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Leleiwi I, Kokkinias K, Kim Y, Baniasad M, Shaffer M, Sabag-Daigle A, Daly RA, Flynn RM, Wysocki VH, Ahmer BMM, Borton MA, Wrighton KC. Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection. bioRxiv 2024:2024.01.16.575907. [PMID: 38293109 PMCID: PMC10827160 DOI: 10.1101/2024.01.16.575907] [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] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.
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McGill BC, Wakefield CE, Tucker KM, Daly RA, Donoghoe MW, Vetsch J, Warby M, Fuentes‐Bolanos NA, Barlow‐Stewart K, Kirk J, Courtney E, O’Brien TA, Marshall GM, Pinese M, Cowley MJ, Tyrrell V, Deyell RJ, Ziegler DS, Hetherington K. Parents' expectations, preferences, and recall of germline findings in a childhood cancer precision medicine trial. Cancer 2023; 129:3620-3632. [PMID: 37382186 PMCID: PMC10952780 DOI: 10.1002/cncr.34917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Germline genome sequencing in childhood cancer precision medicine trials may reveal pathogenic or likely pathogenic variants in cancer predisposition genes in more than 10% of children. These findings can have implications for diagnosis, treatment, and the child's and family's future cancer risk. Understanding parents' perspectives of germline genome sequencing is critical to successful clinical implementation. METHODS A total of 182 parents of 144 children (<18 years of age) with poor-prognosis cancers enrolled in the Precision Medicine for Children with Cancer trial completed a questionnaire at enrollment and after the return of their child's results, including clinically relevant germline findings (received by 13% of parents). Parents' expectations of germline genome sequencing, return of results preferences, and recall of results received were assessed. Forty-five parents (of 43 children) were interviewed in depth. RESULTS At trial enrollment, most parents (63%) believed it was at least "somewhat likely" that their child would receive a clinically relevant germline finding. Almost all expressed a preference to receive a broad range of germline genomic findings, including variants of uncertain significance (88%). Some (29%) inaccurately recalled receiving a clinically relevant germline finding. Qualitatively, parents expressed confusion and uncertainty after the return of their child's genome sequencing results by their child's clinician. CONCLUSIONS Many parents of children with poor-prognosis childhood cancer enrolled in a precision medicine trial expect their child may have an underlying cancer predisposition syndrome. They wish to receive a wide scope of information from germline genome sequencing but may feel confused by the reporting of trial results.
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Borton MA, McGivern BB, Willi KR, Woodcroft BJ, Mosier AC, Bambakidis T, Singleton DM, Liu F, Edirisinghe JN, Faria JP, Leleiwi I, Daly RA, Goldman AE, Wilkins MJ, Hall EK, Pennacchio C, Roux S, Eloe-Fadrosh EA, Sullivan MB, Henry CS, Wood-Charlson EM, Ross MRV, Miller CS, Crump BC, Stegen JC, Wrighton KC. A functional microbiome catalog crowdsourced from North American rivers. bioRxiv 2023:2023.07.22.550117. [PMID: 37502915 PMCID: PMC10370164 DOI: 10.1101/2023.07.22.550117] [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] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices.
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Leleiwi I, Rodriguez-Ramos J, Shaffer M, Sabag-Daigle A, Kokkinias K, Flynn RM, Daly RA, Kop LFM, Solden LM, Ahmer BMM, Borton MA, Wrighton KC. Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers. Microbiome 2023; 11:114. [PMID: 37210515 PMCID: PMC10199544 DOI: 10.1186/s40168-023-01529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. RESULTS Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. CONCLUSIONS This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.
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Affiliation(s)
- Ikaia Leleiwi
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Josué Rodriguez-Ramos
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Katherine Kokkinias
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
| | - Rory M. Flynn
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Rebecca A. Daly
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Linnea F. M. Kop
- Department of Microbiology, RIBES, Radbound University, Nijmegen, The Netherlands
- Department of Microbiology and Biophysics, The Ohio State University, Columbus, OH USA
| | - Lindsey M. Solden
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Brian M. M. Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Mikayla A. Borton
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Kelly C. Wrighton
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
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5
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Vega MAP, Scholes RC, Brady AR, Daly RA, Narrowe AB, Vanzin GF, Wrighton KC, Sedlak DL, Sharp JO. Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat. Environ Sci Technol 2023; 57:7240-7253. [PMID: 37099683 DOI: 10.1021/acs.est.2c09314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as Methylotetracoccus. Inhibition microcosms provided independent confirmation that methane oxidation was mediated by the pMMO. In these same incubations, sulfamethoxazole biotransformation was stimulated proportional to aerobic methane-oxidizing activity and exhibited negligible removal in the absence of methane, in the presence of methane and pMMO inhibitors, and under anoxia. Nitrate reduction was similarly enhanced under aerobic methane-oxidizing conditions with rates several times faster than for canonical denitrification. Collectively, our results provide convergent in situ and laboratory evidence that methane-oxidizing activity can enhance sulfamethoxazole biotransformation, with possible implications for the combined removal of nitrogen and trace organic contaminants in wetland sediments.
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Affiliation(s)
- Michael A P Vega
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
| | - Rachel C Scholes
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Adam R Brady
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Gary F Vanzin
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - David L Sedlak
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Jonathan O Sharp
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
- Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
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Schwartz DA, Rodríguez-Ramos JA, Shaffer M, Flynn RM, Daly RA, Wrighton KC, Lennon JT. Human-Gut Phages Harbor Sporulation Genes. mBio 2023:e0018223. [PMID: 37042671 DOI: 10.1128/mbio.00182-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-carried sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially carried by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notably spo0A, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments. IMPORTANCE Phages acquire bacterial genes and use them to alter host metabolism in ways that enhance phage fitness. To date, most auxiliary genes replace or modulate enzymes that are used by the host for nutrition or energy production. However, phage fitness is affected by all aspects of host physiology, including decisions that reduce the metabolic activity of the cell. Here, we focus on endosporulation, a complex and ancient form of dormancy found among the Bacillota that involves hundreds of genes. By coupling homology searches with host classification, we identified 31 phage-carried homologs of sporulation genes that are mostly limited to phages infecting spore-forming bacteria. Nearly one-third of the homologs recovered were regulatory genes, suggesting that phages may manipulate host genetic networks by tapping into their control elements. Our findings also suggest a mechanism by which phages can overcome the defensive strategy of dormancy, which may be involved in coevolutionary dynamics of spore-forming bacteria.
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Affiliation(s)
- Daniel A Schwartz
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Josué A Rodríguez-Ramos
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Rory M Flynn
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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7
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Rodríguez-Ramos J, Oliverio A, Borton MA, Danczak R, Mueller BM, Schulz H, Ellenbogen J, Flynn RM, Daly RA, Schopflin L, Shaffer M, Goldman A, Lewandowski J, Stegen JC, Wrighton KC. Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream. bioRxiv 2023:2023.04.04.535500. [PMID: 37066413 PMCID: PMC10104031 DOI: 10.1101/2023.04.04.535500] [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] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Although river ecosystems comprise less than 1% of Earth's total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.
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Vega MAP, Scholes RC, Brady AR, Daly RA, Narrowe AB, Bosworth LB, Wrighton KC, Sedlak DL, Sharp JO. Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat. Environ Sci Technol 2022; 56:14462-14477. [PMID: 36197061 DOI: 10.1021/acs.est.2c03566] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.
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Affiliation(s)
- Michael A P Vega
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), https://www.renuwit.org
| | - Rachel C Scholes
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), https://www.renuwit.org
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Adam R Brady
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), https://www.renuwit.org
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lily B Bosworth
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), https://www.renuwit.org
- Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - David L Sedlak
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), https://www.renuwit.org
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Jonathan O Sharp
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), https://www.renuwit.org
- Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
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9
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Nelson AR, Narrowe AB, Rhoades CC, Fegel TS, Daly RA, Roth HK, Chu RK, Amundson KK, Young RB, Steindorff AS, Mondo SJ, Grigoriev IV, Salamov A, Borch T, Wilkins MJ. Wildfire-dependent changes in soil microbiome diversity and function. Nat Microbiol 2022; 7:1419-1430. [PMID: 36008619 PMCID: PMC9418001 DOI: 10.1038/s41564-022-01203-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 09/01/2021] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, and the frequency and size of severe fires have increased owing to climate change. Fires affect ecosystem recovery and modify soil microbiomes and microbially mediated biogeochemical processes. To study wildfire-dependent changes in soil microbiomes, we characterized functional shifts in the soil microbiota (bacteria, fungi and viruses) across burn severity gradients (low, moderate and high severity) 1 yr post fire in coniferous forests in Colorado and Wyoming, USA. We found severity-dependent increases of Actinobacteria encoding genes for heat resistance, fast growth, and pyrogenic carbon utilization that might enhance post-fire survival. We report that increased burn severity led to the loss of ectomycorrhizal fungi and less tolerant microbial taxa. Viruses remained active in post-fire soils and probably influenced carbon cycling and biogeochemistry via turnover of biomass and ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link post-fire soil microbial taxonomy to functions and reveal the complexity of post-fire soil microbiome activity. Wildfires have unknown impacts on soil microbes and biogeochemistry. Using metagenomics across forest burn gradients, here the authors show severity-dependent losses in microbiome diversity and functional shifts that underpin post-fire survival.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.,Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, PA, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kaela K Amundson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Andrei S Steindorff
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.,Department of Chemistry, Colorado State University, Fort Collins, CO, USA.,Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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Baniasad M, Kim Y, Shaffer M, Sabag-Daigle A, Leleiwi I, Daly RA, Ahmer BMM, Wrighton KC, Wysocki VH. Optimization of proteomics sample preparation for identification of host and bacterial proteins in mouse feces. Anal Bioanal Chem 2022; 414:2317-2331. [PMID: 35106611 PMCID: PMC9393048 DOI: 10.1007/s00216-022-03885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/03/2021] [Accepted: 01/07/2022] [Indexed: 11/01/2022]
Abstract
Bottom-up proteomics is a powerful method for the functional characterization of mouse gut microbiota. To date, most of the bottom-up proteomics studies of the mouse gut rely on limited amounts of fecal samples. With mass-limited samples, the performance of such analyses is highly dependent on the protein extraction protocols and contaminant removal strategies. Here, protein extraction protocols (using different lysis buffers) and contaminant removal strategies (using different types of filters and beads) were systematically evaluated to maximize quantitative reproducibility and the number of identified proteins. Overall, our results recommend a protein extraction method using a combination of sodium dodecyl sulfate (SDS) and urea in Tris-HCl to yield the greatest number of protein identifications. These conditions led to an increase in the number of proteins identified from gram-positive bacteria, such as Firmicutes and Actinobacteria, which is a challenging task. Our analysis further confirmed these conditions led to the extraction of non-abundant bacterial phyla such as Proteobacteria. In addition, we found that, when coupled to our optimized extraction method, suspension trap (S-Trap) outperforms other contaminant removal methods by providing the most reproducible method while producing the greatest number of protein identifications. Overall, our optimized sample preparation workflow is straightforward and fast, and requires minimal sample handling. Furthermore, our approach does not require high amounts of fecal samples, a vital consideration in proteomics studies where mice produce smaller amounts of feces due to a particular physiological condition. Our final method provides efficient digestion of mouse fecal material, is reproducible, and leads to high proteomic coverage for both host and microbiome proteins.
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Affiliation(s)
- Maryam Baniasad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Yongseok Kim
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO, USA
| | - Anice Sabag-Daigle
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Ikaia Leleiwi
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO, USA
| | - Brian M M Ahmer
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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11
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Amundson KK, Borton MA, Daly RA, Hoyt DW, Wong A, Eder E, Moore J, Wunch K, Wrighton KC, Wilkins MJ. Correction to: Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation. Microbiome 2022; 10:30. [PMID: 35148809 PMCID: PMC8840777 DOI: 10.1186/s40168-022-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Kaela K Amundson
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Mikayla A Borton
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Rebecca A Daly
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Allison Wong
- Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | | | | | - Kelly C Wrighton
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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12
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Amundson KK, Borton MA, Daly RA, Hoyt DW, Wong A, Eder E, Moore J, Wunch K, Wrighton KC, Wilkins MJ. Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation. Microbiome 2022; 10:5. [PMID: 35034639 PMCID: PMC8762873 DOI: 10.1186/s40168-021-01194-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. RESULTS We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. CONCLUSIONS These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.
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Affiliation(s)
- Kaela K. Amundson
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - Mikayla A. Borton
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - Rebecca A. Daly
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - David W. Hoyt
- Environmental Molecular Sciences Laboratory, Richland, WA USA
| | - Allison Wong
- Environmental Molecular Sciences Laboratory, Richland, WA USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Richland, WA USA
| | | | | | - Kelly C. Wrighton
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - Michael J. Wilkins
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
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13
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Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, Liu P, Narrowe AB, Rodríguez-Ramos J, Bolduc B, Gazitúa MC, Daly RA, Smith GJ, Vik DR, Pope PB, Sullivan MB, Roux S, Wrighton KC. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res 2020; 48:8883-8900. [PMID: 32766782 PMCID: PMC7498326 DOI: 10.1093/nar/gkaa621] [Citation(s) in RCA: 299] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/29/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
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Affiliation(s)
- Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Bridget B McGivern
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Lindsey M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Pengfei Liu
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Josué Rodríguez-Ramos
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - M Consuelo Gazitúa
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Garrett J Smith
- Department of Microbiology, Radboud University, Nijmegen 6525, Netherlands
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Phil B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas 1432, Norway
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Simon Roux
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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14
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Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nat Microbiol 2020; 5:527. [PMID: 32047285 PMCID: PMC7608142 DOI: 10.1038/s41564-020-0681-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Cliffe L, Nixon SL, Daly RA, Eden B, Taylor KG, Boothman C, Wilkins MJ, Wrighton KC, Lloyd JR. Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters. Front Microbiol 2020; 11:286. [PMID: 32153553 PMCID: PMC7046593 DOI: 10.3389/fmicb.2020.00286] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/07/2020] [Indexed: 12/26/2022] Open
Abstract
Produced waters from hydraulically fractured shale formations give insight into the microbial ecology and biogeochemical conditions down-well. This study explores the potential for sulfide production by persistent microorganisms recovered from produced water samples collected from the Marcellus shale formation. Hydrogen sulfide is highly toxic and corrosive, and can lead to the formation of “sour gas” which is costly to refine. Furthermore, microbial colonization of hydraulically fractured shale could result in formation plugging and a reduction in well productivity. It is vital to assess the potential for sulfide production in persistent microbial taxa, especially when considering the trend of reusing produced waters as input fluids, potentially enriching for problematic microorganisms. Using most probable number (MPN) counts and 16S rRNA gene sequencing, multiple viable strains of bacteria were identified from stored produced waters, mostly belonging to the Genus Halanaerobium, that were capable of growth via fermentation, and produced sulfide when supplied with thiosulfate. No sulfate-reducing bacteria (SRB) were detected through culturing, despite the detection of relatively low numbers of sulfate-reducing lineages by high-throughput 16S rRNA gene sequencing. These results demonstrate that sulfidogenic produced water populations remain viable for years post production and, if left unchecked, have the potential to lead to natural gas souring during shale gas extraction.
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Affiliation(s)
- Lisa Cliffe
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Sophie L Nixon
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Bob Eden
- Rawwater Engineering Company Limited, Culcheth, United Kingdom
| | - Kevin G Taylor
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Christopher Boothman
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
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16
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Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol 2019; 4:1895-1906. [PMID: 31332386 PMCID: PMC6813254 DOI: 10.1038/s41564-019-0510-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/05/2019] [Indexed: 01/02/2023]
Abstract
Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications. A machine learning approach was used to recover over 10,000 inovirus-like sequences from existing microbial genomes and metagenomes, consequently proposing the reclassification of the Inoviridae family to a viral order, and uncover the previously unrecognized diversity of these viruses across hosts and environments.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Walnut Creek, CA, USA.
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Adair L Borges
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Allison Sharrar
- Department of Earth & Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, USA
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17
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Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ. Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp. Appl Environ Microbiol 2019; 85:e00018-19. [PMID: 30979840 PMCID: PMC6544827 DOI: 10.1128/aem.00018-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 01/04/2019] [Accepted: 04/10/2019] [Indexed: 01/12/2023] Open
Abstract
Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.
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Affiliation(s)
- Anne E Booker
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tea Meulia
- College of Food, Agricultural, and Environmental Sciences, Ohio State University, Columbus, Ohio, USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Rebecca A Daly
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Joseph D Moore
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Kenneth Wunch
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Paula J Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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18
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Borton MA, Daly RA, O'Banion B, Hoyt DW, Marcus DN, Welch S, Hastings SS, Meulia T, Wolfe RA, Booker AE, Sharma S, Cole DR, Wunch K, Moore JD, Darrah TH, Wilkins MJ, Wrighton KC. Comparative genomics and physiology of the genus
Methanohalophilus
, a prevalent methanogen in hydraulically fractured shale. Environ Microbiol 2018; 20:4596-4611. [DOI: 10.1111/1462-2920.14467] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 11/28/2022]
Affiliation(s)
| | - Rebecca A. Daly
- Soil and Crop Sciences, Colorado State UniversityFort CollinsCOUSA
| | | | | | | | - Susan Welch
- School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
| | | | - Tea Meulia
- Molecular and Cellular Imaging Center, The Ohio State University Wooster OH USA
| | - Richard A. Wolfe
- Soil and Crop Sciences, Colorado State UniversityFort CollinsCOUSA
| | - Anne E. Booker
- Depatment of MicrobiologyThe Ohio State UniversityColumbusOHUSA
| | - Shikha Sharma
- Department of Geology and Geography West Virginia University Morgantown WV USA
| | - David R. Cole
- School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
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19
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Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, Hoyt DW, Meulia T, Wolfe RA, Hanson AJ, Mouser PJ, Moore JD, Wunch K, Sullivan MB, Wrighton KC, Wilkins MJ. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol 2018; 4:352-361. [DOI: 10.1038/s41564-018-0312-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]
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20
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Evans MV, Panescu J, Hanson AJ, Welch SA, Sheets JM, Nastasi N, Daly RA, Cole DR, Darrah TH, Wilkins MJ, Wrighton KC, Mouser PJ. Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin. Front Microbiol 2018; 9:2646. [PMID: 30498478 PMCID: PMC6249378 DOI: 10.3389/fmicb.2018.02646] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 07/18/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.
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Affiliation(s)
- Morgan V Evans
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Jenny Panescu
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Andrea J Hanson
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, United States
| | - Susan A Welch
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Julia M Sheets
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Nicholas Nastasi
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - David R Cole
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Thomas H Darrah
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Michael J Wilkins
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Paula J Mouser
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States.,Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
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21
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Abstract
A large portion of the earth's biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5 km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.
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Affiliation(s)
- Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Michael J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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22
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Booker AE, Borton MA, Daly RA, Welch SA, Nicora CD, Hoyt DW, Wilson T, Purvine SO, Wolfe RA, Sharma S, Mouser PJ, Cole DR, Lipton MS, Wrighton KC, Wilkins MJ. Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales. mSphere 2017; 2:e00257-17. [PMID: 28685163 PMCID: PMC5497025 DOI: 10.1128/mspheredirect.00257-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 11/20/2022] Open
Abstract
Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as "souring") is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.
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Affiliation(s)
- Anne E. Booker
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Mikayla A. Borton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Susan A. Welch
- School of Earth Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Carrie D. Nicora
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - David W. Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Travis Wilson
- Department of Geology and Geography, West Virginia University, Morgantown, West Virginia, USA
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Richard A. Wolfe
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Shikha Sharma
- Department of Geology and Geography, West Virginia University, Morgantown, West Virginia, USA
| | - Paula J. Mouser
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
| | - David R. Cole
- School of Earth Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Mary S. Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Michael J. Wilkins
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- School of Earth Sciences, The Ohio State University, Columbus, Ohio, USA
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Borton MA, Sabag-Daigle A, Wu J, Solden LM, O’Banion BS, Daly RA, Wolfe RA, Gonzalez JF, Wysocki VH, Ahmer BMM, Wrighton KC. Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome. Microbiome 2017; 5:47. [PMID: 28449706 PMCID: PMC5408407 DOI: 10.1186/s40168-017-0264-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Salmonella is one of the most significant food-borne pathogens to affect humans and agriculture. While it is well documented that Salmonella infection triggers host inflammation, the impacts on the gut environment are largely unknown. A CBA/J mouse model was used to evaluate intestinal responses to Salmonella-induced inflammation. In parallel, we evaluated chemically induced inflammation by dextran sodium sulfate (DSS) and a non-inflammation control. We profiled gut microbial diversity by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from fecal and cecal samples. These data were correlated to the inflammation marker lipocalin-2 and short-chain fatty acid concentrations. RESULTS We demonstrated that inflammation, chemically or biologically induced, restructures the chemical and microbial environment of the gut over a 16-day period. We observed that the ten mice within the Salmonella treatment group had a variable Salmonella relative abundance, with three high responding mice dominated by >46% Salmonella at later time points and the remaining seven mice denoted as low responders. These low- and high-responding Salmonella groups, along with the chemical DSS treatment, established an inflammation gradient with chemical and low levels of Salmonella having at least 3 log-fold lower lipocalin-2 concentration than the high-responding Salmonella mice. Total short-chain fatty acid and individual butyrate concentrations each negatively correlated with inflammation levels. Microbial communities were also structured along this inflammation gradient. Low levels of inflammation, regardless of chemical or biological induction, enriched for Akkermansia spp. in the Verrucomicrobiaceae and members of the Bacteroidetes family S24-7. Relative to the control or low inflammation groups, high levels of Salmonella drastically decreased the overall microbial diversity, specifically driven by the reduction of Alistipes and Lachnospiraceae in the Bacteroidetes and Firmicutes phyla, respectively. Conversely, members of the Enterobacteriaceae and Lactobacillus were positively correlated to high levels of Salmonella-induced inflammation. CONCLUSIONS Our results show that enteropathogenic infection and intestinal inflammation are interrelated factors modulating gut homeostasis. These findings may prove informative with regard to prophylactic or therapeutic strategies to prevent disruption of microbial communities, or promote their restoration.
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Affiliation(s)
- Mikayla A. Borton
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Jikang Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Lindsey M. Solden
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Bridget S. O’Banion
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Richard A. Wolfe
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Juan F. Gonzalez
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Brian M. M. Ahmer
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
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Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS. High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. Environ Microbiol 2017; 19:2192-2209. [DOI: 10.1111/1462-2920.13703] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Adrienne B. Narrowe
- Department of Integrative Biology; University of Colorado Denver; Denver CO USA
| | - Jordan C. Angle
- Department of Microbiology; The Ohio State University; Columbus OH USA
| | - Rebecca A. Daly
- Department of Microbiology; The Ohio State University; Columbus OH USA
| | - Kay C. Stefanik
- School of Environment and Natural Resources; The Ohio State University; Columbus OH USA
| | - Kelly C. Wrighton
- Department of Microbiology; The Ohio State University; Columbus OH USA
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25
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Solden LM, Hoyt DW, Collins WB, Plank JE, Daly RA, Hildebrand E, Beavers TJ, Wolfe R, Nicora CD, Purvine SO, Carstensen M, Lipton MS, Spalinger DE, Firkins JL, Wolfe BA, Wrighton KC. New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11. ISME J 2016; 11:691-703. [PMID: 27959345 PMCID: PMC5322302 DOI: 10.1038/ismej.2016.150] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 09/29/2016] [Accepted: 10/05/2016] [Indexed: 11/24/2022]
Abstract
Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives. We show that BS11 are cosmopolitan host-associated bacteria prevalent in gastrointestinal tracts of ruminants and other mammals. Metagenomic reconstruction yielded the first four BS11 genomes; phylogenetically resolving two genera within this previously taxonomically undefined family. Genome-enabled metabolic analyses uncovered multiple pathways for fermenting hemicellulose monomeric sugars to short-chain fatty acids (SCFA), metabolites vital for ruminant energy. Active hemicellulosic sugar fermentation and SCFA production was validated by shotgun proteomics and rumen metabolites, illuminating the role BS11 have in carbon transformations within the rumen. Our results also highlight the currently unknown metabolic potential residing in the rumen that may be vital for sustaining host energy in response to a changing vegetative environment.
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Affiliation(s)
- Lindsey M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - David W Hoyt
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - William B Collins
- Alaska Department of Fish and Game, Division of Wildlife Conservation, Palmer, AK, USA
| | - Johanna E Plank
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Erik Hildebrand
- Minnesota Department of Natural Resources, Division of Fish and Wildlife, Wildlife Health Program, Forest Lake, MN, USA
| | - Timothy J Beavers
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Richard Wolfe
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Sam O Purvine
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michelle Carstensen
- Minnesota Department of Natural Resources, Division of Fish and Wildlife, Wildlife Health Program, Forest Lake, MN, USA
| | - Mary S Lipton
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Donald E Spalinger
- Department of Biology, University of Alaska Anchorage, Anchorage, AK, USA
| | - Jeffrey L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Barbara A Wolfe
- Department of Veterinary Preventative Medicine, Colllege of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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26
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Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Kountz DJ, Wolfe RA, Welch SA, Marcus DN, Trexler RV, MacRae JD, Krzycki JA, Cole DR, Mouser PJ, Wrighton KC. Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nat Microbiol 2016; 1:16146. [PMID: 27595198 DOI: 10.1038/nmicrobiol.2016.146] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/15/2016] [Indexed: 01/22/2023]
Abstract
Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.
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Affiliation(s)
- Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Mikayla A Borton
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Michael J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA.,School of Earth Sciences, The Ohio State University, Columbus, Ohio 43214, USA
| | - David W Hoyt
- EMSL, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Duncan J Kountz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Richard A Wolfe
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Susan A Welch
- School of Earth Sciences, The Ohio State University, Columbus, Ohio 43214, USA
| | - Daniel N Marcus
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Ryan V Trexler
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Jean D MacRae
- Department of Civil and Environmental Engineering, University of Maine, Orono, Maine 04469, USA
| | - Joseph A Krzycki
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - David R Cole
- School of Earth Sciences, The Ohio State University, Columbus, Ohio 43214, USA
| | - Paula J Mouser
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
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Wilkins MJ, Daly RA, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Peterson L, Pfiffner SM, Phelps TJ, Schrenk MO. Trends and future challenges in sampling the deep terrestrial biosphere. Front Microbiol 2014; 5:481. [PMID: 25309520 PMCID: PMC4162470 DOI: 10.3389/fmicb.2014.00481] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 07/25/2014] [Accepted: 08/27/2014] [Indexed: 11/28/2022] Open
Abstract
Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.
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Affiliation(s)
- Michael J. Wilkins
- School of Earth Sciences, The Ohio State UniversityColumbus, OH, USA
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Paula J. Mouser
- Department of Engineering, The Ohio State UniversityColumbus, OH, USA
| | - Ryan Trexler
- Department of Engineering, The Ohio State UniversityColumbus, OH, USA
| | - Shihka Sharma
- Department of Geology and Geography, West Virginia UniversityMorgantown, WV, USA
| | - David R. Cole
- School of Earth Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Jennifer F. Biddle
- College of Earth, Ocean, and Environment, University of DelawareLewes, DE, USA
| | | | - Jim K. Fredrickson
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | | | | | | | - Susan M. Pfiffner
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA
| | - Tommy J. Phelps
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA
| | - Matthew O. Schrenk
- Department of Geological Sciences, Michigan State UniversityEast Lansing, MI, USA
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28
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Doll HM, Armitage DW, Daly RA, Emerson JB, Goltsman DSA, Yelton AP, Kerekes J, Firestone MK, Potts MD. Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains. BMC Microbiol 2013; 13:259. [PMID: 24238386 PMCID: PMC3840555 DOI: 10.1186/1471-2180-13-259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/07/2013] [Indexed: 12/02/2022] Open
Abstract
Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology.
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Affiliation(s)
- Hannah M Doll
- Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.
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29
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Blazewicz SJ, Barnard RL, Daly RA, Firestone MK. Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J 2013; 7:2061-8. [PMID: 23823491 PMCID: PMC3806256 DOI: 10.1038/ismej.2013.102] [Citation(s) in RCA: 433] [Impact Index Per Article: 39.4] [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: 10/31/2012] [Revised: 05/02/2013] [Accepted: 05/22/2013] [Indexed: 12/26/2022]
Abstract
Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the 'active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.
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Affiliation(s)
- Steven J Blazewicz
- The Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Romain L Barnard
- The Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Rebecca A Daly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mary K Firestone
- The Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Allan S, Daly RA, Yoganathan Y, Barrett S, Joseph A, Tariq A, Saing CW, Williams C, Lane C, Sikorska J. British HIV and ageing study. HIV and ageing: older people with HIV, who are they? J Int AIDS Soc 2010. [PMCID: PMC3113061 DOI: 10.1186/1758-2652-13-s4-p57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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31
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Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One 2010; 5:e11044. [PMID: 20585638 PMCID: PMC2890402 DOI: 10.1371/journal.pone.0011044] [Citation(s) in RCA: 327] [Impact Index Per Article: 23.4] [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: 10/04/2009] [Accepted: 05/19/2010] [Indexed: 02/07/2023] Open
Abstract
Bacterial communities in the airways of cystic fibrosis (CF) patients are, as in other ecological niches, influenced by autogenic and allogenic factors. However, our understanding of microbial colonization in younger versus older CF airways and the association with pulmonary function is rudimentary at best. Using a phylogenetic microarray, we examine the airway microbiota in age stratified CF patients ranging from neonates (9 months) to adults (72 years). From a cohort of clinically stable patients, we demonstrate that older CF patients who exhibit poorer pulmonary function possess more uneven, phylogenetically-clustered airway communities, compared to younger patients. Using longitudinal samples collected form a subset of these patients a pattern of initial bacterial community diversification was observed in younger patients compared with a progressive loss of diversity over time in older patients. We describe in detail the distinct bacterial community profiles associated with young and old CF patients with a particular focus on the differences between respective "early" and "late" colonizing organisms. Finally we assess the influence of Cystic Fibrosis Transmembrane Regulator (CFTR) mutation on bacterial abundance and identify genotype-specific communities involving members of the Pseudomonadaceae, Xanthomonadaceae, Moraxellaceae and Enterobacteriaceae amongst others. Data presented here provides insights into the CF airway microbiota, including initial diversification events in younger patients and establishment of specialized communities of pathogens associated with poor pulmonary function in older patient populations.
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Affiliation(s)
- Michael J. Cox
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Martin Allgaier
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Byron Taylor
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Marshall S. Baek
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Yvonne J. Huang
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Adult Cystic Fibrosis Program, University of California San Francisco, San Francisco, California, United States of America
| | - Rebecca A. Daly
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology University of California, Berkeley, California, United States of America
| | - Ulas Karaoz
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gary L. Andersen
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Ronald Brown
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Kei E. Fujimura
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Brian Wu
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Pediatric Cystic Fibrosis Program, University of California San Francisco, San Francisco, California, United States of America
| | - Diem Tran
- Pediatric Cystic Fibrosis Program, University of California San Francisco, San Francisco, California, United States of America
| | - Jonathan Koff
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Adult Cystic Fibrosis Program, University of California San Francisco, San Francisco, California, United States of America
| | - Mary Ellen Kleinhenz
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Adult Cystic Fibrosis Program, University of California San Francisco, San Francisco, California, United States of America
| | - Dennis Nielson
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Pediatric Cystic Fibrosis Program, University of California San Francisco, San Francisco, California, United States of America
| | - Eoin L. Brodie
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Susan V. Lynch
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
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Abstract
HilA, a Salmonella transcription factor, activates the invF-1 and prgH promoters through binding to the HilA box, which contains 2 copies of a TTKHAT motif separated by a T centered at -45 relative to the start sites of transcription. The N-terminal 112 amino acids of HilA are similar to winged helix-turn-helix DNA binding/transcription activation domains (wHTH DBDs). The remaining 441 amino acids are not similar in sequence to any other well-characterized transcription factors. Here, we report that the wHTH DBD is essential for activation of both promoters, but amino acids 113-554 are only required for normal activation of invF-1. Some alanine substitutions in the putative alpha loop, which connects the recognition and positioning helices in wHTH DBDs, cause a loss-of-activation phenotype. A hilA allele encoding a protein with an alanine substituted for arginine at position 71 in the alpha loop has a loss-of-activation defect exclusively at the prgH promoter. The results suggest distinct roles for one or more domains formed by amino acids 113-554 and for arginine 71 in activation of the 2 promoters.
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Affiliation(s)
- Rebecca A Daly
- Department of Biology, Colorado College, 14 E Cache La Poudre Avenue, Colorado Springs, CO 80903, USA
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Tokunaga TK, Wan J, Kim Y, Daly RA, Brodie EL, Hazen TC, Herman D, Firestone MK. Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment. Environ Sci Technol 2008; 42:8901-8907. [PMID: 19192816 DOI: 10.1021/es8019947] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Remediation of uranium-contaminated sediments through in situ stimulation of bioreduction to insoluble UO2 is a potential treatment strategy under active investigation. Previously, we found that newly reduced U(IV) can be reoxidized under reducing conditions sustained by a continuous supply of organic carbon (OC) because of residual reactive Fe(III) and enhanced U(VI) solubilitythrough complexation with carbonate generated through OC oxidation. That finding motivated this investigation directed at identifying a range of OC supply rates that is optimal for establishing U bioreduction and immobilization in initially oxidizing sediments. The effects of OC supply rate, from 0 to 580 mmol of OC (kg of sediment)(-1) year(-1), and OC form (lactate and acetate) on U bioreduction were tested in flow-through columns containing U-contaminated sediments. An intermediate supply rate on the order of 150 mmol of OC (kg of sediment)(-1) year(-1) was determined to be most effective at immobilizing U. At lower OC supply rates, U bioreduction was not achieved, and U(VI) solubilitywas enhanced by complexation with carbonate (from OC oxidation). At the highest OC supply rate, the resulting highly carbonate-enriched solutions also supported elevated levels of U(VI), even though strongly reducing conditions were established. Lactate and acetate were found to have very similar geochemical impacts on effluent U concentrations (and other measured chemical species), when compared at equivalent OC supply rates. While the catalysts of U(VI) reduction to U(IV) are presumably bacteria, the composition of the bacterial community,the Fe-reducing community, and the sulfate-reducing community had no direct relationship with effluent U concentrations. The OC supply rate has competing effects of driving reduction of U(VI) to low-solubility U(IV) solids, as well as causing formation of highly soluble U(VI)-carbonato complexes. These offsetting influences will require careful control of OC supply rates in order to optimize bioreduction-based U stabilization.
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Affiliation(s)
- Tetsu K Tokunaga
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, and University of California, Berkeley, California 94720, USA.
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Affiliation(s)
- R A Daly
- Department of Geology and Geography, Harvard University
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Daly RA, Carter HB. Fleece growth of young Lincoln, Corriedale, Polwarth, and fine Merino maiden ewes grazed on an unimproved paspalum pasture. ACTA ACUST UNITED AC 1956. [DOI: 10.1071/ar9560076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two young maiden ewes of each of the Lincoln, Corriedale, Polwarth, and fine Merino breeds were kept together on 3 acres of unimproved paspalum dominant pasture at Castle Hill, near Sydney, for 42 weeks. In this time 44½ in. of rain were recorded, with fairly uniform monthly incidence. The response of the sheep to these conditions was studied and compared with that of similar sheep which were kept in housed, single pens and fed unrestricted quantities of a high-quality diet (Daly and Carter 1955). Liveweight and wool production of the field sheep were dependent on seasonal trends in pasture quality and were consistently lower than for the housed, well-fed sheep. Rain removed appreciable quantities of wax and suint from the fleeces of Lincolns, Corriedales, and Polwarths and altered the pattern of distribution of these components in them. In warm, wet conditions "canary stain" and bacterial discoloration became conspicuous in Corriedale and Polwarth fleeces but not in Lincoln and fine Merino fleeces. In all respects the fine Merino fleeces were least affected by the relatively severe climatic conditions.
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Daly RA, Carter HB. The fleece growth of young Lincoln, Corriedale, Polwarth, and fine Merino maiden ewes under housed conditions and unrestricted and progressively restricted feeding on a standard diet. ACTA ACUST UNITED AC 1955. [DOI: 10.1071/ar9550476] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two experiments have been conducted with young Lincoln, Corriedale, Polwarth, and fine Merino maiden ewes to compare the growth of fleece by these breeds and to assess relations between the growth of fleece and some factors, nutritional and non-nutritional, likely to influence its growth. In both experiments four representatives of each breed were kept in a sheep house in single pens and fed a high quality diet of constant composition. The second experiment followed immediately on the first and the same sheep were used except for necessary replacements. In the first experiment, which lasted for about one year, the intake of the diet was continuously unrestricted; in the second the intake of the diet was progressively restricted by ordered steps and was finally maintained for 12 weeks at one-fifth of the unrestricted intake of the first 4 weeks of the experiment. With few exceptions, the absolute or relative values of the characters measured formed a smooth series from the fine Merino through the Polwarth and Corriedale to the Lincoln-either in ascending order (e.g. food and water intake; liveweight and chest dimensions; fibre thickness, length, and volume; clean wool, suint, and total skin products output; clean wool and suint output per unit food intake) or descending order (e.g. total and primary follicle density; ratio of secondaries to primaries; wax output and wax output per unit food intake) or showed little or no difference between the breeds (e.g. body length and height; food intake per unit net liveweight; total skin products per unit food intake). The relative positions of the breeds as shown in the first experiment mere generally maintained in the second as food intake was progressively reduced. The results of the two experiments were combined for the individuals and a series of partial regression analyses were undertaken to determine the regression of some variables of fleece production on the level of food intake, atmospheric temperature, fleece weight, and experimental time. Self-selected food intake decreased with increase in fleece weight and less obviously with increase in experimental time (or, possibly, with deposition of subcutaneous fat). Water intake increased with both increase in food intake and rise in atmospheric temperature. Wool weight produced, and fibre thickness, length, and volume growth, all increased with increase in food intake, and within the limits of observed food intake the relation between wool growth and food intake was adequately represented by linear regression. Increase in atmospheric temperature exerted no significant influence on wool growth, except by the Lincolns (through fibre thickness). A positive regression of wool growth rate on fleece weight, acting through fibre length growth, was found, but change in fibre thickness was not related to increase in fleece weight. Wax production was positively related to increase in food intake and negatively to rise in atmospheric temperature. Suint production was positively related to both food intake and fleece weight. Wool, wax and suint production per unit food intake decreased with increase in food intake. Wax per unit food intake decreased with rise in temperature and suint per unit food intake increased with increase in fleece weight.
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Daly RA, Carter HB. A method of fractionating raw fleece samples and some errors encountered in its use in experimental studies of fleece growth. ACTA ACUST UNITED AC 1954. [DOI: 10.1071/ar9540327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A routine quantitative method of separating raw fleece samples into five fractions is described. Moisture content at a known temperature and relative humidity is determined as the loss of weight on drying a t 105°C, wax is Soxhlet-extracted with carbon tetrachloride, suint is extracted by subsequent washings with cold distilled water, dirt is removed by washing and handpicking, and clean wool fibre remains after these fractions have been removed. Some errors detected in the extensive use of this method to provide simple criteria in a variety of field and laboratory studies of fleece growth have been examined. Recovery of original sample weight after fractionation was satisfactory and there was good agreement between the results for duplicate samples. There was a tendency for incomplete separation of suint and for ethyl-alcohol-soluble material, of the order of 1 per cent. by weight, to remain on the clean wool fibre.
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Affiliation(s)
- R A Daly
- Department of Geology, Harvard University
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Daly RA. Gardiner on Coral Reefs. Science 1931; 74:566-7. [PMID: 17807633 DOI: 10.1126/science.74.1927.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Affiliation(s)
- R A Daly
- Department of Geology and Geography, Harvard University
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Affiliation(s)
- R A Daly
- Department of Geology and Geography, Harvard University
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Daly RA. Machine-Made Line Drawings for the Illustration of Scientific Papers. Science 1905; 22:91-3. [PMID: 17817687 DOI: 10.1126/science.22.551.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Daly RA. Notes on Oceanography. Science 1901; 13:951-4. [PMID: 17733661 DOI: 10.1126/science.13.337.951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Daly RA. SCIENTIFIC EXPEDITION TO ICELAND, GREENLAND AND LABRADOR. Science 1901; 13:192. [PMID: 17816318 DOI: 10.1126/science.13.318.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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