1
|
Povedano-Priego C, Jroundi F, Morales-Hidalgo M, Pinel-Cabello M, Peula-Ruiz E, Merroun ML, Martin-Sánchez I. Unveiling fungal diversity in uranium and glycerol-2-phosphate-amended bentonite microcosms: Implications for radionuclide immobilization within the Deep Geological Repository system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168284. [PMID: 37924892 DOI: 10.1016/j.scitotenv.2023.168284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
Uranium (U) represents the preeminent hazardous radionuclide within the context of nuclear waste repositories. Indigenous microorganisms in bentonite can influence radionuclide speciation and migration in Deep Geological Repositories (DGRs) for nuclear waste storage. While bacterial communities in bentonite samples have been extensively studied, the impact of fungi has been somewhat overlooked. Here, we investigate the geomicrobiological processes in bentonite microcosms amended with uranyl nitrate and glycerol-2-phosphate (G2P) for six-month incubation. ITS sequencing revealed that the fungal community was mainly composed of Ascomycota (96.6 %). The presence of U in microcosms enriched specific fungal taxa, such as Penicillium and Fusarium, potentially associated with uranium immobilization mechanisms. Conversely, the amendment of U into G2P-suplemented samples exhibited minimal impact, resulting in a fungal community akin to the control group. Several fungal strains were isolated from bentonite microcosms to explore their potential in the U biomineralization, including Fusarium oxysporum, Aspergillus sp., Penicillium spp., among others. High Annular Angle Dark-Field Scanning Transmission Electron Microscopy (HAADF) analyses showed the capacity of F. oxysporum B1 to form U-phosphate mineral phases, likely mediated by phosphatase activity. Therefore, our study emphasizes the need to take into account indigenous bentonite fungi in the overall assessment of the impact of microbial processes in the immobilization of U within DGRs environments.
Collapse
Affiliation(s)
- Cristina Povedano-Priego
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| | - Fadwa Jroundi
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| | - Mar Morales-Hidalgo
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| | - María Pinel-Cabello
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| | - Esther Peula-Ruiz
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| | - Mohamed L Merroun
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| | - Inés Martin-Sánchez
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
| |
Collapse
|
2
|
Newman-Portela AM, Krawczyk-Bärsch E, Lopez-Fernandez M, Bok F, Kassahun A, Drobot B, Steudtner R, Stumpf T, Raff J, Merroun ML. Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7227-7245. [PMID: 38157180 PMCID: PMC10821841 DOI: 10.1007/s11356-023-31530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.
Collapse
Affiliation(s)
- Antonio M Newman-Portela
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Evelyn Krawczyk-Bärsch
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
| | - Frank Bok
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Andrea Kassahun
- WISMUT GmbH, Jagdschänkenstraße 29, 09117, Chemnitz, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Thorsten Stumpf
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
| |
Collapse
|
3
|
Wise BR, Roane TM, Mosier AC. Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment. MICROBIAL ECOLOGY 2020; 79:562-575. [PMID: 31446448 DOI: 10.1007/s00248-019-01420-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.
Collapse
Affiliation(s)
- Ben R Wise
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Timberley M Roane
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.
| |
Collapse
|
4
|
Fomina M, Hong JW, Gadd GM. Effect of depleted uranium on a soil microcosm fungal community and influence of a plant-ectomycorrhizal association. Fungal Biol 2019; 124:289-296. [PMID: 32389290 DOI: 10.1016/j.funbio.2019.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/18/2019] [Accepted: 08/03/2019] [Indexed: 01/23/2023]
Abstract
Fungi are one of the most biogeochemically active components of the soil microbiome, becoming particularly important in metal polluted terrestrial environments. There is scant information on the mycobiota of uranium (U) polluted sites and the effect of metallic depleted uranium (DU) stress on fungal communities in soil has not been reported. The present study aimed to establish the effect of DU contamination on a fungal community in soil using a culture-independent approach, fungal ribosomal intergenic spacer analysis (F-RISA). Experimental soil microcosms also included variants with plants (Pinus silvestris) and P. silvestris/Rhizopogon rubescens ectomycorrhizal associations. Soil contamination with DU resulted in the appearance of RISA bands of the ITS fragments of fungal metagenomic DNA that were characteristic of the genus Mortierella (Mortierellomycotina: Mucoromycota) in pine-free microcosms and for ectomycorrhizal fungi of the genus Scleroderma (Basidiomycota) in microcosms with mycorrhizal pines. The precise taxonomic affinity of the ITS fragments from the band appearing for non-mycorrhizal pines combined with DU remained uncertain, the most likely being related to the subphylum Zoopagomycotina. Thus, soil contamination by thermodynamically unstable metallic depleted uranium can cause a significant change in a soil fungal community under experimental conditions. These changes were also strongly affected by the presence of pine seedlings and their mycorrhizal status which impacted on DU biocorrosion and the release of bioavailable uranium species.
Collapse
Affiliation(s)
- Marina Fomina
- Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, 03143, Ukraine; Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Ji Won Hong
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Seocheon, Chungcheongnam-do, 33662, South Korea
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom.
| |
Collapse
|
5
|
Ma M, Jiang X, Wang Q, Ongena M, Wei D, Ding J, Guan D, Cao F, Zhao B, Li J. Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols. Microbiologyopen 2018; 7:e00597. [PMID: 29573192 PMCID: PMC6182557 DOI: 10.1002/mbo3.597] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 11/07/2022] Open
Abstract
How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.
Collapse
Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Qingfeng Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Marc Ongena
- Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianli Ding
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| |
Collapse
|
6
|
Ma X, Vikram A, Casson L, Bibby K. Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7648-7657. [PMID: 28562026 DOI: 10.1021/acs.est.7b00768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.
Collapse
Affiliation(s)
- Xiao Ma
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | - Amit Vikram
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | - Leonard Casson
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
- Graduate School of Public Health, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
- Department of Computational and Systems Biology, University of Pittsburgh Medical School , Pittsburgh, Pennsylvania 15261, United States
| |
Collapse
|
7
|
Auld RR, Mykytczuk NC, Leduc LG, Merritt TJ. Seasonal variation in an acid mine drainage microbial community. Can J Microbiol 2017; 63:137-152. [DOI: 10.1139/cjm-2016-0215] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Environmental oxidation and microbial metabolism drive production of acid mine drainage (AMD). Understanding changes in the microbial community, due to geochemical and seasonal characteristics, is fundamental to AMD monitoring and remediation. Using direct sequencing of the 16S and 18S rRNA genes to identify bacterial, archaeal, and eukaryotic members of the microbial community at an AMD site in Northern Ontario, Canada, we found a dynamic community varying significantly across winter and summer sampling times. Community composition was correlated with physical and chemical properties, including water temperature, pH, conductivity, winter ice thickness, and metal concentrations. Within Bacteria, Acidithiobacillus was the dominant genus during winter (11%–57% of sequences) but Acidiphilium was dominant during summer (47%–87%). Within Eukarya, Chrysophyceae (1.5%–94%) and Microbotrymycetes (8%–92%) dominated the winter community, and LKM11 (4%–62%) and Chrysophyceae (25%–87%) the summer. There was less diversity and variability within the Archaea, with similar summer and winter communities mainly comprising Thermoplasmata (33%–64%) and Thermoprotei (5%–20%) classes but also including a large portion of unclassified reads (∼40%). Overall, the active AMD community varied significantly between winter and summer, with changing community profiles closely correlated to specific differences in AMD geochemical and physical properties, including pH, water temperature, ice thickness, and sulfate and metal concentrations.
Collapse
Affiliation(s)
- Ryan R. Auld
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | | | - Leo G. Leduc
- Department of Biology, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Thomas J.S. Merritt
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
| |
Collapse
|
8
|
Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE. Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. Appl Environ Microbiol 2016; 82:2919-2928. [PMID: 26969694 PMCID: PMC4959062 DOI: 10.1128/aem.00243-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Members of the Fungi convert nitrate (NO3 (-)) and nitrite (NO2 (-)) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3 (-) or NO2 (-) in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2 (-) Novel PCR primers targeting the p450nor gene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum Ascomycota and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from NO2 (-), whereas nirK (encoding the NO-forming NO2 (-) reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation. IMPORTANCE A comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal p450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.
Collapse
Affiliation(s)
- Steven A Higgins
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allana Welsh
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Robert A Sanford
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Christopher W Schadt
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| |
Collapse
|
9
|
Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF. Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Front Microbiol 2016; 7:238. [PMID: 26973616 PMCID: PMC4776211 DOI: 10.3389/fmicb.2016.00238] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 11/22/2022] Open
Abstract
The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.
Collapse
Affiliation(s)
- Annika C. Mosier
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Christopher S. Miller
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Kyle R. Frischkorn
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Robin A. Ohm
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Zhou Li
- Oak Ridge National LaboratoryOak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National LaboratoryKnoxville, TN, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Alla Lapidus
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Cindy Chen
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Jenifer Johnson
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | | | - Chongle Pan
- Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | | | - Steven W. Singer
- Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
| |
Collapse
|
10
|
Mueller RC, Belnap J, Kuske CR. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland. Front Microbiol 2015; 6:891. [PMID: 26388845 PMCID: PMC4559666 DOI: 10.3389/fmicb.2015.00891] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 or 0-10 cm) across the N-amendment gradient (0, 7, and 15 kg ha(-1) yr(-1)). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.
Collapse
Affiliation(s)
- Rebecca C Mueller
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Jayne Belnap
- Southwest Biological Science Center, United States Geological Survey Moab, UT, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| |
Collapse
|
11
|
Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure. Appl Environ Microbiol 2015; 81:7143-58. [PMID: 26253672 DOI: 10.1128/aem.02188-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/23/2015] [Indexed: 01/06/2023] Open
Abstract
Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem.
Collapse
|