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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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2
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Cremin K, Duxbury SJN, Rosko J, Soyer OS. Formation and emergent dynamics of spatially organized microbial systems. Interface Focus 2023; 13:20220062. [PMID: 36789239 PMCID: PMC9912014 DOI: 10.1098/rsfs.2022.0062] [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: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 02/12/2023] Open
Abstract
Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.
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Affiliation(s)
- Kelsey Cremin
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Jerko Rosko
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Orkun S. Soyer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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3
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Adler A, Poirier S, Pagni M, Maillard J, Holliger C. Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environ Microbiol 2022; 24:2136-2156. [PMID: 35315560 PMCID: PMC9311429 DOI: 10.1111/1462-2920.15947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/19/2022] [Indexed: 11/26/2022]
Abstract
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon Poirier
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,IFP Energie nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison Cedex, France
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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Kushkevych I, Hýžová B, Vítězová M, Rittmann SKMR. Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats. Int J Mol Sci 2021; 22:4007. [PMID: 33924516 PMCID: PMC8069399 DOI: 10.3390/ijms22084007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/01/2022] Open
Abstract
This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Blanka Hýžová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria
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6
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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.
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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
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Dekas AE, Parada AE, Mayali X, Fuhrman JA, Wollard J, Weber PK, Pett-Ridge J. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Front Microbiol 2019; 10:2682. [PMID: 31920997 PMCID: PMC6927911 DOI: 10.3389/fmicb.2019.02682] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/05/2019] [Indexed: 11/28/2022] Open
Abstract
Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle—chemoautotrophic or heterotrophic—of each cell. Most cells (>90%) were anabolically active during the incubation, and 4–17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.
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Affiliation(s)
- Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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8
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Falås P, Jewell KS, Hermes N, Wick A, Ternes TA, Joss A, Nielsen JL. Transformation, CO 2 formation and uptake of four organic micropollutants by carrier-attached microorganisms. WATER RESEARCH 2018; 141:405-416. [PMID: 29859473 DOI: 10.1016/j.watres.2018.03.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 05/27/2023]
Abstract
A tiered process was developed to assess the transformation, CO2 formation and uptake of four organic micropollutants by carrier-attached microorganisms from two municipal wastewater treatment plants. At the first tier, primary transformation of ibuprofen, naproxen, diclofenac, and mecoprop by carrier-attached microorganisms was shown by the dissipation of the target compounds and the formation of five transformation products using LC-tandem MS. At the second tier, the microbial cleavage of the four organic micropollutants was confirmed with 14C-labeled micropollutants through liquid scintillation counting of the 14CO2 formed. At the third tier, microautoradiography coupled with fluorescence in situ hybridization (MAR-FISH) was used to screen carrier-attached microorganisms for uptake of the four radiolabeled micropollutants. Results from the MAR-FISH screening indicated that only a small fraction of the microbial community (≤1‰) was involved in the uptake of the radiolabeled micropollutants and that the responsible microorganisms differed between the compounds. At the fourth tier, the microbial community structure of the carrier-attached biofilms was analyzed by 16S rRNA gene amplicon sequencing. The sequencing results showed that the MAR-FISH screening targeted ∼80% of the microbial community and that several taxonomic families within the FISH-probed populations with MAR-positive signals (i.e. Firmicutes, Gammaproteobacteria, and Deltaproteobacteria) were present in both biofilms. From the broader perspective of organic micropollutant removal in biological wastewater treatment, the MAR-FISH results of this study indicate a high degree of microbial substrate specialization that could explain differences in transformation rates and patterns between micropollutants and microbial communities.
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Affiliation(s)
- Per Falås
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland; Water and Environmental Engineering, Department of Chemical Engineering, Lund University, 221 00 Lund, Sweden.
| | - Kevin S Jewell
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Nina Hermes
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Arne Wick
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Adriano Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
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10
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Matsubayashi M, Shimada Y, Li YY, Harada H, Kubota K. Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters. PLoS One 2017; 12:e0172888. [PMID: 28264042 PMCID: PMC5338771 DOI: 10.1371/journal.pone.0172888] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic communities in aerobic wastewater treatment processes are well characterized, but little is known about them in anaerobic processes. In this study, abundance, diversity and morphology of eukaryotes in anaerobic sludge digesters were investigated by quantitative real-time PCR (qPCR), 18S rRNA gene clone library construction and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken from four different anaerobic sludge digesters in Japan. Results of qPCR of rRNA genes revealed that Eukarya accounted from 0.1% to 1.4% of the total number of microbial rRNA gene copy numbers. The phylogenetic affiliations of a total of 251 clones were Fungi, Alveolata, Viridiplantae, Amoebozoa, Rhizaria, Stramenopiles and Metazoa. Eighty-five percent of the clones showed less than 97.0% sequence identity to described eukaryotes, indicating most of the eukaryotes in anaerobic sludge digesters are largely unknown. Clones belonging to the uncultured lineage LKM11 in Cryptomycota of Fungi were most abundant in anaerobic sludge, which accounted for 50% of the total clones. The most dominant OTU in each library belonged to either the LKM11 lineage or the uncultured lineage A31 in Alveolata. Principal coordinate analysis indicated that the eukaryotic and prokaryotic community structures were related. The detection of anaerobic eukaryotes, including the members of the LKM11 and A31 lineages in anaerobic sludge digesters, by CARD-FISH revealed their sizes in the range of 2–8 μm. The diverse and uncultured eukaryotes in the LKM11 and the A31 lineages are common and ecologically relevant members in anaerobic sludge digester.
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Affiliation(s)
- Miri Matsubayashi
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Yusuke Shimada
- Department of Frontier Science for Advanced Environment, Tohoku University, Sendai, Miyagi, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
- * E-mail:
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Lebuhn M, Weiß S, Munk B, Guebitz GM. Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 151:1-40. [PMID: 26337842 DOI: 10.1007/978-3-319-21993-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.
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Affiliation(s)
- Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture (LfL), Lange Point 6, 85354, Freising, Germany
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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.
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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
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13
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Neu TR, Lawrence JR. Investigation of microbial biofilm structure by laser scanning microscopy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 146:1-51. [PMID: 24840778 DOI: 10.1007/10_2014_272] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.
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Affiliation(s)
- Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Brueckstrasse 3a, 39114, Magdeburg, Germany,
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14
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Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW. Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotechnol 2013; 27:55-64. [PMID: 24863897 DOI: 10.1016/j.copbio.2013.11.004] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 01/08/2023]
Abstract
Over the last decade there has been a rapid development in culture-independent techniques for exploring microbial communities, which have led to new insights into their structure and function in both natural environments and engineered systems. This review focuses on some of the most important recent advances and their applications to the diverse microbial communities associated with anaerobic digestion. The use of these approaches in combination with complementary imaging techniques, chemical isotope analyses and detailed reactor performance measurements provides a new opportunity to develop a fundamental understanding of how microbial community dynamics, interactions and functionality influence digester efficiency and stability.
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Affiliation(s)
- Inka Vanwonterghem
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia; Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul D Jensen
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Dang P Ho
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Damien J Batstone
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Gene W Tyson
- Advanced Water Management Center (AWMC), School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia; Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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15
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Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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16
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Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C. Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 2013; 37:384-406. [PMID: 23480449 DOI: 10.1111/1574-6976.12019] [Citation(s) in RCA: 446] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/30/2022] Open
Abstract
Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.
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Affiliation(s)
- Brandon E L Morris
- Microbiology, Institute for Biology II, University of Freiburg, Freiburg, Germany
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17
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Ziegler S, Dolch K, Geiger K, Krause S, Asskamp M, Eusterhues K, Kriews M, Wilhelms-Dick D, Goettlicher J, Majzlan J, Gescher J. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. THE ISME JOURNAL 2013; 7:1725-37. [PMID: 23619304 PMCID: PMC3749503 DOI: 10.1038/ismej.2013.64] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 11/09/2022]
Abstract
Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.
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Affiliation(s)
- Sibylle Ziegler
- Department of Microbiology, Albert-Ludwigs University, Freiburg, Germany
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Kerstin Dolch
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katharina Geiger
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Susanne Krause
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Maximilian Asskamp
- Department of Microbiology, Albert-Ludwigs University, Freiburg, Germany
| | - Karin Eusterhues
- Department of Mineralogy, Friedrich Schiller University, Jena, Germany
| | - Michael Kriews
- Department of Geosciences/Glaciology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | | | - Joerg Goettlicher
- Institute for Synchrotron Radiation, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Juraj Majzlan
- Department of Mineralogy, Friedrich Schiller University, Jena, Germany
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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18
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Ito T, Yoshiguchi K, Ariesyady HD, Okabe S. Identification and quantification of key microbial trophic groups of methanogenic glucose degradation in an anaerobic digester sludge. BIORESOURCE TECHNOLOGY 2012; 123:599-607. [PMID: 22944494 DOI: 10.1016/j.biortech.2012.07.108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/23/2012] [Accepted: 07/28/2012] [Indexed: 05/23/2023]
Abstract
We investigated the major phylogenetic groups and population size of glucose-, propionate-, and acetate-degrading bacteria in the glucose-degrading anaerobic digester sludge by stable-isotope probing analysis of 16S rRNA (RNA-SIP) with [(13)C(6)]glucose followed by time course analysis of microautoradiography combined with fluorescent in situ hybridization (MAR-FISH) with [U-(14)C]glucose. The results indicated that glucose was predominately degraded to CH(4) and CO(2) by glucose-degrading Propionibacterium and Olsenella that are belonging to the phylum Actinobacteria, propionate-degrading Smithella and Syntrophobacter, and acetate-degrading Methanosaeta and Synergistes group 4 in this anaerobic sludge. The population size of propionate degraders was the smallest among three trophic groups and the specific degradation rate of propionate was also low. The specific degradation rate of acetate was low even though their population size was comparable to the glucose degraders. These results could explain why the degradation of propionate and acetate was the rate-limiting step in methanogenic glucose degradation.
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Affiliation(s)
- Tsukasa Ito
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
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19
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Sebastián M, Pitta P, González JM, Thingstad TF, Gasol JM. Bacterioplankton groups involved in the uptake of phosphate and dissolved organic phosphorus in a mesocosm experiment with P-starved Mediterranean waters. Environ Microbiol 2012; 14:2334-47. [PMID: 22564346 DOI: 10.1111/j.1462-2920.2012.02772.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The use of inorganic phosphate (Pi) and dissolved organic phosphorus (DOP) by different bacterial groups was studied in experimental mesocosms of P-starved eastern Mediterranean waters in the absence (control mesocosms) and presence of additional Pi (P-amended mesocosms). The low Pi turnover times in the control mesocosms and the increase in heterotrophic prokaryotic abundance and production upon Pi addition confirmed that the bacterial community was originally P-limited. The bacterioplankton groups taking up Pi and DOP were identified by means of microautoradiography combined with catalysed reporter deposition fluorescence in situ hybridization. Incubations with leucine were also performed for comparative purposes. All the probe-identified groups showed a high percentage of cells taking up Pi and DOP in the control, P-limited, mesocosms throughout the experiment. However, in response to Pi addition two contrasting scenarios in Pi use were observed: (i) on day 1 of the experiment Pi addition caused a clear reduction in the percentage of SAR11 cells taking up Pi, whereas Gammaproteobacteria, Roseobacter and Bacteroidetes showed similar percentages to the ones in the control mesocosms and (ii) on day 4 of the experiment, probably when the bacterial community had fully responded to the P input, all the probe-identified groups showed low percentages of cells taking up the substrate as compared with the control mesocosms. These differences are likely related to different P requirements among the bacterial groups and point out to the existence of two contrasting strategies in P use.
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Affiliation(s)
- Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain.
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20
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Tips and tricks for high quality MAR-FISH preparations: focus on bacterioplankton analysis. Syst Appl Microbiol 2012; 35:503-12. [PMID: 22502862 DOI: 10.1016/j.syapm.2012.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 11/20/2022]
Abstract
The combination of microautoradiography and fluorescence in situ hybridization (MAR-FISH) is a powerful technique for tracking the incorporation of radiolabelled compounds by specific bacterial populations at a single cell resolution. It has been widely applied in aquatic microbial ecology as a tool to unveil key ecophysiological features, shedding light on relevant ecological issues such as bacterial biomass production, the role of different bacterioplankton groups in the global carbon and sulphur cycle, and, at the same time, providing insights into the life styles and niche differentiation of cosmopolitan members of the aquatic microbial communities. Despite its great potential, its application has remained restricted to a few laboratories around the world, in part due to its reputation as a "difficult technique". Therefore, the objective of this minireview is to highlight the impact of MAR-FISH application on aquatic microbial ecology, and also to provide basic concepts, as well as practical tips, for processing MAR-FISH preparations, thus aiming to contribute to a more widespread application of this powerful method.
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21
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Graue J, Engelen B, Cypionka H. Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes. THE ISME JOURNAL 2012; 6:660-9. [PMID: 21918576 PMCID: PMC3280128 DOI: 10.1038/ismej.2011.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 07/29/2011] [Accepted: 07/29/2011] [Indexed: 11/08/2022]
Abstract
To follow the anaerobic degradation of organic matter in tidal-flat sediments, a stimulation experiment with (13)C-labeled Spirulina biomass (130 mg per 21 g sediment slurry) was conducted over a period of 24 days. A combination of microcalorimetry to record process kinetics, chemical analyses of fermentation products and RNA-based stable-isotope probing (SIP) to follow community changes was applied. Different degradation phases could be identified by microcalorimetry: Within 2 days, heat output reached its maximum (55 μW), while primary fermentation products were formed (in μmol) as follows: acetate 440, ethanol 195, butyrate 128, propionate 112, H(2) 127 and smaller amounts of valerate, propanol and butanol. Sulfate was depleted within 7 days. Thereafter, methanogenesis was observed and secondary fermentation proceeded. H(2) and alcohols disappeared completely, whereas fatty acids decreased in concentration. Three main degraders were identified by RNA-based SIP and denaturant gradient gel electrophoresis. After 12 h, two phylotypes clearly enriched in (13)C: (i) Psychrilyobacter atlanticus, a fermenter known to produce hydrogen and acetate and (ii) bacteria distantly related to Propionigenium. A Cytophaga-related bacterium was highly abundant after day 3. Sulfate reduction appeared to be performed by incompletely oxidizing species, as only sulfate-reducing bacteria related to Desulfovibrio were labeled as long as sulfate was available.
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Affiliation(s)
- Jutta Graue
- Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Niedersachsen, Germany
| | - Bert Engelen
- Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Niedersachsen, Germany
| | - Heribert Cypionka
- Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Niedersachsen, Germany
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22
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Okabe S, Oshiki M, Kamagata Y, Yamaguchi N, Toyofuku M, Yawata Y, Tashiro Y, Nomura N, Ohta H, Ohkuma M, Hiraishi A, Minamisawa K. A great leap forward in microbial ecology. Microbes Environ 2011; 25:230-40. [PMID: 21576878 DOI: 10.1264/jsme2.me10178] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.
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Affiliation(s)
- Satoshi Okabe
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060–8628, Japan.
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Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge. ISME JOURNAL 2011; 5:1844-56. [PMID: 21562600 DOI: 10.1038/ismej.2011.59] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Major acetate-utilizing bacterial and archaeal populations in methanogenic anaerobic digester sludge were identified and quantified by radioisotope- and stable-isotope-based functional analyses, microautoradiography-fluorescence in situ hybridization (MAR-FISH) and stable-isotope probing of 16S rRNA (RNA-SIP) that can directly link 16S rRNA phylogeny with in situ metabolic function. First, MAR-FISH with (14)C-acetate indicated the significant utilization of acetate by only two major groups, unidentified bacterial cells and Methanosaeta-like filamentous archaeal cells, in the digester sludge. To identify the acetate-utilizing unidentified bacteria, RNA-SIP was conducted with (13)C(6)-glucose and (13)C(3)-propionate as sole carbon source, which were followed by phylogenetic analysis of 16S rRNA. We found that bacteria belonging to Synergistes group 4 were commonly detected in both 16S rRNA clone libraries derived from the sludge incubated with (13)C-glucose and (13)C-propionate. To confirm that this bacterial group can utilize acetate, specific FISH probe targeting for Synergistes group 4 was newly designed and applied to the sludge incubated with (14)C-acetate for MAR-FISH. The MAR-FISH result showed that bacteria belonging to Synergistes group 4 significantly took up acetate and their active population size was comparable to that of Methanosaeta in this sludge. In addition, as bacteria belonging to Synergistes group 4 had high K(m) for acetate and maximum utilization rate, they are more competitive for acetate over Methanosaeta at high acetate concentrations (2.5-10 mM). To our knowledge, it is the first time to report the acetate-utilizing activity of uncultured bacteria belonging to Synergistes group 4 and its competitive significance to acetoclastic methanogen, Methanosaeta.
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24
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Kumar S, Dagar SS, Mohanty AK, Sirohi SK, Puniya M, Kuhad RC, Sangu KPS, Griffith GW, Puniya AK. Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften 2011; 98:457-72. [PMID: 21475941 DOI: 10.1007/s00114-011-0791-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/19/2011] [Accepted: 03/20/2011] [Indexed: 10/18/2022]
Abstract
Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.
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Affiliation(s)
- Sanjay Kumar
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132001, India
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25
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Ecophysiology of uncultured filamentous anaerobes belonging to the phylum KSB3 that cause bulking in methanogenic granular sludge. Appl Environ Microbiol 2011; 77:2081-7. [PMID: 21257808 DOI: 10.1128/aem.02475-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A filamentous bulking of a methanogenic granular sludge caused by uncultured filamentous bacteria of the candidate phylum KSB3 in an upflow anaerobic sludge blanket (UASB) system has been reported. To characterize the physiological traits of the filaments, a polyphasic approach consisting of rRNA-based activity monitoring of the KSB3 filaments using the RNase H method and substrate uptake profiling using microautoradiography combined with fluorescence in situ hybridization (MAR-FISH) was conducted. On the basis of rRNA-based activity, the monitoring of a full-scale UASB reactor operated continuously revealed that KSB3 cells became active and predominant (up to 54% of the total 16S rRNA) in the sludge when the carbohydrate loading to the system increased. Batch experiments with a short incubation of the sludge with maltose, glucose, fructose, and maltotriose at relatively low concentrations (approximately 0.1 mM) in the presence of yeast extract also showed an increase in KSB3 rRNA levels under anaerobic conditions. MAR-FISH confirmed that the KSB3 cells took up radioisotopic carbons from [(14)C]maltose and [(14)C]glucose under the same incubation conditions in the batch experiments. These results suggest that one of the important ecophysiological characteristics of KSB3 cells in the sludge is carbohydrate degradation in wastewater and that high carbohydrate loadings may trigger an outbreak of KSB3 bacteria, causing sludge bulking in UASB systems.
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26
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A Polyphasic Approach to Study Ecophysiology of Complex Multispecies Nitrifying Biofilms. Methods Enzymol 2011; 496:163-84. [DOI: 10.1016/b978-0-12-386489-5.00007-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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27
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Iguchi A, Terada T, Narihiro T, Yamaguchi T, Kamagata Y, Sekiguchi Y. In Situ Detection and Quantification of Uncultured Members of the Phylum Nitrospirae Abundant in Methanogenic Wastewater Treatment Systems. Microbes Environ 2009; 24:97-104. [DOI: 10.1264/jsme2.me08562] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Akinori Iguchi
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Environmental Systems Engineering, Nagaoka University of Technology
| | - Takeshi Terada
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology
| | - Yoichi Kamagata
- Department of Environmental Systems Engineering, Nagaoka University of Technology
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yuji Sekiguchi
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Environmental Systems Engineering, Nagaoka University of Technology
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28
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Fujii Y, Hiraishi A. Combined Use of Cyanoditolyl Tetrazolium Staining and Flow Cytometry for Detection of Metabolically Active Bacteria in a Fed-batch Composting Process. Microbes Environ 2009; 24:57-63. [DOI: 10.1264/jsme2.me08553] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yasuyuki Fujii
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Akira Hiraishi
- Department of Ecological Engineering, Toyohashi University of Technology
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29
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Zang K, Kurisu F, Kasuga I, Furumai H, Yagi O. Analysis of the phylogenetic diversity of estrone-degrading bacteria in activated sewage sludge using microautoradiography-fluorescence in situ hybridization. Syst Appl Microbiol 2008; 31:206-14. [PMID: 18513907 DOI: 10.1016/j.syapm.2008.03.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 03/24/2008] [Accepted: 03/26/2008] [Indexed: 01/11/2023]
Abstract
In situ uptake of [2,4,6,7-3H(N)]estrone ([3H]E1) by the major phylogenetic groups present in activated sludge samples from two different municipal wastewater treatment plants was investigated using microautoradiography-fluorescence in situ hybridization (MAR-FISH). Approximately 1-2% of the total cells confined in the samples by an EUB probe mix contributed to E1 assimilation. Almost all the detected E1-assimilating cells involved in the early phase of E1 degradation were affiliated with the Beta- and Gammaproteobacteria. In the early phase of E1 degradation, no E1-assimilating cells affiliated with the Alphaproteobacteria, Actinobacteria, the Cytophaga-Flavobacterium cluster of phylum Bacteroidetes, or the phyla Chloroflexi, Nitrospira and Planctomycetes were detected. Bacteria affiliated with the Betaproteobacteria in the shape of long rods or chains of rods were found to contribute most to in situ E1 degradation. They contributed 61% and 82% of total E1-assimilating cells in cultures from two sources of activated sludge spiked with [3H]E1. The E1-degrading bacteria related to the Betaproteobacteria differed phylogenetically from the aerobic E1-degrading bacterial isolates reported in previous studies. In addition, MAR-FISH revealed the significant contribution of E1-degrading bacteria affiliated with the Gammaproteobacteria in the degradation of E1 in activated sludge.
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Affiliation(s)
- Kaisai Zang
- Department of Urban Engineering, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
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30
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Hattori S. Syntrophic Acetate-Oxidizing Microbes in Methanogenic Environments. Microbes Environ 2008; 23:118-27. [DOI: 10.1264/jsme2.23.118] [Citation(s) in RCA: 326] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Satoshi Hattori
- Department of Bioresource Engineering, Faculty of Agriculture, Yamagata University
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31
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Miura Y, Watanabe Y, Okabe S. Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:7787-7794. [PMID: 18075089 DOI: 10.1021/es071263x] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We operated pilot-scale submerged membrane bioreactors (MBR) treating real municipal wastewater for over 3 months and observed an interesting phenomenon that carbohydrate concentrations in the MBRs rapidly increased, which consequently resulted in membrane fouling, when relative abundance of the member of uncultured Chloroflexi decreased from over 30% of total Bacteria to less than 10%. We, therefore, hypothesized that the uncultured Chloroflexi present in the MBRs could preferentially degrade carbohydrates and consequently prevent membrane fouling. To test this hypothesis, we investigated the phylogenetic identity, diversity, and in situ physiology (substrate utilization characteristics) of Chloroflexi residing in the MBR by using 16S rRNA gene sequencing analysis and microautoradiography combined with fluorescence in situ hybridization (MAR-FISH) technique. Most of the clones related to the phylum Chloroflexiwere affiliated with the Chloroflexi subphylum 1 containing only a few cultured representatives. The MAR-FISH revealed that the members of Chloroflexi were metabolically versatile and could preferentially utilize glucose and N-acetyl glucosamine (a main substantial constituent of the cell wall peptidoglycan) under oxic and anoxic conditions. The utilization of these compounds was low at low pH. These findings suggest that the members of Chloroflexi are ecologically significant in the MBR treating municipal wastewater and are responsible for degradation of SMP including carbohydrates and cellular materials, which consequently reduces membrane fouling potential.
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Affiliation(s)
- Yuki Miura
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, North-13, West-8, Kita-ku, 060-8628 Sapporo, Japan
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Ginige MP, Carvalho G, Keller J, Blackall LL. Eco-physiological characterization of fluorescence in situ hybridization probe-targeted denitrifiers in activated sludge using culture-independent methods. Lett Appl Microbiol 2007; 44:399-405. [PMID: 17397478 DOI: 10.1111/j.1472-765x.2006.02089.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS This study proposes the application of a culture-independent method [fluorescence in situ hybridization (FISH)] and a bioreactor operation control strategy to characterize environmental micro-organisms according to their survival strategies in a mixed suspension culture. Eco-physiological characteristics of two 16S rRNA probe-targeted denitrifiers (DEN581 and DEN124) were investigated against the availability of two resources. METHODS AND RESULTS Four sequencing batch reactors were operated with manipulation of the sludge retention times to enforce limited and excess availability of two nutrients, namely acetate and nitrite, to the biomass. DEN581 FISH probe-targeted denitrifiers demonstrated dominance when the ratio of either acetate or nitrite to biomass was in excess, while DEN124-targeted organisms dominated when the above were limited. CONCLUSIONS The study demonstrated that microbial populations in mixed cultures can be selected by changing the substrate availability (Rs) to biomass (X) ratio. The manipulation of the specific resource availability (Rs/X) determined which one of the studied probe-targeted denitrifiers (DEN124 or DEN581) became dominant. Rs/X provides a basis to study the physiology of micro-organisms that cannot be isolated in pure culture from activated sludge. SIGNIFICANCE AND IMPACT OF THE STUDY The eco-physiological characterization of micro-organisms responsible for biological nutrient removal is anticipated to assist process designers and operators to optimize a specific biological process, such as denitrification.
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Affiliation(s)
- M P Ginige
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, Qld, Australia
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Sekiguchi Y. Yet-to-be Cultured Microorganisms Relevant to Methane Fermentation Processes. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yuji Sekiguchi
- Microbial and Genetic Resources Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST) Central 6
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Yoshida N, Fujii Y, Hiraishi A. A Modified Cyanoditolyl Tetrazolium Reduction Method for Differential Detection of Metabolically Active Gram-positive and Gram-negative Bacteria. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.272] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Naoko Yoshida
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Yasuyuki Fujii
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Akira Hiraishi
- Department of Ecological Engineering, Toyohashi University of Technology
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