1
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Sivaguru M, Todorov LG, Miller CAH, Fouke CE, Munro CMO, Fouke KW, Fouke KE, Baughman ME, Fouke BW. Author Correction: Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature. Sci Rep 2023; 13:19479. [PMID: 37945791 PMCID: PMC10636029 DOI: 10.1038/s41598-023-45562-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Lauren G Todorov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carly A H Miller
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Courtney E Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, Denison University, Granville, OH, USA
| | - Cara M O Munro
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Ecology and Evolutionary Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Kyle W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kaitlyn E Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, Denison University, Granville, OH, USA
- The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Todorov LG, Sivaguru M, Krambeck AE, Lee MS, Lieske JC, Fouke BW. GeoBioMed perspectives on kidney stone recurrence from the reactive surface area of SWL-derived particles. Sci Rep 2022; 12:18371. [PMID: 36319741 PMCID: PMC9626463 DOI: 10.1038/s41598-022-23331-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/29/2022] [Indexed: 11/18/2022] Open
Abstract
Shock wave lithotripsy (SWL) is an effective and commonly applied clinical treatment for human kidney stones. Yet the success of SWL is counterbalanced by the risk of retained fragments causing recurrent stone formation, which may require retreatment. This study has applied GeoBioMed experimental and analytical approaches to determine the size frequency distribution, fracture patterns, and reactive surface area of SWL-derived particles within the context of their original crystal growth structure (crystalline architecture) as revealed by confocal autofluorescence (CAF) and super-resolution autofluorescence (SRAF) microscopy. Multiple calcium oxalate (CaOx) stones were removed from a Mayo Clinic patient using standard percutaneous nephrolithotomy (PCNL) and shock pulse lithotripsy (SPL). This produced approximately 4-12 mm-diameter PCNL-derived fragments that were experimentally treated ex vivo with SWL to form hundreds of smaller particles. Fractures propagated through the crystalline architecture of PCNL-derived fragments in a variety of geometric orientations to form rectangular, pointed, concentrically spalled, and irregular SWL-derived particles. Size frequency distributions ranged from fine silt (4-8 μm) to very fine pebbles (2-4 mm), according to the Wentworth grain size scale, with a mean size of fine sand (125-250 μm). Importantly, these SWL-derived particles are smaller than the 3-4 mm-diameter detection limit of clinical computed tomography (CT) techniques and can be retained on internal kidney membrane surfaces. This creates clinically undetectable crystallization seed points with extremely high reactive surface areas, which dramatically enhance the multiple events of crystallization and dissolution (diagenetic phase transitions) that may lead to the high rates of CaOx kidney stone recurrence after SWL treatment.
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Affiliation(s)
- Lauren G. Todorov
- grid.35403.310000 0004 1936 9991Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Mayandi Sivaguru
- grid.35403.310000 0004 1936 9991Cytometry and Microscopy to Omics Facility, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Amy E. Krambeck
- grid.66875.3a0000 0004 0459 167XDepartment of Urology, Mayo Clinic, Rochester, MN USA ,grid.16753.360000 0001 2299 3507Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Matthew S. Lee
- grid.16753.360000 0001 2299 3507Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - John C. Lieske
- grid.66875.3a0000 0004 0459 167XDivision of Nephrology and Hypertension, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Bruce W. Fouke
- grid.35403.310000 0004 1936 9991Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL USA
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3
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Sivaguru M, Fouke BW. Renal Macrophages and Multinucleated Giant Cells: Ferrymen of the River Styx? Kidney360 2022; 3:1616-1619. [PMID: 36245644 PMCID: PMC9528364 DOI: 10.34067/kid.0003992022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/22/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Mayandi Sivaguru
- Cytometry and Microscopy to Omics Facility, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Bruce W. Fouke
- Cytometry and Microscopy to Omics Facility, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Biocomplexity Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois
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4
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Ranoa DRE, Holland RL, Alnaji FG, Green KJ, Wang L, Fredrickson RL, Wang T, Wong GN, Uelmen J, Maslov S, Weiner ZJ, Tkachenko AV, Zhang H, Liu Z, Ibrahim A, Patel SJ, Paul JM, Vance NP, Gulick JG, Satheesan SP, Galvan IJ, Miller A, Grohens J, Nelson TJ, Stevens MP, Hennessy PM, Parker RC, Santos E, Brackett C, Steinman JD, Fenner MR, Dohrer K, DeLorenzo M, Wilhelm-Barr L, Brauer BR, Best-Popescu C, Durack G, Wetter N, Kranz DM, Breitbarth J, Simpson C, Pryde JA, Kaler RN, Harris C, Vance AC, Silotto JL, Johnson M, Valera EA, Anton PK, Mwilambwe L, Bryan SP, Stone DS, Young DB, Ward WE, Lantz J, Vozenilek JA, Bashir R, Moore JS, Garg M, Cooper JC, Snyder G, Lore MH, Yocum DL, Cohen NJ, Novakofski JE, Loots MJ, Ballard RL, Band M, Banks KM, Barnes JD, Bentea I, Black J, Busch J, Conte A, Conte M, Curry M, Eardley J, Edwards A, Eggett T, Fleurimont J, Foster D, Fouke BW, Gallagher N, Gastala N, Genung SA, Glueck D, Gray B, Greta A, Healy RM, Hetrick A, Holterman AA, Ismail N, Jasenof I, Kelly P, Kielbasa A, Kiesel T, Kindle LM, Lipking RL, Manabe YC, Mayes J́, McGuffin R, McHenry KG, Mirza A, Moseley J, Mostafa HH, Mumford M, Munoz K, Murray AD, Nolan M, Parikh NA, Pekosz A, Pflugmacher J, Phillips JM, Pitts C, Potter MC, Quisenberry J, Rear J, Robinson ML, Rosillo E, Rye LN, Sherwood M, Simon A, Singson JM, Skadden C, Skelton TH, Smith C, Stech M, Thomas R, Tomaszewski MA, Tyburski EA, Vanwingerden S, Vlach E, Watkins RS, Watson K, White KC, Killeen TL, Jones RJ, Cangellaris AC, Martinis SA, Vaid A, Brooke CB, Walsh JT, Elbanna A, Sullivan WC, Smith RL, Goldenfeld N, Fan TM, Hergenrother PJ, Burke MD. Mitigation of SARS-CoV-2 transmission at a large public university. Nat Commun 2022. [DOI: doi.org/10.1038/s41467-022-30833-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
AbstractIn Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.
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5
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Ranoa DRE, Holland RL, Alnaji FG, Green KJ, Wang L, Fredrickson RL, Wang T, Wong GN, Uelmen J, Maslov S, Weiner ZJ, Tkachenko AV, Zhang H, Liu Z, Ibrahim A, Patel SJ, Paul JM, Vance NP, Gulick JG, Satheesan SP, Galvan IJ, Miller A, Grohens J, Nelson TJ, Stevens MP, Hennessy PM, Parker RC, Santos E, Brackett C, Steinman JD, Fenner MR, Dohrer K, DeLorenzo M, Wilhelm-Barr L, Brauer BR, Best-Popescu C, Durack G, Wetter N, Kranz DM, Breitbarth J, Simpson C, Pryde JA, Kaler RN, Harris C, Vance AC, Silotto JL, Johnson M, Valera EA, Anton PK, Mwilambwe L, Bryan SP, Stone DS, Young DB, Ward WE, Lantz J, Vozenilek JA, Bashir R, Moore JS, Garg M, Cooper JC, Snyder G, Lore MH, Yocum DL, Cohen NJ, Novakofski JE, Loots MJ, Ballard RL, Band M, Banks KM, Barnes JD, Bentea I, Black J, Busch J, Conte A, Conte M, Curry M, Eardley J, Edwards A, Eggett T, Fleurimont J, Foster D, Fouke BW, Gallagher N, Gastala N, Genung SA, Glueck D, Gray B, Greta A, Healy RM, Hetrick A, Holterman AA, Ismail N, Jasenof I, Kelly P, Kielbasa A, Kiesel T, Kindle LM, Lipking RL, Manabe YC, Mayes J, McGuffin R, McHenry KG, Mirza A, Moseley J, Mostafa HH, Mumford M, Munoz K, Murray AD, Nolan M, Parikh NA, Pekosz A, Pflugmacher J, Phillips JM, Pitts C, Potter MC, Quisenberry J, Rear J, Robinson ML, Rosillo E, Rye LN, Sherwood M, Simon A, Singson JM, Skadden C, Skelton TH, Smith C, Stech M, Thomas R, Tomaszewski MA, Tyburski EA, Vanwingerden S, Vlach E, Watkins RS, Watson K, White KC, Killeen TL, Jones RJ, Cangellaris AC, Martinis SA, Vaid A, Brooke CB, Walsh JT, Elbanna A, Sullivan WC, Smith RL, Goldenfeld N, Fan TM, Hergenrother PJ, Burke MD. Mitigation of SARS-CoV-2 transmission at a large public university. Nat Commun 2022; 13:3207. [PMID: 35680861 PMCID: PMC9184485 DOI: 10.1038/s41467-022-30833-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 10/13/2021] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university. Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.
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Affiliation(s)
- Diana Rose E Ranoa
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robin L Holland
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kelsie J Green
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard L Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tong Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - George N Wong
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Johnny Uelmen
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zachary J Weiner
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Hantao Zhang
- Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhiru Liu
- Department of Physics, Stanford University, Palo Alto, CA, USA
| | - Ahmed Ibrahim
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sanjay J Patel
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John M Paul
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Nickolas P Vance
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph G Gulick
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Isaac J Galvan
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Miller
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph Grohens
- Department of English, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Todd J Nelson
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary P Stevens
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Robert C Parker
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Julie D Steinman
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melvin R Fenner
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kirstin Dohrer
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Michael DeLorenzo
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Laura Wilhelm-Barr
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Catherine Best-Popescu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gary Durack
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Tekmill, Champaign, IL, USA
| | | | - David M Kranz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica Breitbarth
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charlie Simpson
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julie A Pryde
- Champaign-Urbana Public Health District, Champaign, IL, USA
| | - Robin N Kaler
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chris Harris
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Allison C Vance
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jodi L Silotto
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark Johnson
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Enrique Andres Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Patricia K Anton
- Housing Division, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lowa Mwilambwe
- Office of the Vice Chancellor for Student Affairs, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stephen P Bryan
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Deborah S Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Danita B Young
- Office of the Vice Chancellor for Student Affairs, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Wanda E Ward
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John Lantz
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John A Vozenilek
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Rashid Bashir
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jeffrey S Moore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mayank Garg
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julian C Cooper
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gillian Snyder
- Interdisciplinary Health Sciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Michelle H Lore
- Interdisciplinary Health Sciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dustin L Yocum
- Office for the Protection of Human Subjects, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Neal J Cohen
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Psychology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jan E Novakofski
- College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melanie J Loots
- Office of the Vice Chancellor for Research and Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Randy L Ballard
- Department of Intercollegiate Athletics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark Band
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kayla M Banks
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph D Barnes
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Iuliana Bentea
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Jessica Black
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jeremy Busch
- Department of Intercollegiate Athletics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Curry
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jennifer Eardley
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - April Edwards
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Therese Eggett
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Judes Fleurimont
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Delaney Foster
- Division of Campus Recreation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Gastala
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Scott A Genung
- Office of the Chief Info Officer, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Declan Glueck
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Brittani Gray
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Andrew Greta
- University of Illinois System Office, Urbana, IL, USA
| | - Robert M Healy
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ashley Hetrick
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Arianna A Holterman
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nahed Ismail
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ian Jasenof
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Patrick Kelly
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Aaron Kielbasa
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Teresa Kiesel
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Lorenzo M Kindle
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rhonda L Lipking
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jade Mayes
- Department of Intercollegiate Athletics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Reubin McGuffin
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kenton G McHenry
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jada Moseley
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melody Mumford
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Kathleen Munoz
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Arika D Murray
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Moira Nolan
- Office of Corporate Relations, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nil A Parikh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Janna Pflugmacher
- University Administration, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Janise M Phillips
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Collin Pitts
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark C Potter
- Department of Family and Community Medicine, College of Medicine, University of Illinois at Chicago, Chicago, USA
| | - James Quisenberry
- Division of Student Affairs, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Janelle Rear
- Office of the Vice President for Economic Development and Innovation, University of Illinois System, Urbana, IL, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Edith Rosillo
- Library Department, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leslie N Rye
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - MaryEllen Sherwood
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anna Simon
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jamie M Singson
- Division of Student Affairs, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carly Skadden
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tina H Skelton
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charlie Smith
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary Stech
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ryan Thomas
- Office of the Chief Info Officer, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Erika A Tyburski
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Emory University School of Medicine, Children's Healthcare of Atlanta, and Georgia Institute of Technology, Atlanta, GA, USA.,Georgia Institute of Technology, Institute for Electronics and Nanotechnology, Atlanta, GA, USA
| | - Scott Vanwingerden
- IT Service Delivery, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Evette Vlach
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ronald S Watkins
- University of Illinois System Office, Urbana, IL, USA.,Office of the President, University of Illinois System, Urbana, IL, USA
| | - Karriem Watson
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Karen C White
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Timothy L Killeen
- Gies College of Business, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Robert J Jones
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Susan A Martinis
- Office of the Vice Chancellor for Research and Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Awais Vaid
- Champaign-Urbana Public Health District, Champaign, IL, USA
| | - Christopher B Brooke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph T Walsh
- Library Department, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ahmed Elbanna
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - William C Sullivan
- Department of Landscape Architecture, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Nigel Goldenfeld
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Physics, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Timothy M Fan
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Martin D Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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6
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Assmus MA, Lee MS, Sivaguru M, Agarwal DK, Large T, Fouke BW, Krambeck AE. Laser fiber degradation following holmium laser enucleation of the prostate utilizing Moses technology versus regular mode. World J Urol 2022; 40:1203-1209. [PMID: 35166893 DOI: 10.1007/s00345-022-03951-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/16/2021] [Accepted: 01/27/2022] [Indexed: 01/08/2023] Open
Abstract
PURPOSE We sought to objectively compare laser fiber degradation for holmium laser enucleation of the prostate (HoLEP) cases performed with 550 μm standard fibers versus 550 μm Moses 2.0 fiber in BPH mode on a macroscopic and microscopic level. METHODS We prospectively collected outcomes for 50 standardized HoLEP cases using 550 μm Moses fiber with 2.0 BPH mode compared to our historical cohort of 50 patients using 550 μm standard fibers on regular mode. Macroscopic degradation length was the difference in length of exposed fiber at the start and end of each case. Five consecutive 550 μm standard fibers, five 550 μm Moses fibers and their respective controls underwent novel utilization of three objective corroborating imaging techniques: Brightfield high resolution microscopy, high resolution 3-D microCT and Confocal Reflection Surface Analysis. Mann-Whitney U, 2-tailed T tests and Chi-squared tests were used. RESULTS Standard fibers demonstrated greater degradation than the Moses fibers with 2.0 BPH mode [2.9 cm (IQR 1.7-4.3 cm) vs 0.2 cm (IQR 0.1-0.4 cm), p < 0.01]. This difference remained significant when comparing degradation per energy used, per minute enucleation and per gram enucleated (all p < 0.05). None of the cases with Moses fiber and 2.0 BPH mode required intraoperative interruption to re-strip the fiber. Objective fiber degradation by three microscopic techniques confirmed more damage to the standard fibers with regular mode. CONCLUSION Overall, use of the 550 μm Moses fiber with 2.0 BPH mode resulted in less fiber degradation compared to a standard 550 μm fiber with regular mode as confirmed using 4 corroborating macroscopic and microscopic techniques.
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Affiliation(s)
- Mark A Assmus
- Department of Urology, Northwestern University, Chicago, USA.
| | - Matthew S Lee
- Department of Urology, Northwestern University, Chicago, USA
| | - Mayandi Sivaguru
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana-Champaign, Champaign, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Champaign, USA
| | - Deepak K Agarwal
- Department of Urology, Indiana University, Indianapolis, IN, USA
| | - Tim Large
- Department of Urology, Indiana University, Indianapolis, IN, USA
| | - Bruce W Fouke
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana-Champaign, Champaign, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Champaign, USA
| | - Amy E Krambeck
- Department of Urology, Northwestern University, Chicago, USA
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7
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Zhou L, Alcalde RE, Deng J, Zuniga B, Sanford RA, Fouke BW, Werth CJ. Impact of antibiotic concentration gradients on nitrate reduction and antibiotic resistance in a microfluidic gradient chamber. Sci Total Environ 2021; 779:146503. [PMID: 34030234 DOI: 10.1016/j.scitotenv.2021.146503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/18/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
In order to explore the impact of antibiotics on the bacterial metabolic cycling of nitrate within contaminated soil and groundwater environments, we compared the effects of polymyxin B (PMB) and ciprofloxacin (CIP) concentration gradients on the distribution and activity of a wild type (WT) and a flagella deficient mutant (Δflag) of Shewanella oneidensis MR-1 in a microfluidic gradient chamber (MGC). Complementary batch experiments were performed to measure bacteriostatic versus bactericidal concentrations of the two antibiotics, as well as their effect on nitrate reduction. Prior work demonstrated that PMB disrupts cell membranes while CIP inhibits DNA synthesis. Consistent with these modes of action, batch results from this work show that PMB is bactericidal at lower concentrations than CIP relative to their respective minimum inhibitory concentrations (MICs) (≥5× MICPMB vs. ≥20× MICCIP). Concentration gradients from 0 to 50× the MIC of both antibiotics were established in the MGC across a 2-cm interconnected pore network, with nutrients injected at both concentration boundaries. The WT cells could only access and reduce nitrate in regions of the MGC with PMB at <18× MICPMB, whereas this occurred with CIP up to 50× MICCIP; and cells extracted from these MGCs showed no antibiotic resistance. The distribution of Δflag cells was further limited to lower antibiotic concentrations (≤1× MICPMB, ≤43× MICCIP) due to inability of movement. These results indicate that S. oneidensis access and reduce nitrate in bactericidal regions via chemotactic migration without development of antibiotic resistance, and that this migration is inhibited by acutely lethal bactericidal levels of antibiotics.
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Affiliation(s)
- Lang Zhou
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Reinaldo E Alcalde
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Jinzi Deng
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Baltazar Zuniga
- College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruce W Fouke
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles J Werth
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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8
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Sivaguru M, Saw JJ, Wilson EM, Lieske JC, Krambeck AE, Williams JC, Romero MF, Fouke KW, Curtis MW, Kear-Scott JL, Chia N, Fouke BW. Human kidney stones: a natural record of universal biomineralization. Nat Rev Urol 2021; 18:404-432. [PMID: 34031587 DOI: 10.1038/s41585-021-00469-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 02/04/2023]
Abstract
GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Jessica J Saw
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Elena M Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amy E Krambeck
- Department of Urology, Mayo Clinic, Rochester, MN, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James C Williams
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael F Romero
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Kyle W Fouke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - Matthew W Curtis
- Carl Zeiss Microscopy LLC, One North Broadway, White Plains, NY, USA
| | | | - Nicholas Chia
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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9
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Sivaguru M, Todorov LG, Miller CAH, Fouke CE, Munro CMO, Fouke KW, Fouke KE, Baughman ME, Fouke BW. Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature. Sci Rep 2021; 11:2230. [PMID: 33500473 PMCID: PMC7838310 DOI: 10.1038/s41598-021-81520-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Lauren G Todorov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carly A H Miller
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Courtney E Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, Denison University, Granville, OH, USA
| | - Cara M O Munro
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Ecology and Evolutionary Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Kyle W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kaitlyn E Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, Denison University, Granville, OH, USA
- The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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10
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Saw JJ, Sivaguru M, Wilson EM, Dong Y, Sanford RA, Fields CJ, Cregger MA, Merkel AC, Bruce WJ, Weber JR, Lieske JC, Krambeck AE, Rivera ME, Large T, Lange D, Bhattacharjee AS, Romero MF, Chia N, Fouke BW. In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis. Kidney360 2020; 2:298-311. [PMID: 35373025 PMCID: PMC8740987 DOI: 10.34067/kid.0006942020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/23/2020] [Indexed: 02/04/2023]
Abstract
Background Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.
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Affiliation(s)
- Jessica J. Saw
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois,Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Elena M. Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Robert A. Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Chris J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Melissa A. Cregger
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Annette C. Merkel
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - William J. Bruce
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Joseph R. Weber
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - John C. Lieske
- Department of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Amy E. Krambeck
- Department of Urology, Mayo Clinic, Rochester, Minnesota,Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Marcelino E. Rivera
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Timothy Large
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dirk Lange
- The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Jack Bell Research Centre, Vancouver, British Columbia, Canada
| | - Ananda S. Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Michael F. Romero
- Department of Individualized Medicine, Mayo Clinic, Rochester, Minnesota,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota,Department of Urology, Mayo Clinic, Rochester, Minnesota
| | - Bruce W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois,Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois,Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois,Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois
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11
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Dong Y, Sanford RA, Boyanov MI, Flynn TM, O'Loughlin EJ, Kemner KM, George S, Fouke KE, Li S, Huang D, Li S, Fouke BW. Controls on Iron Reduction and Biomineralization over Broad Environmental Conditions as Suggested by the Firmicutes Orenia metallireducens Strain Z6. Environ Sci Technol 2020; 54:10128-10140. [PMID: 32693580 DOI: 10.1021/acs.est.0c03853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial iron reduction is a ubiquitous biogeochemical process driven by diverse microorganisms in a variety of environments. However, it is often difficult to separate the biological from the geochemical controls on bioreduction of Fe(III) oxides. Here, we investigated the primary driving factor(s) that mediate secondary iron mineral formation over a broad range of environmental conditions using a single dissimilatory iron reducer, Orenia metallireducens strain Z6. A total of 17 distinct geochemical conditions were tested with differing pH (6.5-8.5), temperature (22-50 °C), salinity (2-20% NaCl), anions (phosphate and sulfate), electron shuttle (anthraquinone-2,6-disulfonate), and Fe(III) oxide mineralogy (ferrihydrite, lepidocrocite, goethite, hematite, and magnetite). The observed rates and extent of iron reduction differed significantly with kint between 0.186 and 1.702 mmol L-1 day-1 and Fe(II) production ranging from 6.3% to 83.7% of the initial Fe(III). Using X-ray absorption and scattering techniques (EXAFS and XRD), we identified and assessed the relationship between secondary minerals and the specific environmental conditions. It was inferred that the observed bifurcation of the mineralization pathways may be mediated by differing extents of Fe(II) sorption on the remaining Fe(III) minerals. These results expand our understanding of the controls on biomineralization during microbial iron reduction and aid the development of practical applications.
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Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Maxim I Boyanov
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Samantha George
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kaitlyn E Fouke
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543, United States
| | - Shuyi Li
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
| | - Dongmei Huang
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
| | - Shuzhen Li
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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12
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amy E Krambeck
- Department of Urology, Mayo Clinic, Rochester, MN, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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13
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Dong Y, Sanford RA, Inskeep WP, Srivastava V, Bulone V, Fields CJ, Yau PM, Sivaguru M, Ahrén D, Fouke KW, Weber J, Werth CR, Cann IK, Keating KM, Khetani RS, Hernandez AG, Wright C, Band M, Imai BS, Fried GA, Fouke BW. Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats. Astrobiology 2019; 19:1442-1458. [PMID: 31038352 PMCID: PMC6918859 DOI: 10.1089/ast.2018.1965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.
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Affiliation(s)
- Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Robert A. Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
- Division School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Christopher J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Peter M. Yau
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dag Ahrén
- Microbial Ecology Group, Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Lund, Sweden
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
| | - Kyle W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology and Environmental Sciences, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Joseph Weber
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Charles R. Werth
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Civil, Architectural and Environmental Engineering, University of Texas Austin, Texas, USA
| | - Isaac K. Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathleen M. Keating
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Radhika S. Khetani
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Chris Wright
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mark Band
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Brian S. Imai
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Glenn A. Fried
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bruce W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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14
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Abstract
Successful Scholar-Athletes are physically, intellectually, and emotionally committed to high-level achievement in both their academic and sport endeavors. This requires development of an integrated skill-set that includes teamwork, a strong work ethic, commitment, leadership, time management, and physical and emotional health. The identity crosses all perceived boundaries of race, gender, ethnicity, sexual orientation, religion, disability, social, and economic status. A nationwide paradigm shift is urgently needed to recognize and tap into these skills for all scholar-athletes, which are the same tools required to succeed in all professions from science and technology to law, medicine, business and the arts. This article addresses the misperceptions and low expectations that much of our society has for the high school and collegiate Scholar-Athlete. While recognizing the efforts of programs that are working to recalibrate the high school athlete's self perceptions, awaken recognition of their own academic potential, and permit them to achieve successful careers and make invaluable professional contributions to society.
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Affiliation(s)
- Joseph L Cross
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Department of Geology, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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15
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Deng J, Zhou L, Sanford RA, Shechtman LA, Dong Y, Alcalde RE, Sivaguru M, Fried GA, Werth CJ, Fouke BW. Adaptive Evolution of Escherichia coli to Ciprofloxacin in Controlled Stress Environments: Contrasting Patterns of Resistance in Spatially Varying versus Uniformly Mixed Concentration Conditions. Environ Sci Technol 2019; 53:7996-8005. [PMID: 31269400 DOI: 10.1021/acs.est.9b00881] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A microfluidic gradient chamber (MGC) and a homogeneous batch culturing system were used to evaluate whether spatial concentration gradients of the antibiotic ciprofloxacin allow development of greater antibiotic resistance in Escherichia coli strain 307 (E. coli 307) compared to exclusively temporal concentration gradients, as indicated in an earlier study. A linear spatial gradient of ciprofloxacin and Luria-Bertani broth (LB) medium was established and maintained by diffusion over 5 days across a well array in the MGC, with relative concentrations along the gradient of 1.7-7.7× the original minimum inhibitory concentration (MICoriginal). The E. coli biomass increased in wells with lower ciprofloxacin concentrations, and only a low level of resistance to ciprofloxacin was detected in the recovered cells (∼2× MICoriginal). Homogeneous batch culture experiments were performed with the same temporal exposure history to ciprofloxacin concentration, the same and higher initial cell densities, and the same and higher nutrient (i.e., LB) concentrations as in the MGC. In all batch experiments, E. coli 307 developed higher ciprofloxacin resistance after exposure, ranging from 4 to 24× MICoriginal in all replicates. Hence, these results suggest that the presence of spatial gradients appears to reduce the driving force for E. coli 307 adaptation to ciprofloxacin, which suggests that results from batch experiments may over predict the development of antibiotic resistance in natural environments.
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Affiliation(s)
- Jinzi Deng
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
| | - Lang Zhou
- Department of Civil, Architectural and Environmental Engineering , University of Texas at Austin , Austin , Texas 78705 United States
| | - Robert A Sanford
- Department of Geology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
| | - Lauren A Shechtman
- Department of Chemistry , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
- Department of Integrative Biology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
| | - Yiran Dong
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
- School of Environmental Studies , China University of Geosciences (Wuhan) , Wuhan , 430074 , China
| | - Reinaldo E Alcalde
- Department of Civil, Architectural and Environmental Engineering , University of Texas at Austin , Austin , Texas 78705 United States
| | - Mayandi Sivaguru
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
| | - Glenn A Fried
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
| | - Charles J Werth
- Department of Civil, Architectural and Environmental Engineering , University of Texas at Austin , Austin , Texas 78705 United States
| | - Bruce W Fouke
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
- Department of Geology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
- Department of Microbiology , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 United States
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16
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Alcalde RE, Michelson K, Zhou L, Schmitz EV, Deng J, Sanford RA, Fouke BW, Werth CJ. Motility of Shewanella oneidensis MR-1 Allows for Nitrate Reduction in the Toxic Region of a Ciprofloxacin Concentration Gradient in a Microfluidic Reactor. Environ Sci Technol 2019; 53:2778-2787. [PMID: 30673286 DOI: 10.1021/acs.est.8b04838] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Subsurface environments often contain mixtures of contaminants in which the microbial degradation of one pollutant may be inhibited by the toxicity of another. Agricultural settings exemplify these complex environments, where antimicrobial leachates may inhibit nitrate bioreduction, and are the motivation to address this fundamental ecological response. In this study, a microfluidic reactor was fabricated to create diffusion-controlled concentration gradients of nitrate and ciprofloxacin under anoxic conditions in order to evaluate the ability of Shewanella oneidenisis MR-1 to reduce the former in the presence of the latter. Results show a surprising ecological response, where swimming motility allow S. oneidensis MR-1 to accumulate and maintain metabolic activity for nitrate reduction in regions with toxic ciprofloxacin concentrations (i.e., 50× minimum inhibitory concentration, MIC), despite the lack of observed antibiotic resistance. Controls with limited nutrient flux and a nonmotile mutant (Δ flag) show that cells cannot colonize antibiotic rich microenvironments, and this results in minimal metabolic activity for nitrate reduction. These results demonstrate that under anoxic, nitrate-reducing conditions, motility can control microbial habitability and metabolic activity in spatially heterogeneous toxic environments.
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Affiliation(s)
- Reinaldo E Alcalde
- Department of Civil, Architectural, and Environmental Engineering , University of Texas at Austin , 301 E. Dean Keeton Street , Austin , Texas 78712 , United States
| | - Kyle Michelson
- Department of Civil, Architectural, and Environmental Engineering , University of Texas at Austin , 301 E. Dean Keeton Street , Austin , Texas 78712 , United States
| | - Lang Zhou
- Department of Civil, Architectural, and Environmental Engineering , University of Texas at Austin , 301 E. Dean Keeton Street , Austin , Texas 78712 , United States
| | - Emily V Schmitz
- McKetta Department of Chemical Engineering , University of Texas at Austin , 200 E Dean Keeton St , Austin , Texas 78712 , United States
| | - Jinzi Deng
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , 1206 W Gregory Dr , Urbana , Illinois 61801 United States
| | - Robert A Sanford
- Department of Geology , University of Illinois at Urbana-Champaign , 1301 West Green Street , Urbana , Illinois 61801 , United States
| | - Bruce W Fouke
- Carl R. Woese Institute of Genomic Biology , University of Illinois Urbana-Champaign , 1206 W Gregory Dr , Urbana , Illinois 61801 United States
- Department of Geology , University of Illinois at Urbana-Champaign , 1301 West Green Street , Urbana , Illinois 61801 , United States
- Department of Microbiology , University of Illinois at Urbana-Champaign , 601 South Goodwin Avenue , Urbana , Illinois 61801 , United States
| | - Charles J Werth
- Department of Civil, Architectural, and Environmental Engineering , University of Texas at Austin , 301 E. Dean Keeton Street , Austin , Texas 78712 , United States
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17
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Thomer AK, Wickett KM, Baker KS, Fouke BW, Palmer CL. Documenting provenance in noncomputational workflows: Research process models based on geobiology fieldwork in Yellowstone National Park. J Assoc Inf Sci Technol 2018. [DOI: 10.1002/asi.24039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andrea K. Thomer
- School of Information, University of Michigan, 105 S. State StreetAnn Arbor Michigan 48109 USA
| | - Karen M. Wickett
- School of InformationUniversity of Texas at Austin, 1616 Guadalupe Suite #5.202Austin Texas 78701‐1213 USA
| | - Karen S. Baker
- INTERACT Research Unit, PO Box 8000, FI‐90014 University of Oulu, Finland; School of Information Sciences, University of Illinois at Urbana‐Champaign, 501 E. Daniel StreetChampaign Illinois 61820 USA
| | - Bruce W. Fouke
- Department of GeologyUniversity of Illinois Urbana‐Champaign, 1301 W. Green StreetUrbana Illinois 61801 USA
- Department of MicrobiologyUniversity of Illinois Urbana‐Champaign, 601 S. Goodwin AvenueUrbana Illinois 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana‐Champaign, 1206 W. Gregory DriveUrbana Illinois 61801 USA
| | - Carole L. Palmer
- Information School, University of Washington, Box 352840, Mary Gates Hall, Ste. 370Seattle Washington 98195‐2840 USA
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18
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Sivaguru M, Saw JJ, Williams JC, Lieske JC, Krambeck AE, Romero MF, Chia N, Schwaderer AL, Alcalde RE, Bruce WJ, Wildman DE, Fried GA, Werth CJ, Reeder RJ, Yau PM, Sanford RA, Fouke BW. Geobiology reveals how human kidney stones dissolve in vivo. Sci Rep 2018; 8:13731. [PMID: 30213974 PMCID: PMC6137216 DOI: 10.1038/s41598-018-31890-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/29/2018] [Indexed: 11/26/2022] Open
Abstract
More than 10% of the global human population is now afflicted with kidney stones, which are commonly associated with other significant health problems including diabetes, hypertension and obesity. Nearly 70% of these stones are primarily composed of calcium oxalate, a mineral previously assumed to be effectively insoluble within the kidney. This has limited currently available treatment options to painful passage and/or invasive surgical procedures. We analyze kidney stone thin sections with a combination of optical techniques, which include bright field, polarization, confocal and super-resolution nanometer-scale auto-fluorescence microscopy. Here we demonstrate using interdisciplinary geology and biology (geobiology) approaches that calcium oxalate stones undergo multiple events of dissolution as they crystallize and grow within the kidney. These observations open a fundamentally new paradigm for clinical approaches that include in vivo stone dissolution and identify high-frequency layering of organic matter and minerals as a template for biomineralization in natural and engineered settings.
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Jessica J Saw
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana- Champaign, Urbana, IL, USA.
- Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA.
| | - James C Williams
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amy E Krambeck
- Department of Urology, Mayo Clinic, Rochester, MN, USA
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael F Romero
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Nicholas Chia
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Department of Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Andrew L Schwaderer
- Department of Pediatric Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Reinaldo E Alcalde
- Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX, USA
| | - William J Bruce
- Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - Derek E Wildman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana- Champaign, Urbana, IL, USA
| | - Glenn A Fried
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charles J Werth
- Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX, USA
| | - Richard J Reeder
- Department of Geosciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Peter M Yau
- Protein Sciences, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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19
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Singh R, Sivaguru M, Fried GA, Fouke BW, Sanford RA, Carrera M, Werth CJ. Real rock-microfluidic flow cell: A test bed for real-time in situ analysis of flow, transport, and reaction in a subsurface reactive transport environment. J Contam Hydrol 2017; 204:28-39. [PMID: 28802767 DOI: 10.1016/j.jconhyd.2017.08.001] [Citation(s) in RCA: 7] [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] [Received: 04/03/2017] [Revised: 07/27/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Physical, chemical, and biological interactions between groundwater and sedimentary rock directly control the fundamental subsurface properties such as porosity, permeability, and flow. This is true for a variety of subsurface scenarios, ranging from shallow groundwater aquifers to deeply buried hydrocarbon reservoirs. Microfluidic flow cells are now commonly being used to study these processes at the pore scale in simplified pore structures meant to mimic subsurface reservoirs. However, these micromodels are typically fabricated from glass, silicon, or polydimethylsiloxane (PDMS), and are therefore incapable of replicating the geochemical reactivity and complex three-dimensional pore networks present in subsurface lithologies. To address these limitations, we developed a new microfluidic experimental test bed, herein called the Real Rock-Microfluidic Flow Cell (RR-MFC). A porous 500μm-thick real rock sample of the Clair Group sandstone from a subsurface hydrocarbon reservoir of the North Sea was prepared and mounted inside a PDMS microfluidic channel, creating a dynamic flow-through experimental platform for real-time tracking of subsurface reactive transport. Transmitted and reflected microscopy, cathodoluminescence microscopy, Raman spectroscopy, and confocal laser microscopy techniques were used to (1) determine the mineralogy, geochemistry, and pore networks within the sandstone inserted in the RR-MFC, (2) analyze non-reactive tracer breakthrough in two- and (depth-limited) three-dimensions, and (3) characterize multiphase flow. The RR-MFC is the first microfluidic experimental platform that allows direct visualization of flow and transport in the pore space of a real subsurface reservoir rock sample, and holds potential to advance our understandings of reactive transport and other subsurface processes relevant to pollutant transport and cleanup in groundwater, as well as energy recovery.
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Affiliation(s)
- Rajveer Singh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA; Energy Bioscience Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA; Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, 205 N. Mathews Avenue, Urbana, IL 61801, USA.
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA
| | - Glenn A Fried
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA; Energy Bioscience Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, 1301 W. Green Street, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois, Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Robert A Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA; Energy Bioscience Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, 1301 W. Green Street, Urbana, IL 61801, USA
| | - Martin Carrera
- BP Biosciences Center, 10628 Science Center Drive, Suite 150, San Diego, CA 92121, USA
| | - Charles J Werth
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, 301 E. Keaton Street, Austin, TX 78712, USA.
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20
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Palmer CL, Thomer AK, Baker KS, Wickett KM, Hendrix CL, Rodman A, Sigler S, Fouke BW. Site-based data curation based on hot spring geobiology. PLoS One 2017; 12:e0172090. [PMID: 28253269 PMCID: PMC5333826 DOI: 10.1371/journal.pone.0172090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Site-Based Data Curation (SBDC) is an approach to managing research data that prioritizes sharing and reuse of data collected at scientifically significant sites. The SBDC framework is based on geobiology research at natural hot spring sites in Yellowstone National Park as an exemplar case of high value field data in contemporary, cross-disciplinary earth systems science. Through stakeholder analysis and investigation of data artifacts, we determined that meaningful and valid reuse of digital hot spring data requires systematic documentation of sampling processes and particular contextual information about the site of data collection. We propose a Minimum Information Framework for recording the necessary metadata on sampling locations, with anchor measurements and description of the hot spring vent distinct from the outflow system, and multi-scale field photography to capture vital information about hot spring structures. The SBDC framework can serve as a global model for the collection and description of hot spring systems field data that can be readily adapted for application to the curation of data from other kinds scientifically significant sites.
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Affiliation(s)
- Carole L. Palmer
- The Information School, University of Washington, Mary Gates Hall, Suite. 370 Seattle, Washington United States of America
| | - Andrea K. Thomer
- School of Information Sciences, University of Illinois Urbana-Champaign, Champaign, Illinois United States of America
- * E-mail:
| | - Karen S. Baker
- School of Information Sciences, University of Illinois Urbana-Champaign, Champaign, Illinois United States of America
| | - Karen M. Wickett
- School of Information, University of Texas at Austin, 1616 Guadalupe Suite #5.202, Austin, Texas, United States of America
| | - Christie L. Hendrix
- Yellowstone Center for Resources, Yellowstone National Park, Yellowstone National Park, Wyoming United States of America
| | - Ann Rodman
- Yellowstone Center for Resources, Yellowstone National Park, Yellowstone National Park, Wyoming United States of America
| | - Stacey Sigler
- Yellowstone Center for Resources, Yellowstone National Park, Yellowstone National Park, Wyoming United States of America
| | - Bruce W. Fouke
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois United States of America
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, Illinois United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, Illinois United States of America
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, 2613 Institute for Genomic Biology, 1206 W. Gregory Drive, Urbana, Illinois United States of America
- Thermal Biology Institute, Montana State University, Leon Johnson Hall, Bozeman, Montana, United States of America
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21
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Dong Y, Sanford RA, Chang YJ, McInerney MJ, Fouke BW. Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6. Environ Sci Technol 2017; 51:232-242. [PMID: 27943672 DOI: 10.1021/acs.est.6b04126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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
Fermentative iron-reducing organisms have been identified in a variety of environments. Instead of coupling iron reduction to respiration, they have been consistently observed to use ferric iron minerals as an electron sink for fermentation. In the present study, a fermentative iron reducer, Orenia metallireducens strain Z6, was shown to use iron reduction to enhance fermentation not only by consuming electron equivalents, but also by generating alkalinity that effectively buffers the pH. Fermentation of glucose by this organism in the presence of a ferric oxide mineral, hematite (Fe2O3), resulted in enhanced glucose decomposition compared with fermentation in the absence of an iron source. Parallel evidence (i.e., genomic reconstruction, metabolomics, thermodynamic analyses, and calculation of electron transfer) suggested hematite reduction as a proton-consuming reaction effectively consumed acid produced by fermentation. The buffering effect of hematite was further supported by a greater extent of glucose utilization by strain Z6 in media with increasing buffer capacity. Such maintenance of a stable pH through hematite reduction for enhanced glucose fermentation complements the thermodynamic interpretation of interactions between microbial iron reduction and other biogeochemical processes. This newly discovered feature of iron reducer metabolism also has significant implications for groundwater management and contaminant remediation by providing microbially mediated buffering systems for the associated microbial and/or chemical reactions.
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Affiliation(s)
| | | | | | - Michael J McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
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22
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Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O’Loughlin EJ, Locke RA, Weber JR, Egan SM, Fouke BW. Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater. Int J Syst Evol Microbiol 2016; 66:3964-3971. [DOI: 10.1099/ijsem.0.001295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yiran Dong
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Robert A. Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Maxim I. Boyanov
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | | | - Randall A. Locke
- Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joseph R. Weber
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sheila M. Egan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Bruce W. Fouke
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
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23
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Srivastava V, Weber JR, Malm E, Fouke BW, Bulone V. Proteomic Analysis of a Poplar Cell Suspension Culture Suggests a Major Role of Protein S-Acylation in Diverse Cellular Processes. Front Plant Sci 2016; 7:477. [PMID: 27148305 PMCID: PMC4828459 DOI: 10.3389/fpls.2016.00477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/24/2016] [Indexed: 05/03/2023]
Abstract
S-acylation is a reversible post-translational modification of proteins known to be involved in membrane targeting, subcellular trafficking, and the determination of a great variety of functional properties of proteins. The aim of this work was to identify S-acylated proteins in poplar. The use of an acyl-biotin exchange method and mass spectrometry allowed the identification of around 450 S-acylated proteins, which were subdivided into three major groups of proteins involved in transport, signal transduction, and response to stress, respectively. The largest group of S-acylated proteins was the protein kinase superfamily. Soluble N-ethylmaleimide-sensitive factor-activating protein receptors, band 7 family proteins and tetraspanins, all primarily related to intracellular trafficking, were also identified. In addition, cell wall related proteins, including cellulose synthases and other glucan synthases, were found to be S-acylated. Twenty four of the identified S-acylated proteins were also enriched in detergent-resistant membrane microdomains, suggesting S-acylation plays a key role in the localization of proteins to specialized plasma membrane subdomains. This dataset promises to enhance our current understanding of the various functions of S-acylated proteins in plants.
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Affiliation(s)
- Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University CentreStockholm, Sweden
- *Correspondence: Vincent Bulone, ; Vaibhav Srivastava,
| | - Joseph R. Weber
- Roy J. Carver Biotechnology Centre, Institute for Genomic Biology, University of Illinois Urbana–ChampaignUrbana, IL, USA
| | - Erik Malm
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University CentreStockholm, Sweden
| | - Bruce W. Fouke
- Roy J. Carver Biotechnology Centre, Institute for Genomic Biology, University of Illinois Urbana–ChampaignUrbana, IL, USA
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University CentreStockholm, Sweden
- ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Waite CampusUrrbrae, SA, Australia
- *Correspondence: Vincent Bulone, ; Vaibhav Srivastava,
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24
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Singh R, Yoon H, Sanford RA, Katz L, Fouke BW, Werth CJ. Metabolism-Induced CaCO3 Biomineralization During Reactive Transport in a Micromodel: Implications for Porosity Alteration. Environ Sci Technol 2015; 49:12094-12104. [PMID: 26348257 DOI: 10.1021/acs.est.5b00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ability of Pseudomonas stutzeri strain DCP-Ps1 to drive CaCO3 biomineralization has been investigated in a microfluidic flowcell (i.e., micromodel) that simulates subsurface porous media. Results indicate that CaCO3 precipitation occurs during NO3(-) reduction with a maximum saturation index (SIcalcite) of ∼1.56, but not when NO3(-) was removed, inactive biomass remained, and pH and alkalinity were adjusted to SIcalcite ∼ 1.56. CaCO3 precipitation was promoted by metabolically active cultures of strain DCP-Ps1, which at similar values of SIcalcite, have a more negative surface charge than inactive strain DCP-Ps1. A two-stage NO3(-) reduction (NO3(-) → NO2(-) → N2) pore-scale reactive transport model was used to evaluate denitrification kinetics, which was observed in the micromodel as upper (NO3(-) reduction) and lower (NO2(-) reduction) horizontal zones of biomass growth with CaCO3 precipitation exclusively in the lower zone. Model results are consistent with two biomass growth regions and indicate that precipitation occurred in the lower zone because the largest increase in pH and alkalinity is associated with NO2(-) reduction. CaCO3 precipitates typically occupied the entire vertical depth of pores and impacted porosity, permeability, and flow. This study provides a framework for incorporating microbial activity in biogeochemistry models, which often base biomineralization only on SI (caused by biotic or abiotic reactions) and, thereby, underpredict the extent of this complex process. These results have wide-ranging implications for understanding reactive transport in relevance to groundwater remediation, CO2 sequestration, and enhanced oil recovery.
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Affiliation(s)
| | - Hongkyu Yoon
- Geoscience Research and Applications, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | | | - Lynn Katz
- Civil, Architectural and Environmental Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | | | - Charles J Werth
- Civil, Architectural and Environmental Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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25
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Dong Y, Sanford RA, Locke RA, Cann IK, Mackie RI, Fouke BW. Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA). Front Microbiol 2014; 5:511. [PMID: 25324834 PMCID: PMC4179719 DOI: 10.3389/fmicb.2014.00511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 02/01/2023] Open
Abstract
The Cambrian-age Mt. Simon Sandstone, deeply buried within the Illinois Basin of the midcontinent of North America, contains quartz sand grains ubiquitously encrusted with iron-oxide cements and dissolved ferrous iron in pore-water. Although microbial iron reduction has previously been documented in the deep terrestrial subsurface, the potential for diagenetic mineral cementation to drive microbial activity has not been well studied. In this study, two subsurface formation water samples were collected at 1.72 and 2.02 km, respectively, from the Mt. Simon Sandstone in Decatur, Illinois. Low-diversity microbial communities were detected from both horizons and were dominated by Halanaerobiales of Phylum Firmicutes. Iron-reducing enrichment cultures fed with ferric citrate were successfully established using the formation water. Phylogenetic classification identified the enriched species to be related to Vulcanibacillus from the 1.72 km depth sample, while Orenia dominated the communities at 2.02 km of burial depth. Species-specific quantitative analyses of the enriched organisms in the microbial communities suggest that they are indigenous to the Mt. Simon Sandstone. Optimal iron reduction by the 1.72 km enrichment culture occurred at a temperature of 40°C (range 20-60°C) and a salinity of 25 parts per thousand (range 25-75 ppt). This culture also mediated fermentation and nitrate reduction. In contrast, the 2.02 km enrichment culture exclusively utilized hydrogen and pyruvate as the electron donors for iron reduction, tolerated a wider range of salinities (25-200 ppt), and exhibited only minimal nitrate- and sulfate-reduction. In addition, the 2.02 km depth community actively reduces the more crystalline ferric iron minerals goethite and hematite. The results suggest evolutionary adaptation of the autochthonous microbial communities to the Mt. Simon Sandstone and carries potentially important implications for future utilization of this reservoir for CO2 injection.
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Affiliation(s)
- Yiran Dong
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Randall A Locke
- Illinois State Geological Survey, Urbana-Champaign Urbana, IL, USA
| | - Isaac K Cann
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Roderick I Mackie
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Bruce W Fouke
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Illinois State Geological Survey, Urbana-Champaign Urbana, IL, USA ; Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
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26
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Sivaguru M, Fried GA, Miller CAH, Fouke BW. Multimodal optical microscopy methods reveal polyp tissue morphology and structure in Caribbean reef building corals. J Vis Exp 2014:e51824. [PMID: 25226350 DOI: 10.3791/51824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
An integrated suite of imaging techniques has been applied to determine the three-dimensional (3D) morphology and cellular structure of polyp tissues comprising the Caribbean reef building corals Montastraeaannularis and M. faveolata. These approaches include fluorescence microscopy (FM), serial block face imaging (SBFI), and two-photon confocal laser scanning microscopy (TPLSM). SBFI provides deep tissue imaging after physical sectioning; it details the tissue surface texture and 3D visualization to tissue depths of more than 2 mm. Complementary FM and TPLSM yield ultra-high resolution images of tissue cellular structure. Results have: (1) identified previously unreported lobate tissue morphologies on the outer wall of individual coral polyps and (2) created the first surface maps of the 3D distribution and tissue density of chromatophores and algae-like dinoflagellate zooxanthellae endosymbionts. Spectral absorption peaks of 500 nm and 675 nm, respectively, suggest that M. annularis and M. faveolata contain similar types of chlorophyll and chromatophores. However, M. annularis and M. faveolata exhibit significant differences in the tissue density and 3D distribution of these key cellular components. This study focusing on imaging methods indicates that SBFI is extremely useful for analysis of large mm-scale samples of decalcified coral tissues. Complimentary FM and TPLSM reveal subtle submillimeter scale changes in cellular distribution and density in nondecalcified coral tissue samples. The TPLSM technique affords: (1) minimally invasive sample preparation, (2) superior optical sectioning ability, and (3) minimal light absorption and scattering, while still permitting deep tissue imaging.
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Affiliation(s)
- Mayandi Sivaguru
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign;
| | - Glenn A Fried
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| | - Carly A H Miller
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Department of Geology, University of Illinois at Urbana-Champaign
| | - Bruce W Fouke
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Department of Geology, University of Illinois at Urbana-Champaign; Department of Microbiology, University of Illinois at Urbana-Champaign;
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27
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Piceno YM, Reid FC, Tom LM, Conrad ME, Bill M, Hubbard CG, Fouke BW, Graff CJ, Han J, Stringfellow WT, Hanlon JS, Hu P, Hazen TC, Andersen GL. Temperature and injection water source influence microbial community structure in four Alaskan North Slope hydrocarbon reservoirs. Front Microbiol 2014; 5:409. [PMID: 25147549 PMCID: PMC4124708 DOI: 10.3389/fmicb.2014.00409] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 04/19/2014] [Accepted: 07/18/2014] [Indexed: 11/29/2022] Open
Abstract
A fundamental knowledge of microbial community structure in petroleum reservoirs can improve predictive modeling of these environments. We used hydrocarbon profiles, stable isotopes, and high-density DNA microarray analysis to characterize microbial communities in produced water from four Alaskan North Slope hydrocarbon reservoirs. Produced fluids from Schrader Bluff (24–27°C), Kuparuk (47–70°C), Sag River (80°C), and Ivishak (80–83°C) reservoirs were collected, with paired soured/non-soured wells sampled from Kuparuk and Ivishak. Chemical and stable isotope data suggested Schrader Bluff had substantial biogenic methane, whereas methane was mostly thermogenic in deeper reservoirs. Acetoclastic methanogens (Methanosaeta) were most prominent in Schrader Bluff samples, and the combined δD and δ13C values of methane also indicated acetoclastic methanogenesis could be a primary route for biogenic methane. Conversely, hydrogenotrophic methanogens (e.g., Methanobacteriaceae) and sulfide-producing Archaeoglobus and Thermococcus were more prominent in Kuparuk samples. Sulfide-producing microbes were detected in all reservoirs, uncoupled from souring status (e.g., the non-soured Kuparuk samples had higher relative abundances of many sulfate-reducers compared to the soured sample, suggesting sulfate-reducers may be living fermentatively/syntrophically when sulfate is limited). Sulfate abundance via long-term seawater injection resulted in greater relative abundances of Desulfonauticus, Desulfomicrobium, and Desulfuromonas in the soured Ivishak well compared to the non-soured well. In the non-soured Ivishak sample, several taxa affiliated with Thermoanaerobacter and Halomonas predominated. Archaea were not detected in the deepest reservoirs. Functional group taxa differed in relative abundance among reservoirs, likely reflecting differing thermal and/or geochemical influences.
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Affiliation(s)
- Yvette M Piceno
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Francine C Reid
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Lauren M Tom
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Mark E Conrad
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Markus Bill
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Christopher G Hubbard
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Bruce W Fouke
- Energy Biosciences Institute Berkeley, CA, USA ; Department of Geology, University of Illinois at Urbana-Champaign, Urbana-Champaign IL, USA
| | - Craig J Graff
- Production Chemistry, BP Exploration Anchorage, AK, USA
| | - Jiabin Han
- Production Chemistry, BP Exploration Anchorage, AK, USA
| | - William T Stringfellow
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA ; Ecological Engineering Research Program, University of the Pacific Stockton, CA, USA
| | - Jeremy S Hanlon
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Ecological Engineering Research Program, University of the Pacific Stockton, CA, USA
| | - Ping Hu
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, TN, USA
| | - Gary L Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
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28
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Gust KA, Najar FZ, Habib T, Lotufo GR, Piggot AM, Fouke BW, Laird JG, Wilbanks MS, Rawat A, Indest KJ, Roe BA, Perkins EJ. Coral-zooxanthellae meta-transcriptomics reveals integrated response to pollutant stress. BMC Genomics 2014; 15:591. [PMID: 25016412 PMCID: PMC4117956 DOI: 10.1186/1471-2164-15-591] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 01/14/2014] [Accepted: 06/18/2014] [Indexed: 11/11/2022] Open
Abstract
Background Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater). Results RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5. Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral/zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (i.e. cytochrome P450 and UDP glucuronosyltransferase 2 family) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production including glycolysis and electron-transport pathways was observed in the coral animal. Conclusions Transcriptional network analysis for central energy metabolism demonstrated highly correlated responses to RDX among the coral animal and zooxanthellae indicative of potential compensatory responses to lost photosynthetic potential within the holobiont. These observations underscore the potential for complex integrated responses to RDX exposure among species comprising the coral holobiont and highlight the need to understand holobiont-species interactions to accurately assess pollutant impacts. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-591) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kurt A Gust
- US Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS 39180, USA.
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Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW. Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir. Environ Microbiol 2013; 16:1695-708. [PMID: 24238218 DOI: 10.1111/1462-2920.12325] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/31/2013] [Indexed: 01/12/2023]
Abstract
A low-diversity microbial community, dominated by the γ-proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for large-scale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole low-contamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaeris-dominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1-V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the geology, geochemistry and present-day environmental conditions of the Mt. Simon Sandstone, implies that H. sulfidaeris-dominated subsurface microbial community may utilize iron and nitrogen metabolisms and extensively recycle indigenous nutrients and substrates. The presence of aromatic compound metabolic pathways suggests this microbial community can readily adapt to and survive subsurface hydrocarbon migration.
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Affiliation(s)
- Yiran Dong
- Energy Biosciences Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, 1301 W. Green Street, Urbana, IL, 61801, USA
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Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings RD, Hengartner NW, Xie G. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Front Microbiol 2013; 4:84. [PMID: 23755042 PMCID: PMC3665934 DOI: 10.3389/fmicb.2013.00084] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [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: 12/01/2012] [Accepted: 03/25/2013] [Indexed: 02/01/2023] Open
Abstract
The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.
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Zhang C, Dehoff K, Hess N, Oostrom M, Wietsma TW, Valocchi AJ, Fouke BW, Werth CJ. Pore-scale study of transverse mixing induced CaCO₃ precipitation and permeability reduction in a model subsurface sedimentary system. Environ Sci Technol 2010; 44:7833-8. [PMID: 20804136 DOI: 10.1021/es1019788] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A microfluidic pore structure etched into a silicon wafer was used as a two-dimensional model subsurface sedimentary system (i.e., micromodel) to study mineral precipitation and permeability reduction relevant to groundwater remediation and geological carbon sequestration. Solutions containing CaCl(2) and Na(2)CO(3) at four different saturation states (Ω = [Ca(2+)][CO(3)(2-)]/K(spCaCO(3))) were introduced through two separate inlets, and they mixed by diffusion transverse to the main flow direction along the center of the micromodel resulting in CaCO(3) precipitation. Precipitation rates increased and the total amount of precipitates decreased with increasing saturation state, and only vaterite and calcite crystals were formed (no aragonite). The relative amount of vaterite increased from 80% at the lowest saturation state (Ω(v) = 2.8 for vaterite) to 95% at the highest saturation state (Ω(v) = 4.5). Fluorescent tracer tests conducted before and after CaCO(3) precipitation indicate that pore spaces were occluded by CaCO(3) precipitates along the transverse mixing zone, thus substantially reducing porosity and permeability, and potentially limiting transformation from vaterite to the more stable calcite. The results suggest that mineral precipitation along plume margins can decrease both reactant mixing during groundwater remediation, and injection and storage efficiency during CO(2) sequestration.
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Affiliation(s)
- Changyong Zhang
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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32
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Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings RD, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 2010; 5:e9773. [PMID: 20333304 PMCID: PMC2841643 DOI: 10.1371/journal.pone.0009773] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [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: 09/13/2009] [Accepted: 02/25/2010] [Indexed: 01/07/2023] Open
Abstract
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs.
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Affiliation(s)
- William P. Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (DBR)
| | - Douglas B. Rusch
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail: (WPI); (DBR)
| | - Zackary J. Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Mark A. Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Richard E. Macur
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Natsuko Hamamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Ryan deM. Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Bruce W. Fouke
- University of Illinois, Urbana, Illinois, United States of America
| | | | - Frank Roberto
- Idaho National Laboratory, Idaho Falls, Idaho, United States of America
| | - Mark Young
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Ariel Schwartz
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Eric S. Boyd
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Eric J. Mathur
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Alice C. Ortmann
- Department of Marine Science, University of South Alabama, Mobile, Alabama, United States of America
| | - Mary Bateson
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Gill Geesey
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Marvin Frazier
- J. Craig Venter Institute, Rockville, Maryland, United States of America
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Klaus JS, Janse I, Heikoop JM, Sanford RA, Fouke BW. Coral microbial communities, zooxanthellae and mucus along gradients of seawater depth and coastal pollution. Environ Microbiol 2007; 9:1291-305. [PMID: 17472641 DOI: 10.1111/j.1462-2920.2007.01249.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The high incidence of coral disease in shallow coastal marine environments suggests seawater depth and coastal pollution have an impact on the microbial communities inhabiting healthy coral tissues. A study was undertaken to determine how bacterial communities inhabiting tissues of the coral Montastraea annularis change at 5 m, 10 m and 20 m water depth in varying proximity to the urban centre and seaport of Willemstad, Curaçao, Netherlands Antilles. Analyses of terminal restriction fragment length polymorphisms (TRFLP) of 16S rRNA gene sequences show significant differences in bacterial communities of polluted and control localities only at the shallowest seawater depth. Furthermore, distinct differences in bacterial communities were found with increasing water depth. Comparisons of TRFLP peaks with sequenced clone libraries indicate the black band disease cyanobacterium clone CD1C11 is common and most abundant on healthy corals in less than 10 m water depth. Similarly, sequences belonging to a previously unrecognized group of likely phototrophic bacteria, herein referred to as CAB-I, were also more common in shallow water. To assess the influence of environmental and physiologic factors on bacterial community structure, canonical correspondence analysis was performed using explanatory variables associated with: (i) light availability; (ii) seawater pollution; (iii) coral mucus composition; (iv) the community structure of symbiotic algae; and (v) the photosynthetic activity of symbiotic algae. Eleven per cent of the variation in bacterial communities was accounted for by covariation with these variables; the most important being photosynthetically active radiation (sunlight) and the coral uptake of sewage-derived compounds as recorded by the delta(15)N of coral tissue.
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Affiliation(s)
- James S Klaus
- Department of Geology, University of Illinois, Urbana, IL 61801, USA.
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Abstract
Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division Firmicutes, two species of the Cytophaga-Flexibacter-Bacteroides (CFB) group, and one species of delta-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of Firmicutes were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a Beggiatoa species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology.
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Affiliation(s)
- Jorge Frias-Lopez
- Department of Geology, University of Illinois, 1301 W. Green St., Urbana, IL 61801, USA.
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Frias-Lopez J, Bonheyo GT, Fouke BW. Identification of differential gene expression in bacteria associated with coral black band disease by using RNA-arbitrarily primed PCR. Appl Environ Microbiol 2004; 70:3687-94. [PMID: 15184174 PMCID: PMC427725 DOI: 10.1128/aem.70.6.3687-3694.2004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA-arbitrarily primed PCR techniques have been applied for the first time to identify differential gene expression in black band disease (BBD), a virulent coral infection that affects reef ecosystems worldwide. The gene activity for the BBD mat on infected surfaces of the brain coral Diploria strigosa was compared with that for portions of the BBD mat that were removed from the coral and suspended nearby in the seawater column. The results obtained indicate that three genes (DD 95-2, DD 95-4, and DD 99-9) were up-regulated in the BBD bacterial mat on the coral surface compared to the transcript base levels observed in the BBD mat suspended in seawater. Clone DD 95-4 has homology with known amino acid ABC transporter systems in bacteria, while clone DD 99-9 exhibits homology with chlorophyll A apoprotein A1 in cyanobacteria. This protein is essential in the final conformation of photosystem I P700. DD 95-2, the only gene that was fully repressed in the BBD mat samples suspended in seawater, exhibited homology with the AraC-type DNA binding domain-containing proteins. These transcriptional activators coordinate the expression of genes essential for virulence in many species of gram-negative bacteria.
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Affiliation(s)
- Jorge Frias-Lopez
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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Abstract
For 30 years it has been assumed that a single species of cyanobacteria, Phormidium corallyticum, is the volumetrically dominant component of all cases of black band disease (BBD) in coral. Cyanobacterium-specific 16S rRNA gene primers and terminal restriction fragment length polymorphism analyses were used to determine the phylogenetic diversity of these BBD cyanobacteria on coral reefs in the Caribbean and Indo-Pacific Seas. These analyses indicate that the cyanobacteria that inhabit BBD bacterial mats collected from the Caribbean and Indo-Pacific Seas belong to at least three different taxa, despite the fact that the corals in each case exhibit similar signs and patterns of BBD mat development.
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Frias-Lopez J, Zerkle AL, Bonheyo GT, Fouke BW. Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl Environ Microbiol 2002; 68:2214-28. [PMID: 11976091 PMCID: PMC127591 DOI: 10.1128/aem.68.5.2214-2228.2002] [Citation(s) in RCA: 249] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2001] [Accepted: 02/25/2002] [Indexed: 11/20/2022] Open
Abstract
Distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (BBD) on the southern Caribbean island of Curaçao, Netherlands Antilles. PCR amplification and sequencing of bacterial 16S rRNA genes (rDNA) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. The molecular sequences exhibited less than 5% similarity in bacterial community composition between seawater and the healthy, black band diseased, and dead coral surfaces. The BBD bacterial mat rapidly migrates across and kills the coral tissue. Clone libraries constructed from the BBD mat were comprised of eight bacterial divisions and 13% unknowns. Several sequences representing bacteria previously found in other marine and terrestrial organisms (including humans) were isolated from the infected coral surfaces, including Clostridium spp., Arcobacter spp., Campylobacter spp., Cytophaga fermentans, Cytophaga columnaris, and Trichodesmium tenue.
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Affiliation(s)
- Jorge Frias-Lopez
- Department of Geology, University of Illinois, Urbana, Illinois 61801, USA
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Fouke BW, Farmer JD, Des Marais DJ, Pratt L, Sturchio NC, Burns PC, Discipulo MK. Depositional facies and aqueous-solid geochemistry of travertine-depositing hot springs (Angel Terrace, Mammoth Hot Springs, Yellowstone National Park, U.S.A.). J Sediment Res A Sediment Petrol Process 2000; 70:565-85. [PMID: 11543518 DOI: 10.1306/2dc40929-0e47-11d7-8643000102c1865d] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [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: 04/16/2023]
Abstract
Petrographic and geochemical analyses of travertine-depositing hot springs at Angel Terrace, Mammoth Hot Springs, Yellowstone National Park, have been used to define five depositional facies along the spring drainage system. Spring waters are expelled in the vent facies at 71 to 73 degrees C and precipitate mounded travertine composed of aragonite needle botryoids. The apron and channel facies (43-72 degrees C) is floored by hollow tubes composed of aragonite needle botryoids that encrust sulfide-oxidizing Aquificales bacteria. The travertine of the pond facies (30-62 degrees C) varies in composition from aragonite needle shrubs formed at higher temperatures to ridged networks of calcite and aragonite at lower temperatures. Calcite "ice sheets", calcified bubbles, and aggregates of aragonite needles ("fuzzy dumbbells") precipitate at the air-water interface and settle to pond floors. The proximal-slope facies (28-54 degrees C), which forms the margins of terracette pools, is composed of arcuate aragonite needle shrubs that create small microterracettes on the steep slope face. Finally, the distal-slope facies (28-30 degrees C) is composed of calcite spherules and calcite "feather" crystals. Despite the presence of abundant microbial mat communities and their observed role in providing substrates for mineralization, the compositions of spring-water and travertine predominantly reflect abiotic physical and chemical processes. Vigorous CO2 degassing causes a +2 unit increase in spring water pH, as well as Rayleigh-type covariations between the concentration of dissolved inorganic carbon and corresponding delta 13C. Travertine delta 13C and delta 18O are nearly equivalent to aragonite and calcite equilibrium values calculated from spring water in the higher-temperature (approximately 50-73 degrees C) depositional facies. Conversely, travertine precipitating in the lower-temperature (< approximately 50 degrees C) depositional facies exhibits delta 13C and delta 18O values that are as much as 4% less than predicted equilibrium values. This isotopic shift may record microbial respiration as well as downstream transport of travertine crystals. Despite the production of H2S and the abundance of sulfide oxidizing microbes, preliminary delta 34S data do not uniquely define the microbial metabolic pathways present in the spring system. This suggests that the high extent of CO2 degassing and large open-system solute reservoir in these thermal systems overwhelm biological controls on travertine crystal chemistry.
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Affiliation(s)
- B W Fouke
- Department of Geology, University of Illinois, Urbana 61801, USA.
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