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Kavagutti VS, Bulzu PA, Chiriac CM, Salcher MM, Mukherjee I, Shabarova T, Grujčić V, Mehrshad M, Kasalický V, Andrei AS, Jezberová J, Seďa J, Rychtecký P, Znachor P, Šimek K, Ghai R. High-resolution metagenomic reconstruction of the freshwater spring bloom. MICROBIOME 2023; 11:15. [PMID: 36698172 PMCID: PMC9878933 DOI: 10.1186/s40168-022-01451-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/16/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. RESULTS We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation. CONCLUSION We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom. Video Abstract.
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Affiliation(s)
- Vinicius S Kavagutti
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Paul-Adrian Bulzu
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Cecilia M Chiriac
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Indranil Mukherjee
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Tanja Shabarova
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Vesna Grujčić
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Present address: Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Present address: Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Vojtěch Kasalický
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Stefan Andrei
- Limnological Station, Microbial Evogenomics Lab (MiEL), University of Zurich, Kilchberg, Switzerland
| | - Jitka Jezberová
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Jaromir Seďa
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Pavel Rychtecký
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Petr Znachor
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Karel Šimek
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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3
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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Freen-van Heeren JJ. Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BIOTECH 2021; 10:21. [PMID: 35822795 PMCID: PMC9245478 DOI: 10.3390/biotech10040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.
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Cahn JKB, Piel J. Anwendungen von Einzelzellmethoden in der mikrobiellen Naturstoffforschung. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201900532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jackson K. B. Cahn
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
| | - Jörn Piel
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
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Cahn JKB, Piel J. Opening up the Single-Cell Toolbox for Microbial Natural Products Research. Angew Chem Int Ed Engl 2021; 60:18412-18428. [PMID: 30748086 DOI: 10.1002/anie.201900532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 02/06/2023]
Abstract
The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.
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Affiliation(s)
- Jackson K B Cahn
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
| | - Jörn Piel
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
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Takahashi H, Horio K, Kato S, Kobori T, Watanabe K, Aki T, Nakashimada Y, Okamura Y. Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification. Sci Rep 2020; 10:9588. [PMID: 32541674 PMCID: PMC7295810 DOI: 10.1038/s41598-020-65864-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/04/2020] [Indexed: 11/11/2022] Open
Abstract
Meta-analyses using next generation sequencing is a powerful strategy for studying microbiota; however, it cannot clarify the role of individual microbes within microbiota. To know which cell expresses what gene is important for elucidation of the individual cell’s function in microbiota. In this report, we developed novel fluorescence in situ hybridization (FISH) procedure using RNase-H-assisted rolling circle amplification to visualize mRNA of interest in microbial cells without reverse transcription. Our results show that this method is applicable to both Gram-negative and Gram-positive microbes without any noise from DNA, and it is possible to visualize the target mRNA expression directly at the single-cell level. Therefore, our procedure, when combined with data of meta-analyses, can help to understand the role of individual microbes in the microbiota.
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Affiliation(s)
- Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.
| | - Kyohei Horio
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Setsu Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Toshiro Kobori
- Division of Food Biotechnology, Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8642, Japan
| | - Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan. .,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.
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8
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Amalfitano S, Levantesi C, Copetti D, Stefani F, Locantore I, Guarnieri V, Lobascio C, Bersani F, Giacosa D, Detsis E, Rossetti S. Water and microbial monitoring technologies towards the near future space exploration. WATER RESEARCH 2020; 177:115787. [PMID: 32315899 DOI: 10.1016/j.watres.2020.115787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.
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Affiliation(s)
- Stefano Amalfitano
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy.
| | - Caterina Levantesi
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
| | - Diego Copetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Fabrizio Stefani
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Ilaria Locantore
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Vincenzo Guarnieri
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Cesare Lobascio
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Francesca Bersani
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Donatella Giacosa
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Emmanouil Detsis
- European Science Foundation, 1 quai Lezay Marnésia, BP 90015, 67080, Strasbourg Cedex, France
| | - Simona Rossetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
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FRET-based fluorescent nanoprobe platform for sorting of active microorganisms by functional properties. Biosens Bioelectron 2019; 148:111832. [PMID: 31706173 DOI: 10.1016/j.bios.2019.111832] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
Fluorescence-activated cell sorting (FACS) has rarely been applied to screening of microorganisms because of poor detection resolution, which is compromised by poor stability, toxicity, or interference from background fluorescence of the fluorescence sensors used. Here, a fluorescence-based rapid high-throughput cell sorting method was first developed using a fluorescence resonance energy transfer (FRET) fluorescent nanoprobe NP-RA, which was constructed by coating a silica nanoparticle with Rhodamine B and methyl-red (an azo dye). Rhodamine B (inner layer) is the FRET donor and methyl-red (outer layer) is the acceptor. This ready-to-use NP-RA is non-fluorescent, but fluoresces once the outer layer is degraded by microorganisms. In our experiment, NP-RA was ultrasensitive to model strain Shewanella decolorationis S12, showing a broad detection range from 8.0 cfu/mL to 8.7 × 108 cfu/mL under confocal laser scanning microscopy, and from 1.1 × 107 to 9.36 × 108 cfu/mL under a fluorometer. In addition, NP-RA bioimaging can clearly identify other azo-respiring cells in the microbial community, including Bosea thiooxidans DSM 9653 and Lysinibacillus pakistanensis NCCP-54. Furthermore, the fluorescent probe NP-RA is compatible with downstream FACS so that azo-respiring cells can be rapidly sorted out directly from an artificial microbial community. To our knowledge, no fluorescent nanoprobe has yet been designed for tracking and sorting azo-respiration functional microorganisms.
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Liu J, Li B, Wang Y, Zhang G, Jiang X, Li X. Passage and community changes of filterable bacteria during microfiltration of a surface water supply. ENVIRONMENT INTERNATIONAL 2019; 131:104998. [PMID: 31330365 DOI: 10.1016/j.envint.2019.104998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/06/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The omnipresence of filterable bacteria that can pass through 0.22-μm membrane filters demands a change in the sterile filtration practice. In this study, we identified that filterable bacteria enriched from a surface water are members of the Bacteroidetes, Proteobacteria, Spirochaetae, Firmicutes, and Actinobacteria. Filterable bacteria displayed superior filterability during the entire bacterial growth phase, especially at the exponential phase. Maximal passage percentages were comparable at different cell densities, and achieved earlier at high cell density. Furthermore, filter retention for the investigated bacteria is independent of liquid temperature. However, cultivation temperature could affect the growth of some specific filterable bacteria and lead to variability in the passage percentage. Additionally, membrane materials, pore size and filtering flux greatly affected the passage of filterable bacteria. The majority of filterable Hylemonella and SAR324 could pass through 0.1-μm polyvinylidene fluoride and polyethersulfone filters but could not pass through 0.1-μm polycarbonate and mixed cellulose esters filters. Taken together, our results demonstrated that the ultra-small size of filterable bacteria, membrane characteristics and filtration operational conditions could challenge the validity of the 0.22/0.1-μm sterilizing grade filters in providing bio-safety barriers.
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Affiliation(s)
- Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China.
| | - Yingying Wang
- College of Environmental Science and Engineering, Nankai University, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China; Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China.
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Song Y, Wang Y, Mao G, Gao G, Wang Y. Impact of planktonic low nucleic acid-content bacteria to bacterial community structure and associated ecological functions in a shallow lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 658:868-878. [PMID: 30678021 DOI: 10.1016/j.scitotenv.2018.12.274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
In this study, 0.45 μm filtration, flow cytometric fingerprint, 16S rRNA amplicon sequencing, and bioinformation tools were adopted to analyze the structural diversity and potential functions of planktonic low nucleic acid (LNA)- content bacteria in a shallow lake. Three bacterial groups, namely, "LNA," "high nucleic acid (HNA)-Small," and "HNA-Large," were classified through flow cytometric fingerprint, among which the "HNA-Small" group was possibly in the proliferation stage of the "LNA" group. Total nitrogen and phosphate were the key factors that influence the growth of LNA bacteria. Results of 16S rRNA amplicon sequencing showed that LNA bacteria were phylogenetically less diverse than HNA bacteria, and Actinobacteria and Proteobacteria (especially Gamma-Proteobacteria) were the dominant phyla in LNA bacterial operational taxonomic units (OTUs). Accordingly, hgcI_clade and Pseudomonas were the most abundant bacterial genera in LNA bacterial OTUs. The fraction of low-abundance LNA bacteria was sensitive to several environmental factors, indicating that environmental factors only determined the fraction distribution of low-abundance bacteria. The prediction of metabolic and ecological functions showed that LNA and HNA bacteria had distinct metabolic and ecological functions, which were mainly attributed to the dominant and exclusive bacterial groups.
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Affiliation(s)
- Yuhao Song
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yufeng Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Guannan Mao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Liu J, Zhao R, Zhang J, Zhang G, Yu K, Li X, Li B. Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant. Front Microbiol 2018; 9:2922. [PMID: 30568635 PMCID: PMC6290093 DOI: 10.3389/fmicb.2018.02922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/14/2018] [Indexed: 12/23/2022] Open
Abstract
Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.
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Affiliation(s)
- Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
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Ghuneim LAJ, Jones DL, Golyshin PN, Golyshina OV. Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function. Front Microbiol 2018; 9:1971. [PMID: 30186275 PMCID: PMC6110929 DOI: 10.3389/fmicb.2018.01971] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/06/2018] [Indexed: 11/13/2022] Open
Abstract
Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and "Candidatus Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.
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Affiliation(s)
- Lydia-Ann J. Ghuneim
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - David L. Jones
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - Peter N. Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
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Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems. ISME JOURNAL 2018; 12:1344-1359. [PMID: 29416124 PMCID: PMC5932017 DOI: 10.1038/s41396-018-0070-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 01/10/2018] [Accepted: 01/12/2018] [Indexed: 11/08/2022]
Abstract
Here we used flow cytometry (FCM) and filtration paired with amplicon sequencing to determine the abundance and composition of small low nucleic acid (LNA)-content bacteria in a variety of freshwater ecosystems. We found that FCM clusters associated with LNA-content bacteria were ubiquitous across several ecosystems, varying from 50 to 90% of aquatic bacteria. Using filter-size separation, we separated small LNA-content bacteria (passing 0.4 µm filter) from large bacteria (captured on 0.4 µm filter) and characterized communities with 16S amplicon sequencing. Small and large bacteria each represented different sub-communities within the ecosystems' community. Moreover, we were able to identify individual operational taxonomical units (OTUs) that appeared exclusively with small bacteria (434 OTUs) or exclusively with large bacteria (441 OTUs). Surprisingly, these exclusive OTUs clustered at the phylum level, with many OTUs appearing exclusively with small bacteria identified as candidate phyla (i.e. lacking cultured representatives) and symbionts. We propose that LNA-content bacteria observed with FCM encompass several previously characterized categories of bacteria (ultramicrobacteria, ultra-small bacteria, candidate phyla radiation) that share many traits including small size and metabolic dependencies on other microorganisms.
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Bruder LM, Dörkes M, Fuchs BM, Ludwig W, Liebl W. Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes. Syst Appl Microbiol 2016; 39:464-475. [DOI: 10.1016/j.syapm.2016.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 01/19/2023]
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