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Shaw AJ, Duffy AM, Nieto-Lugilde M, Aguero B, Schuette S, Robinson S, Loveland J, Hicks KA, Weston D, Piatkowski B, Kolton M, Koska JE, Healey AL. Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex. Ann Bot 2023; 132:77-94. [PMID: 37417448 PMCID: PMC10550268 DOI: 10.1093/aob/mcad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND AND AIMS Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. METHODS Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. KEY RESULTS All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. CONCLUSIONS These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Aaron M Duffy
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Marta Nieto-Lugilde
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Scott Schuette
- Pennsylvania Natural Heritage Program, Western Pennsylvania Conservancy, Pittsburgh, PA, 15222, USA
| | - Sean Robinson
- Department of Biology, SUNY Oneonta, Oneonta, NY, 13820, USA
| | - James Loveland
- Department of Biology, Kenyon College, Gambier, OH 43022, USA
| | - Karen A Hicks
- Department of Biology, Kenyon College, Gambier, OH 43022, USA
| | - David Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Max Kolton
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
| | - Joel E Koska
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Adam L Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Anand U, Pal T, Yadav N, Singh VK, Tripathi V, Choudhary KK, Shukla AK, Sunita K, Kumar A, Bontempi E, Ma Y, Kolton M, Singh AK. Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability. Microb Ecol 2023; 86:1455-1486. [PMID: 36917283 PMCID: PMC10497456 DOI: 10.1007/s00248-023-02190-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.
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Affiliation(s)
- Uttpal Anand
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreshet Ben-Gurion, Israel.
| | - Tarun Pal
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Niraj Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya, 224123, Uttar Pradesh, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, 211007, Uttar Pradesh, India
| | - Krishna Kumar Choudhary
- Department of Botany, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya, 224123, Uttar Pradesh, India
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Ajay Kumar
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7505101, Rishon, Lezion, Israel
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123, Brescia, Italy.
| | - Ying Ma
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Max Kolton
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College (A constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur, 812007, Bihar, India.
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Sun X, Kong T, Huang D, Chen Z, Kolton M, Yang J, Huang Y, Cao Y, Gao P, Yang N, Li B, Liu H, Sun W. Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots. J Hazard Mater 2023; 454:131458. [PMID: 37099912 DOI: 10.1016/j.jhazmat.2023.131458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Zhenyu Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Max Kolton
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Jinchan Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Yuqing Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yue Cao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Peng Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Huaqing Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control,Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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Song T, Liu Y, Kolton M, Wilson RM, Keller JK, Rolando JL, Chanton JP, Kostka JE. Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog. FEMS Microbiol Ecol 2023; 99:fiad060. [PMID: 37280172 DOI: 10.1093/femsec/fiad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023] Open
Abstract
Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.
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Affiliation(s)
- Tianze Song
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Yutong Liu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- Department of Civil & Environmental Engineering, Pennsylvania State University, University Park, University Park, PA 16802, United States
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, 8499000, Israel
| | - Rachel M Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Jason K Keller
- Schmid College of Science and Technology, Chapman University, 1 University Dr, Orange, CA 92866, United States
| | - Jose L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Jeffrey P Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30318, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, United States
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5
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Xu R, Kolton M, Tao W, Sun X, Su P, Huang D, Zhang M, Yang Z, Guo Z, Gao H, Wang Q, Li B, Chen C, Sun W. Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics. J Hazard Mater 2023; 457:131834. [PMID: 37327607 DOI: 10.1016/j.jhazmat.2023.131834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (SeIVRB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative SeIVRB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative SeIVRB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.
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Affiliation(s)
- Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Duanyi Huang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Miaomiao Zhang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Hanbing Gao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Chengyu Chen
- College of Natural Resources and Environment, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou 510642, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control (Ministry of Education), Henan Normal University, Xinxiang 453007, PR China.
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Li Y, Guo L, Kolton M, Yang R, Zhang M, Qi F, Soleimani M, Sun X, Li B, Gao W, Yan G, Xu R, Sun W. Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats. Environ Sci Technol 2023; 57:231-243. [PMID: 36525577 DOI: 10.1021/acs.est.2c06424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N2. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N2 fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fangjie Qi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan 83111-84156, Iran
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Wenlong Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China
| | - Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Li Y, Yang R, Häggblom MM, Li M, Guo L, Li B, Kolton M, Cao Z, Soleimani M, Chen Z, Xu Z, Gao W, Yan B, Sun W. Correction: Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis). Microbiome 2022; 10:232. [PMID: 36527128 PMCID: PMC9756636 DOI: 10.1186/s40168-022-01445-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Yongbin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Rui Yang
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Lifang Guo
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University, of the Negev, Beer Sheva, Israel
| | - Zhiguo Cao
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Zhimin Xu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Wenlong Gao
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Bei Yan
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China.
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
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Sun X, Chen Z, Kong T, Chen Z, Dong Y, Kolton M, Cao Z, Zhang X, Zhang H, Liu G, Gao P, Yang N, Lan L, Xu Y, Sun W. Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems. Environ Sci Technol 2022; 56:15705-15717. [PMID: 36288260 DOI: 10.1021/acs.est.2c05346] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) contamination is a serious global environmental problem. Plastic contamination has attracted extensive attention during the past decades. While physiochemical weathering may influence the properties of MPs, biodegradation by microorganisms could ultimately mineralize plastics into CO2. Compared to the well-studied marine ecosystems, the MP biodegradation process in riverine ecosystems, however, is less understood. The current study focuses on the MP biodegradation in one of the world's most plastic contaminated rivers, Pearl River, using micropolyethylene (mPE) as a model substrate. Mineralization of 13C-labeled mPE into 13CO2 provided direct evidence of mPE biodegradation by indigenous microorganisms. Several Actinobacteriota genera were identified as putative mPE degraders. Furthermore, two Mycobacteriaceae isolates related to the putative mPE degraders, Mycobacterium sp. mPE3 and Nocardia sp. mPE12, were retrieved, and their ability to mineralize 13C-mPE into 13CO2 was confirmed. Pangenomic analysis reveals that the genes related to the proposed mPE biodegradation pathway are shared by members of Mycobacteriaceae. While both Mycobacterium and Nocardia are known for their pathogenicity, these populations on the plastisphere in this study were likely nonpathogenic as they lacked virulence factors. The current study provided direct evidence for MP mineralization by indigenous biodegraders and predicted their biodegradation pathway, which may be harnessed to improve bioremediation of MPs in urban rivers.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zhenyu Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva 849900, Israel
| | - Zhiguo Cao
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Xin Zhang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Guoqiang Liu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Ling Lan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yating Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Li Y, Yang R, Häggblom MM, Li M, Guo L, Li B, Kolton M, Cao Z, Soleimani M, Chen Z, Xu Z, Gao W, Yan B, Sun W. Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis). Microbiome 2022; 10:186. [PMID: 36329505 PMCID: PMC9632085 DOI: 10.1186/s40168-022-01379-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/22/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments. RESULTS Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using 15N2 identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth. CONCLUSIONS This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.
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Affiliation(s)
- Yongbin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Rui Yang
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Lifang Guo
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zhiguo Cao
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Zhimin Xu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Wenlong Gao
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Bei Yan
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China.
- Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. Microbiome 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Sun W, Sun X, Häggblom MM, Kolton M, Lan L, Li B, Dong Y, Xu R, Li F. Identification of Antimonate Reducing Bacteria and Their Potential Metabolic Traits by the Combination of Stable Isotope Probing and Metagenomic-Pangenomic Analysis. Environ Sci Technol 2021; 55:13902-13912. [PMID: 34581566 DOI: 10.1021/acs.est.1c03967] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microorganisms play an important role in altering antimony (Sb) speciation, mobility, and bioavailability, but the understanding of the microorganisms responsible for Sb(V) reduction has been limited. In this study, DNA-stable isotope probing (DNA-SIP) and metagenomics analysis were combined to identify potential Sb(V)-reducing bacteria (SbRB) and predict their metabolic pathways for Sb(V) reduction. Soil slurry cultures inoculated with Sb-contaminated paddy soils from two Sb-contaminated sites demonstrated the capability to reduce Sb(V). DNA-SIP identified bacteria belonging to the genera Pseudomonas and Geobacter as putative SbRB in these two Sb-contaminated sites. In addition, bacteria such as Lysinibacillus and Dechloromonas may potentially participate in Sb(V) reduction. Nearly complete draft genomes of putative SbRB (i.e., Pseudomonas and Geobacter) were obtained, and the genes potentially responsible for arsenic (As) and Sb reduction (i.e., respiratory arsenate reductase (arrA) and antimonate reductase (anrA)) were examined. Notably, bins affiliated with Geobacter contained arrA and anrA genes, supporting our hypothesis that they are putative SbRB. Further, pangenomic analysis indicated that various Geobacter-associated genomes obtained from diverse habitats also contained arrA and anrA genes. In contrast, Pseudomonas may use a predicted DMSO reductase closely related to sbrA (Sb(V) reductase gene) clade II to reduce Sb(V), which may need further experiments to verify. This current work represents a demonstration of using DNA-SIP and metagenomic-binning to identify SbRB and their key genes involved in Sb(V) reduction and provides valuable data sets to link bacterial identities with Sb(V) reduction.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Ling Lan
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430070, China
| | - Rui Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
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Zhang M, Kolton M, Li Z, Lin H, Li F, Lu G, Gao P, Sun X, Xu R, Xu F, Sun W. Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics. FEMS Microbiol Ecol 2021; 97:6206827. [PMID: 33791784 DOI: 10.1093/femsec/fiab057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/29/2021] [Indexed: 12/23/2022] Open
Abstract
Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity of SbOB. In this study, Sb(III)-oxidizing microcosms were set up using Sb-contaminated rice paddies as inocula. Sb(III) oxidation driven by microorganisms was observed in the microcosms. The increasing copies and transcription of the arsenate-oxidizing gene, aioA, in the microcosms during biotic Sb(III) oxidation indicated that microorganisms mediated Sb(III) oxidation via the aioA genes. Furthermore, a novel combination of DNA-SIP and shotgun metagenomic was applied to identify the SbOB and predict their metabolic potential. Several putative SbOB were identified, including Paracoccus, Rhizobium, Achromobacter and Hydrogenophaga. Furthermore, the metagenomic analysis indicated that all of these putative SbOB contained aioA genes, confirming their roles in Sb(III) oxidation. These results suggested the concept of proof of combining DNA-SIP and shotgun metagenomics directly. In addition, the identification of the novel putative SbOB expands the current knowledge regarding the diversity of SbOB.
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Affiliation(s)
- Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zhe Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guimei Lu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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13
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Liu H, Kong T, Qiu L, Xu R, Li F, Kolton M, Lin H, Zhang L, Lin L, Chen J, Sun X, Gao P, Sun W. Solar-driven, self-sustainable electrolysis for treating eutrophic river water: Intensified nutrient removal and reshaped microbial communities. Sci Total Environ 2021; 764:144293. [PMID: 33385655 DOI: 10.1016/j.scitotenv.2020.144293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/15/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
River ecosystems are the most important resource of surface freshwater, but they have frequently been contaminated by excessive nutrient input of nitrogen (N) and phosphorus (P) in particular. An efficient and economic river water treatment technology that possesses the capacity of simultaneous N and P removal is urgently required. In this study, a solar-driven, self-sustainable electrolytic treatment was conducted in situ to intensify N and P removal from eutrophic river water. Solar panel was applied to provide the electrolysis setups with energy (voltage 10 ± 0.5 V), and the current density was controlled to be 0.06 ± 0.02 mA cm-2. Results indicated that the average removal efficiencies of total N (TN) and total P (TP) under electrolysis conditions reached 72.4 ± 11.7 and 13.8 ± 5.3 mg m-2 d-1, which were 3.7- and 4.7-fold higher compared to untreated conditions. Enhanced TN removal mainly reflected the abatement of nitrate N (NO3--N) (80.6 ± 4.1%). The formation of ferric ions through the electro-dissolution of the sacrificial iron anode improved TP removal by coprecipitation with SPS. Combined high-throughput sequencing and statistical analyses revealed that electrolysis significantly reshaped the microbial communities in both the sediment-water interface and suspended sediment (SPS), and hydrogenotrophic denitrifiers (e.g., Hydrogenophaga) were highly enriched under electrolysis conditions. These findings indicated that in situ electrolysis is a feasible and effective technology for intensified nutrient removal from river water.
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Affiliation(s)
- Huaqing Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lang Qiu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lei Zhang
- Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou 510665, PR China
| | - Lan Lin
- Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou 510665, PR China
| | - Jiazhi Chen
- Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou 510665, PR China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China.
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14
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Kolton M, Rolando JL, Kostka JE. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol Ecol 2020; 96:5813622. [PMID: 32227167 DOI: 10.1093/femsec/fiaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.
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Affiliation(s)
- Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - José L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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15
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Sun X, Qiu L, Kolton M, Häggblom M, Xu R, Kong T, Gao P, Li B, Jiang C, Sun W. V V Reduction by Polaromonas spp. in Vanadium Mine Tailings. Environ Sci Technol 2020; 54:14442-14454. [PMID: 33125214 DOI: 10.1021/acs.est.0c05328] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Vanadium (V) is an important metal with critical industrial and medical applications. Elevated V contamination, however, can be a threat to the environment and human health. Microorganisms can reduce the more toxic and mobile VV to the less toxic and immobile VIV, which could be a detoxification and energy metabolism strategy adopted by V-reducing bacteria (VRB). The limited understanding of microbial responses to V contamination and the mechanisms for VV reduction, however, hamper our capability to attenuate V contamination. This study focused on determining the microbial responses to elevated V concentration and the mechanisms of VV reduction in V tailings. The bacterial communities were characterized and compared between the V tailings and the less contaminated adjacent mineral soils. Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction. Retrieved metagenome-assembled genomes (MAGs) suggested that the Polaromonas spp. encoded genes (cymA, omcA, and narG) were responsible for VV reduction. Additionally, Polaromonas spp. was metabolically versatile and could use both organic and inorganic electron donors. The metabolic versatility of Polaromonas spp. may be important for its ability to flourish in the V tailings.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Lang Qiu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Max Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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16
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Sun X, Kong T, Häggblom MM, Kolton M, Li F, Dong Y, Huang Y, Li B, Sun W. Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings. Environ Sci Technol 2020; 54:6082-6093. [PMID: 32216300 DOI: 10.1021/acs.est.9b07835] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.
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Affiliation(s)
- Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqing Huang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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17
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Hopple AM, Wilson RM, Kolton M, Zalman CA, Chanton JP, Kostka J, Hanson PJ, Keller JK, Bridgham SD. Massive peatland carbon banks vulnerable to rising temperatures. Nat Commun 2020; 11:2373. [PMID: 32398638 PMCID: PMC7217827 DOI: 10.1038/s41467-020-16311-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/17/2020] [Indexed: 11/10/2022] Open
Abstract
Peatlands contain one-third of the world's soil carbon (C). If destabilized, decomposition of this vast C bank could accelerate climate warming; however, the likelihood of this outcome remains unknown. Here, we examine peatland C stability through five years of whole-ecosystem warming and two years of elevated atmospheric carbon dioxide concentrations (eCO2). Warming exponentially increased methane (CH4) emissions and enhanced CH4 production rates throughout the entire soil profile; although surface CH4 production rates remain much greater than those at depth. Additionally, older deeper C sources played a larger role in decomposition following prolonged warming. Most troubling, decreases in CO2:CH4 ratios in gas production, porewater concentrations, and emissions, indicate that the peatland is becoming more methanogenic with warming. We observed limited evidence of eCO2 effects. Our results suggest that ecosystem responses are largely driven by surface peat, but that the vast C bank at depth in peatlands is responsive to prolonged warming.
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Affiliation(s)
- A M Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA. .,Schmid College of Science and Technology, Chapman University, Orange, CA, 92866, USA. .,Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - R M Wilson
- Earth, Ocean, and Atmospheric Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - M Kolton
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - C A Zalman
- Schmid College of Science and Technology, Chapman University, Orange, CA, 92866, USA
| | - J P Chanton
- Earth, Ocean, and Atmospheric Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - J Kostka
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - P J Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - J K Keller
- Schmid College of Science and Technology, Chapman University, Orange, CA, 92866, USA
| | - S D Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
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18
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Shin B, Bociu I, Kolton M, Huettel M, Kostka JE. Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach. Sci Rep 2019; 9:19401. [PMID: 31852991 PMCID: PMC6920467 DOI: 10.1038/s41598-019-55625-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/02/2019] [Indexed: 01/06/2023] Open
Abstract
The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.
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Affiliation(s)
- Boryoung Shin
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ioana Bociu
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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19
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Carrell AA, Kolton M, Glass JB, Pelletier DA, Warren MJ, Kostka JE, Iversen CM, Hanson PJ, Weston DJ. Experimental warming alters the community composition, diversity, and N 2 fixation activity of peat moss (Sphagnum fallax) microbiomes. Glob Chang Biol 2019; 25:2993-3004. [PMID: 31148286 PMCID: PMC6852288 DOI: 10.1111/gcb.14715] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 05/19/2023]
Abstract
Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.
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Affiliation(s)
- Alyssa A. Carrell
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Max Kolton
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | | | - Melissa J. Warren
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
- Present address:
CH2MAtlantaGeorgia30328USA
| | - Joel E. Kostka
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | - Colleen M. Iversen
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - David J. Weston
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
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Kolton M, Marks A, Wilson RM, Chanton JP, Kostka JE. Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States). Front Microbiol 2019; 10:870. [PMID: 31105668 PMCID: PMC6498409 DOI: 10.3389/fmicb.2019.00870] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/04/2019] [Indexed: 11/17/2022] Open
Abstract
Climate warming is predicted to increase heterotrophic metabolism in northern peatland soils leading to enhanced greenhouse gas emissions. However, the specific relationships between temperature and the greenhouse gas producing microbial communities are poorly understood. Thus, in this study, the temperature dependence of carbon dioxide (CO2) and methane (CH4) production rates along with abundance and composition of microbial communities were investigated in peat from a Sphagnum-dominated peatland, S1 bog (Minnesota, United States). Whereas CH4 production rates increased with temperature up to 30°C, CO2 production did not, resulting in a lower CO2:CH4 ratio with increasing temperature. CO2 production showed both psychrophilic and mesophilic maxima at 4 and 20°C, respectively, and appears to be mediated by two anaerobic microbial communities, one that operates under psychrophilic conditions that predominate for much of the year, and another that is more active under warmer conditions during the growing season. In incubations at 10°C above the ambient range, members of the Clostridiaceae and hydrogenotrophic methanogens of the Methanobacteriaceae dominated. Moreover, a significant negative correlation between temperature and microbial diversity was observed. Results indicate that the potential consequences of warming surface peat in northern peatlands include a large stimulation in CH4 production and a significant loss of microbial diversity.
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Affiliation(s)
- Max Kolton
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ansley Marks
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Rachel M. Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Jeffrey P. Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Joel E. Kostka
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
- School of Earth and Atmospheric Science, Georgia Institute of Technology, Atlanta, GA, United States
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Kolton M, Graber ER, Tsehansky L, Elad Y, Cytryn E. Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere. New Phytol 2017; 213:1393-1404. [PMID: 27780299 DOI: 10.1111/nph.14253] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/01/2016] [Indexed: 05/03/2023]
Abstract
The 'biochar effect' depicts a phenomenon in which biochar soil amendment enhances plant performance by promoting growth and suppressing disease. Although this phenomenon has been observed in numerous studies, the mode of action that explains it is currently unknown. In order to elucidate mechanisms responsible for the 'biochar effect', we comprehensively monitored tomato plant development and resistance to the foliar fungal pathogen Botrytis cinerea, in biochar-amended and nonamended soils using native biochar and washed biochar, striped of labile chemical constituents. We concomitantly assessed bacterial community succession in the rhizosphere by high-throughput 16S rRNA gene amplicon sequencing and carbon-source utilization profiling. Biochar had little impact on plant physiological parameters. However, both native and washed biochar treatments were characterized by higher rhizosphere bacterial diversity and enhanced carbohydrate and phenolic compound utilization rates coupled to stimulation of bacteria known to degrade phenolic compounds. This study indicates that the 'biochar effect' is at least partially dictated by increased diversity and changes in metabolic potential in the rhizosphere microbiome, which is primarily triggered by the recalcitrant carbon backbone of the biochar and tightly bound compounds. It corresponds to the growing consensus that soil amendments which enhance microbial diversity have important benefits to ecosystem functioning.
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Affiliation(s)
- Max Kolton
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Ellen R Graber
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
| | - Ludmila Tsehansky
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
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22
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Wilson RM, Hopple AM, Tfaily MM, Sebestyen SD, Schadt CW, Pfeifer-Meister L, Medvedeff C, McFarlane KJ, Kostka JE, Kolton M, Kolka R, Kluber LA, Keller JK, Guilderson TP, Griffiths NA, Chanton JP, Bridgham SD, Hanson PJ. Stability of peatland carbon to rising temperatures. Nat Commun 2016; 7:13723. [PMID: 27958276 PMCID: PMC5159855 DOI: 10.1038/ncomms13723] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/27/2016] [Indexed: 01/22/2023] Open
Abstract
Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20-30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.
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Affiliation(s)
- R. M. Wilson
- Earth, Ocean and Atmospheric Sciences, Florida State University, 117 N Woodward Avenue, Tallahassee, Florida 32306, USA
| | - A. M. Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - M. M. Tfaily
- Environmental Molecular Sciences Laboratory—Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - S. D. Sebestyen
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota 55744, USA
| | - C. W. Schadt
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - L. Pfeifer-Meister
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - C. Medvedeff
- Schmid College of Science and Technology, Chapman University, Orange, California 92866, USA
| | - K. J. McFarlane
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - J. E. Kostka
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M. Kolton
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R.K. Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota 55744, USA
| | - L. A. Kluber
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J. K. Keller
- Schmid College of Science and Technology, Chapman University, Orange, California 92866, USA
| | - T. P. Guilderson
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - N. A. Griffiths
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J. P. Chanton
- Earth, Ocean and Atmospheric Sciences, Florida State University, 117 N Woodward Avenue, Tallahassee, Florida 32306, USA
| | - S. D. Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - P. J. Hanson
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Kolton M, Frenkel O, Elad Y, Cytryn E. Potential role of Flavobacterial gliding-motility and type IX secretion system complex in root colonization and plant defense. Mol Plant Microbe Interact 2014; 27:1005-1013. [PMID: 24921925 DOI: 10.1094/mpmi-03-14-0067-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Members of the Flavobacterium genus are often highly abundant in the rhizosphere. Nevertheless, the physiological characteristics associated with their enhanced rhizosphere competence are currently an enigma. Flavobacteria possess a unique gliding-motility complex that is tightly associated with a recently characterized Bacteroidetes-specific type IX protein secretion system, which distinguishes them from the rest of the rhizosphere microbiome. We hypothesize that proper functionality of this complex may confer a competitive advantage in the rhizosphere. To test this hypothesis, we constructed mutant and complement root-associated flavobacterial variants with dysfunctional secretion and gliding motility, and tested them in a series of in planta experiments. These mutants demonstrated significantly lower rhizosphere persistence (approximately 10-fold), plant root colonization (approximately fivefold), and seed adhesion capacity (approximately sevenfold) than the wild-type strains. Furthermore, the biocontrol capacity of the mutant strain toward foliar-applied Clavibacter michiganensis was significantly impaired relative to the wild-type strain, suggesting a role of the gliding and secretion complex in plant protection. Collectively, these results provide an initial link between the high abundance of flavobacteria in the rhizosphere and their unique physiology, indicating that the flavobacterial gliding-motility and secretion complex may play a central role in root colonization and plant defense.
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Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013; 8:e76704. [PMID: 24086761 PMCID: PMC3784431 DOI: 10.1371/journal.pone.0076704] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022] Open
Abstract
Flavobacteria are important members of aquatic and terrestrial bacterial communities, displaying extreme variations in lifestyle, geographical distribution and genome size. They are ubiquitous in soil, but are often strongly enriched in the rhizosphere and phyllosphere of plants. In this study, we compared the genome of a root-associated Flavobacterium that we recently isolated, physiologically characterized and sequenced, to 14 additional Flavobacterium genomes, in order to pinpoint characteristics associated with its high abundance in the rhizosphere. Interestingly, flavobacterial genomes vary in size by approximately two-fold, with terrestrial isolates having predominantly larger genomes than those from aquatic environments. Comparative functional gene analysis revealed that terrestrial and aquatic Flavobacteria generally segregated into two distinct clades. Members of the aquatic clade had a higher ratio of peptide and protein utilization genes, whereas members of the terrestrial clade were characterized by a significantly higher abundance and diversity of genes involved in metabolism of carbohydrates such as xylose, arabinose and pectin. Interestingly, genes encoding glycoside hydrolase (GH) families GH78 and GH106, responsible for rhamnogalacturonan utilization (exclusively associated with terrestrial plant hemicelluloses), were only present in terrestrial clade genomes, suggesting adaptation of the terrestrial strains to plant-related carbohydrate metabolism. The Peptidase/GH ratio of aquatic clade Flavobacteria was significantly higher than that of terrestrial strains (1.7±0.7 and 9.7±4.7, respectively), supporting the concept that this relation can be used to infer Flavobacterium lifestyles. Collectively, our research suggests that terrestrial Flavobacteria are highly adapted to plant carbohydrate metabolism, which appears to be a key to their profusion in plant environments.
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Affiliation(s)
- Max Kolton
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
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Keren I, Bezawork-Geleta A, Kolton M, Maayan I, Belausov E, Levy M, Mett A, Gidoni D, Shaya F, Ostersetzer-Biran O. AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria. RNA 2009; 15:2299-311. [PMID: 19946041 PMCID: PMC2779688 DOI: 10.1261/rna.1776409] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 09/15/2009] [Indexed: 05/18/2023]
Abstract
Mitochondria (mt) in plants house about 20 group-II introns, which lie within protein-coding genes required in both organellar genome expression and respiration activities. While in nonplant systems the splicing of group-II introns is mediated by proteins encoded within the introns themselves (known as "maturases"), only a single maturase ORF (matR) has retained in the mitochondrial genomes in plants; however, its putative role(s) in the splicing of organellar introns is yet to be established. Clues to other proteins are scarce, but these are likely encoded within the nucleus as there are no obvious candidates among the remaining ORFs within the mtDNA. Intriguingly, higher plants genomes contain four maturase-related genes, which exist in the nucleus as self-standing ORFs, out of the context of their evolutionary-related group-II introns "hosts." These are all predicted to reside within mitochondria and may therefore act "in-trans" in the splicing of organellar-encoded introns. Here, we analyzed the intracellular locations of the four nuclear-encoded maturases in Arabidopsis and established the roles of one of these genes, At5g46920 (AtnMat2), in the splicing of several mitochondrial introns, including the single intron within cox2, nad1 intron2, and nad7 intron2.
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Affiliation(s)
- Ido Keren
- Volcani Center, Institute of Plant Sciences, Agricultural Research Organization, Bet Dagan 50250, Israel
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Keren I, Klipcan L, Bezawork-Geleta A, Kolton M, Shaya F, Ostersetzer-Biran O. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains. J Biol Chem 2008; 283:23333-42. [PMID: 18559344 DOI: 10.1074/jbc.m710488200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.
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Affiliation(s)
- Ido Keren
- Institute of Plant Sciences, Agricultural Research Organization, Bet Dagan 50250, Israel
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Shah H, Patel R, Kolton M, Mack E, Kuske R. Toxicity and cosmetic outcomes of high dose rate interstitial accelerated partial breast irradiation. Int J Radiat Oncol Biol Phys 2003. [DOI: 10.1016/s0360-3016(03)01185-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kavanagh BP, Ngo C, Raymer K, Yang H, Alhashemi JA, Lui ACP, Reid D, Cicutti N, Krepski B, Wood G, Heyland DK, Badner NH, Murkin JM, Mohr J, McKenzie FN, van der Starre PJA, van Rooyen-Butijn WT, Wilson-Yang K, Teoh K, Lee RMKW, Hossain I, Cheng D, Karski J, Asokumar B, Sandier A, St-Amand MA, Murkin JM, Menkis AH, Downey DB, Nantau W, Adams S, Dowd N, Cheng D, Wong D, Carroll-Munro J, Trachuk C, Cregg N, Cheng DCH, Williams WG, Karski JM, Siu S, Webb G, Cheng DCH, Wong DT, Kustra R, Karski J, Tibshirani RJ, Côté DL, Lacey DE, LeDez KM, Smith JA, Crosby ET, Orkin FK, Fisher A, Volgyesi G, Silverman J, Edelstein S, Rucker J, Sommer L, Dunington S, Roy L, Crochetière C, Arsenault MY, Villeneuve E, Lortie L, Grange CS, Douglas MJ, Adams TJ, Merrick PM, Lucas SB, Morgan PJ, Halpern S, Lo J, Giesinger CL, Halpern SH, Breen TW, Vishnubala S, Shetty GR, De Kock M, Lagmiche A, Scholtes JL, Grodecki W, Duffy PJ, Hull KA, Hawboldt GS, Clark AJ, Smith JB, Norman RW, Beattie WS, Sandier A, Jewett M, Valiquette L, Katz J, Fradet Y, Redelmeier D, Sampson H, Cole J, Chedore T, Snedden W, Green RG, Sosis MB, Robles PI, Lazar ER, Jolly DT, Tarn YK, Tawfik SR, Clanachan AS, Milne A, Beamish T, Cuillerier DJ, Sharpe MD, Lee JK, Basta M, Krahn AD, Klein GJ, Yee R, Vakharia N, Francis H, Scheepers L, Vaghadia H, Carrier J, Martin R, Pirlet M, Claprood Y, Tétrault JP, Wong TD, Ryner L, Kozlowski P, Scarth G, Warrian RK, Lefevre G, Thiessen D, Girling L, Doiron L, McCudden C, Saunders J, Mutch WAC, Duffy PJ, Langevin S, Lessard MR, Trépanier CA, Hare GMT, Ngan JCS, Viskari D, Berrill A, Jodoin C, Couture J, Bellemare F, Farmer S, Muir H, Money P, Milne B, Parlow J, Raymond J, Williams JM, Craen RA, Novick T, Komar W, Frenette L, Cox J, Lockhart B, McArdle P, Eckhoff D, Bynon S, Dobkowski WB, Grant DR, Wall WJ, Chedrawy EG, Hall RI, Nedelcu V, Parlow J, Viale JP, Bégou G, Sagnard P, Hughson R, Quintin L, Troncy É, Collet JP, Shapiro S, Guimond JG, Blair L, Ducruet T, Francœur M, Charbonneau M, Blaise G, Snedden W, Bernadska E, Manson HI, Kutt JL, Mezon BY, Nishida O, Arellano R, Boylen P, DeMajo W, Archer DP, Roth SH, Raman S, Manninen P, Boyle K, Cenic A, Lee TY, Gelb AW, Reinders FX, Brown JIM, Baker AJ, Moulton RJ, Schlichtert L, Schwarz SKW, Puil E, Finegan BA, Finucane BT, Kurrek MM, Devitt JH, Morgan PJ, Cleave-Hogg D, Bradley J, Byrick R, Spadafora SM, Fuller JG, Gelula MH, Mayson K, Forster B, Byrick RJ, McKnight DJ, Kurrek M, Kolton M, Cleave-Hogg D, Haughton J, Halpern S, Kronberg J, Shysh S, Eagle C, Dagnone AJ, Parlow JL, Blaise G, Yang F, Nguyen H, Troncy E, Czaika G, Wachowski I, Basta M, Krahn AD, Yee R, Deladrière H, Cambier C, Pendeville P, Hung OR, Coonan E, Whynot SC, Mezei M, Coonan E, Whynot SC, Ho AMH, Luchsinger IS, Ling E, Mashava D, Chinyanga HM, Cohen MM, Shaw M, Robblee JA, Labow RS, Rubens FD, Diemunsch AM, Gervais R, Rose DK, Cohen MM, O’Brien-Pallas L, Copplestone C, Rose DK, Karkouti K, Sykora K, Cheung SLW, Booker PD, Franks R, Pozzi M, Guard B, Sikich N, Lerman J, Levine M, Swan H, Cox P, Montgomery C, Dunn G, Bourne R, Kinahan A, McCormack J, Dunn GS, Reimer EJ, Sanderson P, Sanderson PM, Montgomery CJ, Betts TA, Orlay GR, Wong DH, Cohen M, Al-Kaisy AA, Chan V, Peng P, Perlas A, Miniad A, Cushing EV, Mills KR, El-Beheiry H, Jahromi SS, Weaver J, Morris M, Carien PL, Cowan RM, Manninen P, Richards J, Robblee JA, Labow RS, Rubens FD, Menkis AH, Adams S, Henderson BT, Hudson RJ, Thomson IR, Moon M, Peterson MD, Rosenbloom M, Davison PJ, Ali M, Ali NS, Searle NR, Thomson I, Roy M, Gagnon L, Lye A, Walsh F, Middleton W, Wong D, Langer A, Errett L, Mazer CD, Karski J, Tibshirani RJ, Williamson KM, Smith G, Gnanendran KP, Bignell SJ, Jones S, Sleigh J, Arnell M, Schultz JAI, Fear DW, Ganapathy S, Moote C, Wassermann R, Watson J, Armstrong K, Calikyan AO, Yilmaz O, Kose Y, Peng P, Chan V, Chung F, Claxton AR, Krishnathas A, Mezei G, Badner NH, Paul TL, Doyle JA, Mehta M, DeLima LGR, Silva LEO, May WL, Maliakkal RJ, Mehta M, Kolesar R, Arellano R, Rafuse S, Fletcher M, Dunn G, Curran M, Bragg P, Chamberlain W, Crossan M, Ganapathy S, Sandhu H, Spadafora S, Mian R, Evans B, Hurst L, Katsiris S. Abstracts. Can J Anaesth 1997. [DOI: 10.1007/bf03022274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Abstract
Pulmonary pressure-flow curves can be easily generated in the intact animal by using a combination of systemic arteriovenous (a-v) fistulas and inferior vena cava (IVC) occlusion. By combining this technique with pulmonary artery occlusion, pulmonary pressure-flow curves may be studied over a broader range of pressures than has been previously been done in the intact, resting animal using pulsatile flow. Pressure-flow curves were generated by varying flow through opening and closing of the a-v fistulas in conjunction with inflating and deflating a balloon in the inferior vena cava. The pressure-flow curves were done under two conditions; (1) with both lungs perfused; (2) with the right lung excluded from the circulation (PA occlusion). PA occlusion resulted in no change in alveolar arterial oxygen tension gradient. The pressure-flow relationships for one lung and two lungs were well described by linear equations (r2 = 0.83 +/- 0.03 and 0.82 +/- 0.04 respectively). The slope of the equations increased with PA occlusion (3.6 +/- 0.4 mmHg.L-1 to 5.9 +/- 0.9 mmHg.L-1). There was no change in the pressure axis intercept with PA occlusion (8.34 +/- 0.8 mmHg pre-occlusion and 8.9 +/- 1.3 mmHg post-occlusion). It is concluded that the pulmonary pressure-flow relationship is well described by a linear function above a mean pulmonary artery pressure (PAP) of 10-12 mmHg.
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Affiliation(s)
- R F McLean
- Department of Anaesthesia, Sunnybrook Health Science Center, Ontario, Canada
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Korzeniewski P, Lang SA, Grant R, Loader C, Vaghadia H, Wong D, Waters T, Merrick P, Ali MJ, Dobkowski W, Cornelius T, Hawkins R, Varkey GP, Claffey L, Plourde G, Trahan M, Morris J, Dean DM, Yamaguchi H, Harukuni I, Naito H, Chan VWS, Mati N, Seyone C, Evans D, Chung F, Joffe D, Plourde G, Villemurc C, Hong M, Milne B, Loomis C, Jhamandas K, Priddy R, Archer D, Tang T, Sabourin M, Samanini N, Cuillerier DJ, Schuben A, Awad IA, Perez-Trepichio AD, Ebrahim ZY, Bloomfield EL, Zexu F, Zhengnua G, Qing Z, Balhua S, Miller DR, Martineau RJ, Wynands JE, Hill JD, Knill RL, Skinner MI, Novick TV, McLean RF, Kolton M, Noble WH, Sullivan PJ, Cheng DCH, Chapman KR, Ong D, Roraanelli J, Smallman B, Nathan HJ, Murphy JT, Hall RI, Moffitt EA, Hudson RJ, Pascoe EA, Anderson BA, Thomson IR, Kassum DA, Shanks A, Rosenbloom M, Sidi A, Gehrig TR, Fool JM, Rush W, Martin AJ, Cooper PD, Maltby JR, Johnson D, Hurst T, Mayers I, Wigglesworth DF, Rose DK, Kay JC, Mazer CD, Yang H, Beattie WS, Doyle DJ, Demajo W, Comfort VK, Code WE, Rooney ME, Clark FJS, Sutton IR, Mutch WAC, Thomson IR, Teskey JM, Thiessen OB, Rosanbloom M, Tang TKK, Robblee JA, Nathan HJ, Wynands JE, Eagle CJ, Belenkle I, Chan KL, Tyberg JV, Stockwell M, Zintel T, Gallagher G, Kavanagh B, Sandier A, Lawson S, Chung F, Ong D, Isabel L, Trépanier CA, Campbell DC, Randall TE, Growe GH, Scarth I, Sawchuk CWT, Ong B, Unruh H, Horan T, Greengrass R, Mark D, Kitts JB, Curran MJ, Lindsay P, Polis T, Coté S, Socci M, Wiesel S, Conway JB, Seyone C, Goldberg J, Chung F, Rose DK, Cohen MM, Rogers KH, Duncan PG, Pope WDB, Tweed WA, Biehl D, Novick TV, Skinner MI, Mathieu A, Villeneuve E, Goldsmith CH, Allen GC, Smith CE, Pinchak AC, Hagen JF, Hudson JC, Gennings C, Tyler BL, Keenan RL, Chung F, Seyone C, Matl N, Ong D, Powell P, Tessler MJ, Kleiman SJ, Wiesel S, Tetzlaff JE, Yoon HJ, Baird B, Walsh M, Hondorp G, Wassef MR, Munshi C, Brooks J, Nimphius N, Tweed WA, Lee TL, Tweed WA, Phua WT, Chong KY, Lim E, Finegan BA, Coulson C, Lopaschuk GD, Clanachan AS, Fournier L, Cloutier R, Major D, Sharpe MD, Wexler HR, Dhamee MS, Rooney R, Ong SK, O’Leary E, McCarroll M, Phelan D, Young T, Coghlan D, O’Leary E, Blunnie WP, Splinter WM, Splinter WM, Ryan T, Maguire M, Bouchier-Hayes D, Cunningham AJ, Kamath MV, Fallen EL, Murkin JM, Shannon NA, Montgomery CJ, Karl HW, Raymond J, Drolet P, Tanguay M, Blaise G, Garceau D, Dumont L, Omri A, Sharkawi M, Billard V, Bourgain JL, Panos A, Mazer CD, Lichtenstein SV, Bevan JC, Popovic V, Baxter MRN, Donati F, Bevan DR, Bachman C, Kopelow M, Donen N, Umôn DT, Kemp S, Hartley E, Sikich N, Roy WL, Lerman J, Cooper RM, Yentis SM, Bissonnette B, Halpern L, Roy L, Burrows FA, Fear DW, Hillier S, Sloan M, Crawford M, Blssonnette B, Sikich N, Friedlander M, Sandier AN, Panos L, Winton T, Benureof J, Karski J, Teasdale S, Cruise C, Skala R, Zulys V, Ong D, Chow F, Packota G, Yip R, Bradley J, Arellano R, Sussman G, Sosis M, Braverman B, Sosis M, Ivankovich AD, Manganas M, Lephay A, Fournier T, Kadri N, Ossart M, Sandier AN, Turner KE, Wick V, Wherrett C, Sullivan PJ, Dyck JB, Varvel J, Shafer SL, Fiset P, Balendran P, Meistelman C, Lira E, Sloan M, Nigrovic V, Banoub M, Splinter WM, Roberts DW, Rhine EJ, MacNeill HB, Bonn GE, Clarke WM, Noel LP, Ryan T, Moriarty J, Bouchier-Hayes D, Cunningham AJ, Sandier AN, Baxter AD, Norman P, Samson B, Hull K, Chung F, Mali N, Evans D, Cruise C, Shumka D, Seyone C, Leung PT, Badner NH, Komar WE, Rajasingham M, Farren B, Vaillancourt G, Cournoyer S, Hollmann C, Breen TW, Janzen JA, Crochetiere CT, McMorland GH, Douglas MJ, Kamani AA, Arora SK, Tunstall M, Ross J, Mayer DC, Weeks SK, Norman P, Daley D, Sandier A, Guay J, Gaudreault P, Boulanger A, Tang A, Lortie L, Dupuis C, Backman SB, Bachoo M, Polosa C, Moudgil GC, Frame B, Blajchman HA, Singal DP, Albert JF, Ratcliff A, Law JC, Varvel J, Hung O, Shafer SL, Fiset P, Balendran P, Burgess PM, Doak GJ, Duke PC, Sloan PA, Mather LE, McLean CF, Rutten AJ, Nation RL, Milne RW, Runciman WB, Somoggi AA, Haack C, Shafer SL, Irish CL, Weisleider L, Mazer CD, Bell RS, Dejonckheere M, Levarlet M, d’Hollander A, Taylor RH, Sikich N, Campbell F, McLeod ME, Swartz J, Spahr-Schopfer I, McIntyre BG, Roy WL, Laycock GJA, Mitchell IM, Morton NS, Logan RW, Campbell F, Yentis SM, Fear D, Halpem L, Sloan M, Badgwell JM, Kleinman S, Yentis SM, Britton JT, Hannallah RS, Schafer PO, Norden JM, Splinter WM, Menard EA, Derdamezi JB, Ghurch JG, Britt BA, Radde IC, Sosis M, Kao YJ, Norton RG, Volgyesi GA, Spahr-Schopfer I, Sosis M, Plum M, Sosis M, Smith CE, Pinchak AC, Hancock DE, Owen P, McMeekin J, Hanson S, Cujec B, Feindel CM, Cruz J, Boylen P, Ong D, Murphy JT, Dupuis JY, Nathan HJ, Cattran C, Wynands JE, Murphy JT, Kinley CE, Sulliyan JA, Landymore RW, Robblee JA, Labow R, Buckley DN, Sharpe MD, Guiraudon G, Klein G, Yee R, Black J, Devitt JH, McLellan BA, Dubbin J, Ehrlich LE, Ralley FE, Robbins GR, Symcs JF, Bourke M, Nathan H, Wynands JE. Abstracts. Can J Anaesth 1991. [DOI: 10.1007/bf03008442] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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McLean RF, Noble WH, Kolton M. Pulmonary pressures at high flows in the intact pulsatile flow perfused lung. Can J Anaesth 1990; 37:S158. [PMID: 2361273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- R F McLean
- Department of Anesthesia, Sunnybrook Medical Centre
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Kolton M, McGhee I, Bryan AC. Tidal volumes required to maintain isocapnia at frequencies from 3 to 30 Hz in the dog. Anesth Analg 1987; 66:523-8. [PMID: 3107431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We ventilated seven mongrel dogs with high frequency oscillatory ventilation (HFO) at frequencies from 3 to 30 Hz. At each frequency, the tidal volume required to achieve isocapnia (VTiso) was measured by plethysmography. In an individual dog, VTiso could be related to frequency by an equation of the form VTiso = KfA. A was similar for the seven dogs, A = -0.54 +/- 0.03. K varied from 179 to 325 cc- Hz-A, reflecting differences between the dogs in dead space, CO2 production and gradient for gas transport. This relation is consistent with that predicted from the data of previous investigators who used different ventilators, circuits and methodology. From 3 to 30 Hz, VTiso decreased from 1.2 to 0.4 times anatomic plus equipment dead space, but minute volumes required to maintain isocapnia increased from 6 to 18 times those required during conventional ventilation. We conclude that low tidal volume ventilation is also high minute volume ventilation.
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Payne BC, Lyons TF, Neuhaus E, Kolton M, Dwarshius L. Method of evaluating and improving ambulatory medical care. Health Serv Res 1984; 19:219-45. [PMID: 6735736 PMCID: PMC1068802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The usefulness of an action-research model is demonstrated in the evaluation and improvement of ambulatory medical care in a variety of settings: solo office practice, prepaid capitation multiple-specialty group practice, and medical school hospital-based outpatient clinic practice. Improvements in the process of medical care are found to relate directly to the intensity and duration of planned interventions by the study group and are demonstrated to follow organizational changes in the participating sites--primarily managerial and support services initiated by policy decisions in each study site. Improvement in performance approaching one standard deviation results from the most intense intervention, about one-half standard deviation at the next level of intervention, and virtually no change from a simple feedback of performance measures. On the basis of these findings and other operational and research efforts to improve physician performance, it is unlikely that simple feedback of performance measures will elicit a change in behavior. However, noncoercive methods involving health care providers in problem identification, problem solving, and solution implementation are demonstrated to be effective.
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Kolton M, Cattran CB, Kent G, Volgyesi G, Froese AB, Bryan AC. Oxygenation during high-frequency ventilation compared with conventional mechanical ventilation in two models of lung injury. Anesth Analg 1982; 61:323-32. [PMID: 7039416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Oxygenation and mean lung volume were investigated during high frequency oscillation (HFO) and conventional mechanical ventilation (CMV) in two models of lung disease and related to the lung mechanics of the lesions. Oleic acid (n = 10) or lung lavage (n = 12) pulmonary injury was induced in a series of rabbits. Each animal was alternately ventilated with HFO (15 Hz sinusoidal wave form) and CMV (flow generator I:E, 1:2; f, 30 breaths/min; VT, 10 to 15 ml/kg) at matched mean airway pressure. Pao2 was measured 5 minutes after onset of ventilation. In the lung lavage model Pao2 was significantly greater during HFO than CMV (Pao2 228 +/- 116 torr vs 71 +/- 42 torr) provided that mean airway pressure was greater than the distinct opening pressure characteristic of this lesion. In the oleic acid model oxygenation was again superior during HFO (Pao2 269 +/- 116 torr vs 110 +/- 83 torr), but only if HFO was preceded by a sustained inflation. Plethysmography in a subset of six rabbits from each group revealed that the improvements in oxygenation were associated with significantly higher mean lung volumes during HFO than CMV (58 +/- 30 ml vs 29 +/- 14 ml lung lavage model, 45 +/- 15 ml vs 30.9 +/- 13 ml on the oleic acid model). The importance of a sustained inflation in rapidly optimizing gas exchange during HFO but not CMV was demonstrated. A sustained inflation resulted in immediate and sustained increases in Pao2 (from 134 +/- 102 torr to 274 +/0 124 torr in the oleic acid model; from 115 +/- 105 torr to 291 +/- 143 torr in the lung lavage model) and mean lung volume (41.8 +/- 11 to 53.8 +/- 9.7 ml in the oleic acid model, 30.9 +/- 7.7 ml to 42.8 +/- 5 ml in the lung lavage model). It is suggested that in these two particular models of lung disease, HFO, when combined with a sustained inflation (to provide opening forces), can more fully exploit the pressure volume hysteresis of unstable lung units than CMV, thereby resulting in the larger mean lung volumes and better oxygenation observed during HFO.
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