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Harzallah B, Grama SB, Bousseboua H, Jouanneau Y, Yang J, Li J. Isolation and characterization of Indigenous Bacilli strains from an oil refinery wastewater with potential applications for phenol/cresol bioremediation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117322. [PMID: 36724594 DOI: 10.1016/j.jenvman.2023.117322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/07/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Phenolic compounds are frequently occurring in wastewaters from various industrial processes at high concentrations, imposing prominent risk to aquatic biosphere and human health. Bioremediation has been proven to be an effective approach to remove these compounds, and hunting for functional organisms is still of primary importance to develop efficient processes. In this study, we report several newly isolated bacillus strains with superior performances in metabolizing phenols, one of which showed paramount efficiencies to metabolize phenol at concentrations up to 1200 mg L-1 and could simultaneously degrade a wide range of other phenolic compounds. The genes encoding for phenol hydroxylase (PH) and catechol-2,3-dioxygenase (C23O) have been detected and characterized, evidencing that phenol degradation occurs via the meta pathway. The GC level of the PH gene was found to be much higher than that of genes from other Bacilli but was quite close to that of the genes from Rhodococcus, and the induction of both enzymes by phenols was confirmed by RT-PCR experiments. We intend to believe this novel strain might be promising to serve as preferred organisms for developing more robust and efficient bioremediation processes of degrading phenolic compounds due to its validated performance.
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Affiliation(s)
- Besma Harzallah
- CEA, DRF, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble F-38054, France; CNRS, UMR 5249, Laboratoire de Chimie et Biologie des Métaux, Grenoble F-38054, France; Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, Grenoble F-38000, France; Université des Frères Mentouri, Laboratoire de Génie Microbiologique et Applications, Constantine 25117, Algeria
| | - Samir B Grama
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, University of Oum El Bouaghi, Oum El Bouaghi 04000, Algeria.
| | - Hacène Bousseboua
- Ecole Nationale Supérieure de Biotechnologies, Constantine 25000, Algeria
| | - Yves Jouanneau
- CEA, DRF, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble F-38054, France; CNRS, UMR 5249, Laboratoire de Chimie et Biologie des Métaux, Grenoble F-38054, France; Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, Grenoble F-38000, France
| | - Jixiang Yang
- Chongqing Institute of Green and Intelligence Technology, Chinese Academy of Science, Chongqing 400714, China
| | - Jian Li
- College of Biological and Chemical Engineering, Panzhihua University, Panzhihua 617000, China.
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2
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Özel Duygan BD, Rey S, Leocata S, Baroux L, Seyfried M, van der Meer JR. Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry. mSystems 2021; 6:e01143-20. [PMID: 33563780 PMCID: PMC7883543 DOI: 10.1128/msystems.01143-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/15/2021] [Indexed: 11/20/2022] Open
Abstract
Compound biodegradability tests with natural microbial communities form an important keystone in the ecological assessment of chemicals. However, biodegradability tests are frequently limited by a singular focus either on the chemical and potential transformation products or on the individual microbial species degrading the compound. Here, we investigated a methodology to simultaneously analyze community compositional changes and biomass growth on dosed test compound from flow cytometry (FCM) data coupled to machine-learned cell type recognition. We quantified the growth of freshwater microbial communities on a range of carbon dosages of three readily biodegradable reference compounds, phenol, 1-octanol, and benzoate, in comparison to three fragrances, methyl jasmonate, myrcene, and musk xylene (as a nonbiodegradable control). Compound mass balances with between 0.1 to 10 mg C · liter-1 phenol or 1-octanol, inferred from cell numbers, parent compound analysis, and CO2 evolution, as well as use of 14C-labeled compounds, showed between 6 and 25% mg C · mg C-1 substrate incorporation into biomass within 2 to 4 days and 25 to 45% released as CO2 In contrast, similar dosage of methyl jasmonate and myrcene supported slower (4 to 10 days) and less (2.6 to 6.6% mg C · mg C-1 with 4.9 to 22% CO2) community growth. Community compositions inferred from machine-learned cell type recognition and 16S rRNA amplicon sequencing showed substrate- and concentration-dependent changes, with visible enrichment of microbial subgroups already at 0.1 mg C · liter-1 phenol and 1-octanol. In general, community compositions were similar at the start and after the stationary phase of the microbial growth, except at the highest used substrate concentrations of 100 to 1,000 mg C · liter-1 Flow cytometry cell counting coupled to deconvolution of communities into subgroups is thus suitable to infer biodegradability of organic chemicals, permitting biomass balances and near-real-time assessment of relevant subgroup changes.IMPORTANCE The manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects. In this study, we benchmark a new method based on machine-learned microbial cell recognition to rapidly follow dynamic changes in aquatic communities. We further determine productive biodegradation upon dosing of a number of well-known readily biodegradable tester compounds at a variety of concentrations. Microbial community growth was quantified using flow cytometry, and the multiple cell parameters measured were used in parallel to deconvolute the community on the basis of similarity to previously standardized cell types. Biodegradation was further confirmed by chemical analysis, showing how distinct changes in specific populations correlate to degradation. The method holds great promise for near-real-time community composition changes and deduction of compound biodegradation in natural microbial communities.
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Affiliation(s)
- B D Özel Duygan
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - S Rey
- Biotechnology and Natural Process Development Department, Firmenich SA, Geneva, Switzerland
| | - S Leocata
- Innovation in Analytical Chemistry Department, Firmenich SA, Geneva, Switzerland
| | - L Baroux
- Innovation in Analytical Chemistry Department, Firmenich SA, Geneva, Switzerland
| | - M Seyfried
- Biotechnology and Natural Process Development Department, Firmenich SA, Geneva, Switzerland
| | - J R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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3
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Mooshammer M, Kitzinger K, Schintlmeister A, Ahmerkamp S, Nielsen JL, Nielsen PH, Wagner M. Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities. THE ISME JOURNAL 2021; 15:348-353. [PMID: 32879458 PMCID: PMC7852690 DOI: 10.1038/s41396-020-00761-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]
Abstract
Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.
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Affiliation(s)
- Maria Mooshammer
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Arno Schintlmeister
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM-Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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4
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Brereton NJB, Gonzalez E, Desjardins D, Labrecque M, Pitre FE. Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135067. [PMID: 31818595 DOI: 10.1016/j.scitotenv.2019.135067] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.
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Affiliation(s)
- N J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada.
| | - E Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC H3A 0G1, Canada; Department of Human Genetics, McGill University, Montreal H3A 1B1, Canada
| | - D Desjardins
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada
| | - M Labrecque
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada; Montreal Botanical Garden, Montreal, QC H1X 2B2, Canada
| | - F E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada; Montreal Botanical Garden, Montreal, QC H1X 2B2, Canada
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5
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Barnett SE, Buckley DH. Simulating metagenomic stable isotope probing datasets with MetaSIPSim. BMC Bioinformatics 2020; 21:37. [PMID: 32000676 PMCID: PMC6993524 DOI: 10.1186/s12859-020-3372-6] [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: 08/13/2019] [Accepted: 01/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Results Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Conclusions Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.
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Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Bradfield Hall, room 705, 306 Tower Rd, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Bradfield Hall, room 705, 306 Tower Rd, Ithaca, NY, 14853, USA.
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Nag P, Shriti S, Das S. Microbiological strategies for enhancing biological nitrogen fixation in nonlegumes. J Appl Microbiol 2020; 129:186-198. [PMID: 31858682 DOI: 10.1111/jam.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 01/17/2023]
Abstract
In an agro-ecosystem, industrially produced nitrogenous fertilizers are the principal sources of nitrogen for plant growth; unfortunately these also serve as the leading sources of pollution. Hence, it becomes imperative to find pollution-free methods of providing nitrogen to crop plants. A diverse group of free-living, plant associative and symbiotic prokaryotes are able to perform biological nitrogen fixation (BNF). BNF is a two component process involving the nitrogen fixing diazotrophs and the host plant. Symbiotic nitrogen fixation is most efficient as it can fix nitrogen inside the nodule formed on the roots of the plant; delivering nitrogen directly to the host. However, most of the important crop plants are nonleguminous and are unable to form symbiotic associations. In this context, the plant associative and endophytic diazotrophs assume importance. BNF in nonlegumes can be encouraged either through the transfer of BNF traits from legumes or by elevating the nitrogen fixing capacity of the associative and endophytic diazotrophs. In this review we discuss mainly the microbiological strategies which may be used in nonleguminous crops for enhancement of BNF.
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Affiliation(s)
- P Nag
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
| | - S Shriti
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
| | - S Das
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
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7
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Stable Isotope Probing Techniques and Methodological Considerations Using 15N. Methods Mol Biol 2019. [PMID: 31407305 DOI: 10.1007/978-1-4939-9721-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nitrogen fixation and assimilation processes are vital to the functioning of any ecosystem. Nevertheless, studying these processes using 15N-based stable isotope probing was so far limited because of technical challenges related to the relative rarity of nitrogen in nucleic acids and proteins compared to carbon, and because of its absence in lipids. However, the recent adoption of high-throughput sequencing and statistical modelling methods to SIP studies increased the sensitivity of the method and enabled overcoming some of the challenges. This chapter describes in detail how to perform DNA- and RNA-SIP using 15N.
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8
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Hara E, Yoshimoto T, Shigeno T, Mayumi D, Suzuki T, Mitsuhashi K, Abe A, Nakajima-Kambe T. Ecological impact evaluation by constructing in situ microcosm with porous ceramic arrowhead. CHEMOSPHERE 2019; 219:202-208. [PMID: 30543954 DOI: 10.1016/j.chemosphere.2018.11.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
In recent years, bioremediation has been used as an effective technique for the cleaning of polluted sites. However, bioremediation treatment efficacy varies considerably; thus, characterization of indigenous pollutant-degrading soil microorganisms and assessment of the changes in microbial composition by pollutants are essential for designing efficient bioremediation methods. In this study, an ecological impact evaluation method that is cost-efficient and has low contamination risk was developed to assess the indigenous microbial composition. An "in situ microcosm" was constructed using a porous ceramic arrowhead. Phenol, a common environmental pollutant, was used to assess the evaluation efficacy of this method. Our data showed that phenol gradually percolated into the soil adjacent to the arrowhead and stimulated unique indigenous microorganisms (Bacillus sp., Streptomyces sp., and Cupriavidus sp.). Furthermore, the arrowhead approach enabled efficient evaluation of the ecological impact of phenol on soil microorganisms. Thus, the arrowhead method will contribute to the development of bioremediation methods.
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Affiliation(s)
- Eri Hara
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Takuya Yoshimoto
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Toshiya Shigeno
- Tsukuba Institute of Environmental Microbiology, 8-1 Sakuragaoka, Tsukuba, Ibaraki, 300-1271, Japan.
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Toshihiro Suzuki
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Kyohei Mitsuhashi
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Akihiro Abe
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Toshiaki Nakajima-Kambe
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
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9
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Angel R. Experimental Setup and Data Analysis Considerations for DNA- and RNA-SIP Experiments in the Omics Era. Methods Mol Biol 2019; 2046:1-15. [PMID: 31407292 DOI: 10.1007/978-1-4939-9721-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Careful and thoughtful experimental design is crucial to the success of any SIP experiment. This chapter discusses the essential aspects of designing a SIP experiment, focusing primarily on DNA- and RNA-SIP. The design aspects discussed here begin with considerations for carrying out the incubation, such as, the effect of choosing different stable isotopes and target biomolecules, to what degree should a labeled substrate be enriched, what concentration to use, and how long should the incubation take. Then tips and pitfalls in the technical execution of SIP are listed, including how much nucleic acids should be loaded, how many fractions to collect, and what centrifuge rotor to use. Lastly, a brief overview of the current methods for analyzing SIP data is presented, focusing on high-throughput amplicon sequencing, together with a discussion on how the choice of analysis method might affect the experimental design.
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Affiliation(s)
- Roey Angel
- Soil and Water Research Infrastructure and Institute of Soil Biology, Biology Centre CAS, České Budějovice, Czech Republic.
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10
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Barnett SE, Youngblut ND, Buckley DH. Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP. Methods Mol Biol 2019; 2046:109-128. [PMID: 31407300 DOI: 10.1007/978-1-4939-9721-3_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). MW-HR-SIP has improved accuracy over other methods and is easily implemented on the statistical platform R. We also discuss key experimental parameters to consider when designing DNA-SIP experiments and how these parameters affect accuracy of analysis.
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Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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11
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Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018; 20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
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Affiliation(s)
- Roland C Wilhelm
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Buck T Hanson
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Subhash Chandra
- Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eugene Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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12
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Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
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13
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Youngblut ND, Barnett SE, Buckley DH. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. PLoS One 2018; 13:e0189616. [PMID: 29298299 PMCID: PMC5751983 DOI: 10.1371/journal.pone.0189616] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022] Open
Abstract
Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (qSIP), and ΔBD. Currently, there is no publicly available software designed specifically for analyzing HTS-SIP data. To address this shortfall, we have developed the HTSSIP R package, an open-source, cross-platform toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/buckleylab/HTSSIP.
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Affiliation(s)
- Nicholas D. Youngblut
- School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Samuel E. Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
| | - Daniel H. Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
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Wastewater Reuse in Agriculture: A Review about Its Limitations and Benefits. SUSTAINABILITY 2017. [DOI: 10.3390/su9101734] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
For centuries, wastewater has been improperly used in agriculture, presenting potential risks to public health and the environment. In the context of scientific development, and confronted by an increasing water crisis, wastewater reuse merits consideration because the practice helps decrease water use pressure and moderates water pollution. Thus, this article presents a literature review that addresses the effects, both positive and negative, of wastewater use in agriculture, emphasizing the effects on the soil environment. The literature review reveals that, until the 1990s, research studies promoted the use of wastewater for irrigation purposes from a treatment approach, while proposing “end of pipe” conventional solutions. However, more recent research studies (2012–2016) reveal that agricultural reuse significantly affects soil texture properties, while also causing possible alterations of the biomass and microbiota. In addition, research in this period has been oriented to the quantitative evaluation of microbiological risk.
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15
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Harzallah B, Bousseboua H, Jouanneau Y. Diversity shift in bacterial phenol hydroxylases driven by alkyl-phenols in oil refinery wastewaters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:14376-14386. [PMID: 28432622 DOI: 10.1007/s11356-017-8950-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Phenol hydroxylases (PHs) play a primary role in the bacterial degradation of phenol and alkylphenols. They are divided into two main classes, single-component and multi-component PHs, having distinctive catalytic subunits designated as PheA1 and LmPH, respectively. The diversity of these enzymes is still largely unexplored. Here, both LmPH and pheA1 gene sequences were examined in activated sludge from oil refinery wastewaters. Phenol, p-cresol, or 3,4-dimethylphenol (3,4-DMP) supplied as extra carbon sources were rapidly mineralized by the microbial community. Analysis of LmPH genes revealed a wide range of sequences, most of which exhibited moderate similarity with homologs found in Proteobacteria. Moreover, the LmPH diversity profiles showed a dramatic shift upon sludge treatment with p-cresol or 3,4-DMP amendment. This resulted in an enrichment in sequences similar to LmPHs from Betaproteobacteria and Gammaproteobacteria. RT-PCR analysis of RNA extracted from wastewater sludge highlighted LmPH genes best expressed in situ. A PCR approach was implemented to analyze the pheA1 gene diversity in the same microbial community. Retrieved sequences fell into four clusters and appeared to be distantly related to pheA1 genes from Actinobacteria. Altogether, our results provide evidence that phenol degraders carrying LmPH are more diverse than PheA1 carrying bacteria and suggest that PHs with best adapted substrate specificity are recruited in response to (methyl)phenol availability.
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Affiliation(s)
- Besma Harzallah
- CEA, DRF, BIG, Laboratoire de Chimie et Biologie des Métaux, F-38054 Cedex 9, Grenoble, France
- CNRS, UMR 5249, F-38054, Grenoble, France
- Université Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire de Génie Microbiologique et Applications, FSNV, Université des Frères Mentouri, BP 325 25117, Constantine, Algeria
- Département de Biologie, FSESNV, Université d'Oum El Bouaghi, BP358 04000, Oum El Bouaghi, Algeria
| | - Hacène Bousseboua
- Ecole Nationale Supérieure de Biotechnologies, BP E66 25100, Constantine, Algeria
| | - Yves Jouanneau
- CEA, DRF, BIG, Laboratoire de Chimie et Biologie des Métaux, F-38054 Cedex 9, Grenoble, France.
- CNRS, UMR 5249, F-38054, Grenoble, France.
- Université Grenoble Alpes, F-38000, Grenoble, France.
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16
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El Moujahid L, Le Roux X, Michalet S, Bellvert F, Weigelt A, Poly F. Effect of plant diversity on the diversity of soil organic compounds. PLoS One 2017; 12:e0170494. [PMID: 28166250 PMCID: PMC5293253 DOI: 10.1371/journal.pone.0170494] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/05/2017] [Indexed: 11/30/2022] Open
Abstract
The effect of plant diversity on aboveground organisms and processes was largely studied but there is still a lack of knowledge regarding the link between plant diversity and soil characteristics. Here, we analyzed the effect of plant identity and diversity on the diversity of extractible soil organic compounds (ESOC) using 87 experimental grassland plots with different levels of plant diversity and based on a pool of over 50 plant species. Two pools of low molecular weight organic compounds, LMW1 and LMW2, were characterized by GC-MS and HPLC-DAD, respectively. These pools include specific organic acids, fatty acids and phenolics, with more organic acids in LMW1 and more phenolics in LMW2. Plant effect on the diversity of LMW1 and LMW2 compounds was strong and weak, respectively. LMW1 richness observed for bare soil was lower than that observed for all planted soils; and the richness of these soil compounds increased twofold when dominant plant species richness increased from 1 to 6. Comparing the richness of LMW1 compounds observed for a range of plant mixtures and for plant monocultures of species present in these mixtures, we showed that plant species richness increases the richness of these ESOC mainly through complementarity effects among plant species associated with contrasted spectra of soil compounds. This could explain previously reported effects of plant diversity on the diversity of soil heterotrophic microorganisms.
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Affiliation(s)
- Lamiae El Moujahid
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire d’Ecologie microbienne, UMR 5557 CNRS, UMR 1418 INRA, Villeurbanne, France
| | - Xavier Le Roux
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire d’Ecologie microbienne, UMR 5557 CNRS, UMR 1418 INRA, Villeurbanne, France
- * E-mail:
| | - Serge Michalet
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire d’Ecologie microbienne, UMR 5557 CNRS, UMR 1418 INRA, Villeurbanne, France
- Université de Lyon, Université Lyon 1, UMR5557 CNRS, UMR 1418 INRA, Centre d’Etude des Substances Naturelles, Villeurbanne, France
| | - Florian Bellvert
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire d’Ecologie microbienne, UMR 5557 CNRS, UMR 1418 INRA, Villeurbanne, France
- Université de Lyon, Université Lyon 1, UMR5557 CNRS, UMR 1418 INRA, Centre d’Etude des Substances Naturelles, Villeurbanne, France
| | - Alexandra Weigelt
- Department of Systematic Botany and Functional Biodiversity, Institute of Biology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Franck Poly
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire d’Ecologie microbienne, UMR 5557 CNRS, UMR 1418 INRA, Villeurbanne, France
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17
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Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community. Appl Environ Microbiol 2017; 83:AEM.02658-16. [PMID: 27913419 DOI: 10.1128/aem.02658-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/25/2016] [Indexed: 11/20/2022] Open
Abstract
Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [13C]benzene enabled us to obtain 13C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities. IMPORTANCE Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.
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18
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Treseder KK, Marusenko Y, Romero-Olivares AL, Maltz MR. Experimental warming alters potential function of the fungal community in boreal forest. GLOBAL CHANGE BIOLOGY 2016; 22:3395-3404. [PMID: 26836961 DOI: 10.1111/gcb.13238] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/18/2016] [Indexed: 06/05/2023]
Abstract
Fungal community composition often shifts in response to warmer temperatures, which might influence decomposition of recalcitrant carbon (C). We hypothesized that evolutionary trade-offs would enable recalcitrant C-using taxa to respond more positively to warming than would labile C-using taxa. Accordingly, we performed a warming experiment in an Alaskan boreal forest and examined changes in the prevalence of fungal taxa. In a complementary field trial, we characterized the ability of fungal taxa to use labile C (glucose), intermediate C (hemicellulose or cellulose), or recalcitrant C (lignin). We also assigned taxa to functional groups (e.g., free-living filamentous fungi, ectomycorrhizal fungi, and yeasts) based on taxonomic identity. We found that response to warming varied most among taxa at the order level, compared to other taxonomic ranks. Among orders, ability to use lignin was significantly related to increases in prevalence in response to warming. However, the relationship was weak, given that lignin use explained only 9% of the variability in warming responses. Functional groups also differed in warming responses. Specifically, free-living filamentous fungi and ectomycorrhizal fungi responded positively to warming, on average, but yeasts responded negatively. Overall, warming-induced shifts in fungal communities might be accompanied by an increased ability to break down recalcitrant C. This change in potential function may reduce soil C storage under global warming.
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Affiliation(s)
- Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Yevgeniy Marusenko
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Adriana L Romero-Olivares
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Mia R Maltz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
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19
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Fischer A, Manefield M, Bombach P. Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies. Curr Opin Biotechnol 2016; 41:99-107. [PMID: 27314918 DOI: 10.1016/j.copbio.2016.04.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 11/25/2022]
Abstract
Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations.
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Affiliation(s)
- Anko Fischer
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany.
| | - Mike Manefield
- Micronovo Py Ltd, 18 Mason St, Maroubra, NSW, 2035, Australia
| | - Petra Bombach
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany
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20
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Dawson KS, Scheller S, Dillon JG, Orphan VJ. Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment. Front Microbiol 2016; 7:774. [PMID: 27303371 PMCID: PMC4881376 DOI: 10.3389/fmicb.2016.00774] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 11/24/2022] Open
Abstract
Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.
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Affiliation(s)
- Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Silvan Scheller
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Jesse G Dillon
- Department of Biological Sciences, California State University Long Beach Long Beach, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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21
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Pepe-Ranney C, Campbell AN, Koechli CN, Berthrong S, Buckley DH. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil. Front Microbiol 2016; 7:703. [PMID: 27242725 PMCID: PMC4867679 DOI: 10.3389/fmicb.2016.00703] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either (13)C-xylose or (13)C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for (13)C-incorporation into DNA from (13)C-xylose and (13)C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated (13)C in the (13)C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These (13)C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes.
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Affiliation(s)
| | | | | | - Sean Berthrong
- Department of Biological Sciences, Butler UniversityIndianapolis, IN, USA
| | - Daniel H. Buckley
- School of Integrative Plant Sciences, Cornell UniversityIthaca, NY, USA
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22
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Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Leewis MC, Uhlik O, Leigh MB. Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil. Sci Rep 2016; 6:22145. [PMID: 26915282 PMCID: PMC4768254 DOI: 10.1038/srep22145] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/08/2016] [Indexed: 11/18/2022] Open
Abstract
Aerobic mineralization of PCBs, which are toxic and persistent organic pollutants, involves the upper (biphenyl, BP) and lower (benzoate, BZ) degradation pathways. The activity of different members of the soil microbial community in performing one or both pathways, and their synergistic interactions during PCB biodegradation, are not well understood. This study investigates BP and BZ biodegradation and subsequent carbon flow through the microbial community in PCB-contaminated soil. DNA stable isotope probing (SIP) was used to identify the bacterial guilds involved in utilizing 13C-biphenyl (unchlorinated analogue of PCBs) and/or 13C-benzoate (product/intermediate of BP degradation and analogue of chlorobenzoates). By performing SIP with two substrates in parallel, we reveal microbes performing the upper (BP) and/or lower (BZ) degradation pathways, and heterotrophic bacteria involved indirectly in processing carbon derived from these substrates (i.e. through crossfeeding). Substrate mineralization rates and shifts in relative abundance of labeled taxa suggest that BP and BZ biotransformations were performed by microorganisms with different growth strategies: BZ-associated bacteria were fast growing, potentially copiotrophic organisms, while microbes that transform BP were oligotrophic, slower growing, organisms. Our findings provide novel insight into the functional interactions of soil bacteria active in processing biphenyl and related aromatic compounds in soil, revealing how carbon flows through a bacterial community.
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Affiliation(s)
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
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24
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Billings AF, Fortney JL, Hazen TC, Simmons B, Davenport KW, Goodwin L, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, DeAngelis KM. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Stand Genomic Sci 2015; 10:106. [PMID: 26594307 PMCID: PMC4653933 DOI: 10.1186/s40793-015-0100-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 11/10/2015] [Indexed: 01/20/2023] Open
Abstract
Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. By characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.
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Affiliation(s)
- Andrew F Billings
- Microbiology Department, University of Massachusetts, Amherst, MA USA
| | - Julian L Fortney
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN USA
| | - Terry C Hazen
- Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN USA ; Department of Microbiology, The University of Tennessee, Knoxville, TN USA ; Department of Earth & Planetary Sciences, The University of Tennessee, Knoxville, TN USA
| | - Blake Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA USA ; Sandia National Lab, Livermore, CA USA
| | | | | | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
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25
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Cho KC, Lee DG, Fuller ME, Hatzinger PB, Condee CW, Chu KH. Application of (13)C and (15)N stable isotope probing to characterize RDX degrading microbial communities under different electron-accepting conditions. JOURNAL OF HAZARDOUS MATERIALS 2015; 297:42-51. [PMID: 25935409 DOI: 10.1016/j.jhazmat.2015.04.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 06/04/2023]
Abstract
This study identified microorganisms capable of using the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or its metabolites as carbon and/or nitrogen sources under different electron-accepting conditions using (13)C and (15)N stable isotope probing (SIP). Mesocosms were constructed using groundwater and aquifer solids from an RDX-contaminated aquifer. The mesocosms received succinate as a carbon source and one of four electron acceptors (nitrate, manganese(IV), iron(III), or sulfate) or no additional electron acceptor (to stimulate methanogenesis). When RDX degradation was observed, subsamples from each mesocosm were removed and amended with (13)C3- or ring-(15)N3-, nitro-(15)N3-, or fully-labeled (15)N6-RDX, followed by additional incubation and isolation of labeled nucleic acids. A total of fifteen 16S rRNA sequences, clustering in α- and γ-Proteobacteria, Clostridia, and Actinobacteria, were detected in the (13)C-DNA fractions. A total of twenty seven sequences were derived from different (15)N-DNA fractions, with the sequences clustered in α- and γ-Proteobacteria, and Clostridia. Interestingly, sequences identified as Desulfosporosinus sp. (in the Clostridia) were not only observed to incorporate the labeled (13)C or (15)N from labeled RDX, but also were detected under each of the different electron-accepting conditions. The data suggest that (13)C- and (15)N-SIP can be used to characterize microbial communities involved in RDX biodegradation, and that the dominant pathway of RDX biodegradation may differ under different electron-accepting conditions.
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Affiliation(s)
- Kun-Ching Cho
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Do Gyun Lee
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | | | | | | | - Kung-Hui Chu
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA.
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26
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Characterization of para-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing. Appl Environ Microbiol 2015. [PMID: 26209677 DOI: 10.1128/aem.01794-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations.
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27
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Jiang L, Song M, Luo C, Zhang D, Zhang G. Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing. PLoS One 2015; 10:e0130846. [PMID: 26098417 PMCID: PMC4476716 DOI: 10.1371/journal.pone.0130846] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/13/2015] [Indexed: 01/20/2023] Open
Abstract
Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.
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Affiliation(s)
- Longfei Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Mengke Song
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- * E-mail:
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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Becerra-Castro C, Lopes AR, Vaz-Moreira I, Silva EF, Manaia CM, Nunes OC. Wastewater reuse in irrigation: a microbiological perspective on implications in soil fertility and human and environmental health. ENVIRONMENT INTERNATIONAL 2015; 75:117-35. [PMID: 25461421 DOI: 10.1016/j.envint.2014.11.001] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/04/2014] [Accepted: 11/04/2014] [Indexed: 05/25/2023]
Abstract
The reuse of treated wastewater, in particular for irrigation, is an increasingly common practice, encouraged by governments and official entities worldwide. Irrigation with wastewater may have implications at two different levels: alter the physicochemical and microbiological properties of the soil and/or introduce and contribute to the accumulation of chemical and biological contaminants in soil. The first may affect soil productivity and fertility; the second may pose serious risks to the human and environmental health. The sustainable wastewater reuse in agriculture should prevent both types of effects, requiring a holistic and integrated risk assessment. In this article we critically review possible effects of irrigation with treated wastewater, with special emphasis on soil microbiota. The maintenance of a rich and diversified autochthonous soil microbiota and the use of treated wastewater with minimal levels of potential soil contaminants are proposed as sine qua non conditions to achieve a sustainable wastewater reuse for irrigation.
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Affiliation(s)
- Cristina Becerra-Castro
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana Rita Lopes
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Elisabete F Silva
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viseu, Campus Politécnico de Repeses, 3504-510 Viseu, Portugal
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal.
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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Auffret MD, Yergeau E, Labbé D, Fayolle-Guichard F, Greer CW. Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis. Appl Microbiol Biotechnol 2014; 99:2419-30. [PMID: 25343979 DOI: 10.1007/s00253-014-6159-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/12/2014] [Indexed: 11/29/2022]
Abstract
A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.
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Affiliation(s)
- Marc D Auffret
- Institut Français du Pétrole (IFP), 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France,
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Uhlik O, Strejcek M, Vondracek J, Musilova L, Ridl J, Lovecka P, Macek T. Bacterial acquisition of hexachlorobenzene-derived carbon in contaminated soil. CHEMOSPHERE 2014; 113:141-145. [PMID: 25065801 DOI: 10.1016/j.chemosphere.2014.04.110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 06/03/2023]
Abstract
Pesticides are a class of xenobiotics intentionally released into the environment. Hexachlorobenzene (HCB) was used as a fungicide from 1945, leaving behind many contaminated sites. Very few studies have examined the biodegradation of HCB or the fate of HCB-derived carbon. Here we report that certain bacterial populations are capable of deriving carbon from HCB in contaminated soil under aerobic conditions. These populations are primarily Proteobacteria, including Methylobacterium and Pseudomonas, which predominated as detected by stable isotope probing (SIP) and 16S rRNA gene amplicon pyrosequencing. Due to the nature of SIP, which can be used as a functional method solely for assimilatory processes, it is not possible to elucidate whether these populations metabolized directly HCB or intermediates of its metabolism produced by different populations. The possibility exists that HCB is degraded via the formation of pentachlorophenol (PCP), which is further mineralized. With this in mind, we designed primers to amplify PCP 4-monooxygenase-coding sequences based on the available pcpB gene sequence from Methylobacterium radiotolerans JCM 2831. Based on 16S rRNA gene analysis, organisms closely related to this strain were detected in (13)C-labeled DNA. Using the designed primers, we were able to amplify pcpB genes in both total community DNA and (13)C-DNA. This indicates that HCB might be transformed into PCP before it gets assimilated. In summary, this study is the first report on which bacterial populations benefit from carbon originating in the pesticide HCB in a contaminated soil.
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Affiliation(s)
- Ondrej Uhlik
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Technicka 3, 166 28 Prague 6, Czech Republic.
| | - Michal Strejcek
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jan Vondracek
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Lucie Musilova
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jakub Ridl
- Institute of Molecular Genetics, Czech Academy of Sciences, Department of Genomics and Bioinformatics, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Petra Lovecka
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Tomas Macek
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Technicka 3, 166 28 Prague 6, Czech Republic.
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Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation. Appl Environ Microbiol 2014; 80:3375-83. [PMID: 24657858 DOI: 10.1128/aem.00166-14] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity.
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Vedler E, Heinaru E, Jutkina J, Viggor S, Koressaar T, Remm M, Heinaru A. Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterised by comparative analysis of catabolic genes. Syst Appl Microbiol 2013; 36:525-32. [DOI: 10.1016/j.syapm.2013.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/10/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
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Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 2013; 4:280. [PMID: 24065962 PMCID: PMC3777014 DOI: 10.3389/fmicb.2013.00280] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
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Affiliation(s)
- Kristen M Deangelis
- Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA
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Solyanikova IP, Suzina NE, Mulyukin AL, El’-Registan GI, Golovleva LA. Effect of a dormant state on the xenobiotic-degrading strain Pseudomonas fluorescens 26K. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713050135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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36
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Rizoulis A, Elliott DR, Rolfe SA, Thornton SF, Banwart SA, Pickup RW, Scholes JD. Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. MICROBIAL ECOLOGY 2013; 66:84-95. [PMID: 23640275 DOI: 10.1007/s00248-013-0233-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 04/14/2013] [Indexed: 06/02/2023]
Abstract
Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.
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Affiliation(s)
- Athanasios Rizoulis
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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Bell TH, Yergeau E, F. Juck D, G. Whyte L, W. Greer C. Alteration of microbial community structure affects diesel biodegradation in an Arctic soil. FEMS Microbiol Ecol 2013; 85:51-61. [DOI: 10.1111/1574-6941.12102] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 02/06/2013] [Accepted: 02/10/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Etienne Yergeau
- National Research Council Canada; EME-Montreal; Montreal; QC; Canada
| | - Dave F. Juck
- National Research Council Canada; EME-Montreal; Montreal; QC; Canada
| | - Lyle G. Whyte
- Department of Natural Resource Sciences; McGill University; Sainte-Anne-de-Bellevue; QC; Canada
| | - Charles W. Greer
- National Research Council Canada; EME-Montreal; Montreal; QC; Canada
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Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T. Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 2012; 31:154-65. [PMID: 23022353 DOI: 10.1016/j.biotechadv.2012.09.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 12/24/2022]
Abstract
Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.
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Affiliation(s)
- Ondrej Uhlik
- Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic.
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Hatton PJ, Remusat L, Zeller B, Derrien D. A multi-scale approach to determine accurate elemental and isotopic ratios by nano-scale secondary ion mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1363-1371. [PMID: 22555930 DOI: 10.1002/rcm.6228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Nano-scale secondary ion mass spectrometry (NanoSIMS) is still hampered by a lack of appropriate calibration method for the quantification of elemental and isotopic ratios in heterogeneous materials such as soil samples. The potential of (13)C-(15)N-labeled density fractions of soil to calibrate the C/N, (13)C/(12)C and (15)N/(14)N ratios provided by NanoSIMS was evaluated. METHODS The spatial organization of soil particles found at the macro- and micro-scales were compared. The C/N, (13)C/(12)C and (15)N/(14)N ratios measured at the macroscopic scale from different density fractions using an elemental analyzer coupled to an isotope ratio mass spectrometer (EA/IRMS) were compared with the corresponding micro-scale NanoSIMS measurements. When the macro- and micro-scales patterns were similar, macroscopic scale measurements obtained by EA/IRMS and the corresponding NanoSIMS C/N and (15)N/(14)N ratios averaged per fraction were used to obtain correction equations. The correction method using the internal calibration procedure was compared with the traditional one using a single organic standard. RESULTS It was demonstrated that the correction method using an internal calibration procedure was applicable for NanoSIMS images acquired on more than 500 µm(2) per fraction and provided more accurate C/N and (15)N/(14)N ratios than the traditional correction method. CONCLUSIONS As long as the NanoSIMS sampling was representative of the macroscopic properties, the correction method using an internal calibration procedure allowed better quantification of the isotope tracers and characterization of the C/N ratios. This method not only produced qualitative images, but also accurate quantitative parameters from which ecological interpretations can be derived.
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Affiliation(s)
- Pierre-Joseph Hatton
- INRA, Laboratoire de Biogéochimie des Ecosystèmes Forestiers, UR 1138, INRA Nancy, 54280 Champenoux, France.
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Musat N, Foster R, Vagner T, Adam B, Kuypers MMM. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev 2012; 36:486-511. [DOI: 10.1111/j.1574-6976.2011.00303.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/22/2011] [Indexed: 11/30/2022] Open
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Penicillium chrysogenum var. halophenolicum, a new halotolerant strain with potential in the remediation of aromatic compounds in high salt environments. Microbiol Res 2012; 167:79-89. [PMID: 21524896 DOI: 10.1016/j.micres.2011.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 03/12/2011] [Accepted: 03/26/2011] [Indexed: 11/24/2022]
Abstract
A halotolerant phenylacetate-degrading fungus Penicillium CLONA2, previously isolated from a salt mine at Algarve (Portugal), was identified as a variant of P. chrysogenum using the ITS-5,8S rDNA and the D1/D2 domain of 28S rDNA sequences. The metabolic features and genetic characteristics suggest that this strain belongs to a subgroup of P. chrysogenum, named var. halophenolicum. The presence of the penicillin biosynthetic cluster was proven by Southern hybridizations using probes internal to the pcbAB and penDE genes and sequencing of the pcbAB-pcbC intergenic region. However the pcbAB-pcbC divergent promoter region contained 20 point modifications with respect to that of the wild type P. chrysogenum NRRL1951. The CLONA2 strain produced non-aromatic natural penicillins rather than benzylpenicillin in a medium containing potassium phenylacetate (the precursor of benzylpenicillin) and was able to grow well on phenylacetatic acid using it as sole carbon source. Due to the ability of P. chrysogenum CLONA2 to degrade aromatic compounds, this strain may be an interesting organism for aromatic compounds remediation in high salinity environments.
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Abstract
Imaging mass spectrometry tools allow the two-dimensional visualization of the distribution of trace metals, metabolites, surface lipids, peptides and proteins directly from biological samples without the need for chemical tagging or antibodies, and are becoming increasingly useful for microbiology applications. These tools, comprising different imaging mass spectrometry techniques, are ushering in an exciting new era of discovery by enabling the generation of chemical hypotheses based on the spatial mapping of atoms and molecules that can correlate to or transcend observed phenotypes. In this Innovation article, we explore the wide range of imaging mass spectrometry techniques that is available to microbiologists and describe the unique applications of these tools to microbiology with respect to the types of samples to be investigated.
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Affiliation(s)
- Jeramie D. Watrous
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Center For Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography
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Cupples AM. The use of nucleic acid based stable isotope probing to identify the microorganisms responsible for anaerobic benzene and toluene biodegradation. J Microbiol Methods 2011; 85:83-91. [DOI: 10.1016/j.mimet.2011.02.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/18/2011] [Accepted: 02/18/2011] [Indexed: 11/26/2022]
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DeAngelis KM, Allgaier M, Chavarria Y, Fortney JL, Hugenholtz P, Simmons B, Sublette K, Silver WL, Hazen TC. Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS One 2011; 6:e19306. [PMID: 21559391 PMCID: PMC3084812 DOI: 10.1371/journal.pone.0019306] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 04/01/2011] [Indexed: 02/01/2023] Open
Abstract
Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.
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Affiliation(s)
- Kristen M DeAngelis
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
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A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites. J Microbiol Methods 2010; 84:46-51. [PMID: 20971136 DOI: 10.1016/j.mimet.2010.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/13/2010] [Accepted: 10/13/2010] [Indexed: 11/20/2022]
Abstract
We modified and tuned a commercial model of a gas chromatography/mass spectrometry (GC/MS) instrument to develop a simple and rapid method for the simultaneous quantification of a variety of gas species. Using the developed method with the newly modified instrument, gas species such as H(2), N(2), O(2), CO, NO, CH(4), CO(2), and N(2)O, which are common components of microbial metabolism, were accurately identified based on their retention times and/or mass-to-charge ratios (m/z) in less than 2.5 min. By examining the sensitivities and dynamic ranges for the detection of H(2), N(2), O(2), CH(4), CO(2), and N(2)O, it was demonstrated that the method developed in this study was sufficient for accurately monitoring the production and the consumption of these gaseous species during microbial metabolism. The utility of the new method was demonstrated by a denitrification study with Pseudomonas aureofaciens ATCC 13985(T). This method will be suitable for a variety of applications requiring the identification of gaseous metabolites in microorganisms, microbial communities, and natural ecosystems.
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Biodegradation of a biocide (Cu-N-cyclohexyldiazenium dioxide) component of a wood preservative by a defined soil bacterial community. Appl Environ Microbiol 2010; 76:8076-83. [PMID: 20952650 DOI: 10.1128/aem.01092-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wood protection industry has refined their products from chrome-, copper-, and arsenate-based wood preservatives toward solely copper-based preservatives in combination with organic biocides. One of these is Cu-HDO, containing the chelation product of copper and N-cyclohexyldiazenium dioxide (HDO). In this study, the fate of isotope-labeled ((13)C) and nonlabeled ((12)C) Cu-HDO incorporated in wood sawdust mixed with soil was investigated. HDO concentration was monitored by high-pressure liquid chromatography. The total carbon and the δ(13)C content of respired CO(2), as well as of the soil-wood-sawdust mixture, were determined with an elemental analyzer-isotopic ratio mass spectrometer. The concentration of HDO decreased significantly after 105 days of incubation, and after 24 days the (13)CO(2) concentration respired from soil increased steadily to a maximum after 64 days of incubation. Phospholipid fatty acid-stable isotope probing (PFA-SIP) analysis revealed that the dominant PFAs C(19:0)d8,9, C(18:0), C(18:1)ω7, C(18:2)ω6,9, C(17:1)d7,8, C(16:0), and C(16:1)ω7 were highly enriched in their δ(13)C content. Moreover, RNA-SIP identified members of the phylum Acidobacteria and the genera Phenylobacterium and Comamonas that were assimilating carbon from HDO exclusively. Cu-HDO as part of a wood preservative effectively decreased fungal wood decay and overall microbial respiration from soil. In turn, a defined bacterial community was stimulated that was able to metabolize HDO completely.
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Xie S, Sun W, Luo C, Cupples AM. Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation 2010; 22:71-81. [PMID: 20549308 DOI: 10.1007/s10532-010-9377-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 05/28/2010] [Indexed: 11/26/2022]
Abstract
The remediation of benzene contaminated groundwater often involves biodegradation and although the mechanisms of aerobic benzene biodegradation in laboratory cultures have been well studied, less is known about the microorganisms responsible for benzene degradation in mixed culture samples or at contaminated sites. To address this knowledge gap, DNA based stable isotope probing (SIP) was utilized to identify active benzene degraders in microcosms constructed with soil from three sources (a contaminated site and two agricultural sites). For this, replicate microcosms were amended with either labeled (¹³C) or unlabeled benzene and the extracted DNA samples were ultracentrifuged, fractioned and subject to terminal restriction fragment length polymorphism (TRFLP). The dominant benzene degraders (responsible for ¹³C uptake) were determined by comparing relative abundance of TRFLP phylotypes in heavy fractions of labeled benzene (¹³C) amended samples to the controls (from unlabeled benzene amended samples). Two phylotypes (a Polaromonas sp. and an Acidobacterium) were the major benzene degraders in the microcosms constructed from the contaminated site soil, whereas one phylotype incorporated the majority of the benzene-derived ¹³C in each of the agricultural soils ("candidate" phylum TM7 and an unclassified Sphingomonadaceae).
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Chen Y, Murrell JC. When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol 2010; 18:157-63. [PMID: 20202846 DOI: 10.1016/j.tim.2010.02.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/26/2022]
Abstract
The application of metagenomics, the culture-independent capture and subsequent analysis of genomic DNA from the environment, has greatly expanded our knowledge of the diversity of microbes and microbial protein families; however, the metabolic functions of many microorganisms remain largely unknown. DNA stable-isotope probing (DNA-SIP) is a recently developed method in which the incorporation of stable isotope from a labelled substrate is used to identify the function of microorganisms in the environment. The technique has now been used in conjunction with metagenomics to establish links between microbial identity and particular metabolic functions. The combination of DNA-SIP and metagenomics not only permits the detection of rare low-abundance species from metagenomic libraries but also facilitates the detection of novel enzymes and bioactive compounds.
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Affiliation(s)
- Yin Chen
- Department of Biological Sciences, the University of Warwick, Coventry CV4 7AL, UK
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Abstract
DNA-stable isotope probing, a method to identify active microorganisms without the prerequisite of cultivation, has been widely applied in the study of microorganisms involved in the degradation of environmental pollutants. Recent advances and technique considerations in applying DNA-SIP in bioremediation are highlighted. A detailed protocol of a DNA-SIP experiment is provided.
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Wagner M. Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 2009; 63:411-29. [PMID: 19514853 DOI: 10.1146/annurev.micro.091208.073233] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An astonishing diversity of microorganisms thrives on our planet and their activities are fundamental for the functioning of all ecosystems including the human body. Consequently, detailed insights into the functions performed by microorganisms in their natural environment are required to understand human biology and the biology of the world around us and to lay the foundations for targeted manipulation of microbial communities. Isotope-labeling techniques combined with molecular detection tools are frequently used by microbial ecologists to directly link structure and function of microbial communities and to monitor metabolic properties of uncultured microbes at the single-cell level. However, only the recent combination of such techniques with Raman microspectroscopy or secondary ion mass spectrometry enables functional studies of microbes on a single-cell level by using stable isotopes as labels. This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago.
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Affiliation(s)
- Michael Wagner
- University of Vienna, Department of Microbial Ecology, Vienna 1090, Austria.
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