1
|
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.
Collapse
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
| |
Collapse
|
2
|
Samanta P, Cooke SF, McNulty R, Hormoz S, Rosenthal A. ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets. Nat Protoc 2024:10.1038/s41596-024-01002-1. [PMID: 38769144 DOI: 10.1038/s41596-024-01002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/12/2024] [Indexed: 05/22/2024]
Abstract
Methods that measure the transcriptomic state of thousands of individual cells have transformed our understanding of cellular heterogeneity in eukaryotic cells since their introduction in the past decade. While simple and accessible protocols and commercial products are now available for the processing of mammalian cells, these existing technologies are incompatible with use in bacterial samples for several fundamental reasons including the absence of polyadenylation on bacterial messenger RNA, the instability of bacterial transcripts and the incompatibility of bacterial cell morphology with existing methodologies. Recently, we developed ProBac sequencing (ProBac-seq), a method that overcomes these technical difficulties and provides high-quality single-cell gene expression data from thousands of bacterial cells by using messenger RNA-specific probes. Here we provide details for designing large oligonucleotide probe sets for an organism of choice, amplifying probe sets to produce sufficient quantities for repeated experiments, adding unique molecular indexes and poly-A tails to produce finalized probes, in situ probe hybridization and single-cell encapsulation and library preparation. This protocol, from the probe amplification to the library preparation, requires ~7 d to complete. ProBac-seq offers several advantages over other methods by capturing only the desired target sequences and avoiding nondesired transcripts, such as highly abundant ribosomal RNA, thus enriching for signal that better informs on cellular state. The use of multiple probes per gene can detect meaningful single-cell signals from cells expressing transcripts to a lesser degree or those grown in minimal media and other environmentally relevant conditions in which cells are less active. ProBac-seq is also compatible with other organisms that can be profiled by in situ hybridization techniques.
Collapse
Affiliation(s)
- Prosenjit Samanta
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Samuel F Cooke
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Ryan McNulty
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sahand Hormoz
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Rosenthal
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
| |
Collapse
|
3
|
Abstract
FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.
Collapse
Affiliation(s)
- Nuno M Guimarães
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
4
|
Barrero-Canosa J, Moraru C. Linking Microbes to Their Genes at Single Cell Level with Direct-geneFISH. Methods Mol Biol 2021; 2246:169-205. [PMID: 33576990 DOI: 10.1007/978-1-0716-1115-9_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Direct-geneFISH is a Fluorescence In Situ Hybridization (FISH) method that directly links gene presence, and thus potential metabolic capabilities, to cell identity. The method uses rRNA-targeting oligonucleotide probes to identify cells and dsDNA polynucleotide probes carrying multiple molecules of the same fluorochrome to detect genes. In addition, direct-geneFISH allows quantification of the cell fraction carrying the targeted gene and the number of target genes per cell. It can be applied to laboratory cultures, for example, enrichments and phage infections, and to environmental samples. This book chapter describes the main steps of the direct-geneFISH protocol: probe design and synthesis, the "core" direct-geneFISH protocol and lastly, microscopy and data analysis.
Collapse
Affiliation(s)
- Jimena Barrero-Canosa
- Department of Environmental Technology, Technische Universität Berlin, Berlin, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.
| |
Collapse
|
5
|
Castillo YM, Sebastián M, Forn I, Grimsley N, Yau S, Moraru C, Vaqué D. Visualization of Viral Infection Dynamics in a Unicellular Eukaryote and Quantification of Viral Production Using Virus Fluorescence in situ Hybridization. Front Microbiol 2020; 11:1559. [PMID: 32765451 PMCID: PMC7379908 DOI: 10.3389/fmicb.2020.01559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/16/2020] [Indexed: 11/13/2022] Open
Abstract
One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.
Collapse
Affiliation(s)
- Yaiza M Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanographic Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Sheree Yau
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanographic Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Cristina Moraru
- Department of the Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| |
Collapse
|
6
|
Mori T, Katayama Y. Signal amplification in flow cytometry for cell surface antigen analysis. J Biochem 2019; 166:205-212. [PMID: 31251348 DOI: 10.1093/jb/mvz052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/25/2019] [Indexed: 01/12/2023] Open
Abstract
Signal enhancing systems have been introduced to enable detection of cell surface antigens by flow cytometry. Cell surface antigens are important targets that describe the function and lineage of cells. Although flow cytometry is an effective tool for analysing cell surface antigens, this technique has poor sensitivity, which prohibits the detection of many important antigens on cell membranes. Thus, signal amplification is essential for developing practical tools for evaluating cell surface antigens by flow cytometry. Using a bright fluorophore or fluorescent polymer incorporated into antibodies is a straightforward strategy to improve flow cytometry sensitivity but may affect the functional characteristics of the labelled antibody. In contrast, enzymatic signal amplification is a more practical and efficient strategy to improve sensitivity that should not affect antibody activity. Although enzymatic signal amplification still has a number of drawbacks, this approach is a promising strategy to analyse cell surface antigens.
Collapse
Affiliation(s)
- Takeshi Mori
- Faculty of Engineering, Department of Chemistry and Biochemistry, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, Japan
| | - Yoshiki Katayama
- Faculty of Engineering, Department of Chemistry and Biochemistry, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, Japan
| |
Collapse
|
7
|
Zhu Y, Wang Y, Yan Y, Xue H. Rapid and Sensitive Quantification of Anammox Bacteria by Flow Cytometric Analysis Based on Catalyzed Reporter Deposition Fluorescence In Situ Hybridization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:6895-6905. [PMID: 31120737 DOI: 10.1021/acs.est.9b01017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The quantification of anammox bacteria is crucial to manipulation and management of anammox biosystems. In this study, we proposed a protocol specifically optimized for quantification of anammox bacteria abundance in anammox sludge samples using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) and flow cytometry (FCM) in combination (Flow-CARD-FISH). We optimized the pretreatment procedures for FCM-compatibility, as well as the permeabilization, hybridization and staining protocols of the CARD-FISH. The developed method was compared with other methods for specific bacteria quantification (standard FISH, 16S rRNA sequencing and quantitative polymerase chain reaction). Anammox sludge samples could be disaggregated effectively by sonication (specific energy of 90 kJ·L-1 with MLVSS of 3-5 g·L-1) with the mixed ionic and nonionic dispersants Triton X-100 (5%) and sodium pyrophosphate (10 mM). Lysozyme treatment for permeabilizing bacterial cell walls and H2O2 incubation for completely quenching endogenous peroxidase of anammox sludges were essential to fluorescence enhancement and false positive signals control, respectively. Horseradish peroxidase molecules labeling at 20 °C for 12 h and the fluorescent tyramide labeling at 25 °C for 30 min with a fluorescent substrate concentration of 1:50 maintained the balance between increasing the signal and preventing nonspecific binding. Flow-CARD-FISH results showed that anammox bacteria absolute abundance in two different sludge samples were (2.31 ± 0.01) × 107 and (1.20 ± 0.06) × 107 cells·mL-1, respectively, with the relative abundances of 36.7 ± 4.1% and 26.5 ± 3.7%, respectively, comparable with those of qPCR and 16S rRNA sequencing analysis. The enhanced fluorescence signals induced by CARD-FISH combined with the high quantitative fluorescence sensitivity of FCM provide a rapid and sensitive method that yields accurate quantification results that will be valuable in future studies of microbial community determination.
Collapse
Affiliation(s)
- Yijing Zhu
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering , Tongji University , Siping Road , Shanghai 200092 , P. R. China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering , Tongji University , Siping Road , Shanghai 200092 , P. R. China
| | - Yuan Yan
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering , Tongji University , Siping Road , Shanghai 200092 , P. R. China
| | - Hao Xue
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering , Tongji University , Siping Road , Shanghai 200092 , P. R. China
| |
Collapse
|
8
|
Yang Y, Li Y, Gu Z, Lu F, Xia S, Hermanowicz S. Quick start-up and stable operation of a one-stage deammonification reactor with a low quantity of AOB and ANAMMOX biomass. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:933-941. [PMID: 30453263 DOI: 10.1016/j.scitotenv.2018.11.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
In this study, a quick start-up of one-stage deammonification in an immobilized aerobic ammonium oxidizing bacteria (AOB) and anoxic ammonium oxidizing (ANAMMOX) bacteria up-flow reactor (IAAR) was successfully achieved. With the aid of gel layers, AOB and ANAMMOX bacteria had excellent spatial distribution, theoretically meeting dissolved oxygen requirements for the simultaneous processes of aerobic and anaerobic ammonium oxidizing. The results indicated that an IAAR containing 0.4 g-VSS L-1 immobilized biomass achieved a nitrogen removal rate (NRR) of 0.53 kg-N m-3 d-1 after only 10 days of operation and subsequently reached a maximum nitrogen removal rate (NRRmax) of 3.73 kg-N m-3 d-1. The micro-profiles of DO and pH were measured using microelectrodes to help understand the stratification of the microbial processes inside the gel layers. The distribution of AOB and ANAMMOX bacteria within the gel layers was verified using fluorescence in situ hybridization (FISH) analysis. The community distribution in the FISH three-dimensional images closely corresponded to the micro-profiles of DO concentration and pH, enabling rapid adaptation and stable operation of the reactor seeded with a quite low quantity of biomass.
Collapse
Affiliation(s)
- Yifeng Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA
| | - Yuan Li
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA; Tsinghua-Berkeley Shenzhen Institute, Tsinghua University Shenzhen, PR China
| | - Zaoli Gu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA
| | - Feng Lu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China.
| | - Slawomir Hermanowicz
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA; Tsinghua-Berkeley Shenzhen Institute, Tsinghua University Shenzhen, PR China
| |
Collapse
|
9
|
Abstract
PhageFISH uses the power of fluorescence in situ hybridization to monitor intracellular phage infections at single cell level. It combines host cell identification via rRNA probes and phage identification via phage-specific gene probes, allowing for the quantification of the infected cell fraction and the discrimination between infection stages. This book chapter covers all aspects of the procedure, from phage probe design and synthesis, to the phageFISH protocol itself, to microscopy and image analysis.
Collapse
|
10
|
Sharafat I, Saeed DK, Yasmin S, Imran A, Zafar Z, Hameed A, Ali N. Interactive effect of trivalent iron on activated sludge digestion and biofilm structure in attached growth reactor of waste tire rubber. ENVIRONMENTAL TECHNOLOGY 2018; 39:130-143. [PMID: 28278106 DOI: 10.1080/09593330.2017.1296894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 02/14/2017] [Indexed: 06/06/2023]
Abstract
Waste tire rubber (WTR) has been introduced as an alternative, novel media for biofilm development in several experimental systems including attached growth bioreactors. In this context, four laboratory-scale static batch bioreactors containing WTR as a support material for biofilm development were run under anoxic condition for 90 days using waste activated sludge as an inoculum under the influence of different concentrations (2.5, 6.5, 8.5 mg/l) of trivalent ferric iron (Fe3+). The data revealed that activated sludge with a Fe3+ concentration of 8.5 mg/l supported the maximum bacterial biomass [4.73E + 10 CFU/ml cm2]; besides, it removed 38% more Chemical oxygen demand compared to Fe3+ free condition from the reactor. Biochemical testing and 16S rDNA phylogenetic analysis of WTR-derived biofilm communities further suggested the role of varying concentrations of Fe3+ on the density and diversity of members of Enterobacteria(ceae), ammonium (AOB) and nitrite oxidizing bacteria. Furthermore, Fluorescent in situ hybridization with phylogenetic oligonucleotide probes and confocal laser scanning microscopy of WTR biofilms indicated a significant increase in density of eubacteria (3.00E + 01 to.05E + 02 cells/cm2) and beta proteobacteria (8.10E + 01 to 1.42E + 02 cells/cm2), respectively, with an increase in Fe3+ concentration in the reactors, whereas, the cell density of gamma proteobacteria in biofilms decreased.
Collapse
Affiliation(s)
- Iqra Sharafat
- a Department of Microbiology , Quaid-i-Azam University Islamabad , Pakistan
| | - Dania Khalid Saeed
- a Department of Microbiology , Quaid-i-Azam University Islamabad , Pakistan
| | - Sumera Yasmin
- b National Institute for Biotechnology and Genetic Engineering (NIBGE) , Faisalabad , Pakistan
| | - Asma Imran
- b National Institute for Biotechnology and Genetic Engineering (NIBGE) , Faisalabad , Pakistan
| | - Zargona Zafar
- a Department of Microbiology , Quaid-i-Azam University Islamabad , Pakistan
| | - Abdul Hameed
- a Department of Microbiology , Quaid-i-Azam University Islamabad , Pakistan
| | - Naeem Ali
- a Department of Microbiology , Quaid-i-Azam University Islamabad , Pakistan
| |
Collapse
|
11
|
Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kačániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C. Critical review on biofilm methods. Crit Rev Microbiol 2016; 43:313-351. [PMID: 27868469 DOI: 10.1080/1040841x.2016.1208146] [Citation(s) in RCA: 541] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.
Collapse
Affiliation(s)
- Joana Azeredo
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Nuno F Azevedo
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Romain Briandet
- c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Nuno Cerca
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Tom Coenye
- d Laboratory of Pharmaceutical Microbiology , Ghent University , Ghent , Belgium
| | - Ana Rita Costa
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Mickaël Desvaux
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Giovanni Di Bonaventura
- f Department of Medical, Oral, and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT) , "G. d'Annunzio" University of Chieti-Pescara , Chieti , Italy
| | - Michel Hébraud
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Zoran Jaglic
- g Department of Food and Feed Safety, Laboratory of Food Bacteriology , Veterinary Research Institute , Brno , Czech Republic
| | - Miroslava Kačániová
- h Department of Microbiology, Faculty of Biotechnology and Food Sciences , Slovak University of Agriculture in Nitra , Nitra , Slovakia
| | - Susanne Knøchel
- i Department of Food Science (FOOD) , University of Copenhagen , Frederiksberg C , Denmark
| | - Anália Lourenço
- j Department of Computer Science , University of Vigo , Ourense , Spain
| | - Filipe Mergulhão
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Rikke Louise Meyer
- k Aarhus University, Interdisciplinary Nanoscience Center (iNANO) , Aarhus , Denmark
| | - George Nychas
- l Agricultural University of Athens, Lab of Microbiology and Biotechnology of Foods , Athens , Greece
| | - Manuel Simões
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Odile Tresse
- m LUNAM Université, Oniris, SECALIM UMR1024 INRA , Université de Nantes , Nantes , France
| | - Claus Sternberg
- n Department of Biotechnology and Biomedicine , Technical University of Denmark , Lyngby, Denmark
| |
Collapse
|
12
|
Guo J, Peng Y, Fan L, Zhang L, Ni BJ, Kartal B, Feng X, Jetten MSM, Yuan Z. Metagenomic analysis of anammox communities in three different microbial aggregates. Environ Microbiol 2016; 18:2979-93. [DOI: 10.1111/1462-2920.13132] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 11/07/2015] [Accepted: 11/11/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Jianhua Guo
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
| | - Lu Fan
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Liang Zhang
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Boran Kartal
- Microbiology, IWWR; Faculty of Science; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Department of Biochemistry and Microbiology; Laboratory of Microbiology; Gent University; Gent 9000 Belgium
| | - Xin Feng
- Research Department of Microbiology; Beijing Genomics Institute (BGI)-Shenzhen; Shenzhen China
| | - Mike S. M. Jetten
- Microbiology, IWWR; Faculty of Science; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Zhiguo Yuan
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| |
Collapse
|
13
|
Dosta J, Vila J, Sancho I, Basset N, Grifoll M, Mata-Álvarez J. Two-step partial nitritation/Anammox process in granulation reactors: Start-up operation and microbial characterization. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 164:196-205. [PMID: 26386756 DOI: 10.1016/j.jenvman.2015.08.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/29/2015] [Accepted: 08/15/2015] [Indexed: 06/05/2023]
Abstract
A two-stage Partial Nitritation (PN)/Anammox process was carried out at lab-scale conditions to treat reject water from a municipal WWTP. PN was achieved in a granular SBR obtaining an effluent with a NH4(+)-N/NO2(-)-N molar ratio around 1.0. The microbial characterization of this reactor revealed a predominance of Betaproteobacteria, with a member of Nitrosomonas as the main autotrophic ammonium oxidizing bacterium (AOB). Nitrite oxidizing bacteria (NOB) were under the detection limit of 16S rRNA gene pyrosequencing, indicating their effective inhibition. The effluent of the PN reactor was fed to an Anammox SBR where stable operation was achieved with a NH4(+)-N:NO2(-)-N:NO3(-)-N stoichiometry of 1:1.25:0.14. The deviation to the theoretical stoichiometry could be attributed to the presence of heterotrophic biomass in the Anammox reactor (mainly members of Chlorobi and Chloroflexi). Planctomycetes accounted for 7% of the global community, being members of Brocadia (1.4% of the total abundance) the main anaerobic ammonium oxidizer detected.
Collapse
Affiliation(s)
- J Dosta
- Department of Chemical Engineering, University of Barcelona, C/Martí i Franquès, No. 1, 6th Floor, 08028 Barcelona, Spain.
| | - J Vila
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - I Sancho
- Department of Chemical Engineering, University of Barcelona, C/Martí i Franquès, No. 1, 6th Floor, 08028 Barcelona, Spain
| | - N Basset
- Department of Chemical Engineering, University of Barcelona, C/Martí i Franquès, No. 1, 6th Floor, 08028 Barcelona, Spain
| | - M Grifoll
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - J Mata-Álvarez
- Department of Chemical Engineering, University of Barcelona, C/Martí i Franquès, No. 1, 6th Floor, 08028 Barcelona, Spain
| |
Collapse
|
14
|
Yamaguchi T, Kawakami S, Hatamoto M, Imachi H, Takahashi M, Araki N, Yamaguchi T, Kubota K. In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms. Environ Microbiol 2015; 17:2532-41. [DOI: 10.1111/1462-2920.12745] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 11/22/2014] [Accepted: 12/06/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Tsuyoshi Yamaguchi
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
| | - Shuji Kawakami
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
- Department of Construction Systems Engineering; Anan National College of Technology; 265 Aoki Minobayashi Anan Tokushima 774-0017 Japan
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR); Japan Agency for Marine-Earth Science & Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
| | - Masanobu Takahashi
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
- Department of Civil and Environmental Engineering; Tohoku University; 6-6-06 Aoba Sendai Miyagi 980-8579 Japan
| | - Nobuo Araki
- Department of Civil Engineering; Nagaoka National College of Technology; 888 Nishikatagai Nagaoka Niigata 940-8532 Japan
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering; Tohoku University; 6-6-06 Aoba Sendai Miyagi 980-8579 Japan
| |
Collapse
|
15
|
Kubota K, Morono Y, Ito M, Terada T, Itezono S, Harada H, Inagaki F. Gold-ISH: a nano-size gold particle-based phylogenetic identification compatible with NanoSIMS. Syst Appl Microbiol 2014; 37:261-6. [PMID: 24702906 DOI: 10.1016/j.syapm.2014.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 02/20/2014] [Accepted: 02/20/2014] [Indexed: 11/25/2022]
Abstract
The linkage of microbial phylogenetic and metabolic analyses by combining ion imaging analysis with nano-scale secondary ion mass spectrometry (NanoSIMS) has become a powerful means of exploring the metabolic functions of environmental microorganisms. Phylogenetic identification using NanoSIMS typically involves probing by horseradish peroxidase-mediated deposition of halogenated fluorescent tyramides, which permits highly sensitive detection of specific microbial cells. However, the methods require permeabilization of target microbial cells and inactivation of endogenous peroxidase activity, and the use of halogens as the target atom is limited because of heavy background signals due to the presence of halogenated minerals in soil and sediment samples. Here, we present "Gold-ISH," a non-halogen phylogenetic probing method in which oligonucleotide probes are directly labeled with Undecagold, an ultra-small gold nanoparticle. Undecagold-labeled probes were generated using a thiol-maleimide chemical coupling reaction and they were purified by polyacrylamide gel electrophoresis. The method was optimized with a mixture of axenic (13)C-labeled Escherichia coli and Methanococcus maripaludis cells and applied to investigate sulfate-reducing bacteria in an anaerobic sludge sample. Clear gold-derived target signals were detected in microbial cells using NanoSIMS ion imaging. It was concluded that Gold-ISH can be a useful approach for metabolic studies of naturally occurring microbial ecosystems using NanoSIMS.
Collapse
Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan; Geobio-Engineering and Technology Group, Submarine Resources Research Project, JAMSTEC, Natsushima-cho 2-15, Yokosuka 237-0061, Japan.
| | - Motoo Ito
- Geochemical Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan; Geobio-Engineering and Technology Group, Submarine Resources Research Project, JAMSTEC, Natsushima-cho 2-15, Yokosuka 237-0061, Japan
| | - Takeshi Terada
- Department of Ocean Drilling Science Technical Support, Marine Works Japan LTD, Yokohama 236-0042, Japan
| | - Shogo Itezono
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hideki Harada
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan; Geobio-Engineering and Technology Group, Submarine Resources Research Project, JAMSTEC, Natsushima-cho 2-15, Yokosuka 237-0061, Japan
| |
Collapse
|
16
|
Schmidt H, Eickhorst T. Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescencein situhybridization. FEMS Microbiol Ecol 2013; 87:390-402. [DOI: 10.1111/1574-6941.12232] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/08/2013] [Accepted: 09/21/2013] [Indexed: 02/05/2023] Open
Affiliation(s)
- Hannes Schmidt
- Soil Microbial Ecology; University of Bremen; Bremen Germany
| | - Thilo Eickhorst
- Soil Microbial Ecology; University of Bremen; Bremen Germany
| |
Collapse
|
17
|
Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
Collapse
Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
| |
Collapse
|
18
|
Brandsma J, van de Vossenberg J, Risgaard-Petersen N, Schmid MC, Engström P, Eurenius K, Hulth S, Jaeschke A, Abbas B, Hopmans EC, Strous M, Schouten S, Jetten MSM, Damsté JSS. A multi-proxy study of anaerobic ammonium oxidation in marine sediments of the Gullmar Fjord, Sweden. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:360-366. [PMID: 23761282 DOI: 10.1111/j.1758-2229.2010.00233.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is an important process for nitrogen removal in marine pelagic and benthic environments and represents a major sink in the global nitrogen cycle. We applied a suite of complementary methods for the detection and enumeration of anammox activity and anammox bacteria in marine sediments of the Gullmar Fjord, and compared the results obtained with each technique. (15) N labelling experiments showed that nitrogen removal through N2 production was essentially limited to the upper 2 cm of the sediment, where anammox contributed 23-47% of the total production. The presence of marine anammox bacteria belonging to the genus 'Candidatus Scalindua' was shown by 16S rRNA gene sequence comparison. FISH counts of anammox bacteria correlated well with anammox activity, while quantitative PCR may have underestimated the number of anammox bacterial 16S rRNA gene copies at this site. Potential nitrogen conversion by anammox ranged from 0.6 to 4.8 fmol N cell(-1) day(-1) , in agreement with previous measurements in the marine environment and in bioreactors. Finally, intact ladderane glycerophospholipid concentrations better reflected anammox activity and abundance than ladderane core lipid concentrations, most likely because the core lipid fraction contained a substantial fossil component, especially deeper in the sediment.
Collapse
Affiliation(s)
- Joost Brandsma
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands. Radboud University Nijmegen, IWWR, Department of Microbiology, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands. Aarhus University, National Environmental Research Institute, Velsøvej 25, DK-8600 Silkeborg, Denmark. University of Gothenburg, Department of Chemistry, SE-412 96 Göteborg, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria. Appl Microbiol Biotechnol 2011; 90:1241-52. [PMID: 21476137 PMCID: PMC3082692 DOI: 10.1007/s00253-011-3230-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 11/28/2022]
Abstract
Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future.
Collapse
|
20
|
Avens HJ, Berron BJ, May AM, Voigt KR, Seedorf GJ, Balasubramaniam V, Bowman CN. Sensitive immunofluorescent staining of cells via generation of fluorescent nanoscale polymer films in response to biorecognition. J Histochem Cytochem 2011; 59:76-87. [PMID: 21339175 DOI: 10.1369/jhc.2010.955948] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Immunofluorescent staining is central to nearly all cell-based research, yet only a few fluorescent signal amplification approaches for cell staining exist, each with distinct limitations. Here, the authors present a novel, fluorescent polymerization-based amplification (FPBA) method that is shown to enable similar signal intensities as the highly sensitive, enzyme-based tyramide signal amplification (TSA) approach. Being non-enzymatic, FPBA is not expected to suffer from nonspecific staining of endogenous enzymes, as occurs with enzyme-based approaches. FPBA employs probes labeled with photopolymerization initiators, which lead to the controlled formation of fluorescent polymer films only at targeted biorecognition sites. Nuclear pore complex proteins (NPCs; in membranes), vimentin (in filaments), and von Willebrand factor (in granules) were all successfully immunostained by FPBA. Also, FPBA was demonstrated to be capable of multicolor immunostaining of multiple antigens. To assess relative sensitivity, decreasing concentrations of anti-NPC antibody were used, indicating that both FPBA and TSA stained NPC down to a 1:100,000 dilution. Nonspecific, cytoplasmic signal resulting from NPC staining was found to be reduced up to 5.5-fold in FPBA as compared to TSA, demonstrating better signal localization with FPBA. FPBA's unique approach affords a combination of preferred attributes, including high sensitivity and specificity not otherwise available with current techniques.
Collapse
Affiliation(s)
- Heather J Avens
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA
| | | | | | | | | | | | | |
Collapse
|
21
|
Almeida C, Azevedo NF, Santos S, Keevil CW, Vieira MJ. Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH). PLoS One 2011; 6:e14786. [PMID: 21479268 PMCID: PMC3066202 DOI: 10.1371/journal.pone.0014786] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 10/11/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Our current understanding of biofilms indicates that these structures are typically composed of many different microbial species. However, the lack of reliable techniques for the discrimination of each population has meant that studies focusing on multi-species biofilms are scarce and typically generate qualitative rather than quantitative data. METHODOLOGY/PRINCIPAL FINDINGS We employ peptide nucleic acid fluorescence in situ hybridization (PNA FISH) methods to quantify and visualize mixed biofilm populations. As a case study, we present the characterization of Salmonella enterica/Listeria monocytogenes/Escherichia coli single, dual and tri-species biofilms in seven different support materials. Ex-situ, we were able to monitor quantitatively the populations of ∼56 mixed species biofilms up to 48 h, regardless of the support material. In situ, a correct quantification remained more elusive, but a qualitative understanding of biofilm structure and composition is clearly possible by confocal laser scanning microscopy (CLSM) at least up to 192 h. Combining the data obtained from PNA FISH/CLSM with data from other established techniques and from calculated microbial parameters, we were able to develop a model for this tri-species biofilm. The higher growth rate and exopolymer production ability of E. coli probably led this microorganism to outcompete the other two [average cell numbers (cells/cm(2)) for 48 h biofilm: E. coli 2,1 × 10(8) (± 2,4 × 10(7)); L. monocytogenes 6,8 × 10(7) (± 9,4 × 10(6)); and S. enterica 1,4 × 10(6) (± 4,1 × 10(5))]. This overgrowth was confirmed by CSLM, with two well-defined layers being easily identified: the top one with E. coli, and the bottom one with mixed regions of L. monocytogenes and S. enterica. SIGNIFICANCE While PNA FISH has been described previously for the qualitative study of biofilm populations, the present investigation demonstrates that it can also be used for the accurate quantification and spatial distribution of species in polymicrobial communities. Thus, it facilitates the understanding of interspecies interactions and how these are affected by changes in the surrounding environment.
Collapse
Affiliation(s)
- Carina Almeida
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Nuno F. Azevedo
- Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sílvio Santos
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
| | - Charles W. Keevil
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Maria J. Vieira
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
| |
Collapse
|
22
|
Song B, Tobias CR. Molecular and Stable Isotope Methods to Detect and Measure Anaerobic Ammonium Oxidation (Anammox) in Aquatic Ecosystems. Methods Enzymol 2011; 496:63-89. [DOI: 10.1016/b978-0-12-386489-5.00003-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
23
|
Parsley LC, Newman MM, Liles MR. Fluorescence in situ hybridization of bacterial cell suspensions. Cold Spring Harb Protoc 2010; 2010:pdb.prot5493. [PMID: 20810640 DOI: 10.1101/pdb.prot5493] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The use of fluorescence in situ hybridization (FISH) to identify and enumerate specific bacteria within a mixed culture or environmental sample has become a powerful tool in combining microscopy with molecular phylogenetic discrimination. However, processing a large number of samples in parallel can be difficult because the bacterial cells are typically fixed and hybridized on microscope slides rather than processed in solution. In addition, gram-positive cells and certain environmental samples present a unique challenge to achievement of adequate cell fixation and uniform hybridization for optimal FISH analysis. Here, we describe a protocol for FISH in solution that can be performed entirely in suspension, in a microcentrifuge tube format, prior to microscopy. This protocol can be applied to both gram-positive and -negative cells, as well as complex microbial assemblages. The method employs a rapid technique for performing multiple hybridizations simultaneously, which may be used to qualitatively assess the presence of specific phylogenetic groups in bacterial cultures or environmental samples, and/or directly quantify fluorescence by fluorometry or flow cytometry.
Collapse
Affiliation(s)
- Larissa C Parsley
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | | | | |
Collapse
|
24
|
Kiely PD, Call DF, Yates MD, Regan JM, Logan BE. Anodic biofilms in microbial fuel cells harbor low numbers of higher-power-producing bacteria than abundant genera. Appl Microbiol Biotechnol 2010; 88:371-80. [DOI: 10.1007/s00253-010-2757-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/22/2010] [Accepted: 06/25/2010] [Indexed: 10/19/2022]
|
25
|
Tang KH, Feng X, Tang YJ, Blankenship RE. Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114. PLoS One 2009; 4:e7233. [PMID: 19794911 PMCID: PMC2749216 DOI: 10.1371/journal.pone.0007233] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Accepted: 09/04/2009] [Indexed: 11/30/2022] Open
Abstract
The Roseobacter clade of aerobic marine proteobacteria, which compose 10–25% of the total marine bacterial community, has been reported to fix CO2, although it has not been determined what pathway is involved. In this study, we report the first metabolic studies on carbohydrate utilization, CO2 assimilation, and amino acid biosynthesis in the phototrophic Roseobacter clade bacterium Roseobacter denitrificans OCh114. We develop a new minimal medium containing defined carbon source(s), in which the requirements of yeast extract reported previously for the growth of R. denitrificans can be replaced by vitamin B12 (cyanocobalamin). Tracer experiments were carried out in R. denitrificans grown in a newly developed minimal medium containing isotopically labeled pyruvate, glucose or bicarbonate as a single carbon source or in combination. Through measurements of 13C-isotopomer labeling patterns in protein-derived amino acids, gene expression profiles, and enzymatic activity assays, we report that: (1) R. denitrificans uses the anaplerotic pathways mainly via the malic enzyme to fix 10–15% of protein carbon from CO2; (2) R. denitrificans employs the Entner-Doudoroff (ED) pathway for carbohydrate metabolism and the non-oxidative pentose phosphate pathway for the biosynthesis of histidine, ATP, and coenzymes; (3) the Embden-Meyerhof-Parnas (EMP, glycolysis) pathway is not active and the enzymatic activity of 6-phosphofructokinase (PFK) cannot be detected in R. denitrificans; and (4) isoleucine can be synthesized from both threonine-dependent (20% total flux) and citramalate-dependent (80% total flux) pathways using pyruvate as the sole carbon source.
Collapse
Affiliation(s)
- Kuo-Hsiang Tang
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Xueyang Feng
- Department of Energy, Environment and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Yinjie J. Tang
- Department of Energy, Environment and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Robert E. Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|