1
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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2
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Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness. mBio 2022; 13:e0032322. [PMID: 35491853 PMCID: PMC9239258 DOI: 10.1128/mbio.00323-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Cellulose is the most abundant polysaccharide in plant biomass and an important precursor of soil organic matter formation. Fungi play a key role in carbon cycling dynamics because they tend to decompose recalcitrant materials. Here, we applied [12C]cellulose and [13C]cellulose to distinguish the effects of application of compost, nitrogen-phosphorus-potassium (NPK) fertilizer, and no fertilizer (control) for 27 years upon cellulose decomposition via RNA-based stable isotope probing (RNA-SIP). The loss ratio of added cellulose C in compost soil was 67.6 to 106.7% higher than in NPK and control soils during their 20-day incubation. Dothideomycetes (mainly members of the genus Cryptococcus) dominated cellulose utilization in compost soil, whereas the copiotrophic Sordariomycetes were more abundant in NPK and unfertilized soils. Compared with NPK and control soils, compost application increased the diversity of 13C-assimilating fungi. The 13C-labeled fungal communities in compost soil were more phylogenetically clustered and exhibited greater species relatedness than those in NPK and control soils, perhaps because of stringent filtering of narrow-spectrum organic resources and biological invasion originating from added compost. These changes led to an augmented decomposition capacity of fungal species for cellulose-rich substrates and reduced cellulose C sequestration efficiency. The RNA-SIP technique is more sensitive to responses of fungi to altered soil resource availability than DNA-SIP. Overall, long-term compost application modified fungal community composition and promoted fungal diversity and phylogenetic relatedness, accelerating the decomposition of substrate cellulose in soil. This work also highlights the RNA-SIP technique’s value for comprehensively assessing the contributions of active fungi to the substrate decomposition process.
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3
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Schwendner P, Nguyen AN, Schuerger AC. Use of NanoSIMS to Identify the Lower Limits of Metabolic Activity and Growth by Serratia liquefaciens Exposed to Sub-Zero Temperatures. Life (Basel) 2021; 11:life11050459. [PMID: 34065549 PMCID: PMC8161314 DOI: 10.3390/life11050459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Serratia liquefaciens is a cold-adapted facultative anaerobic astrobiology model organism with the ability to grow at a Martian atmospheric pressure of 7 hPa. Currently there is a lack of data on its limits of growth and metabolic activity at sub-zero temperatures found in potential habitable regions on Mars. Growth curves and nano-scale secondary ion mass spectrometry (NanoSIMS) were used to characterize the growth and metabolic threshold for S. liquefaciens ATCC 27,592 grown at and below 0 °C. Cells were incubated in Spizizen medium containing three stable isotopes substituting their unlabeled counterparts; i.e., 13C-glucose, (15NH4)2SO4, and H218O; at 0, −1.5, −3, −5, −10, or −15 °C. The isotopic ratios of 13C/12C, 15N/14N, and 18O/16O and their corresponding fractions were determined for 240 cells. NanoSIMS results revealed that with decreasing temperature the cellular amounts of labeled ions decreased indicating slower metabolic rates for isotope uptake and incorporation. Metabolism was significantly reduced at −1.5 and −3 °C, almost halted at −5 °C, and shut-down completely at or below −10 °C. While growth was observed at 0 °C after 5 days, samples incubated at −1.5 and −3 °C exhibited significantly slower growth rates until growth was detected at 70 days. In contrast, cell densities decreased by at least half an order of magnitude over 70 days in cultures incubated at ≤ −5 °C. Results suggest that S. liquefaciens, if transported to Mars, might be able to metabolize and grow in shallow sub-surface niches at temperatures above −5 °C and might survive—but not grow—at temperatures below −5 °C.
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Affiliation(s)
- Petra Schwendner
- Space Life Sciences Lab, Department of Plant Pathology, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL 32953, USA;
- Correspondence:
| | - Ann N. Nguyen
- Jacobs, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Andrew C. Schuerger
- Space Life Sciences Lab, Department of Plant Pathology, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL 32953, USA;
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4
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Viana TFC, Campelo APS, Baldani JI, Fernandes-Júnior PI, Baldani VLD, Silva WM, Paggi GM, Brasil MS. Cultivable bacterial diversity associated with bromeliad roots from ironstone outcrops in central Brazil. BRAZ J BIOL 2020; 80:872-880. [PMID: 31967279 DOI: 10.1590/1519-6984.224982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022] Open
Abstract
Studies on the bacterial diversity associated with wild plants are rare, especially on those that grow in association with bromeliads. In the present study, we isolated and identified epiphytic and endophytic bacteria from the roots of the bromeliads Dyckia excelsa, Dyckia leptostachya and Deuterocohnia meziana occurring in the "cangas" in the Pantanal from Mato Grosso do Sul State, Brazil. The epiphytic bacteria were isolated from washed roots, while the endophytic bacteria were isolated from surface disinfested roots. Bacterial representatives corresponding to each BOX-PCR fingerprint, as well as those that did not result in amplicons, were selected for 16S rDNA gene sequence analysis. The BOX-PCR data showed intrageneric and intraspecific diversity and could discriminate strains and identify their phenotypic characteristics. The 16S rDNA gene sequence and phylogeny analysis showed a higher occurrence of strains belonging to the genus Bacillus than Mycobacterium and Brevibacterium, which were found in lower numbers. Species from the Bacillus genus are well known for their sporulation capacity and longer survival in arid locations, such as the "cangas". This study clearly showed that the bromeliad species represent a vast reservoir of bacterial community diversity, and the cultivable strains represent a new source for biotechnological prospecting.
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Affiliation(s)
- T F C Viana
- Programa de Pós-graduação em Biologia Vegetal, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul - UFMS, Av. Costa e Silva, s/n, Bairro Universitário, CEP 79070-900, Campo Grande, MS, Brasil.,Ciências Biológicas, Laboratório de Microbiologia, Universidade Federal de Mato Grosso do Sul - UFMS, do Pantanal, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil
| | - A P S Campelo
- Programa de Pós-graduação em Biologia Vegetal, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul - UFMS, Av. Costa e Silva, s/n, Bairro Universitário, CEP 79070-900, Campo Grande, MS, Brasil.,Ciências Biológicas, Laboratório de Microbiologia, Universidade Federal de Mato Grosso do Sul - UFMS, do Pantanal, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil
| | - J I Baldani
- Embrapa Agrobiologia, Rodovia, BR-465, Km 7 (antiga Rodovia Rio/São Paulo), Bairro Ecologia, CEP 23891-000, Seropédica, RJ, Brasil
| | | | - V L D Baldani
- Embrapa Agrobiologia, Rodovia, BR-465, Km 7 (antiga Rodovia Rio/São Paulo), Bairro Ecologia, CEP 23891-000, Seropédica, RJ, Brasil
| | - W M Silva
- Ciências Biológicas, Laboratório de Ecologia, do Pantanal, Universidade Federal de Mato Grosso do Sul - UFMS, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil
| | - G M Paggi
- Programa de Pós-graduação em Biologia Vegetal, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul - UFMS, Av. Costa e Silva, s/n, Bairro Universitário, CEP 79070-900, Campo Grande, MS, Brasil.,Ciências Biológicas, Laboratório de Microbiologia, Universidade Federal de Mato Grosso do Sul - UFMS, do Pantanal, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil.,Ciências Biológicas, Laboratório de Genética, do Pantanal, Universidade Federal de Mato Grosso do Sul - UFMS, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil
| | - M S Brasil
- Ciências Biológicas, Laboratório de Microbiologia, Universidade Federal de Mato Grosso do Sul - UFMS, do Pantanal, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil.,Ciências Biológicas, Laboratório de Genética, do Pantanal, Universidade Federal de Mato Grosso do Sul - UFMS, Av. Rio Branco, 1.270, Bairro Universitário, CEP 79304-902, Corumbá, MS, Brasil
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5
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Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M. Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. J Proteomics 2020; 222:103791. [PMID: 32335296 DOI: 10.1016/j.jprot.2020.103791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/08/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023]
Abstract
Stable isotope probing (SIP) approaches are a suitable tool to identify active organisms in bacterial communities, but adding isotopically labeled substrate can alter both the structure and the functionality of the community. Here, we validated and demonstrated a substrate-independent protein-SIP protocol using isotopically labeled water that captures the entire microbial activity of a community. We found that 18O yielded a higher incorporation rate into peptides and thus comprised a higher sensitivity. We then applied the method to an in vitro model of a human distal gut microbial ecosystem grown in two medium formulations, to evaluate changes in microbial activity between a high-fiber and high-protein diet. We showed that only little changes are seen in the community structure but the functionality varied between the diets. In conclusion, our approach can detect species-specific metabolic activity in complex bacterial communities and more specifically to quantify the amount of amino acid synthesis. Heavy water makes possible to analyze the activity of bacterial communities for which adding an isotopically labeled energy and nutrient sources is not easily feasible. SIGNIFICANCE: Heavy stable isotopes allow for the detection of active key players in complex ecosystems where many organisms are thought to be dormant. Opposed to the labelling with energy or nutrient sources, heavy water could be a suitable replacement to trace activity, which has been shown for DNA and RNA. Here we validate, quantify and compare the incorporation of heavy water either labeled with deuterium or 18‑oxygen into proteins of Escherichia coli K12 and of an in vitro model of a human gut microbial ecosystem. The significance of our research is in providing a freely available pipeline to analyze the incorporation of deuterium and 18‑oxygen into proteins together with the validation of the applicability of tracing heavy water as a proxy for activity. Our approach unveils the relative functional contribution of microbiota in complex ecosystems, which will improve our understanding of both animal- and environment-associated microbiomes and in vitro models.
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Affiliation(s)
- Robert Starke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Timo Sachsenberg
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany; Center for Bioinformatics, University of Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany; Center for Bioinformatics, University of Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany.
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6
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Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
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7
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Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
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8
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van der Waals MJ, Plugge C, Meima-Franke M, de Waard P, Bodelier PLE, Smidt H, Gerritse J. Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater. WATER RESEARCH 2019; 148:314-323. [PMID: 30391860 DOI: 10.1016/j.watres.2018.10.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using 13C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with 13C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the 13C and 12C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.
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Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands; Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Caroline Plugge
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Marion Meima-Franke
- The Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Pieter de Waard
- Wageningen University & Research, BioNanoTechnology, Bornse Weilanden 9, 6700 EK, Wageningen, the Netherlands
| | - Paul L E Bodelier
- The Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands
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9
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Papp K, Hungate BA, Schwartz E. Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H 218O. Appl Environ Microbiol 2018; 84:e02441-17. [PMID: 29439990 PMCID: PMC5881069 DOI: 10.1128/aem.02441-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/07/2018] [Indexed: 02/01/2023] Open
Abstract
Growing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with H218O. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with H218O. The positive correlation between 18O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA-to-DNA ratios obtained from sequencing libraries and the atom percent excess (APE) 18O values of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division and suggest that nondividing taxa do not dominate soil metabolic activity.IMPORTANCE Using quantitative stable isotope probing of microbial RNA and DNA with H218O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with 18O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Additionally, our results indicate that relative sequence abundance-based RNA-to-DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.
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Affiliation(s)
- Katerina Papp
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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10
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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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11
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Uksa M, Buegger F, Gschwendtner S, Lueders T, Kublik S, Kautz T, Athmann M, Köpke U, Munch JC, Schloter M, Fischer D. Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:729-741. [PMID: 28892269 DOI: 10.1111/1758-2229.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, 13 C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in 13 C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in 13 C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear 13 C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.
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Affiliation(s)
- Marie Uksa
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Tillmann Lueders
- Institute for Groundwater Ecology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Timo Kautz
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Miriam Athmann
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Ulrich Köpke
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Jean Charles Munch
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Chair for Soil Science, Research Department Ecology and Ecosystem Management, Technische Universität München, D-85350 Freising-Weihenstephan, Germany
| | - Doreen Fischer
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
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12
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Schwartz E, Hayer M, Hungate BA, Koch BJ, McHugh TA, Mercurio W, Morrissey EM, Soldanova K. Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples. Curr Opin Biotechnol 2016; 41:14-18. [DOI: 10.1016/j.copbio.2016.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/27/2016] [Accepted: 03/01/2016] [Indexed: 11/17/2022]
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13
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Lueders T, Dumont MG, Bradford L, Manefield M. RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes. Curr Opin Biotechnol 2016; 41:83-89. [PMID: 27269505 DOI: 10.1016/j.copbio.2016.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/27/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
Abstract
Stable isotope probing of RNA has enthused researchers right from its first introduction in 2002. The concept of a labelling-based detection of process-targeted microbes independent of cellular replication or growth has allowed for a much more direct handle on functionally relevant microbiota than by labelling of other biomarkers. This has led to a widespread application of the technology, and breakthroughs in our understanding of carbon flow in natural microbiomes, autotrophic and heterotrophic physiologies, microbial food webs, host-microbe interactions and environmental biotechnology. Recent studies detecting labelled mRNA demonstrate that RNA-SIP is not limited to the analysis of rRNA, but is currently developing towards an approach for accessing targeted transcriptomes. In combination with next-generation sequencing and other methodological advances, RNA-SIP will continue to deliver invaluable insights into the functioning of microbial communities.
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Affiliation(s)
- Tillmann Lueders
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute for Groundwater Ecology, Neuherberg, Germany.
| | - Marc G Dumont
- Centre for Biological Sciences (CfBS), University of Southampton, Southampton, United Kingdom
| | - Lauren Bradford
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute for Groundwater Ecology, Neuherberg, Germany
| | - Mike Manefield
- Centre for Marine Bioinnovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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14
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Ladino-Orjuela G, Gomes E, da Silva R, Salt C, Parsons JR. Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 237:105-121. [PMID: 26613990 DOI: 10.1007/978-3-319-23573-8_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.
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Affiliation(s)
- Guillermo Ladino-Orjuela
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Eleni Gomes
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Roberto da Silva
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Christopher Salt
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
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