetta
- Marine Biodiversity, Exploitation and Conservation, Centre National de la Recherche Scientifique, Institut Français de Recherche pour l'Exploitation de la Mer, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Francesca Vidussi
- Marine Biodiversity, Exploitation and Conservation, Centre National de la Recherche Scientifique, Institut Français de Recherche pour l'Exploitation de la Mer, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Cécile Roques
- Marine Biodiversity, Exploitation and Conservation, Centre National de la Recherche Scientifique, Institut Français de Recherche pour l'Exploitation de la Mer, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Marco Scotti
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Behzad Mostajir
- Marine Biodiversity, Exploitation and Conservation, Centre National de la Recherche Scientifique, Institut Français de Recherche pour l'Exploitation de la Mer, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
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Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile. Microorganisms 2020; 8:microorganisms8071077. [PMID: 32698305 PMCID: PMC7409041 DOI: 10.3390/microorganisms8071077] [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: 06/24/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.
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Tada Y, Marumoto K, Takeuchi A. Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea. Front Microbiol 2020; 11:1369. [PMID: 32719662 PMCID: PMC7347909 DOI: 10.3389/fmicb.2020.01369] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
In natural environments, the production of neurotoxic and bioaccumulative methylmercury (MeHg) is mediated by microorganisms carrying the genes hgcA and hgcB. However, the contribution of these microorganisms to mercury (Hg) methylation or MeHg accumulation in the ocean is poorly understood. Here we determined the total Hg (THg) and MeHg concentrations in seawater samples and conducted a metagenomic survey of the hgcAB genes and functional modules involved in metabolic pathways in the East China Sea (ECS). In the metagenomic analyses, we used paired-end reads and assembled contigs for hgcAB enumeration and phylogenetic analyses in the seawater column. To evaluate the relative abundance of hgcAB in the metagenomic data, we estimated the abundance of recA (single-copy gene of bacteria) as well and then compared them. Moreover, the profiles of prokaryotic community composition were analyzed by 16S rRNA gene (V4 region) deep-sequencing. In the mesopelagic layers, the hgcA sequences were detected, and there was a positive correlation between hgcA abundance relative to the recA and MeHg concentrations. Thus, the quantification of the hgcA sequences could provide valuable information to evaluate the potential environments of microbial MeHg accumulation in the seawater column. A phylogenetic analysis using the assembled contigs revealed that all of the hgcA sequences in the mesopelagic layers were affiliated with Nitrospina-like sequences. The 16S rRNA gene analysis revealed that Nitrospinae were abundant in the mesopelagic layers. Although the lineages of Deltaproteobacteria, Firmicutes, and Spirochaetes were detected in the seawater column, their hgcAB sequences were not detected in our metagenomes, despite the fact that they are closely related to previously identified Hg methylators. The metabolic pathway analysis revealed that the modules related to sulfur and methane metabolism were prominent in the mesopelagic layers. However, no hgcA sequences affiliated with sulfate-reducing bacteria (SRB) or methanogens were detected in these layers, suggesting that these bacteria could not be strongly involved in the Hg accumulation in the seawater column. Our results indicate that Nitrospina-like bacteria with hgcAB genes could play a critical role in microbial Hg accumulation in the oxygenated mesopelagic layers of the ECS.
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Affiliation(s)
- Yuya Tada
- Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan
| | - Kohji Marumoto
- Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan
| | - Akinori Takeuchi
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Ibaraki, Japan
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Wei M, Xu K. New Insights Into the Virus-to-Prokaryote Ratio (VPR) in Marine Sediments. Front Microbiol 2020; 11:1102. [PMID: 32547525 PMCID: PMC7272709 DOI: 10.3389/fmicb.2020.01102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/04/2020] [Indexed: 11/13/2022] Open
Abstract
The virus-to-prokaryote ratio (VPR), which reflects the numerical dominance of viruses over their hosts, has been proposed as a proxy for assessing the relationship between viruses and prokaryotes. Previous studies showed that VPR values fluctuate over six orders of magnitude within and across various benthic ecosystems, with an average value of approximately 10. We hypothesize that this high VPR value is largely due to the inaccurate enumeration of viruses and prokaryotes (e.g., centrifugation treatments may lead to a three-fourfold overestimation of VPR). In this study, we evaluated the impact of processing methods on the determination of VPR values. Using an optimized procedure, we investigated the marine benthic VPR at 31 sites, from intertidal zones through continental shelves to abyssal plains, and assessed its monthly variation in two contrasting intertidal habitats (muddy-sand and sandy). By compiling 135 VPR data points of surface sediments from 37 publications, we reveal the effect of centrifugation on published VPR values and describe the spatial distribution of VPR values on a larger scale based on reliable data. The results showed that the commonly used centrifugation method may result in an overestimation of VPR values that are approximately one order of magnitude higher than those obtained using the dilution method, while other processing steps had a limited impact on the VPR. Our analysis indicates that the benthic VPR value is low and less varied across temporal and spatial scales, fluctuating mostly within 10, and the average VPR is approximately 2 in both marine and freshwater habitats. An insignificant seasonal pattern in the VPR was observed in the intertidal zone, with lower VPR values occurring at high temperatures. The VPR spatial distribution was primarily associated with sediment phaeophytin a, suggesting that the trophic conditions of the upper water column and the sedimentation of organic matter to the bottom are the key factors affecting VPR values. The mean VPR in benthic habitats is approximately one order of magnitude lower and much less varied than that observed in pelagic habitats, indicating that the virus-host relationship and the ecological function of viruses in the two ecosystems may be very different.
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Affiliation(s)
- Miao Wei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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25
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Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage. mSystems 2020; 5:5/2/e00586-19. [PMID: 32234774 PMCID: PMC7112961 DOI: 10.1128/msystems.00586-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prochlorococcus cyanobacteria grow in diurnal rhythms driven by diel cycles. Their ecology depends on light, nutrients, and top-down mortality processes, including lysis by viruses. Cyanophage, viruses that infect cyanobacteria, are also impacted by light. For example, the extracellular viability and intracellular infection kinetics of some cyanophage vary between light and dark conditions. Nonetheless, it remains unclear whether light-dependent viral life history traits scale up to influence population-level dynamics. Here, we examined the impact of diel forcing on both cellular- and population-scale dynamics in multiple Prochlorococcus-phage systems. To do so, we developed a light-driven population model, including both cellular growth and viral infection dynamics. We then tested the model against measurements of experimental infection dynamics with diel forcing to examine the extent to which population level changes in both viral and host abundances could be explained by light-dependent life history traits. Model-data integration reveals that light-dependent adsorption can improve fits to population dynamics for some virus-host pairs. However, light-dependent variation alone does not fully explain realized host and virus population dynamics. Instead, we show evidence consistent with lysis saturation at relatively high virus-to-cell ratios. Altogether, our study represents a quantitative approach to integrate mechanistic models to reconcile Prochlorococcus-virus dynamics spanning cellular-to-population scales.IMPORTANCE The cyanobacterium Prochlorococcus is an essential member of global ocean ecosystems. Light rhythms drive Prochlorococcus photosynthesis, ecology, and interactions with potentially lethal viruses. At present, the impact of light on Prochlorococcus-virus interactions is not well understood. Here, we analyzed Prochlorococcus and virus population dynamics with a light-driven population model and compared our results with experimental data. Our approach revealed that light profoundly drives both cellular- and population-level dynamics for some host-virus systems. However, we also found that additional mechanisms, including lysis saturation, are required to explain observed host-virus dynamics at the population scale. This study provides the basis for future work to understand the intertwined fates of Prochlorococcus and associated viruses in the surface ocean.
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26
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Mayr MJ, Besemer K, Sieczko A, Demeter K, Peduzzi P. Bacterial community composition and function along spatiotemporal connectivity gradients in the Danube floodplain (Vienna, Austria). AQUATIC SCIENCES 2020; 82:28. [PMID: 32165802 PMCID: PMC7045780 DOI: 10.1007/s00027-020-0700-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 05/25/2023]
Abstract
It is well recognized that river-floodplain systems contribute significantly to riverine ecosystem metabolism, and that bacteria are key players in the aquatic organic carbon cycle, but surprisingly few studies have linked bacterial community composition (BCC), function and carbon quality in these hydrologically highly dynamic habitats. We investigated aquatic BCC and extracellular enzymatic activity (EEA) related to dissolved organic carbon quality and algae composition, including the impact of a major flood event in one of the last remaining European semi-natural floodplain-systems. We found that surface connectivity of floodplain pools homogenizes BCC and EEA, whereas low connectivity led to increased BCC and EEA heterogeneity, supported by their relationship to electrical conductivity, an excellent indicator for surface connection strength. Hydrogeochemical parameters best explained variation of both BCC and EEA, while the algal community and chromophoric DOM properties explained only minor fractions of BCC variation. We conclude that intermittent surface connectivity and especially permanent isolation of floodplain pools from the main river channel may severely alter BCC and EEA, with potential consequences for nutrient cycling, ecological services and greenhouse gas emissions. Disentangling microbial structure-function coupling is therefore crucial, if we are to understand and predict the consequences of human alterations on these dynamic systems.
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Affiliation(s)
- Magdalena J. Mayr
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Katharina Besemer
- WasserCluster Lunz, Dr. Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
| | - Anna Sieczko
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
- Department of Thematic Studies–Environmental Change, Linköping University, Tema M, Campus Valla, 581 83 Linköping, Sweden
| | - Katalin Demeter
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Peter Peduzzi
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
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27
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Liu X, Tang K, Zhang D, Li Y, Liu Z, Yao J, Wood TK, Wang X. Symbiosis of a P2‐family phage and deep‐sea
Shewanella putrefaciens. Environ Microbiol 2019; 21:4212-4232. [DOI: 10.1111/1462-2920.14781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Dali Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention Guangdong Provincial Institute of Public Health Guangzhou 511430 China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Thomas K. Wood
- Department of Chemical Engineering Pennsylvania State University University Park PA 16802‐4400 USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
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28
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Abstract
To adapt to the daily light–dark cycle, diurnal rhythms are used by the photosynthetic cyanobacteria Prochlorococcus and Synechococcus, which are the most abundant photosynthetic organisms on earth. Field studies revealed that cyanobacterial virus (cyanophage) populations in the oceans showed transcriptional rhythms. To explore the underlying mechanism, we used cyanophage laboratory cultures to find that some showed adsorption rhythms and all showed transcriptional rhythms. We discovered that the cyanophage transcriptional rhythm is partially caused by the photosynthetic activity of host cells, explaining transcriptional rhythms of field cyanophage populations. Our study shows that cultured viruses have diurnal infection rhythms which are critical for understanding how light–dark cycles shape the interaction of cyanophages and their hosts in the oceans. As an adaptation to the daily light–dark (diel) cycle, cyanobacteria exhibit diurnal rhythms of gene expression and cell cycle. The light–dark cycle also affects the life cycle of viruses (cyanophages) that infect the unicellular picocyanobacteria Prochlorococcus and Synechococcus, which are the major primary producers in the oceans. For example, the adsorption of some cyanophages to the host cells depends on light, and the burst sizes of cyanophages are positively correlated to the length of light exposure during infection. Recent metatranscriptomic studies revealed transcriptional rhythms of field cyanophage populations. However, the underlying mechanism remains to be determined, as cyanophage laboratory cultures have not been shown to exhibit diurnal transcriptional rhythms. Here, we studied variation in infection patterns and gene expression of Prochlorococcus phages in laboratory culture conditions as a function of light. We found three distinct diel-dependent life history traits in dark conditions (diel traits): no adsorption (cyanophage P-HM2), adsorption but no replication (cyanophage P-SSM2), and replication (cyanophage P-SSP7). Under light–dark cycles, each cyanophage exhibited rhythmic transcript abundance, and cyanophages P-HM2 and P-SSM2 also exhibited rhythmic adsorption patterns. Finally, we show evidence to link the diurnal transcriptional rhythm of cyanophages to the photosynthetic activity of the host, thus providing a mechanistic explanation for the field observations of cyanophage transcriptional rhythms. Our study identifies that cultured viruses can exhibit diurnal rhythms during infection, which might impact cyanophage population-level dynamics in the oceans.
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29
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Yang C, Huang K. Clinical Applications of Virus-like Particles: Opportunities and Challenges. Curr Protein Pept Sci 2019; 20:488-489. [PMID: 30942144 DOI: 10.2174/138920372005190327120752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Chen Yang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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30
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Martin‐Cuadrado A, Senel E, Martínez‐García M, Cifuentes A, Santos F, Almansa C, Moreno‐Paz M, Blanco Y, García‐Villadangos M, Cura MÁG, Sanz‐Montero ME, Rodríguez‐Aranda JP, Rosselló‐Móra R, Antón J, Parro V. Prokaryotic and viral community of the sulfate‐rich crust from Peñahueca ephemeral lake, an astrobiology analogue. Environ Microbiol 2019; 21:3577-3600. [DOI: 10.1111/1462-2920.14680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ece Senel
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Manuel Martínez‐García
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Ana Cifuentes
- Department of Ecology and Marine Resources, Marine Microbiology GroupMediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | - Fernando Santos
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Cristina Almansa
- Research Technical Services (SSTTI), Microscopy UnitUniversity of Alicante Alicante Spain
| | - Mercedes Moreno‐Paz
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | - Yolanda Blanco
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | | | | | | | | | - Ramon Rosselló‐Móra
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Josefa Antón
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Víctor Parro
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
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31
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The utility of flow cytometry for potable reuse. Curr Opin Biotechnol 2019; 57:42-49. [PMID: 30684865 DOI: 10.1016/j.copbio.2018.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/03/2018] [Accepted: 12/16/2018] [Indexed: 11/22/2022]
Abstract
Protecting public health from pathogens is critical when treating wastewater to drinking water standards (i.e., planned water reuse). Viruses are a principal concern, yet real-time monitoring strategies do not currently measure virus removal through reuse processes. Flow cytometry (FCM) has enabled rapid and sensitive bacteria monitoring in water treatment applications, but methods for virus and protozoa monitoring remain immature. We discuss recent advances in the FCM field and FCM applications for quantifying microorganisms in water. We focus on flow virometry (FVM) developments, as virus enumeration methods show promise for water reuse applications. Ultimately, we propose FVM for near real-time monitoring across treatment to more accurately validate virus particle removal and for pilot studies to characterize removal through understudied unit processes.
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32
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Evans MV, Panescu J, Hanson AJ, Welch SA, Sheets JM, Nastasi N, Daly RA, Cole DR, Darrah TH, Wilkins MJ, Wrighton KC, Mouser PJ. Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin. Front Microbiol 2018; 9:2646. [PMID: 30498478 PMCID: PMC6249378 DOI: 10.3389/fmicb.2018.02646] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.
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Affiliation(s)
- Morgan V Evans
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Jenny Panescu
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Andrea J Hanson
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, United States
| | - Susan A Welch
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Julia M Sheets
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Nicholas Nastasi
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - David R Cole
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Thomas H Darrah
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Michael J Wilkins
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Paula J Mouser
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States.,Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
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33
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Wang H, Nche-Fambo FA, Yu Z, Chen F. Using microalgal communities for high CO2-tolerant strain selection. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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34
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Eissler Y, Gálvez MJ, Dorador C, Hengst M, Molina V. Active microbiome structure and its association with environmental factors and viruses at different aquatic sites of a high-altitude wetland. Microbiologyopen 2018; 8:e00667. [PMID: 30062777 PMCID: PMC6436485 DOI: 10.1002/mbo3.667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/04/2018] [Accepted: 04/21/2018] [Indexed: 01/23/2023] Open
Abstract
Salar de Huasco is a high‐altitude wetland characterized by a highly diverse microbial life adapted to extreme climatic and environmental conditions. Our study aims to determine active microbial community structure changes within different aquatic sites and its relationship with environmental factors and viruses as potential drivers of diversification in different aquatic areas of this ecosystem. In this study, bacteria and archaea composition (16S rRNA subunit pyrolibraries) and picoplankton and viral abundance were determined at ponds, springs and lagoon sites of the wetland during wet and dry seasons (February and July 2012, respectively). In general, mixosaline waters (1,400–51,000 μS/cm) usually found in ponds and lagoon presented higher picoplanktonic abundances compared to freshwater (<800 μS/cm) spring sites, ranging from 1.07 × 105 to 1.83 × 107 cells/ml. Viral abundance and viral to picoplankton ratio (VPR) also presented greater values at ponds compared to spring sites, reaching up to 4.78 × 108 viruses‐like particles and up to 351 for VPR. In general, ponds hold a higher microbial diversity and complexity associated also with the presence of microbial mats compared with water sources or lagoon (Shannon index H′ 2.6–3.9 vs. <2.0). A greater richness of archaea was also detected in ponds characterized by functional groups such as known methanogens and ammonia oxidizers, and uncultured groups. In total, our results indicate that among the different aquatic sites of the wetland, ponds presented a great microbial community diversification associated to a higher top‐down control by viruses which may influence nutrient and greenhouse gases cycling.
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Affiliation(s)
- Yoanna Eissler
- Facultad de Ciencias, Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Universidad de Valparaíso, Valparaíso, Chile
| | - María-Jesús Gálvez
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Santiago, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Santiago, Chile.,Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
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35
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Bone S, Alum A, Markovski J, Hristovski K, Bar-Zeev E, Kaufman Y, Abbaszadegan M, Perreault F. Physisorption and chemisorption of T4 bacteriophages on amino functionalized silica particles. J Colloid Interface Sci 2018; 532:68-76. [PMID: 30077067 DOI: 10.1016/j.jcis.2018.07.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
Bacteriophages, or phages, are receiving increasing interest as recognition tools for the design of bioactive surfaces. However, to maintain the activity of surface-bound phages, the immobilization strategy must provide the right orientation and not compromise the phages' integrity. The objectives of this study were to characterize the phage sorption capacity and the immobilized phage activity for aminated silica particles functionalized with T4 phages. Two functionalization strategies were compared; physisorption, based on electrostatic adhesion, and chemisorption, where the phage and the particle are coupled using a carbodiimide cross-linker. We report that chemisorption, at maximum adsorption conditions on 1 µm particles, yielded 16 functional phages per particle, which is 2.5 times more than by the physisorption method. Particle diameter is shown to have an important impact on phage attachment and 1.8 µm particles were found to have ∼4 times more phages per surface area than 0.5 µm particles. Higher surface coverage is attributed to the lower steric hindrance on bigger particles. These findings provide important guidelines for the design of phage-functionalized particles for environmental, biomedical, or sensing applications.
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Affiliation(s)
- Stephanie Bone
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, United States; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, AZ, United States
| | - Absar Alum
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, United States; National Science Foundation Water & Environmental Technology Center, United States
| | - Jasmina Markovski
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, AZ, United States; The Polytechnic School, Arizona State University, Mesa, AZ 85212, United States
| | - Kiril Hristovski
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, AZ, United States; The Polytechnic School, Arizona State University, Mesa, AZ 85212, United States
| | - Edo Bar-Zeev
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Israel
| | - Yair Kaufman
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Israel
| | - Morteza Abbaszadegan
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, United States; National Science Foundation Water & Environmental Technology Center, United States
| | - François Perreault
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, United States; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, AZ, United States.
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36
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Kropinski AM. Bacteriophage research - What we have learnt and what still needs to be addressed. Res Microbiol 2018; 169:481-487. [PMID: 29777837 DOI: 10.1016/j.resmic.2018.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/28/2018] [Accepted: 05/07/2018] [Indexed: 12/21/2022]
Abstract
Research on bacteriophages has significantly enhanced our understanding of molecular biology, the genomes of prokaryotic cells, and viral ecology. Phages and lysins offer a viable alternative to the declining utility of antibiotics in this post-antibiotic era. They also provide ideal teaching tools for genomics and bioinformatics. This article touches on the first 100 years of phage research with the author commenting on what he thinks are the highlights, and what needs to be addressed.
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Affiliation(s)
- Andrew M Kropinski
- Departments of Food Science and Pathobiology, University of Guelph, Guelph, Ontario, N1G 1W1, Canada.
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37
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Parikka KJ, Jacquet S, Colombet J, Guillaume D, Le Romancer M. Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands. Polar Biol 2018. [DOI: 10.1007/s00300-018-2288-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Yoshida M, Mochizuki T, Urayama SI, Yoshida-Takashima Y, Nishi S, Hirai M, Nomaki H, Takaki Y, Nunoura T, Takai K. Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. Front Microbiol 2018; 9:75. [PMID: 29467725 PMCID: PMC5807898 DOI: 10.3389/fmicb.2018.00075] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 11/25/2022] Open
Abstract
Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach.
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Affiliation(s)
- Mitsuhiro Yoshida
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Tomohiro Mochizuki
- Project Team for Analyses of Changes in East Japan Marine Ecosystems, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Syun-Ichi Urayama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Shinro Nishi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Hidetaka Nomaki
- Project Team for Analyses of Changes in East Japan Marine Ecosystems, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.,Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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39
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Rosario K, Fierer N, Miller S, Luongo J, Breitbart M. Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1014-1027. [PMID: 29298386 DOI: 10.1021/acs.est.7b04203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diverse bacterial and fungal communities inhabit human-occupied buildings and circulate in indoor air; however, viral diversity in these man-made environments remains largely unknown. Here we investigated DNA and RNA viruses circulating in the air of 12 university dormitory rooms by analyzing dust accumulated over a one-year period on heating, ventilation, and air conditioning (HVAC) filters. A metagenomic sequencing approach was used to determine the identity and diversity of viral particles extracted from the HVAC filters. We detected a broad diversity of viruses associated with a range of hosts, including animals, arthropods, bacteria, fungi, humans, plants, and protists, suggesting that disparate organisms can contribute to indoor airborne viral communities. Viral community composition and the distribution of human-infecting papillomaviruses and polyomaviruses were distinct in the different dormitory rooms, indicating that airborne viral communities are variable in human-occupied spaces and appear to reflect differential rates of viral shedding from room occupants. This work significantly expands the known airborne viral diversity found indoors, enabling the design of sensitive and quantitative assays to further investigate specific viruses of interest and providing new insight into the likely sources of viruses found in indoor air.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida , Saint Petersburg, Florida 33701, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado , Boulder, Colorado 80309, United States
| | - Shelly Miller
- Department of Mechanical Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Julia Luongo
- Department of Mechanical Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida , Saint Petersburg, Florida 33701, United States
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40
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Zamora JLR, Aguilar HC. Flow virometry as a tool to study viruses. Methods 2017; 134-135:87-97. [PMID: 29258922 DOI: 10.1016/j.ymeth.2017.12.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 12/10/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023] Open
Abstract
In the last few decades, flow cytometry has redefined the field of biology, exponentially enhancing our understanding of cells, immunology, and microbiology. Flow cytometry recently gave birth to flow virometry, a new way to detect, analyze, and characterize single viral particles. Detection of viruses by flow cytometry is possible due to improvements in current flow cytometers, calibration, and tuning methods. We summarize the recent birth and novel uses of flow virometry and the progressive evolution of this tool to advance the field of virology. We also discuss the various flow virometry methods used to identify and analyze viruses. We briefly summarize other applications of flow virometry, including: virus detection, quantification, population discrimination, and viral particles' antigenic properties. Finally, we summarize how viral sorting will allow further progress of flow virometry to relate viral surface characteristics to infectivity properties.
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Affiliation(s)
| | - Hector C Aguilar
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA.
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41
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Corinaldesi C, Tangherlini M, Dell'Anno A. From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments. Sci Rep 2017; 7:8355. [PMID: 28827715 PMCID: PMC5566222 DOI: 10.1038/s41598-017-08783-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/13/2017] [Indexed: 11/09/2022] Open
Abstract
Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing. The procedure based on a physical-chemical dislodgment of viral particles from the sediments, followed by vacuum filtration was much more efficient allowing us to recover >85% of the extractable viruses. By using this procedure, a high fraction of viral DNA was recovered and new viromes from different benthic deep-sea sites were generated. Such viromes were diversified in terms of both viral families and putative functions. Overall, the results presented here provide new insights for evaluating benthic deep-sea viral diversity through metagenomic analyses, and reveal that deep-sea sediments are a hot spot of novel viral genotypes and functions.
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Affiliation(s)
- Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Michael Tangherlini
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
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42
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Oliveira J, Mahony J, Hanemaaijer L, Kouwen TRHM, Neve H, MacSharry J, van Sinderen D. Detecting Lactococcus lactis Prophages by Mitomycin C-Mediated Induction Coupled to Flow Cytometry Analysis. Front Microbiol 2017; 8:1343. [PMID: 28769907 PMCID: PMC5515857 DOI: 10.3389/fmicb.2017.01343] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
Most analyzed Lactococcus lactis strains are predicted to harbor one or more prophage genomes within their chromosome; however, the true extent of the inducibility and functionality of such prophages cannot easily be deduced from sequence analysis alone. Chemical treatment of lysogenic strains with Mitomycin C is known to cause induction of temperate phages, though it is not always easy to clearly identify a lysogenic strain or to measure the number of released phage particles. Here, we report the application of flow cytometry as a reliable tool for the detection and enumeration of released lactococcal prophages using the green dye SYTO-9.
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Affiliation(s)
- Joana Oliveira
- School of Microbiology, University College CorkCork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | | | | | | | - John MacSharry
- APC Microbiome Institute, University College CorkCork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
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43
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Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates. ISME JOURNAL 2016; 11:394-404. [PMID: 27824343 DOI: 10.1038/ismej.2016.134] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/12/2016] [Accepted: 08/19/2016] [Indexed: 01/17/2023]
Abstract
Diverse microbes release membrane-bound extracellular vesicles from their outer surfaces into the surrounding environment. Vesicles are found in numerous habitats including the oceans, where they likely have a variety of functional roles in microbial ecosystems. Extracellular vesicles are known to contain a range of biomolecules including DNA, but the frequency with which DNA is packaged in vesicles is unknown. Here, we examine the quantity and distribution of DNA associated with vesicles released from five different bacteria. The average quantity of double-stranded DNA and size distribution of DNA fragments released within vesicles varies among different taxa. Although some vesicles contain sufficient DNA to be visible following staining with the SYBR fluorescent DNA dyes typically used to enumerate viruses, this represents only a small proportion (<0.01-1%) of vesicles. Thus DNA is packaged heterogeneously within vesicle populations, and it appears that vesicles are likely to be a minor component of SYBR-visible particles in natural sea water compared with viruses. Consistent with this hypothesis, chloroform treatment of coastal and offshore seawater samples reveals that vesicles increase epifluorescence-based particle (viral) counts by less than an order of magnitude and their impact is variable in space and time.
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44
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Kan J, Clingenpeel S, Dow CL, McDermott TR, Macur RE, Inskeep WP, Nealson KH. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake. Front Microbiol 2016; 7:210. [PMID: 26973602 PMCID: PMC4770039 DOI: 10.3389/fmicb.2016.00210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/08/2016] [Indexed: 11/13/2022] Open
Abstract
Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.
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Affiliation(s)
- Jinjun Kan
- Stroud Water Research Center, Avondale PA, USA
| | | | | | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Richard E Macur
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles CA, USA
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45
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Skvortsov T, de Leeuwe C, Quinn JP, McGrath JW, Allen CCR, McElarney Y, Watson C, Arkhipova K, Lavigne R, Kulakov LA. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland. PLoS One 2016; 11:e0150361. [PMID: 26927795 PMCID: PMC4771703 DOI: 10.1371/journal.pone.0150361] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.
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Affiliation(s)
- Timofey Skvortsov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Colin de Leeuwe
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John P. Quinn
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John W. McGrath
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Yvonne McElarney
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Catherine Watson
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Ksenia Arkhipova
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leonid A. Kulakov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
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46
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Dann LM, Paterson JS, Newton K, Oliver R, Mitchell JG. Distributions of Virus-Like Particles and Prokaryotes within Microenvironments. PLoS One 2016; 11:e0146984. [PMID: 26785114 PMCID: PMC4718716 DOI: 10.1371/journal.pone.0146984] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022] Open
Abstract
Microbial interactions are important for ecosystem function, but occur at the microscale and so are difficult to observe. Previous studies in marine systems have shown significant shifts in microbial community abundance and composition over scales of micrometres to centimetres. This study investigates the microscale abundance distributions of virus-like particles (VLPs) and prokaryotes in the lower reaches of a river to determine the extent to which microscale microbial patchiness exists in freshwater systems. Here we report local hotspots surrounded by gradients that reach a maximum 80 and 107 fold change in abundance over 0.9 cm for prokaryotic and VLP subpopulations. Changes in prokaryotic and VLP hotspots were tightly coupled. There were no gradients at tens of centimetres across the boundary layers, which is consistent with strong mixing and turbulence-driven aggregation found in river systems. Quantification of the patchiness shows a marked asymmetry with patches 10 times greater than background common, but depletions being rare or absent in most samples. This consistent asymmetry suggests that coldspots depleted by grazing and lysis are rapidly mixed to background concentrations, while the prevalence of hotspots indicates persistence against disruption. The hotspot to coldspot relative abundance may be useful for understanding microbial river dynamics. The patchiness indicates that the mean- field approach of bulk phase sampling misses the microbially relevant community variation and may underestimate the concentrations of these important microbial groups.
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Affiliation(s)
- Lisa M. Dann
- School of Biological Sciences at Flinders University, Adelaide, South Australia
- * E-mail:
| | - James S. Paterson
- School of Biological Sciences at Flinders University, Adelaide, South Australia
| | - Kelly Newton
- School of Biological Sciences at Flinders University, Adelaide, South Australia
| | - Rod Oliver
- Land and Water Research Division at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia
| | - James G. Mitchell
- School of Biological Sciences at Flinders University, Adelaide, South Australia
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47
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Zheng X, Lu Y, Zhao J, Zhang Y, Ren W, Liu D, Lu J, Piper JA, Leif RC, Liu X, Jin D. High-Precision Pinpointing of Luminescent Targets in Encoder-Assisted Scanning Microscopy Allowing High-Speed Quantitative Analysis. Anal Chem 2015; 88:1312-9. [DOI: 10.1021/acs.analchem.5b03767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xianlin Zheng
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
| | - Yiqing Lu
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jiangbo Zhao
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
| | - Yuhai Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Wei Ren
- Institute
for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Deming Liu
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jie Lu
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
| | - James A. Piper
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
| | - Robert C. Leif
- Newport Instruments, 3345 Hopi
Place, San Diego, California 92117-3516, United States
| | - Xiaogang Liu
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Institute
of Materials
Research and Engineering, A*STAR (Agency for Science, Technology and
Research), 3 Research Link, Singapore 117602, Singapore
| | - Dayong Jin
- Advanced
Cytometry Laboratories, ARC Centre of Excellence for Nanoscale BioPhotonics
(CNBP), Macquarie University, Sydney, New South Wales 2109, Australia
- Institute
for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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48
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Liang Y, Bai X, Jiang Y, Wang M, He J, McMinn A. Distribution of marine viruses and their potential hosts in Prydz Bay and adjacent Southern Ocean, Antarctic. Polar Biol 2015. [DOI: 10.1007/s00300-015-1787-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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49
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Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality. ISME JOURNAL 2015; 10:491-9. [PMID: 26251870 DOI: 10.1038/ismej.2015.129] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Predation on bacteria and accompanying mortality are important mechanisms in controlling bacterial populations and recycling of nutrients through the microbial loop. The agents most investigated and seen as responsible for bacterial mortality are viruses and protists. However, a body of evidence suggests that predatory bacteria such as the Halobacteriovorax (formerly Bacteriovorax), a Bdellovibrio-like organism, contribute substantially to bacterial death. Until now, conclusive evidence has been lacking. The goal of this study was to better understand the contributors to bacterial mortality by addressing the poorly understood role of Halobacteriovorax and how their role compares with that of viruses. The results revealed that when a concentrated suspension of Vibrio parahaemolyticus was added into microcosms of estuarine waters, the native Halobacteriovorax were the predators that responded first and most rapidly. Their numbers increased by four orders of magnitude, whereas V. parahaemolyticus prey numbers decreased by three orders of magnitude. In contrast, the extant virus population showed little increase and produced little change in the prey density. An independent experiment with stable isotope probing confirmed that Halobacteriovorax were the predators primarily responsible for the mortality of the V. parahaemolyticus. The results show that Halobacteriovorax have the potential to be significant contributors to bacterial mortality, and in such cases, predation by Halobacteriovorax may be an important mechanism of nutrient recycling. These conclusions add another dimension to bacterial mortality and the recycling of nutrients.
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50
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Holmes DE, Giloteaux L, Chaurasia AK, Williams KH, Luef B, Wilkins MJ, Wrighton KC, Thompson CA, Comolli LR, Lovley DR. Evidence of Geobacter-associated phage in a uranium-contaminated aquifer. THE ISME JOURNAL 2015; 9:333-46. [PMID: 25083935 PMCID: PMC4303627 DOI: 10.1038/ismej.2014.128] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/27/2014] [Accepted: 06/14/2014] [Indexed: 11/08/2022]
Abstract
Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
- Western New England University, Springfield, MA, USA
| | - Ludovic Giloteaux
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Akhilesh K Chaurasia
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Birgit Luef
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Kelly C Wrighton
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Courtney A Thompson
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
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