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Bicaldo IEC, Padilla KSAR, Tu TH, Chen WT, Mendoza-Pascual MU, Vicera CVB, de Leon JR, Poblete KN, Austria ES, Lopez MLD, Kobayashi Y, Shiah FK, Papa RDS, Okuda N, Wang PL, Lin LH. The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia. Front Microbiol 2024; 15:1410666. [PMID: 39044952 PMCID: PMC11263035 DOI: 10.3389/fmicb.2024.1410666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.
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Affiliation(s)
- Iona Eunice C. Bicaldo
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Karol Sophia Agape R. Padilla
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
- Department of Science and Technology, Science Education Institute, Taguig, Philippines
| | - Tzu-Hsuan Tu
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan Ting Chen
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Milette U. Mendoza-Pascual
- Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines
| | | | - Justine R. de Leon
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | | | | | - Mark Louie D. Lopez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Yuki Kobayashi
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Rey Donne S. Papa
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
- Research Center for Inland Seas, Kobe University, Kobe, Japan
- Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024; 6:1209-1224. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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Snaidr L, Mühlhahn P, Beimfohr C, Kreuzer C, Richly C, Snaidr J. Specific cultivation-independent enumeration of viable cells in probiotic products using a combination of fluorescence in situ hybridization and flow cytometry. Front Microbiol 2024; 15:1410709. [PMID: 38933029 PMCID: PMC11199854 DOI: 10.3389/fmicb.2024.1410709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
This study introduces an optimized integration of flow cytometry and fluorescence in situ hybridization (Flow-FISH) as an approach for the specific enumeration of gram-positive bacteria in probiotic products, overcoming the limitations of conventional methods. The enhanced Flow-FISH technique synergizes the rapid and automated capabilities of flow cytometry with the high specificity of FISH, facilitating the differentiation of viable cells at the species level within probiotic blends. By analyzing lyophilized samples of Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Bifidobacterium animalis subsp. lactis, and a commercial product, the study highlights the optimized Flow-FISH protocol's advantages, including reduced hybridization times to 1.5 h and elimination of centrifugation steps. Comparative evaluations with the widely accepted enumeration methods plate count and Live/Dead (L/D) staining were conducted. The study revealed that Flow-FISH produces higher viable cell counts than plate count, thereby challenging the traditional "gold standard" by highlighting its predisposition to underestimate actual viable cell numbers. Against L/D staining, Flow-FISH achieved comparable results, which, despite the different foundational premises of each technique, confirms the accuracy and reliability of our method. In conclusion, the optimized Flow-FISH protocol represents a significant leap forward in probiotic research and quality control. This method provides a rapid, robust, and highly specific alternative for the enumeration of probiotic bacteria, surpassing traditional methodologies. Its ability to enable a more detailed and reliable analysis of probiotic products paves the way for precise quality control and research insights, underscoring its potential to improve the field significantly.
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Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [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: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
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Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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Sousa M, Rocha R, Araújo D, Castro J, Barbosa A, Azevedo NF, Cerqueira L, Almeida C. A New Peptide Nucleic Acid Fluorescence In Situ Hybridization Probe for the Specific Detection of Salmonella Species in Food Matrices. Foodborne Pathog Dis 2024; 21:298-305. [PMID: 38484326 DOI: 10.1089/fpd.2023.0127] [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] [Indexed: 05/12/2024] Open
Abstract
Salmonella spp. is among the most central etiological agents in foodborne bacterial disorders. To identify Salmonella spp., numerous new molecular techniques have been developed conversely to the traditional culture-based methods. In this work, a new peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method was developed for the specific detection of Salmonella species, allowing a faster analysis compared with the traditional methods (ISO 6579-1: 2017). The method was optimized based on a novel PNA probe (SalPNA1692) combined with a blocker probe to detect Salmonella in food samples through an assessment of diverse-rich and selective enrichment broths. Our findings indicated that the best outcome was obtained using a 24-h pre-enrichment step in buffered peptone water, followed by RambaQuick broth selective enrichment for 16 h. For the enrichment step performance validation, fresh ground beef was artificially contaminated with two ranges of concentration of inoculum: a low level (0.2-2 colony-forming units [CFUs]/25 g) and a high level (2-10 CFUs/25 g). The new PNA-FISH method presented a specificity of 100% and a detection limit of 0.5 CFU/25 g of food sample, which confirms the great potential of applying PNA probes in food analysis.
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Affiliation(s)
- Mário Sousa
- Biomode SA, Av. Mestre José Veiga, Braga, Portugal
| | - Rui Rocha
- Biomode SA, Av. Mestre José Veiga, Braga, Portugal
- Center of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
- Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, Viana do Castelo, Portugal
| | - Daniela Araújo
- Center of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Joana Castro
- Center of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Ana Barbosa
- Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- AliCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Nuno F Azevedo
- Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- AliCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Laura Cerqueira
- Biomode SA, Av. Mestre José Veiga, Braga, Portugal
- Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- AliCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Carina Almeida
- Biomode SA, Av. Mestre José Veiga, Braga, Portugal
- Center of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
- Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
- AliCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
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Stojan I, Šantić D, Villena-Alemany C, Trumbić Ž, Matić F, Vrdoljak Tomaš A, Lepen Pleić I, Piwosz K, Kušpilić G, Ninčević Gladan Ž, Šestanović S, Šolić M. Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network. ENVIRONMENTAL MICROBIOME 2024; 19:28. [PMID: 38685092 PMCID: PMC11059731 DOI: 10.1186/s40793-024-00573-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of the microbial food chain. Despite their considerable contribution to the transformation of organic matter in marine environments, relatively little is still known about their community structure and ecology at fine-scale taxonomic resolution. Up to date, there is no comprehensive (i.e. qualitative and quantitative) analysis of their community composition in the Adriatic Sea. RESULTS Analysis was based on pufM gene metabarcoding and quantitative FISH-IR approach with the use of artificial neural network. Significant seasonality was observed with regards to absolute abundances (maximum average abundances in spring 2.136 ± 0.081 × 104 cells mL-1, minimum in summer 0.86 × 104 cells mL-1), FISH-IR groups (Roseobacter clade prevalent in autumn, other Alpha- and Gammaproteobacteria in summer) and pufM sequencing data agglomerated at genus-level. FISH-IR results revealed heterogeneity with the highest average relative contribution of AAPs assigned to Roseobacter clade (37.66%), followed by Gammaproteobacteria (35.25%) and general Alphaproteobacteria (31.15%). Community composition obtained via pufM sequencing was dominated by Gammaproteobacteria clade NOR5/OM60, specifically genus Luminiphilus, with numerous rare genera present in relative abundances below 1%. The use of artificial neural network connected this community to biotic (heterotrophic bacteria, HNA and LNA bacteria, Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic nanoflagellates, bacterial production) and abiotic environmental factors (temperature, salinity, chlorophyll a and nitrate, nitrite, ammonia, total nitrogen, silicate, and orthophosphate concentration). A type of neural network, neural gas analysis at order-, genus- and ASV-level, resulted in five distinct best matching units (representing particular environments) and revealed that high diversity was generally independent of temperature, salinity, and trophic status of the environment, indicating a potentially dissimilar behaviour of aerobic anoxygenic phototrophs compared to the general bacterioplankton. CONCLUSION This research represents the first comprehensive analysis of aerobic anoxygenic phototrophs in the Adriatic Sea on a trophic gradient during a year-round period. This study is also one of the first reports of their genus-level ecology linked to biotic and abiotic environmental factors revealed by unsupervised neural network algorithm, paving the way for further research of substantial contribution of this important bacterial functional group to marine ecosystems.
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Affiliation(s)
- Iva Stojan
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Danijela Šantić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia.
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Frano Matić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Ana Vrdoljak Tomaš
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Ivana Lepen Pleić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Kasia Piwosz
- Department of Fisheries, Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Grozdan Kušpilić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | | | - Stefanija Šestanović
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Mladen Šolić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
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Liu X, Yang H, Liu J, Liu K, Jin L, Zhang Y, Khan MR, Zhong K, Cao J, He Q, Xia X, Deng R. In Situ Cas12a-Based Allele-Specific PCR for Imaging Single-Nucleotide Variations in Foodborne Pathogenic Bacteria. Anal Chem 2024; 96:2032-2040. [PMID: 38277772 DOI: 10.1021/acs.analchem.3c04532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
In situ profiling of single-nucleotide variations (SNVs) can elucidate drug-resistant genotypes with single-cell resolution. The capacity to directly "see" genetic information is crucial for investigating the relationship between mutated genes and phenotypes. Fluorescence in situ hybridization serves as a canonical tool for genetic imaging; however, it cannot detect subtle sequence alteration including SNVs. Herein, we develop an in situ Cas12a-based amplification refractory mutation system-PCR (ARMS-PCR) method that allows the visualization of SNVs related to quinolone resistance inside cells. The capacity of discriminating SNVs is enhanced by incorporating optimized mismatched bases in the allele-specific primers, thus allowing to specifically amplify quinolone-resistant related genes. After in situ ARMS-PCR, we employed a modified Cas12a/CRISPR RNA to tag the amplicon, thereby enabling specific binding of fluorophore-labeled DNA probes. The method allows to precisely quantify quinolone-resistant Salmonella enterica in the bacterial mixture. Utilizing this method, we investigated the survival competition capacity of quinolone-resistant and quinolone-sensitive bacteria toward antimicrobial peptides and indicated the enrichment of quinolone-resistant bacteria under colistin sulfate stress. The in situ Cas12a-based ARMS-PCR method holds the potential for profiling cellular phenotypes and gene regulation with single-nucleotide resolution at the single-cell level.
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Affiliation(s)
- Xinmiao Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hao Yang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jun Liu
- Chengdu Customs Technology Center, Chengdu 610041, China
| | - Kerui Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Lulu Jin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kai Zhong
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, Liaoning 116600, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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Liao Y. Emerging tools for uncovering genetic and transcriptomic heterogeneities in bacteria. Biophys Rev 2024; 16:109-124. [PMID: 38495445 PMCID: PMC10937887 DOI: 10.1007/s12551-023-01178-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/11/2023] [Indexed: 03/19/2024] Open
Abstract
Bacterial communities display an astonishing degree of heterogeneities among their constituent cells across both the genomic and transcriptomic levels, giving rise to diverse social interactions and stress-adaptation strategies indispensable for proliferating in the natural environment (Ackermann in Nat Rev Microbiol 13:497-508, 2015). Our knowledge about bacterial heterogeneities and their physiological ramifications critically depends on our ability to unambiguously resolve the genetic and phenotypic states of the individual cells that make up the population. In this short review, I highlight several recently developed methods for studying bacterial heterogeneities, primarily focusing on single-cell techniques based on advanced sequencing and microscopy technologies. I will discuss the working principle of each technique as well as the types of problems each technique is best positioned to address. With significant improvements in resolution and throughput, these emerging tools together offer unprecedented and complementary views of various types of heterogeneities found within bacterial populations, paving the way for mechanistic dissections and systematic interventions in laboratory and clinical settings.
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Affiliation(s)
- Yi Liao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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10
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Liyanage SH, Yan M. Maltose-Derivatized Fluorescence Turn-On Imaging Probe for Bacteria Detection. ACS Infect Dis 2023; 9:2560-2571. [PMID: 37936289 DOI: 10.1021/acsinfecdis.3c00403] [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] [Indexed: 11/09/2023]
Abstract
We report a maltose-derivatized fluorescence turn-on imaging probe, Mal-Cz, to detect E. coli and Staphylococci. The fluorescence turn-on is achieved through an intramolecular C-H insertion reaction of the perfluoroaryl azide-functionalized carbazole to give a fluorescent product. Confocal fluorescence microscopy confirmed the successful uptake of Mal-Cz by E. coli and Staphylococci upon photoactivation. The Mal-Cz probe could selectively detect E. coli and S. epidermidis in the presence of P. aeruginosa and M. smegmatis without interference from these bacteria. Both the photoactivation and bacteria detection can be accomplished using a hand-held UV lamp at 365 nm, with the limit of detection of 103 CFU/mL by the naked eye. Mal-Cz could also be used to detect E. coli and S. epidermidis spiked in milk by the naked eye under a hand-held UV lamp. The uptake of Mal-Cz requires metabolically active bacteria: the uptake was reduced in stationary phase bacteria and was diminished in bacteria that were killed by heating or treating with antibiotics or sodium azide. The uptake decreased with increasing concentration of added free maltose, indicating that Mal-Cz hijacked the maltose uptake pathways. In E. coli, the maltose transport systems, including maltoporin LamB, maltose binding protein MBP, and the maltose ATP binding cassette (ABC) transporter MalFGK2, are all critical for the transport of Mal-Cz. The uptake was diminished in the deletion mutants ΔLamB, ΔMalE, ΔMalF, and ΔMalK.
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Affiliation(s)
- Sajani H Liyanage
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
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11
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Koike K, Honda R, Aoki M, Yamamoto‐Ikemoto R, Syutsubo K, Matsuura N. A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:497-511. [PMID: 37465846 PMCID: PMC10667660 DOI: 10.1111/1758-2229.13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
The method of spiking synthetic internal standard genes (ISGs) to samples for amplicon sequencing, generating sequences and converting absolute gene numbers from read counts has been used only for phylogenetic markers and has not been applied to functional markers. In this study, we developed ISGs, including gene sequences of the 16S rRNA, pmoA, encoding a subunit of particulate methane monooxygenase and amoA, encoding a subunit of ammonia monooxygenase. We added ISGs to the samples, amplified the target genes and performed amplicon sequencing. For the mock community, the copy numbers converted from read counts using ISGs were equivalent to those obtained by the quantitative real-time polymerase chain reaction (4.0 × 104 versus 4.1 × 104 and 3.0 × 103 versus 4.0 × 103 copies μL-DNA-1 for 16S rRNA and pmoA genes, respectively), but we also identified underestimation, possibly due to primer coverage (7.8 × 102 versus 3.7 × 103 μL-DNA-1 for amoA gene). We then applied this method to environmental samples and analysed phylogeny, functional diversity and absolute quantities. One Methylocystis population was most abundant in the sludge samples [16S rRNA gene (3.8 × 109 copies g-1 ) and the pmoA gene (2.3 × 109 copies g-1 )] and were potentially interrelated. This study demonstrates that ISG spiking is useful for evaluating sequencing data processing and quantifying functional markers.
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Affiliation(s)
- Kazuyoshi Koike
- Graduate School of Natural Science and TechnologyKanazawa UniversityKanazawaJapan
| | - Ryo Honda
- Faculty of Geosciences and Civil EngineeringKanazawa UniversityKanazawaJapan
| | - Masataka Aoki
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | | | - Kazuaki Syutsubo
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
- Research Center for Water Environment Technology, School of Engineeringthe University of TokyoTokyoJapan
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil EngineeringKanazawa UniversityKanazawaJapan
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12
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Sousa C, Ferreira R, Santos SB, Azevedo NF, Melo LDR. Advances on diagnosis of Helicobacter pylori infections. Crit Rev Microbiol 2023; 49:671-692. [PMID: 36264672 DOI: 10.1080/1040841x.2022.2125287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
The association of Helicobacter pylori to several gastric diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer, and its high prevalence worldwide, raised the necessity to use methods for a proper and fast diagnosis and monitoring the pathogen eradication. Available diagnostic methods can be classified as invasive or non-invasive, and the selection of the best relies on the clinical condition of the patient, as well as on the sensitivity, specificity, and accessibility of the diagnostic test. This review summarises all diagnostic methods currently available, including the invasive methods: endoscopy, histology, culture, and molecular methods, and the rapid urease test (RUT), as well as the non-invasive methods urea breath test (UBT), serological assays, biosensors, and microfluidic devices and the stool antigen test (SAT). Moreover, it lists the diagnostic advantages and limitations, as well as the main advances for each methodology. In the end, research on the development of new diagnostic methods, such as bacteriophage-based H. pylori diagnostic tools, is also discussed.
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Affiliation(s)
- Cláudia Sousa
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Rute Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Sílvio B Santos
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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13
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Huang Z, Wang D, Zhou J, He H, Wei C. The Improvement of Fluorescence In Situ Hybridization Technique Based on Explorations of Symbionts in Cicadas. Int J Mol Sci 2023; 24:15838. [PMID: 37958818 PMCID: PMC10650757 DOI: 10.3390/ijms242115838] [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: 09/27/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is widely used for the identification of microbes in complex samples, but it suffers from some limitations resulting in the weak or even absence of fluorescence signals of microbe(s), which may lead to the underestimation or misunderstanding of a microbial community. Herein, we explored symbionts in the bacteriomes and fat bodies of cicadas using modified FISH, aiming to improve this technique. We initially revealed that the probes of Candidatus Sulcia muelleri (Sulcia) and the yeast-like fungal symbiont (YLS) are suitable for detection of these symbionts in all cicadas and some other species of Auchenorrhyncha, whereas the probe of Candidatus Hodgkinia cicadicola (Hodgkinia) is only suitable for detection of Hodgkinia in a few cicada species. The fluorescence signal of Sulcia, Hodgkinia and YLS exhibited weak intensity without the addition of unlabeled oligonucleotides (helpers) and heat shock in some cicadas; however, it can be significantly improved by the addition of both helpers and heat shock. Results of this study suggest that heat shock denaturing rRNA and proteins of related microbe(s) together with helpers binding to the adjacent region of the probe's target sites prevent the re-establishment of the native secondary structure of rRNA; therefore, suitable probe(s) can more easily access to the probe's target sites of rRNA. Our results provide new information for the significant improvement of hybridization signal intensities of microbes in the FISH experiment, making it possible to achieve a more precise understanding of the microbial distribution, community and density in complex samples.
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Affiliation(s)
- Zhi Huang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Z.H.); (D.W.); (J.Z.)
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Dandan Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Z.H.); (D.W.); (J.Z.)
| | - Jinrui Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Z.H.); (D.W.); (J.Z.)
| | - Hong He
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Z.H.); (D.W.); (J.Z.)
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14
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Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. THE NEW PHYTOLOGIST 2023; 240:439-451. [PMID: 37381111 PMCID: PMC10962543 DOI: 10.1111/nph.19112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.
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Affiliation(s)
- Hannes Schmidt
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Doctoral School in Microbiology and Environmental ScienceUniversity of ViennaVienna1030Austria
| | - David Seki
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
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15
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Bourceau P, Geier B, Suerdieck V, Bien T, Soltwisch J, Dreisewerd K, Liebeke M. Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling. Nat Protoc 2023; 18:3050-3079. [PMID: 37674095 DOI: 10.1038/s41596-023-00864-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/31/2023] [Indexed: 09/08/2023]
Abstract
Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.
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Affiliation(s)
- Patric Bourceau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tanja Bien
- Institute of Hygiene, University of Münster, Münster, Germany
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Institute of Human Nutrition and Food Sciences, University of Kiel, Kiel, Germany.
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16
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Brüwer JD, Orellana LH, Sidhu C, Klip HCL, Meunier CL, Boersma M, Wiltshire KH, Amann R, Fuchs BM. In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls. mSystems 2023; 8:e0128722. [PMID: 37195198 PMCID: PMC10308942 DOI: 10.1128/msystems.01287-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 05/18/2023] Open
Abstract
Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls. IMPORTANCE The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom-up and top-down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates in situ. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (Bacteroidetes and Aurantivirga) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top-down control. Microscopy remains the method of choice to understand ecological processes like top-down and bottom-up control on a cellular level.
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Affiliation(s)
- Jan D. Brüwer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helena C. L. Klip
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Cédric L. Meunier
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- University of Bremen, Bremen, Germany
| | - Karen H. Wiltshire
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Wattenmeerstation, List auf Sylt, Bremerhaven, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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17
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Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
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Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
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18
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Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [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: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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19
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Estève PO, Vishnu US, Chin HG, Pradhan S. NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells. Methods Mol Biol 2023; 2611:293-302. [PMID: 36807075 DOI: 10.1007/978-1-0716-2899-7_16] [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] [Indexed: 02/23/2023]
Abstract
A novel genome-wide accessible chromatin visualization, quantitation, and sequencing method is described, which allows in situ fluorescence visualization and sequencing of the accessible chromatin in the mammalian cell. The cells are fixed by formaldehyde crosslinking, and processed using a modified nick translation method, where a nicking enzyme nicks one strand of DNA, and DNA polymerase incorporates biotin-conjugated dCTP, 5-methyl-dCTP, Fluorescein-12-dATP or Texas Red-5-dATP, dGTP, and dTTP. This allows accessible chromatin DNA to be labeled for visualization and on bead NGS library preparation. This technology allows cellular level chromatin accessibility quantification and genomic analysis of the epigenetic information in the chromatin, particularly accessible promoter, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding.
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Affiliation(s)
| | | | - Hang Gyeong Chin
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA.
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20
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Liu YY. Controlling the human microbiome. Cell Syst 2023; 14:135-159. [PMID: 36796332 PMCID: PMC9942095 DOI: 10.1016/j.cels.2022.12.010] [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: 06/06/2022] [Revised: 10/18/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
We coexist with a vast number of microbes that live in and on our bodies. Those microbes and their genes are collectively known as the human microbiome, which plays important roles in human physiology and diseases. We have acquired extensive knowledge of the organismal compositions and metabolic functions of the human microbiome. However, the ultimate proof of our understanding of the human microbiome is reflected in our ability to manipulate it for health benefits. To facilitate the rational design of microbiome-based therapies, there are many fundamental questions to be addressed at the systems level. Indeed, we need a deep understanding of the ecological dynamics associated with such a complex ecosystem before we rationally design control strategies. In light of this, this review discusses progress from various fields, e.g., community ecology, network science, and control theory, that are helping us make progress toward the ultimate goal of controlling the human microbiome.
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Affiliation(s)
- Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
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21
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A Study on Symbiotic Systems of Cicadas Provides New Insights into Distribution of Microbial Symbionts and Improves Fluorescence In Situ Hybridization Technique. Int J Mol Sci 2023; 24:ijms24032434. [PMID: 36768757 PMCID: PMC9917331 DOI: 10.3390/ijms24032434] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 01/28/2023] Open
Abstract
Nutritional symbionts of sap-sucking auchenorrhynchan insects of Hemiptera are usually confined to the bacteriomes and/or fat bodies. Knowledge is limited about the distribution of microbial symbionts in other organs. We investigated the distribution of obligate symbionts in the salivary glands, gut tissues, reproductive organs, bacteriomes, and fat bodies of two cicada species, Karenia caelatata and Tanna sp., using integrated methods, including a modified fluorescence in situ hybridization (FISH) technique, which can greatly enhance the FISH signal intensity of related symbionts. We revealed that Candidatus Sulcia muelleri (Sulcia) and a yeast-like fungal symbiont (YLS) were harbored in the bacteriomes and fat bodies, respectively. Both of Sulcia and YLS can be transmitted to the offspring via ovaries, forming a "symbiont ball" in each egg. Neither Sulcia nor YLS were harbored in the salivary glands, gut tissues and testes. Phylogenetic trees of both Sulcia and cicadas confirm that K. caelatata is a member of the tribe Dundubiini, and the tribe Leptopsaltriini that comprises Ta. sp. is not monophyletic. YLS of K. caelatata is embedded inside the lineage of YLS of Dundubiini, whereas YLS of Ta. sp. is closely related to the clade comprising both cicada-parasitizing fungi Ophiocordyceps and YLS of Mogannia conica and Meimuna mongolica, suggesting an evolutionary replacement of YLS in Ta. sp. from an Ophiocordyceps fungus to another Ophiocordyceps fungus. Our results provide new insights into the symbiosis between Cicadidae and related symbionts. Modification through the addition of helpers and heat shock greatly enhanced the FISH signal intensity of YLS, which may provide guidelines for enhancement of the hybridization signal intensity of other symbiont(s) in the FISH experiments.
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22
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Dirren-Pitsch G, Bühler D, Salcher MM, Bassin B, Le Moigne A, Schuler M, Pernthaler J, Posch T. FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates. Front Microbiol 2022; 13:1070232. [PMID: 36578568 PMCID: PMC9790926 DOI: 10.3389/fmicb.2022.1070232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.
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Affiliation(s)
- Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland,*Correspondence: Gianna Dirren-Pitsch,
| | - Dominique Bühler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M. Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budĕjovice, Czechia
| | - Barbara Bassin
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Alizée Le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Martina Schuler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
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23
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Application of Fluorescence In Situ Hybridization (FISH) in Oral Microbial Detection. Pathogens 2022; 11:pathogens11121450. [PMID: 36558784 PMCID: PMC9788346 DOI: 10.3390/pathogens11121450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Varieties of microorganisms reside in the oral cavity contributing to the occurrence and development of microbes associated with oral diseases; however, the distribution and in situ abundance in the biofilm are still unclear. In order to promote the understanding of the ecosystem of oral microbiota and the diagnosis of oral diseases, it is necessary to monitor and compare the oral microorganisms from different niches of the oral cavity in situ. The fluorescence in situ hybridization (FISH) has proven to be a powerful tool for representing the status of oral microorganisms in the oral cavity. FISH is one of the most routinely used cytochemical techniques for genetic detection, identification, and localization by a fluorescently labeled nucleic acid probe, which can hybridize with targeted nucleic acid sequences. It has the advantages of rapidity, safety, high sensitivity, and specificity. FISH allows the identification and quantification of different oral microorganisms simultaneously. It can also visualize microorganisms by combining with other molecular biology technologies to represent the distribution of each microbial community in the oral biofilm. In this review, we summarized and discussed the development of FISH technology and the application of FISH in oral disease diagnosis and oral ecosystem research, highlighted its advantages in oral microbiology, listed the existing problems, and provided suggestions for future development..
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24
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Vulcano F, Hahn CJ, Roerdink D, Dahle H, Reeves EP, Wegener G, Steen IH, Stokke R. Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents. FEMS Microbiol Ecol 2022; 98:6747120. [PMID: 36190327 PMCID: PMC9576274 DOI: 10.1093/femsec/fiac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 01/21/2023] Open
Abstract
The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.
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Affiliation(s)
- F Vulcano
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
| | - C J Hahn
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany
| | - D Roerdink
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - H Dahle
- Computational Biological Unit, Department of Informatics, Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - E P Reeves
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - G Wegener
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany,MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, 28359, Germany,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - I H Steen
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - R Stokke
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
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25
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Selective single-bacteria extraction based on capture and release of microemulsion droplets. Sci Rep 2022; 12:15461. [PMID: 36104374 PMCID: PMC9474873 DOI: 10.1038/s41598-022-19844-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
Human host-associated microbial communities in body sites can reflect health status based on the population distribution and specific microbial properties in the heterogeneous community. Bacteria identification at the single-cell level provides a reliable biomarker and pathological information for clinical diagnosis. Nevertheless, biosamples obtained from some body sites cannot offer sufficient sample volume and number of target cells as required by most of the existing single-cell isolation methods such as flow cytometry. Herein we report a novel integrated microfluidic system, which consists of a microemulsion module for single-bacteria encapsulation and a sequential microdroplet capture and release module for selectively extracting only the single-bacteria encapsulated in microdroplets. We optimize the system for a success rate of the single-cell extraction to be > 38%. We further verify applicability of the system with prepared cell mixtures (Methylorubrum extorquens AM1 and Methylomicrobium album BG8) and biosamples collected from human skin, to quantify the population distribution of multiple key species in a heterogeneous microbial community. Results indicate perfect viability of the single-cell extracts and compatibility with downstream analyses such as PCR. Together, this research demonstrates that the reported single-bacteria extraction system can be applied in microbiome and pathology research and clinical diagnosis as a clinical or point-of-care device.
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26
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Jo T, Yamanaka H. Fine‐tuning the performance of abundance estimation based on environmental
DNA
(
eDNA
) focusing on
eDNA
particle size and marker length. Ecol Evol 2022. [DOI: 10.1002/ece3.9234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Toshiaki Jo
- Faculty of Advanced Science and Technology Ryukoku University Otsu City Japan
- Ryukoku Center for Biodiversity Science Otsu City Japan
- Research Fellow of Japan Society for the Promotion of Science Chiyoda‐ku Japan
| | - Hiroki Yamanaka
- Faculty of Advanced Science and Technology Ryukoku University Otsu City Japan
- Ryukoku Center for Biodiversity Science Otsu City Japan
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27
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Nácher-Vázquez M, Barbosa A, Armelim I, Azevedo AS, Almeida GN, Pizarro C, Azevedo NF, Almeida C, Cerqueira L. Development of a Novel Peptide Nucleic Acid Probe for the Detection of Legionella spp. in Water Samples. Microorganisms 2022; 10:1409. [PMID: 35889127 PMCID: PMC9318766 DOI: 10.3390/microorganisms10071409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
Legionella are opportunistic intracellular pathogens that are found throughout the environment. The Legionella contamination of water systems represents a serious social problem that can lead to severe diseases, which can manifest as both Pontiac fever and Legionnaires' disease (LD) infections. Fluorescence in situ hybridization using nucleic acid mimic probes (NAM-FISH) is a powerful and versatile technique for bacterial detection. By optimizing a peptide nucleic acid (PNA) sequence based on fluorescently selective binding to specific bacterial rRNA sequences, we established a new PNA-FISH method that has been successfully designed for the specific detection of the genus Legionella. The LEG22 PNA probe has shown great theoretical performance, presenting 99.9% specificity and 96.9% sensitivity. We also demonstrated that the PNA-FISH approach presents a good signal-to-noise ratio when applied in artificially contaminated water samples directly on filtration membranes or after cells elution. For water samples with higher turbidity (from cooling tower water systems), there is still the need for further method optimization in order to detect cellular contents and to overcome interferents' autofluorescence, which hinders probe signal visualization. Nevertheless, this work shows that the PNA-FISH approach could be a promising alternative for the rapid (3-4 h) and accurate detection of Legionella.
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Affiliation(s)
- Montserrat Nácher-Vázquez
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
| | - Ana Barbosa
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Inês Armelim
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
| | - Andreia Sofia Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Gonçalo Nieto Almeida
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
| | - Cristina Pizarro
- INSA—National Institute of Health Doutor Ricardo Jorge, Rua Alexandre Herculano 321, 4000-055 Porto, Portugal;
| | - Nuno Filipe Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carina Almeida
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Laura Cerqueira
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Biodeterioration Assessment of a Unique Old Pharaonic Kingdom Wooden Statue Using Advanced Diagnostic Techniques. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A recently discovered Egyptian wooden statue of King Djedefre was studied together with some surrounding burial soil samples for assessing the statue biodeterioration. The wooden morphological characterisation identified the hardwood Acacia nilotica as the wood type. X-ray diffraction, micro-FT-IR spectroscopy, and scanning electron microscopy with an X-ray spectrometer were used to evaluate the wood deterioration degree and the soil contribution in wood biodeterioration. Microbiological analyses (fluorescent in situ hybridisation and polymerase chain reaction) were also performed to detect the microbial attack on the statue. The prolonged interaction of the statue with the burial environment caused a strong wood decay due to biotic (fungi and bacteria) and abiotic factors (e.g., humidity fluctuations of the burial environment), which caused the severe cracking and collapsing of the wood structures. The analyses of the burial soil mineral composition were relevant for obtaining an overall picture of the statue deterioration. The results are useful for planning the right conservation procedures for this very particular and important wooden statue. Furthermore, analysis of the woody cell wall will help in the selection of appropriate consolidation and recovery treatments. Because the statue is a unique single piece of wood, and the morphological observations indicated that it is a bald woman in a sitting position, this statue will provide new and interesting knowledge of Egyptian culture.
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Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R. Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME COMMUNICATIONS 2022; 2:52. [PMID: 37938730 PMCID: PMC9723565 DOI: 10.1038/s43705-022-00134-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 05/08/2023]
Abstract
Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.
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Affiliation(s)
- George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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30
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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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31
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Saurabh A, Niekamp S, Sgouralis I, Pressé S. Modeling Non-additive Effects in Neighboring Chemically Identical Fluorophores. J Phys Chem B 2022; 126:10.1021/acs.jpcb.2c01889. [PMID: 35649158 PMCID: PMC9712593 DOI: 10.1021/acs.jpcb.2c01889] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative fluorescence analysis is often used to derive chemical properties, including stoichiometries, of biomolecular complexes. One fundamental underlying assumption in the analysis of fluorescence data─whether it be the determination of protein complex stoichiometry by super-resolution, or step-counting by photobleaching, or the determination of RNA counts in diffraction-limited spots in RNA fluorescence in situ hybridization (RNA-FISH) experiments─is that fluorophores behave identically and do not interact. However, recent experiments on fluorophore-labeled DNA origami structures such as fluorocubes have shed light on the nature of the interactions between identical fluorophores as these are brought closer together, thereby raising questions on the validity of the modeling assumption that fluorophores do not interact. Here, we analyze photon arrival data under pulsed illumination from fluorocubes where distances between dyes range from 2 to 10 nm. We discuss the implications of non-additivity of brightness on quantitative fluorescence analysis.
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Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Stefan Niekamp
- Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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32
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Delangiz N, Aliyar S, Pashapoor N, Nobaharan K, Asgari Lajayer B, Rodríguez-Couto S. Can polymer-degrading microorganisms solve the bottleneck of plastics' environmental challenges? CHEMOSPHERE 2022; 294:133709. [PMID: 35074325 DOI: 10.1016/j.chemosphere.2022.133709] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Increasing world population and industrial activities have enhanced anthropogenic pollution, plastic pollution being especially alarming. So, plastics should be recycled and/or make them biodegradable. Chemical and physical remediating methods are usually energy consuming and costly. In addition, they are not ecofriendly and usually produce toxic byproducts. Bioremediation is a proper option as it is cost-efficient and environmentally friendly. Plastic production and consumption are increasing daily, and, as a consequence, more microorganisms are exposed to these nonbiodegradable polymers. Therefore, investigating new efficient microorganisms and increasing the knowledge about their biology can pave the way for efficient and feasible plastic bioremediation processes. In this sense, omics, systems biology and bioinformatics are three important fields to analyze the biodegradation pathways in microorganisms. Based on the above-mentioned technologies, researchers can engineer microorganisms with specific desired properties to make bioremediation more efficient.
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Affiliation(s)
- Nasser Delangiz
- Department of Plant Biotechnology and Breeding, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Sajad Aliyar
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Neda Pashapoor
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | | | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Susana Rodríguez-Couto
- Department of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, FI-50130 Mikkeli, Finland
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33
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Rebrosova K, Samek O, Kizovsky M, Bernatova S, Hola V, Ruzicka F. Raman Spectroscopy—A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings. Front Cell Infect Microbiol 2022; 12:866463. [PMID: 35531343 PMCID: PMC9072635 DOI: 10.3389/fcimb.2022.866463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rapid and accurate identification of pathogens causing infections is one of the biggest challenges in medicine. Timely identification of causative agents and their antimicrobial resistance profile can significantly improve the management of infection, lower costs for healthcare, mitigate ever-growing antimicrobial resistance and in many cases, save lives. Raman spectroscopy was shown to be a useful—quick, non-invasive, and non-destructive —tool for identifying microbes from solid and liquid media. Modifications of Raman spectroscopy and/or pretreatment of samples allow single-cell analyses and identification of microbes from various samples. It was shown that those non-culture-based approaches could also detect antimicrobial resistance. Moreover, recent studies suggest that a combination of Raman spectroscopy with optical tweezers has the potential to identify microbes directly from human body fluids. This review aims to summarize recent advances in non-culture-based approaches of identification of microbes and their virulence factors, including antimicrobial resistance, using methods based on Raman spectroscopy in the context of possible use in the future point-of-care diagnostic process.
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Affiliation(s)
- Katarina Rebrosova
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Martin Kizovsky
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Silvie Bernatova
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Veronika Hola
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
- *Correspondence: Veronika Hola,
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
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Caldara M, Belgiovine C, Secchi E, Rusconi R. Environmental, Microbiological, and Immunological Features of Bacterial Biofilms Associated with Implanted Medical Devices. Clin Microbiol Rev 2022; 35:e0022120. [PMID: 35044203 PMCID: PMC8768833 DOI: 10.1128/cmr.00221-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spread of biofilms on medical implants represents one of the principal triggers of persistent and chronic infections in clinical settings, and it has been the subject of many studies in the past few years, with most of them focused on prosthetic joint infections. We review here recent works on biofilm formation and microbial colonization on a large variety of indwelling devices, ranging from heart valves and pacemakers to urological and breast implants and from biliary stents and endoscopic tubes to contact lenses and neurosurgical implants. We focus on bacterial abundance and distribution across different devices and body sites and on the role of environmental features, such as the presence of fluid flow and properties of the implant surface, as well as on the interplay between bacterial colonization and the response of the human immune system.
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Affiliation(s)
- Marina Caldara
- Interdepartmental Center on Safety, Technologies, and Agri-food Innovation (SITEIA.PARMA), University of Parma, Parma, Italy
| | - Cristina Belgiovine
- IRCCS Humanitas Research Hospital, Rozzano–Milan, Italy
- Scuola di Specializzazione in Microbiologia e Virologia, Università degli Studi di Pavia, Pavia, Italy
| | - Eleonora Secchi
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Roberto Rusconi
- IRCCS Humanitas Research Hospital, Rozzano–Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele–Milan, Italy
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Kao YT, Calabrese S, Borst N, Lehnert M, Lai YK, Schlenker F, Juelg P, Zengerle R, Garstecki P, von Stetten F. Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification. BIOSENSORS 2022; 12:bios12040237. [PMID: 35448297 PMCID: PMC9032532 DOI: 10.3390/bios12040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 02/06/2023]
Abstract
We demonstrate detection and quantification of bacterial load with a novel microfluidic one-pot wash-free fluorescence in situ hybridization (FISH) assay in droplets. The method offers minimal manual workload by only requiring mixing of the sample with reagents and loading it into a microfluidic cartridge. By centrifugal microfluidic step emulsification, our method partitioned the sample into 210 pL (73 µm in diameter) droplets for bacterial encapsulation followed by in situ permeabilization, hybridization, and signal detection. Employing locked nucleic acid (LNA)/DNA molecular beacons (LNA/DNA MBs) and NaCl-urea based hybridization buffer, the assay was characterized with Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The assay performed with single-cell sensitivity, a 4-log dynamic range from a lower limit of quantification (LLOQ) at ~3 × 103 bacteria/mL to an upper limit of quantification (ULOQ) at ~3 × 107 bacteria/mL, anda linearity R2 = 0.976. The total time-to-results for detection and quantification was around 1.5 hours.
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Affiliation(s)
- Yu-Ting Kao
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Nadine Borst
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Yu-Kai Lai
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Franziska Schlenker
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
- Correspondence: ; Tel.: +49-761-203-73243
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Dalimot JJ, Smith IMC, Gerkrath J, Hartmann S, Cornely OA, Lee SC, Heitman J, Rickerts V. Identification of Mucormycosis by Fluorescence In Situ Hybridization Targeting Ribosomal RNA in Tissue Samples. J Fungi (Basel) 2022; 8:jof8030289. [PMID: 35330291 PMCID: PMC8949899 DOI: 10.3390/jof8030289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/17/2022] Open
Abstract
Mucormycosis is an invasive fungal infection associated with high mortality, partly due to delayed diagnosis and inadequate empiric therapy. As fungal cultures often fail to grow Mucorales, identification of respective hyphae in tissue is frequently needed for diagnosis but may be challenging. We studied fluorescence in situ hybridization (FISH) targeting specific regions of the fungal ribosomal RNA (rRNA) of Mucorales to improve diagnosis of mucormycosis from tissue samples. We generated a probe combination specifically targeting Mucorales. Probe specificity was verified in silico and using cultivated fungi. Mucorales hyphae in tissue of a mouse model demonstrated a bright cytoplasmatic hybridization signal. In tissue samples of patients with mucormycosis, a positive signal was seen in 7 of 12 (58.3%) samples. However, autofluorescence in 3 of 7 (42.9%) samples impaired the diagnostic yield. Subsequent experiments suggested that availability of nutrients and antifungal therapy may impact on the FISH signal obtained with Mucorales hyphae. Diagnosis of mucormycosis from tissue might be improved by rRNA FISH in a limited number of cases only. FISH signals may reflect different physiological states of fungi in tissue. Further studies are needed to define the value of FISH to diagnose mucormycosis from other clinical samples.
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Affiliation(s)
- Jill Jasmine Dalimot
- Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch Institute (RKI), 13353 Berlin, Germany; (J.J.D.); (I.M.C.S.); (J.G.)
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ilka Mc Cormick Smith
- Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch Institute (RKI), 13353 Berlin, Germany; (J.J.D.); (I.M.C.S.); (J.G.)
| | - Jasmin Gerkrath
- Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch Institute (RKI), 13353 Berlin, Germany; (J.J.D.); (I.M.C.S.); (J.G.)
| | - Sylvia Hartmann
- Senckenberg Institute for Pathology, Johann Wolfgang Goethe University Frankfurt, 60323 Frankfurt am Main, Germany;
| | - Oliver A. Cornely
- Excellence Center for Medical Mycology (ECMM), Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany;
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Chair Translational Research, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany
- Clinical Trials Centre Cologne (ZKS Köln), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 50923 Cologne, Germany
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; (S.C.L.); (J.H.)
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Molecular Microbiology and Immunology, The University of Texas, San Antonio, TX 78249, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; (S.C.L.); (J.H.)
| | - Volker Rickerts
- Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch Institute (RKI), 13353 Berlin, Germany; (J.J.D.); (I.M.C.S.); (J.G.)
- Correspondence:
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Design and Experimental Evaluation of a New RNA-FISH Probe to Detect and Identify Paenibacillus sp. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Paenibacillus, rod-saped gram-positive endospores forming aerobic or facultative anaerobic bacteria, colonize diverse ecosystems and are involved in the biodegradation of cultural heritage assets. Biodeteriogenic microorganisms can be easily detected/identified by ribonucleic acid- fluorescent in situ hybridization RNA-FISH with specific probes. In this work, probes designed in silico were analyzed to calculate hybridization efficiency and specificity by varying the formamide concentration in the hybridization. The Pab489 probe showed excellent in silico performance with high theoretical maximum efficiency hybridization (99.99%) and specificity and was selected for experimental assays with target Paenibacillus sp. and non-target biodeteriogenic microorganisms. Results assessed by epifluorescence microscopy and flow cytometry revealed that, regardless of the formamide concentration, it was possible to observe that the Pab489-Cy3 probe had a similar signal intensity to the EUB338-Cy3 probe (positive control), so the presence of formamide, a highly toxic and carcinogenic compound used to aid the hybridization process, is not necessary. The designed probe used in FISH assays allows specific in situ identification of Paenibacillus spp. in microbial communities in a culture-independent way. This approach can be employed for screening Paenibacillus spp., showing great potential for future application in biodeterioration of heritage assets, in the search for Paenibacillus strains that produce compounds with biotechnological or medical potential.
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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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Xu H, Chen D, Jia L. Intelligent assembly of Y-shaped DNA nanostructures for intracellular microRNA imaging. Anal Chim Acta 2022; 1189:338701. [PMID: 34815048 DOI: 10.1016/j.aca.2021.338701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 11/26/2022]
Abstract
Highly sensitive and specific imaging of low-level microRNAs (miRNAs) in cytoplasm is vital for early diagnosis of cancers. In this work, we have developed the amplification strategies for miRNA-155 detection based on the combination the nicked rolling circle amplification (N-RCA) and catalyzed hairpin assembly (CHA). In this system, the target miRNA-155 acts as a polymerase primer to activate N-RCA to produce nicked fragment1 (NF1) and NF2. NF1 acted as new primer could further initiate a new N-RCA reaction over and over. Then, the NF2s could serve as triggers to induce the CHA reaction, and the Y-shaped DNA nanostructure (Y-SDN) was formed. Thus, an amplified fluorescence signal was obtained based on the multiple amplification. Under the optimized experimental conditions, a high sensitivity with a detection limit as low as 1.8 pM at 3σ miRNA-155 and excellent specificity in buffer condition have been achieved by applying this method. Meanwhile, the proposed method enables the application in miRNA-155 detection in human serum. Moreover, we have shown that the method performs well for the intracellular miRNA-155 imaging in cellular environments. Therefore, the present strategy was expected to apply into the clinical disease diagnosis effectively.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China.
| | - Danlong Chen
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
| | - Lee Jia
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China.
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Ma H, Zhao Y, Yang K, Wang Y, Zhang C, Ji M. Application oriented bioaugmentation processes: Mechanism, performance improvement and scale-up. BIORESOURCE TECHNOLOGY 2022; 344:126192. [PMID: 34710609 DOI: 10.1016/j.biortech.2021.126192] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Bioaugmentation is an optimization method with great potential to improve the treatment effect by introducing specific strains into the biological treatment system. In this study, a comprehensive review of the mechanism of bioaugmentation from the aspect of microbial community structure, the optimization methods facilitating application as well as feasible approaches of scale-up application has been provided. The different contribution of indigenous and exogenous strains was critically analyzed, the relationship between microbial community variation and system performance was clarified. Operation regulation and immobilization technologies are effective methods to deal with the possible failure of bioaugmentation. The gradual expansion from lab-scale, pilot scale to full-scale, the transformation and upgrading of wastewater treatment plants through the combination of direct dosing and biofilm, and the application of side-stream reactors are feasible ways to realize the full-scale application. The future challenges and prospects in this field were also proposed.
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Affiliation(s)
- Huilin Ma
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Kaichao Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yue Wang
- School of Environmental Science and Engineering, Tiangong University, Tianjin 300387, China
| | - Chenggong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
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Comprehensive Assessment of the Virulence Factors sub 3, sub 6 and mcpA in the Zoonotic Dermatophyte Trichophyton benhamiae Using FISH and qPCR. J Fungi (Basel) 2021; 8:jof8010024. [PMID: 35049964 PMCID: PMC8778074 DOI: 10.3390/jof8010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Skin infections by keratinophilic fungi are commonly referred to as dermatophytosis and represent a major health burden worldwide. Although patient numbers are on the rise, data on virulence factors, their function and kinetics are scarce. We employed an ex vivo infection model based on guinea pig skin explants (GPSE) for the zoonotic dermatophyte Trichophyton (T.) benhamiae to investigate kinetics of the virulence factors subtilisin (sub) 3, sub 6, metallocarboxypeptidase A (mcpA) and isocitrate lyase (isol) at gene level for ten days. Fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR) were used to detect and quantify the transcripts, respectively. Kingdom-spanning, species-specific and virulence factor-specific probes were successfully applied to isolated fungal elements showing inhomogeneous fluorescence signals along hyphae. Staining results for inoculated GPSE remained inconsistent despite thorough optimization. qPCR revealed a significant increase of sub 3- and mcpA-transcripts toward the end of culture, sub 6 and isol remained at a low level throughout the entire culture period. Sub 3 is tightly connected to the de novo formation of conidia during culture. Since sub 6 is considered an in vivo disease marker. However, the presented findings urgently call for further research on the role of certain virulence factors during infection and disease.
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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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43
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Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis. WATER 2021. [DOI: 10.3390/w13243551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.
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Cruz A, Condinho M, Carvalho B, Arraiano CM, Pobre V, Pinto SN. The Two Weapons against Bacterial Biofilms: Detection and Treatment. Antibiotics (Basel) 2021; 10:1482. [PMID: 34943694 PMCID: PMC8698905 DOI: 10.3390/antibiotics10121482] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial biofilms are defined as complex aggregates of bacteria that grow attached to surfaces or are associated with interfaces. Bacteria within biofilms are embedded in a self-produced extracellular matrix made of polysaccharides, nucleic acids, and proteins. It is recognized that bacterial biofilms are responsible for the majority of microbial infections that occur in the human body, and that biofilm-related infections are extremely difficult to treat. This is related with the fact that microbial cells in biofilms exhibit increased resistance levels to antibiotics in comparison with planktonic (free-floating) cells. In the last years, the introduction into the market of novel compounds that can overcome the resistance to antimicrobial agents associated with biofilm infection has slowed down. If this situation is not altered, millions of lives are at risk, and this will also strongly affect the world economy. As such, research into the identification and eradication of biofilms is important for the future of human health. In this sense, this article provides an overview of techniques developed to detect and imaging biofilms as well as recent strategies that can be applied to treat biofilms during the several biofilm formation steps.
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Affiliation(s)
- Adriana Cruz
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Manuel Condinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Beatriz Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Sandra N. Pinto
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Zhang Z, Huang X, Liu K, Lan T, Wang Z, Zhu Z. Recent Advances in Electrical Impedance Sensing Technology for Single-Cell Analysis. BIOSENSORS 2021; 11:470. [PMID: 34821686 PMCID: PMC8615761 DOI: 10.3390/bios11110470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 05/10/2023]
Abstract
Cellular heterogeneity is of significance in cell-based assays for life science, biomedicine and clinical diagnostics. Electrical impedance sensing technology has become a powerful tool, allowing for rapid, non-invasive, and label-free acquisition of electrical parameters of single cells. These electrical parameters, i.e., equivalent cell resistance, membrane capacitance and cytoplasm conductivity, are closely related to cellular biophysical properties and dynamic activities, such as size, morphology, membrane intactness, growth state, and proliferation. This review summarizes basic principles, analytical models and design concepts of single-cell impedance sensing devices, including impedance flow cytometry (IFC) to detect flow-through single cells and electrical impedance spectroscopy (EIS) to monitor immobilized single cells. Then, recent advances of both electrical impedance sensing systems applied in cell recognition, cell counting, viability detection, phenotypic assay, cell screening, and other cell detection are presented. Finally, prospects of impedance sensing technology in single-cell analysis are discussed.
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Affiliation(s)
- Zhao Zhang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing 210018, China; (Z.Z.); (K.L.); (T.L.)
| | - Xiaowen Huang
- The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Department of Orthopedics, Nanjing 210029, China;
| | - Ke Liu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing 210018, China; (Z.Z.); (K.L.); (T.L.)
| | - Tiancong Lan
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing 210018, China; (Z.Z.); (K.L.); (T.L.)
| | - Zixin Wang
- School of Electronics and Information Technology, Sun Yat-Sen University, Xingang Xi Road 135, Guangzhou 510275, China;
| | - Zhen Zhu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing 210018, China; (Z.Z.); (K.L.); (T.L.)
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Schneider M, Bäumler M, Lee NM, Weuster-Botz D, Ehrenreich A, Liebl W. Monitoring co-cultures of Clostridium carboxidivorans and Clostridium kluyveri by fluorescence in situ hybridization with specific 23S rRNA oligonucleotide probes. Syst Appl Microbiol 2021; 44:126271. [PMID: 34735802 DOI: 10.1016/j.syapm.2021.126271] [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: 07/17/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
The development of co-cultures of clostridial strains which combine different physiological traits represents a promising strategy to achieve the environmentally friendly production of biofuels and chemicals. For the optimization of such co-cultures it is essential to monitor their composition and stability throughout fermentation. FISH is a quick and sensitive method for the specific labeling and quantification of cells within microbial communities. This technique is neither limited by the anaerobic fermenter environment nor by the need of prior genetic modification of strains. In this study, two specific 23S rRNA oligonucleotide probes, ClosKluy and ClosCarb, were designed for the monitoring of C. kluyveri and C. carboxidivorans, respectively. After the optimization of hybridization conditions for both probes, which was achieved at 30% (v/v) formamide, a high specificity was observed with epifluorescence microscopy using cells from different pure reference strains. The discriminating properties of the ClosKluy and ClosCarb probes was verified with samples from heterotrophic co-cultures in anaerobic flasks as well as autotrophic stirred-tank bioreactor co-cultures of C. kluyveri and C. carboxidivorans. Besides being suited to monitor defined co-cultures of these two species, the new specific FISH oligonucleotide probes for C. kluyveri and C. carboxidivorans additionally have potential to be applied in environmental studies.
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Affiliation(s)
- Martina Schneider
- Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany
| | - Miriam Bäumler
- Department of Mechanical Engineering, Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Natuschka M Lee
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Research Infrastructure Fluorescence in Situ Hybridization (FISH), Chemical Biological Centre, Umeå University, Umeå, Sweden
| | - Dirk Weuster-Botz
- Department of Mechanical Engineering, Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Armin Ehrenreich
- Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany.
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany
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Jia Z, Dong Y, Xu H, Wang F. Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol for detection of microbes in sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:529-541. [PMID: 37073263 PMCID: PMC10077247 DOI: 10.1007/s42995-021-00098-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/17/2021] [Indexed: 05/03/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a canonical tool commonly used in environmental microbiology research to visualize targeted cells. However, the problems of low signal intensity and false-positive signals impede its widespread application. Alternatively, the signal intensity can be amplified by incorporating Hybridization Chain Reaction (HCR) with FISH, while the specificity can be improved through protocol modification and proper counterstaining. Here we optimized the HCR-FISH protocol for studying microbes in environmental samples, particularly marine sediments. Firstly, five sets of HCR initiator/amplifier pairs were tested on the laboratory-cultured bacterium Escherichia coli and the archaeon Methanococcoides methylutens, and two sets displayed high hybridization efficiency and specificity. Secondly, we tried to find the best combination of sample pretreatment methods and HCR-FISH protocol for environmental sample analysis with the aim of producing less false positive signals. Various detachment methods, extraction methods and formulas of hybridization buffer were tested using sediment samples. Thirdly, an image processing method was developed to enhance the DAPI signal of microbial cells against that of abiotic particles, providing a reliable reference for FISH imaging. In summary, our optimized HCR-FISH protocol showed promise to serve as an addendum to traditional FISH for research on environmental microbes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00098-8.
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Affiliation(s)
- Zeyu Jia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Heng Xu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240 China
- Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240 China
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Evaluation of RNA later as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses. Microbiol Spectr 2021; 9:e0142921. [PMID: 34704828 PMCID: PMC8549751 DOI: 10.1128/spectrum.01429-21] [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
Field studies are central to environmental microbiology and microbial ecology, because they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows investigators to study these communities "in situ," which requires protein preservation directly in the field because protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is nonhazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability under field conditions when targeted for metaproteomic analyses is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater storage after 1 day, 1 week, and 4 weeks at room temperature (22°C to 23°C). We evaluated protein preservation using one-dimensional liquid chromatography-tandem mass spectrometry. We found that RNAlater and flash freezing preserved proteins equally well in terms of total numbers of identified proteins and relative abundances of individual proteins, and none of the test time points was altered, compared to time zero. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomic data and the logistical requirements for field deployment, we recommend RNAlater for protein preservation of field-collected samples targeted for metaproteomic analyses. IMPORTANCE Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory setups, samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations, due to their hazardous nature and transport restrictions. Our study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses. We show that RNAlater preserves the metaproteome equally well, compared to flash freezing, and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature.
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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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50
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Sun H, Jiang S, Jiang C, Wu C, Gao M, Wang Q. A review of root exudates and rhizosphere microbiome for crop production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54497-54510. [PMID: 34431053 DOI: 10.1007/s11356-021-15838-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/02/2021] [Indexed: 05/04/2023]
Abstract
Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.
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Affiliation(s)
- Haishu Sun
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shanxue Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China
| | - Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chuanfu Wu
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Ming Gao
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Qunhui Wang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China.
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