Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils
Abstract
Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis ofmore »
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1560692
- Grant/Contract Number:
- AC09-08SR22470
- Resource Type:
- Published Article
- Journal Name:
- Microorganisms
- Additional Journal Information:
- Journal Name: Microorganisms Journal Volume: 7 Journal Issue: 9; Journal ID: ISSN 2076-2607
- Publisher:
- MDPI AG
- Country of Publication:
- Switzerland
- Language:
- English
Citation Formats
Jaswal, Rajneesh, Pathak, Ashish, and Chauhan, Ashvini. Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils. Switzerland: N. p., 2019.
Web. doi:10.3390/microorganisms7090324.
Jaswal, Rajneesh, Pathak, Ashish, & Chauhan, Ashvini. Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils. Switzerland. https://doi.org/10.3390/microorganisms7090324
Jaswal, Rajneesh, Pathak, Ashish, and Chauhan, Ashvini. Fri .
"Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils". Switzerland. https://doi.org/10.3390/microorganisms7090324.
@article{osti_1560692,
title = {Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils},
author = {Jaswal, Rajneesh and Pathak, Ashish and Chauhan, Ashvini},
abstractNote = {Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.},
doi = {10.3390/microorganisms7090324},
journal = {Microorganisms},
number = 9,
volume = 7,
place = {Switzerland},
year = {Fri Sep 06 00:00:00 EDT 2019},
month = {Fri Sep 06 00:00:00 EDT 2019}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3390/microorganisms7090324
https://doi.org/10.3390/microorganisms7090324
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 10 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Metabolically active microbial communities in uranium-contaminated subsurface sediments: Microbial communities in uranium-contaminated sediments
journal, January 2007
- Akob, Denise M.; Mills, Heath J.; Kostka, Joel E.
- FEMS Microbiology Ecology, Vol. 59, Issue 1
Metal Toxicity Affects Fungal and Bacterial Activities in Soil Differently
journal, May 2004
- Rajapaksha, R. M. C. P.; Tobor-Kaplon, M. A.; Baath, E.
- Applied and Environmental Microbiology, Vol. 70, Issue 5
Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
journal, April 2019
- Jaswal,
- Genes, Vol. 10, Issue 5
Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site
journal, December 2011
- Green, Stefan J.; Prakash, Om; Jasrotia, Puja
- Applied and Environmental Microbiology, Vol. 78, Issue 4
Spatial Distribution of an Uranium-Respiring Betaproteobacterium at the Rifle, CO Field Research Site
journal, April 2015
- Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora
- PLOS ONE, Vol. 10, Issue 4
Isolation of Previously Uncultured Slow-Growing Bacteria by Using a Simple Modification in the Preparation of Agar Media
journal, July 2018
- Kato, Souichiro; Yamagishi, Ayasa; Daimon, Serina
- Applied and Environmental Microbiology, Vol. 84, Issue 19
Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress
journal, December 2018
- Agarwal, Meenakshi; Pathak, Ashish; Rathore, Rajesh
- Cells, Vol. 7, Issue 12
Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA
journal, June 2017
- Pathak, Ashish; Chauhan, Ashvini; Stothard, Paul
- Genomics Data, Vol. 12
Microbial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure
journal, August 2008
- Moreels, David; Crosson, Garry; Garafola, Craig
- Environmental Science and Pollution Research, Vol. 15, Issue 6
Microbial Community Changes in Response to Ethanol or Methanol Amendments for U(VI) Reduction
journal, July 2010
- Vishnivetskaya, T. A.; Brandt, C. C.; Madden, A. S.
- Applied and Environmental Microbiology, Vol. 76, Issue 17
Effective Soil Extraction Method for Cultivating Previously Uncultured Soil Bacteria
journal, October 2018
- Nguyen, Tuan Manh; Seo, Chan; Ji, Moongi
- Applied and Environmental Microbiology, Vol. 84, Issue 24
Metagenomic analysis of microbial community and function involved in cd-contaminated soil
journal, February 2018
- Feng, Gang; Xie, Tian; Wang, Xin
- BMC Microbiology, Vol. 18, Issue 1
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments
journal, February 2013
- Miller, Christopher S.; Handley, Kim M.; Wrighton, Kelly C.
- PLoS ONE, Vol. 8, Issue 2
Effects of Growth Medium, Inoculum Size, and Incubation Time on Culturability and Isolation of Soil Bacteria
journal, February 2005
- Davis, K. E. R.; Joseph, S. J.; Janssen, P. H.
- Applied and Environmental Microbiology, Vol. 71, Issue 2
Novel diesel-oil-degrading bacteria and fungi from the Ecuadorian Amazon rainforest
journal, May 2015
- Maddela, N. R.; Masabanda, M.; Leiva-Mora, M.
- Water Science and Technology, Vol. 71, Issue 10
Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate
journal, August 2004
- North, N. N.; Dollhopf, S. L.; Petrie, L.
- Applied and Environmental Microbiology, Vol. 70, Issue 8
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies
journal, October 2015
- Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 18, Issue 5
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
journal, October 2018
- Nilsson, Rolf Henrik; Larsson, Karl-Henrik; Taylor, Andy F. S.
- Nucleic Acids Research, Vol. 47, Issue D1
Nonlinear partial differential equations and applications: Cultivating the uncultured
journal, November 2002
- Zengler, K.; Toledo, G.; Rappe, M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 24
Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil
journal, December 2012
- Ormeno-Orrillo, E.; Rogel, M. A.; Chueire, L. M. O.
- Journal of Bacteriology, Vol. 194, Issue 24
Uranium and Fungi
journal, June 2011
- Gadd, Geoffrey M.; Fomina, Marina
- Geomicrobiology Journal, Vol. 28, Issue 5-6
Effect of gelling agent on colony formation in solid cultivation of microbial community in lake sediment
journal, July 2009
- Tamaki, Hideyuki; Hanada, Satoshi; Sekiguchi, Yuji
- Environmental Microbiology, Vol. 11, Issue 7
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
Short Peptide Induces an "Uncultivable" Microorganism To Grow In Vitro
journal, May 2008
- Nichols, D.; Lewis, K.; Orjala, J.
- Applied and Environmental Microbiology, Vol. 74, Issue 15
Biodegradation of petroleum hydrocarbons in the presence of nickel and cobalt: Petroleum hydrocarbon biodegradation in heavy metal-rich system
journal, March 2013
- Oyetibo, Ganiyu Oladunjoye; Ilori, Matthew Olusoji; Obayori, Oluwafemi Sunday
- Journal of Basic Microbiology, Vol. 53, Issue 11
Heavy metal tolerance traits of filamentous fungi isolated from gold and gemstone mining sites
journal, January 2018
- Oladipo, Oluwatosin Gbemisola; Awotoye, Olusegun Olufemi; Olayinka, Akinyemi
- Brazilian Journal of Microbiology, Vol. 49, Issue 1
Fungi outcompete bacteria under increased uranium concentration in culture media
journal, June 2013
- Mumtaz, Saqib; Streten-Joyce, Claire; Parry, David L.
- Journal of Environmental Radioactivity, Vol. 120
Cyclic AMP and Acyl Homoserine Lactones Increase the Cultivation Efficiency of Heterotrophic Bacteria from the Central Baltic Sea
journal, August 2002
- Bruns, A.; Cypionka, H.; Overmann, J.
- Applied and Environmental Microbiology, Vol. 68, Issue 8
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
journal, October 2013
- Zhang, J.; Kobert, K.; Flouri, T.
- Bioinformatics, Vol. 30, Issue 5
Isolation and Physiology of Bacteria from Contaminated Subsurface Sediments
journal, September 2010
- Bollmann, A.; Palumbo, A. V.; Lewis, K.
- Applied and Environmental Microbiology, Vol. 76, Issue 22
Incubation of Environmental Samples in a Diffusion Chamber Increases the Diversity of Recovered Isolates
journal, August 2007
- Bollmann, A.; Lewis, K.; Epstein, S. S.
- Applied and Environmental Microbiology, Vol. 73, Issue 20
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
journal, April 2017
- Dhariwal, Achal; Chong, Jasmine; Habib, Salam
- Nucleic Acids Research, Vol. 45, Issue W1
Effects of uranium concentration on microbial community structure and functional potential
journal, August 2017
- Sutcliffe, Brodie; Chariton, Anthony A.; Harford, Andrew J.
- Environmental Microbiology, Vol. 19, Issue 8
Common Features of Environmental and Potentially Beneficial Plant-Associated Burkholderia
journal, August 2011
- Suárez-Moreno, Zulma Rocío; Caballero-Mellado, Jesús; Coutinho, Bruna G.
- Microbial Ecology, Vol. 63, Issue 2
Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria
journal, December 2003
- Joseph, S. J.; Hugenholtz, P.; Sangwan, P.
- Applied and Environmental Microbiology, Vol. 69, Issue 12
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
journal, July 2014
- Tikhonov, Mikhail; Leach, Robert W.; Wingreen, Ned S.
- The ISME Journal, Vol. 9, Issue 1
Tapping into microbial diversity
journal, February 2004
- Keller, Martin; Zengler, Karsten
- Nature Reviews Microbiology, Vol. 2, Issue 2
A trap for in situ cultivation of filamentous actinobacteria
journal, March 2008
- Gavrish, Ekaterina; Bollmann, Annette; Epstein, Slava
- Journal of Microbiological Methods, Vol. 72, Issue 3
Bioleaching remediation of heavy metal-contaminated soils using Burkholderia sp. Z-90
journal, January 2016
- Yang, Zhihui; Zhang, Zhi; Chai, Liyuan
- Journal of Hazardous Materials, Vol. 301
Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils
journal, January 2018
- Chauhan, Ashvini; Pathak, Ashish; Jaswal, Rajneesh
- Genes, Vol. 9, Issue 1
Metagenomic analysis of microbial community in uranium-contaminated soil
journal, October 2015
- Yan, Xun; Luo, Xuegang; Zhao, Min
- Applied Microbiology and Biotechnology, Vol. 100, Issue 1
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
25 years of serving the community with ribosomal RNA gene reference databases and tools
journal, November 2017
- Glöckner, Frank Oliver; Yilmaz, Pelin; Quast, Christian
- Journal of Biotechnology, Vol. 261
Endogenous Stress Caused by Faulty Oxidation Reactions Fosters Evolution of 2,4-Dinitrotoluene-Degrading Bacteria
journal, August 2013
- Pérez-Pantoja, Danilo; Nikel, Pablo I.; Chavarría, Max
- PLoS Genetics, Vol. 9, Issue 8
The Uncultured Microbial Majority
journal, October 2003
- Rappé, Michael S.; Giovannoni, Stephen J.
- Annual Review of Microbiology, Vol. 57, Issue 1
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
journal, October 2015
- Hemme, Christopher L.; Tu, Qichao; Shi, Zhou
- Frontiers in Microbiology, Vol. 6