1
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Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. THE ISME JOURNAL 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
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Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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2
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Pacheco AR, Vorholt JA. Resolving metabolic interaction mechanisms in plant microbiomes. Curr Opin Microbiol 2023; 74:102317. [PMID: 37062173 DOI: 10.1016/j.mib.2023.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/18/2023]
Abstract
Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those of plants. However, disentangling the molecular basis of these interactions and their specific roles remains a major challenge. Here, we review recent applications of experimental and computational methods toward the elucidation of metabolic interactions in plant-associated microbiomes. We highlight studies that span various scales of taxonomic and environmental complexity, including those that test interaction outcomes in vitro and in planta by deconstructing microbial communities. We also discuss how the continued integration of multiple methods can further reveal the general ecological characteristics of plant microbiomes, as well as provide strategies for applications in areas such as improved plant protection, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Alan R Pacheco
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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3
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Li X, Yao S, Bolan N, Wang Z, Jiang X, Song Y. Combined maize straw-biochar and oxalic acids induced a relay activity of abundant specific degraders for efficient phenanthrene degradation: Evidence based on the DNA-SIP technology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119867. [PMID: 35940483 DOI: 10.1016/j.envpol.2022.119867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/08/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Biochar-oxalic acid composite application (BCOA) have shown to be efficient in the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil, but the functional degraders and the mechanism of improving biodegradation remains unclear. In this study, with the help of stable isotope probing technology of phenanthrene (Phe), we determined that BCOA significantly improved Phe mineralization by 2.1 times, which was ascribed to the increased numbers and abundances of functional degraders. The BCOA increased contents of dissolved organic carbon and available nutrients and decreased pH values in soil, thus promoting the activity, diversity and close cooperation of the functional Phe-degraders, and stimulating their functions associated with Phe degradation. In addition, there is a relay activity among more and diverse functional Phe-degraders in the soil with BCOA. Specifically, Pullulanibacillus persistently participated in Phe-degradation in the soil with BCOA throughout the incubation period. Moreover, Pullulanibacillus, Blastococcus, Alsobacter, Ramlibacter, and Mizugakiibacter were proved to be potential Phe-degraders in soil for the first time. The specific Phe degraders and their relay and cooperation activity in soils as impacted by BCOA were first identified with DNA-stable isotope probing technology. Our findings provided a novel perspective to understand the efficient degradation of PAH in the BCOA treatments, revealed the potential of soil native microbes in the efficient bioremediation of PAH-contaminated natural soil, and provided a basis for the development of in-situ phytoremediation technologies to remediate PAH pollution in future.
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Affiliation(s)
- Xiaona Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Institute of Environmental Processes and Pollution Control, And School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shi Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nanthi Bolan
- School of Agriculture and Environment, UWA Institute of Agriculture, The University of Western Australia, Nedland, WA, 6009, Australia
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, And School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Duan H, He P, Shao L, Lü F. Functional genome-centric view of the CO-driven anaerobic microbiome. THE ISME JOURNAL 2021; 15:2906-2919. [PMID: 33911204 PMCID: PMC8443622 DOI: 10.1038/s41396-021-00983-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 02/02/2023]
Abstract
CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.
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Affiliation(s)
- Haowen Duan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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5
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Yun J, Crombie AT, Ul Haque MF, Cai Y, Zheng X, Wang J, Jia Z, Murrell JC, Wang Y, Du W. Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau. Environ Microbiol 2021; 23:6520-6535. [PMID: 34390603 DOI: 10.1111/1462-2920.15697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023]
Abstract
The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using 13 C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H4 MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.
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Affiliation(s)
- Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 10049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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6
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Liang J, Gao S, Wu Z, Rijnaarts HHM, Grotenhuis T. DNA-SIP identification of phenanthrene-degrading bacteria undergoing bioaugmentation and natural attenuation in petroleum-contaminated soil. CHEMOSPHERE 2021; 266:128984. [PMID: 33234305 DOI: 10.1016/j.chemosphere.2020.128984] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/08/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
DNA-stable isotope probing (SIP) with 13C labeled phenanthrene (PHE) as substrate was used to identify specific bacterial degraders during natural attenuation (NA) and bioaugmentation (BA) in petroleum contaminated soil. BA, with the addition of a bacterial suspension mixture named GZ, played a significant role in PHE degradation with a higher PHE removal rate (∼90%) than that of NA (∼80%) during the first 3 days, and remarkably altered microbial communities. Of the five strains introduced in BA, only two genera, particularly, Ochrobactrum, Rhodococcus were extensively responsible for PHE-degradation. Six (Bacillus sp., Acinetobacter sp., Xanthomonas sp., Conexibacter sp., Acinetobacter sp. and Staphylococcus sp.) and seven (Ochrobactrum sp., Rhodococcus sp., Alkanindiges sp., Williamsia sp., Sphingobium sp., Gillisia sp. and Massilia sp.) bacteria responsible for PHE degradation were identified in NA and BA treatments, respectively. This study reports for the first time the association of Xanthomonas sp., Williamsia sp., and Gillisia sp. to PHE degradation.
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Affiliation(s)
- Jidong Liang
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Sha Gao
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; Department of Environmental Technology, Wageningen University and Research, Wageningen, 6700AA, the Netherlands
| | - Zijun Wu
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Huub H M Rijnaarts
- Department of Environmental Technology, Wageningen University and Research, Wageningen, 6700AA, the Netherlands
| | - Tim Grotenhuis
- Department of Environmental Technology, Wageningen University and Research, Wageningen, 6700AA, the Netherlands
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7
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Starke R, Schäpe SS, Jehmlich N, von Bergen M. Protein stable isotope probing with H 2 18 O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8941. [PMID: 32885498 DOI: 10.1002/rcm.8941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Tracing isotopically labeled water into proteins allows for the detection of species-specific metabolic activity in complex communities. However, a stress response may alter the newly synthesized proteins. METHODS We traced 18-oxygen from heavy water into proteins of Escherichia coli K12 grown from permissive to retardant temperatures. All samples were analyzed using UPLC/Orbitrap Q-Exactive-MS/MS operating in positive electrospray ionization mode. RESULTS We found that warmer temperatures resulted in significantly (P-value < 0.05) higher incorporation of 18-oxygen as seen by both substrate utilization as relative isotope abundance (RIA) and growth as labeling ratio (LR). However, the absolute number of peptides with incorporation of 18-oxygen showed no significant correlation to temperature, potentially caused by the synthesis of different proteins at low temperatures, namely, proteins related to cold stress response. CONCLUSIONS Our results unveil the species-specific cold stress response of E. coli K12 that could be misinterpreted as general growth; this is why the quantity as RIA and LR but also the quality as absolute number of peptides with incorporation (relative abundance, RA) and their function must be considered to fully understand the activity of microbial communities.
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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
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - 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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8
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Walker LP, Buhler D. Catalyzing Holistic Agriculture Innovation Through Industrial Biotechnology. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2020.29222.lpw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Larry P. Walker
- Biosystems and Agricultural Engineering Department, Michigan State University, East Lansing, Michigan, USA
- Somaiya Vidyavihar University, Mumbai, India
- Biological and Environmental Engineering Department, Cornell University, Ithaca, New York, USA
| | - Douglas Buhler
- Michigan State University AgBioResearch and Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
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9
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Waseem H, Ali J, Syed JH, Jones KC. Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114676. [PMID: 33618452 DOI: 10.1016/j.envpol.2020.114676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.
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Affiliation(s)
- Hassan Waseem
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA; Department of Biotechnology, University of Sialkot, Sialkot, Punjab 51310, Pakistan
| | - Jafar Ali
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS University, Tarlai Kalan Park Road, Islamabad, 45550, Pakistan.
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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10
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Couradeau E, Sasse J, Goudeau D, Nath N, Hazen TC, Bowen BP, Chakraborty R, Malmstrom RR, Northen TR. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat Commun 2019; 10:2770. [PMID: 31235780 PMCID: PMC6591230 DOI: 10.1038/s41467-019-10542-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/07/2019] [Indexed: 01/17/2023] Open
Abstract
The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (Tennessee, USA) and find that a maximum of 25-70% of the extractable cells are active. Analysis of 16S rRNA sequences from BONCAT-positive cells recovered by fluorescence-activated cell sorting (FACS) reveals that the phylogenetic composition of the active fraction is distinct from the total population of extractable cells. Some members of the community are found to be active at both depths independently of their abundance rank, suggesting that the incubation conditions favor the activity of similar organisms. We conclude that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new approach for uncovering the links between soil processes and specific microbial groups.
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Affiliation(s)
- Estelle Couradeau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joelle Sasse
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Nandita Nath
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Terry C Hazen
- University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ben P Bowen
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Romy Chakraborty
- Earth Science and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA.
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11
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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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12
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Abstract
Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.
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Affiliation(s)
- Eileen Kröber
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Landscape Research, Müncheberg, Germany
| | - Özge Eyice
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
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13
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Egert M, Weis S, Schnell S. RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Methods 2018; 149:25-30. [PMID: 29857194 DOI: 10.1016/j.ymeth.2018.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 12/15/2022] Open
Abstract
The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.
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Affiliation(s)
- Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany; Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Germany
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Arcand MM, Levy-Booth DJ, Helgason BL. Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use. Front Microbiol 2017; 8:2293. [PMID: 29230199 PMCID: PMC5711833 DOI: 10.3389/fmicb.2017.02293] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/06/2017] [Indexed: 01/06/2023] Open
Abstract
Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal calorimetry was combined with 13C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of Proteobacteria and Actinobacteria, with a higher Proteobacteria:Actinobacteria ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of Firmicutes. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to ıcritical biological processes that underpin soil health.
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Affiliation(s)
- Melissa M Arcand
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - David J Levy-Booth
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Bobbi L Helgason
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
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