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Kumar V, Sarma VV, Thambugala KM, Huang JJ, Li XY, Hao GF. Ecology and Evolution of Marine Fungi With Their Adaptation to Climate Change. Front Microbiol 2021; 12:719000. [PMID: 34512597 PMCID: PMC8430337 DOI: 10.3389/fmicb.2021.719000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change agitates interactions between organisms and the environment and forces them to adapt, migrate, get replaced by others, or extinct. Marine environments are extremely sensitive to climate change that influences their ecological functions and microbial community including fungi. Fungi from marine habitats are engaged and adapted to perform diverse ecological functions in marine environments. Several studies focus on how complex interactions with the surrounding environment affect fungal evolution and their adaptation. However, a review addressing the adaptation of marine fungi to climate change is still lacking. Here we have discussed the adaptations of fungi in the marine environment with an example of Hortaea werneckii and Aspergillus terreus which may help to reduce the risk of climate change impacts on marine environments and organisms. We address the ecology and evolution of marine fungi and the effects of climate change on them to explain the adaptation mechanism. A review of marine fungal adaptations will show widespread effects on evolutionary biology and the mechanism responsible for it.
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Affiliation(s)
- Vinit Kumar
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | | | - Kasun M. Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Xiang-Yang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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Wang Y, Hu Z, Shen L, Liu C, Islam ARMT, Wu Z, Dang H, Chen S. The process of methanogenesis in paddy fields under different elevated CO 2 concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145629. [PMID: 33940739 DOI: 10.1016/j.scitotenv.2021.145629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH4 production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO2 concentrations (e[CO2]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH4 flux in paddy fields under various (e[CO2]). CH4 flux and CH4 production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO2 concentration), C1 (C + 160 ppm CO2), and C2 (C + 200 ppm CO2) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C2 treatment significantly increased CH4 flux and MPP at the tillering stage. E[CO2] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO2] did not significantly change the overall community structure and diversity of methanogens, C2 treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH4 flux under e[CO2]. Overall, our results demonstrated that CH4 flux in paddy fields under e[CO2] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhenghua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
| | - Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
| | - Chao Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - A R M Towfiqul Islam
- Department of Disaster Management, Disaster Management E-Learning Centre, Begum Rokeya University, Rangpur 5400, Bangladesh
| | - Zhurong Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Huihui Dang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Shutao Chen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
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Diversity, Concentration and Dynamics of Culturable Fungal Bioaerosols at Doha, Qatar. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 18:ijerph18010182. [PMID: 33383754 PMCID: PMC7796145 DOI: 10.3390/ijerph18010182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/02/2022]
Abstract
This research was conducted to investigate the dynamics of airborne fungi using viable culture collection and in respect to different abiotic variables, including seasonal and intra-diurnal variations. A gravimetric method was used to sample airborne fungal deposition on potato dextrose agar plates on alternate days, for a year between April 2015 to March 2016. From 176 settle plate exposures, a total of 1197 mould and 283 yeast colony-forming units (CFU), 21 genera and 62 species were retrieved. The highest fungal spore count was recorded in February 2016, whereas the lowest count occurred in August 2015. The main constituents of the fungal airspora were attributed to Cladosporium (60.2%), Aspergillus (10.4%), Fusarium (9.4%), Alternaria (8.5%), and Ganoderma spp. (2.3%). Temperature was negatively correlated with total colony count (r = −0.231, p ≤ 0.05) or species richness (r = −0.267, p ≤ 0.001), while wind speed was positively correlated with total colony count (r = 0.484, p ≤ 0.001) or species richness (r = 0.257, p ≤ −0.001). The highest dispersal of fungal spores was obtained at 18:00, whereas the lowest fungal spores release was recorded at 00:00 (midnight). There were no significant differences in species composition and richness of the airborne fungal population between two study sites, the Industrial area and Qatar University Campus. The count of Alternaria spp. and Fusarium spp. were significantly higher at the Industrial area site, which corresponds to a higher CO2 level than the Qatar University site. This study lays the foundation for future work to assess the implications of such aeromycological data on public health.
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Chen W, Wang J, Meng Z, Xu R, Chen J, Zhang Y, Hu T. Fertility-related interplay between fungal guilds underlies plant richness-productivity relationships in natural grasslands. THE NEW PHYTOLOGIST 2020; 226:1129-1143. [PMID: 31863600 DOI: 10.1111/nph.16390] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
The plant richness-productivity relationship is a central subject in ecology, yet the mechanisms behind this pattern remain debated. Soil fungi are closely associated with the dynamics of plant communities, however empirical evidence on how fungal communities integrate into the richness-productivity relationships of natural environments is lacking. We used Illumina high-throughput sequencing to identify rhizosphere fungal communities across a natural plant richness gradient at two sites with different fertility conditions, and related the subsequent information to plant richness and productivity to elucidate the role of fungal guilds in integrating the linkages of both plant components. Saprotrophs, mycorrhizal fungi and potential plant pathogens interacted differently between the sites, with saprotrophic and mycorrhizal fungal abundances being positively correlated at the high-nutrient site and abundances of mycorrhizal fungi and potential plant pathogens being negatively correlated at the low-nutrient site. The synergistic associations between these fungal guilds with plant richness and productivity operated in concert to promote positive richness-productivity relationships. Our findings provide empirical evidence for the importance of soil fungal guilds in integrating the linkages of plant richness and productivity, and suggest that future work incorporating soil fungal communities into richness-productivity relationships would advance our mechanistic understanding of their linkages.
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Affiliation(s)
- Wenqing Chen
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jianyu Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zexin Meng
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ran Xu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun Chen
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yingjun Zhang
- Department of Grassland Science, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Barnes CJ, van der Gast CJ, McNamara NP, Rowe R, Bending GD. Extreme rainfall affects assembly of the root-associated fungal community. THE NEW PHYTOLOGIST 2018; 220:1172-1184. [PMID: 29350759 PMCID: PMC6282977 DOI: 10.1111/nph.14990] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/03/2017] [Indexed: 05/31/2023]
Abstract
Global warming is resulting in increased frequency of weather extremes. Root-associated fungi play important roles in terrestrial biogeochemical cycling processes, but the way in which they are affected by extreme weather is unclear. Here, we performed long-term field monitoring of the root-associated fungus community of a short rotation coppice willow plantation, and compared community dynamics before and after a once in 100 yr rainfall event that occurred in the UK in 2012. Monitoring of the root-associated fungi was performed over a 3-yr period by metabarcoding the fungal internal transcribed spacer (ITS) region. Repeated soil testing and continuous climatic monitoring supplemented community data, and the relative effects of environmental and temporal variation were determined on the root-associated fungal community. Soil saturation and surface water were recorded throughout the early growing season of 2012, following extreme rainfall. This was associated with a crash in the richness and relative abundance of ectomycorrhizal fungi, with each declining by over 50%. Richness and relative abundance of saprophytes and pathogens increased. We conclude that extreme rainfall events may be important yet overlooked determinants of root-associated fungal community assembly. Given the integral role of ectomycorrhizal fungi in biogeochemical cycles, these events may have considerable impacts upon the functioning of terrestrial ecosystems.
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Affiliation(s)
- Christopher J. Barnes
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
- Present address:
National History Museum of Denmar University of Copenhagen 83 SølvgadeMadison1800Denmark
| | | | - Niall P. McNamara
- NERC Centre for Ecology & HydrologyLancaster Environment CentreLibrary AvenueBailriggLancasterLA1 4APUK
| | - Rebecca Rowe
- NERC Centre for Ecology & HydrologyLancaster Environment CentreLibrary AvenueBailriggLancasterLA1 4APUK
| | - Gary D. Bending
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
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Yin P, Yin M, Cai Z, Wu G, Lin G, Zhou J. Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO 2. MARINE ENVIRONMENTAL RESEARCH 2018; 140:422-432. [PMID: 30055835 DOI: 10.1016/j.marenvres.2018.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Rhizosphere microbial communities play an important role in mediating the decomposition of soil organic matter. Increased CO2 concentration may increase plant growth by stimulating photosynthesis or improving water use efficiency. However, possible eco-physiological influences of this greenhouse gas in mangrove plants are not well understood, especially how rhizosphere microbial communities respond to CO2 increase. We characterized the effect of elevated CO2 (eCO2) on rhizospheric microbial communities associated with the mangrove plant Kandelia candel for 20 weeks, eCO2 increased plant chlorophyll a levels and root microbial biomass. Operational taxonomic unit analysis revealed no significant effects of eCO2 on rhizospheric bacterial communities; however, some influence on archaeal community structure was observed, especially on the ammonia-oxidizing archaea. Principal component analysis showed that microbial biomass C, total nitrogen, C/N ratio, nitrate nitrogen, and salinity were the main factors structuring the microbial community. The relative contribution of environmental parameters to variability among samples was 31.0%. In addition, functional analysis by average well color development showed that carbon source utilization under eCO2 occurred in the order amino acids > carbohydrates > polymers > carboxylic acids > amines > phenolic acids; whereas, sugars, amino acids, and carboxylic acids were the preferred carbon sources in control groups. Differences in utilization ability of carbohydrates and amino acids resulted in changes in carbon metabolism between the two groups. Rhizosphere microbial communities appear to have some buffering ability in response to short-term (20 weeks) CO2 increase, during which the metabolic efficiency of carbon sources is changed. The results will help better understand the structural inflexibility and functional plasticity of the rhizosphere microbiome in mangrove plants facing a changing environment (such as global climate change).
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Affiliation(s)
- Panqing Yin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China; The School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, Gansu Province, PR China
| | - Mengqing Yin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Guoqiang Wu
- The School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, Gansu Province, PR China
| | - Guanghui Lin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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7
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Sayer EJ, Oliver AE, Fridley JD, Askew AP, Mills RTE, Grime JP. Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. Ecol Evol 2017; 7:855-862. [PMID: 28168022 PMCID: PMC5288249 DOI: 10.1002/ece3.2700] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/30/2016] [Accepted: 11/27/2016] [Indexed: 11/09/2022] Open
Abstract
Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species‐rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short‐term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community‐weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon‐to‐nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long‐term climate change effects, especially in nutrient‐poor systems with slow‐growing vegetation.
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Affiliation(s)
- Emma J Sayer
- Lancaster Environment Centre Lancaster University Lancaster UK; Smithsonian Tropical Research Institute Panama Republic of Panama; Department of Environment, Earth and Ecosystems The Open University Milton Keynes UK
| | | | | | - Andrew P Askew
- Department of Biology Syracuse University Syracuse NY USA
| | | | - J Philip Grime
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
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Veresoglou SD, Anderson IC, de Sousa NMF, Hempel S, Rillig MC. Resilience of Fungal Communities to Elevated CO2. MICROBIAL ECOLOGY 2016; 72:493-5. [PMID: 27273090 DOI: 10.1007/s00248-016-0795-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/23/2023]
Abstract
Soil filamentous fungi play a prominent role in regulating ecosystem functioning in terrestrial ecosystems. This necessitates understanding their responses to climate change drivers in order to predict how nutrient cycling and ecosystem services will be influenced in the future. Here, we provide a quantitative synthesis of ten studies on soil fungal community responses to elevated CO2. Many of these studies reported contradictory diversity responses. We identify the duration of the study as an influential parameter that determines the outcome of experimentation. Our analysis reconciles the existing globally distributed experiments on fungal community responses to elevated CO2 and provides a framework for comparing results of future CO2 enrichment studies.
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Affiliation(s)
- Stavros D Veresoglou
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany.
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Natalia M F de Sousa
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Stefan Hempel
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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Burke DJ. Effects of annual and interannual environmental variability on soil fungi associated with an old-growth, temperate hardwood forest. FEMS Microbiol Ecol 2015; 91:fiv053. [PMID: 25979478 DOI: 10.1093/femsec/fiv053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2015] [Indexed: 11/14/2022] Open
Abstract
Seasonal and interannual variability in temperature, precipitation and chemical resources may regulate fungal community structure in forests but the effect of such variability is still poorly understood. In this study, I examined changes in fungal communities over two years and how these changes were correlated to natural variation in soil conditions. Soil cores were collected every month for three years from permanent plots established in an old-growth hardwood forest, and molecular methods were used to detect fungal species. Species richness and diversity were not consistent between years with richness and diversity significantly affected by season in one year but significantly affected by depth in the other year. These differences were associated with variation in late winter snow cover. Fungal communities significantly varied by plot location, season and depth and differences were consistent between years but fungal species within the community were not consistent in their seasonality or in their preference for certain soil depths. Some fungal species, however, were found to be consistently correlated with soil chemistry across sampled years. These results suggest that fungal community changes reflect the behavior of the individual species within the community pool and how those species respond to local resource availability.
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Affiliation(s)
- David J Burke
- The Holden Arboretum, 9500 Sperry Road, Kirtland, OH 44094, USA The Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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11
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Oliver AE, Newbold LK, Whiteley AS, van der Gast CJ. Marine bacterial communities are resistant to elevated carbon dioxide levels. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:574-582. [PMID: 25756110 DOI: 10.1111/1758-2229.12159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It is well established that the release of anthropogenic-derived CO2 into the atmosphere will be mainly absorbed by the oceans, with a concomitant drop in pH, a process termed ocean acidification. As such, there is considerable interest in how changes in increased CO2 and lower pH will affect marine biota, such as bacteria, which play central roles in oceanic biogeochemical processes. Set within an ecological framework, we investigated the direct effects of elevated CO2, contrasted with ambient conditions on the resistance and resilience of marine bacterial communities in a replicated temporal seawater mesocosm experiment. The results of the study strongly indicate that marine bacterial communities are highly resistant to the elevated CO2 and lower pH conditions imposed, as demonstrated from measures of turnover using taxa–time relationships and distance–decay relationships. In addition, no significant differences in community abundance, structure or composition were observed. Our results suggest that there are no direct effects on marine bacterial communities and that the bacterial fraction of microbial plankton holds enough flexibility and evolutionary capacity to withstand predicted future changes from elevated CO2 and subsequent ocean acidification.
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12
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Terminal RFLP analysis to determine the oral microbiota with hyposalivation. Arch Microbiol 2014; 196:489-96. [DOI: 10.1007/s00203-014-0987-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/15/2014] [Indexed: 11/30/2022]
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13
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Hungate BA, Dijkstra P, Wu Z, Duval BD, Day FP, Johnson DW, Megonigal JP, Brown ALP, Garland JL. Cumulative response of ecosystem carbon and nitrogen stocks to chronic CO₂ exposure in a subtropical oak woodland. THE NEW PHYTOLOGIST 2013; 200:753-766. [PMID: 23718224 PMCID: PMC4282374 DOI: 10.1111/nph.12333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/10/2013] [Indexed: 05/05/2023]
Abstract
Rising atmospheric carbon dioxide (CO₂) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11 yr of exposure to elevated CO₂. We used open-top chambers to manipulate CO₂ during regrowth after fire, and measured C, N and tracer (15) N in ecosystem components throughout the experiment. Elevated CO₂ increased plant C and tended to increase plant N but did not significantly increase whole-system C or N. Elevated CO₂ increased soil microbial activity and labile soil C, but more slowly cycling soil C pools tended to decline. Recovery of a long-term (15) N tracer indicated that CO₂ exposure increased N losses and altered N distribution, with no effect on N inputs. Increased plant C accrual was accompanied by higher soil microbial activity and increased C losses from soil, yielding no statistically detectable effect of elevated CO₂ on net ecosystem C uptake. These findings challenge the treatment of terrestrial ecosystems responses to elevated CO₂ in current biogeochemical models, where the effect of elevated CO₂ on ecosystem C balance is described as enhanced photosynthesis and plant growth with decomposition as a first-order response.
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Affiliation(s)
- Bruce A Hungate
- Department of Biological Sciences and The Center for Ecosystem Science and Society, Northern Arizona UniversityFlagstaff, AZ, 86011, USA
| | - Paul Dijkstra
- Department of Biological Sciences and The Center for Ecosystem Science and Society, Northern Arizona UniversityFlagstaff, AZ, 86011, USA
| | - Zhuoting Wu
- Department of Biological Sciences and The Center for Ecosystem Science and Society, Northern Arizona UniversityFlagstaff, AZ, 86011, USA
- US Geological SurveyFlagstaff, AZ, 86001, USA
| | - Benjamin D Duval
- Department of Biological Sciences and The Center for Ecosystem Science and Society, Northern Arizona UniversityFlagstaff, AZ, 86011, USA
- US Dairy Forage Research Center, USDA-ARSMadison, WI, 53706, USA
| | - Frank P Day
- Department of Biological Sciences, Old Dominion UniversityNorfolk, VA, 23529, USA
| | - Dale W Johnson
- Department of Natural Resources and Environmental Science, University of NevadaReno, NV, 89557, USA
| | | | - Alisha L P Brown
- Department of Biological Sciences, Old Dominion UniversityNorfolk, VA, 23529, USA
| | - Jay L Garland
- Environmental Protection Agency, Microbiological and Chemical Exposure Assessment Research DivisionCincinnati, OH, 45268, USA
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Day FP, Schroeder RE, Stover DB, Brown ALP, Butnor JR, Dilustro J, Hungate BA, Dijkstra P, Duval BD, Seiler TJ, Drake BG, Hinkle CR. The effects of 11 yr of CO₂ enrichment on roots in a Florida scrub-oak ecosystem. THE NEW PHYTOLOGIST 2013; 200:778-787. [PMID: 23528147 DOI: 10.1111/nph.12246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/19/2013] [Indexed: 06/02/2023]
Abstract
Uncertainty surrounds belowground plant responses to rising atmospheric CO₂ because roots are difficult to measure, requiring frequent monitoring as a result of fine root dynamics and long-term monitoring as a result of sensitivity to resource availability. We report belowground plant responses of a scrub-oak ecosystem in Florida exposed to 11 yr of elevated atmospheric CO₂ using open-top chambers. We measured fine root production, turnover and biomass using minirhizotrons, coarse root biomass using ground-penetrating radar and total root biomass using soil cores. Total root biomass was greater in elevated than in ambient plots, and the absolute difference was larger than the difference aboveground. Fine root biomass fluctuated by more than a factor of two, with no unidirectional temporal trend, whereas leaf biomass accumulated monotonically. Strong increases in fine root biomass with elevated CO₂ occurred after fire and hurricane disturbance. Leaf biomass also exhibited stronger responses following hurricanes. Responses after fire and hurricanes suggest that disturbance promotes the growth responses of plants to elevated CO₂. Increased resource availability associated with disturbance (nutrients, water, space) may facilitate greater responses of roots to elevated CO₂. The disappearance of responses in fine roots suggests limits on the capacity of root systems to respond to CO₂ enrichment.
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Affiliation(s)
- Frank P Day
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - Rachel E Schroeder
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - Daniel B Stover
- Office of Biological and Environmental Research, US Department of Energy, Washington, DC, 20585, USA
| | - Alisha L P Brown
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - John R Butnor
- Southern Research Station, USDA Forest Service, Burlington, VT, 05405, USA
| | - John Dilustro
- Department of Biology, Chowan University, Murfreesboro, NC, 27855, USA
| | - Bruce A Hungate
- Department of Biological Sciences and the Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Paul Dijkstra
- Department of Biological Sciences and the Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Benjamin D Duval
- Global Change Solutions, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Bert G Drake
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - C Ross Hinkle
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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16
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Hayden HL, Mele PM, Bougoure DS, Allan CY, Norng S, Piceno YM, Brodie EL, Desantis TZ, Andersen GL, Williams AL, Hovenden MJ. Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil. Environ Microbiol 2012; 14:3081-96. [PMID: 23039205 DOI: 10.1111/j.1462-2920.2012.02855.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 07/22/2012] [Indexed: 11/28/2022]
Abstract
The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([CO2]) (ambient, +550 ppm) and temperatures (ambient, + 2°C) under different plant functional types (C3 and C4 grasses) and at two soil depths (0-5 cm and 5-10 cm). Archaeal community diversity was influenced by elevated [CO2], while under warming archaeal 16S rRNA gene copy numbers increased for C4 plant Themeda triandra and decreased for the C3 plant community (P < 0.05). Fungal community diversity resulted in three groups based upon elevated [CO2], elevated [CO2] plus warming and ambient [CO2]. Overall bacterial community diversity was influenced primarily by depth. Specific bacterial taxa changed in richness and relative abundance in response to climate change factors when assessed by a high-resolution 16S rRNA microarray (PhyloChip). Operational taxonomic unit signal intensities increased under elevated [CO2] for both Firmicutes and Bacteroidetes, and increased under warming for Actinobacteria and Alphaproteobacteria. For the interaction of elevated [CO2] and warming there were 103 significant operational taxonomic units (P < 0.01) representing 15 phyla and 30 classes. The majority of these operational taxonomic units increased in abundance for elevated [CO2] plus warming plots, while abundance declined in warmed or elevated [CO2] plots. Bacterial abundance (16S rRNA gene copy number) was significantly different for the interaction of elevated [CO2] and depth (P < 0.05) with decreased abundance under elevated [CO2] at 5-10 cm, and for Firmicutes under elevated [CO2] (P < 0.05). Bacteria, archaea and fungi in soil responded differently to elevated [CO2], warming and their interaction. Taxa identified as significantly climate-responsive could show differing trends in the direction of response ('+' or '-') under elevated CO2 or warming, which could then not be used to predict their interactive effects supporting the need to investigate interactive effects for climate change. The approach of focusing on specific taxonomic groups provides greater potential for understanding complex microbial community changes in ecosystems under climate change.
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Affiliation(s)
- Helen L Hayden
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, Bundoora, Victoria, 3083, Australia.
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Anderson IC, Drigo B, Keniry K, Ghannoum O, Chambers SM, Tissue DT, Cairney JW. Interactive effects of preindustrial, current and future atmospheric CO2concentrations and temperature on soil fungi associated with twoEucalyptusspecies. FEMS Microbiol Ecol 2012; 83:425-37. [DOI: 10.1111/1574-6941.12001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/07/2012] [Accepted: 08/27/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Ian C. Anderson
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
| | - Barbara Drigo
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
| | - Kerry Keniry
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
| | - Susan M. Chambers
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
| | - David T. Tissue
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
| | - John W.G. Cairney
- Hawkesbury Institute for the Environment, University of Western Sydney; Penrith; NSW; Australia
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Quantification of ectomycorrhizal mycelium in soil by real-time PCR compared to conventional quantification techniques. FEMS Microbiol Ecol 2012; 45:283-92. [PMID: 19719597 DOI: 10.1016/s0168-6496(03)00163-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mycelial biomass estimates in soils are usually obtained by measuring total hyphal length or by measuring the amount of fungal-specific biomarkers such as ergosterol and phospholipid fatty acids (PLFAs). These methods determine the biomass of the fungal community as a whole and do not allow species-specific identification. Molecular methods based on the extraction of total soil DNA and the use of genes as biomarkers enable identification of mycelia directly from the environment. Three molecular techniques were compared to determine the most reliable method for determining the biomass of individual fungal species in soil. The growth of extramatrical mycelium of two ectomycorrhizal (EM) fungal species (Suillus bovinus and Paxillus involutus) in soil was monitored by denaturing gradient gel electrophoresis, a cloning technique and real-time quantitative polymerase chain reaction, and the results were compared with those obtained with hyphal length determination and PLFA analysis. The molecular methods enabled identification and relative quantification of both species separately in an environment with several fungal species present and showed consistent results. Amounts of target DNA per gram soil were used to quantitatively compare soil samples. Increasing amounts of S. bovinus DNA and decreasing amounts of P. involutus DNA were detected over time in an environment containing a more complex community. This work demonstrates that molecular methods provide tools to determine the biomass of individual fungal species in soil.
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Lott M, Eldridge M, Hose G, Power M. Nematode community structure in the brush-tailed rock-wallaby, Petrogale penicillata: Implications of captive breeding and the translocation of wildlife. Exp Parasitol 2012; 132:185-92. [DOI: 10.1016/j.exppara.2012.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 06/26/2012] [Accepted: 06/27/2012] [Indexed: 11/29/2022]
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Sistla SA, Schimel JP. Stoichiometric flexibility as a regulator of carbon and nutrient cycling in terrestrial ecosystems under change. THE NEW PHYTOLOGIST 2012; 196:68-78. [PMID: 22924404 DOI: 10.1111/j.1469-8137.2012.04234.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ecosystems across the biosphere are subject to rapid changes in elemental balance and climatic regimes. A major force structuring ecological responses to these perturbations lies in the stoichiometric flexibility of systems - the ability to adjust their elemental balance whilst maintaining function. The potential for stoichiometric flexibility underscores the utility of the application of a framework highlighting the constraints and consequences of elemental mass balance and energy cycling in biological systems to address global change phenomena. Improvement in the modeling of ecological responses to disturbance requires the consideration of the stoichiometric flexibility of systems within and across relevant scales. Although a multitude of global change studies over various spatial and temporal scales exist, the explicit consideration of the role played by stoichiometric flexibility in linking micro-scale to macro-scale biogeochemical processes in terrestrial ecosystems remains relatively unexplored. Focusing on terrestrial systems under change, we discuss the mechanisms by which stoichiometric flexibility might be expressed and connected from organisms to ecosystems. We suggest that the transition from the expression of stoichiometric flexibility within individuals to the community and ecosystem scales is a key mechanism regulating the extent to which environmental perturbation may alter ecosystem carbon and nutrient cycling dynamics.
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Affiliation(s)
- Seeta A Sistla
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93108, USA
| | - Joshua P Schimel
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93108, USA
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21
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Elevated CO2 impacts ectomycorrhiza-mediated forest soil carbon flow: fungal biomass production, respiration and exudation. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Das S, Bhattacharyya P, Adhya TK. Interaction effects of elevated CO₂ and temperature on microbial biomass and enzyme activities in tropical rice soils. ENVIRONMENTAL MONITORING AND ASSESSMENT 2011; 182:555-569. [PMID: 21340550 DOI: 10.1007/s10661-011-1897-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 01/27/2011] [Indexed: 05/30/2023]
Abstract
The impacts of elevated CO(2) and temperature on microbial biomass and soil enzyme activities in four physicochemically different types of tropical rice soils (Aeric Endoaquept, Aeric Tropoaquept, Ultic Haplustalf and Udic Rhodostalf) were investigated in a laboratory incubation study. Soil samples were incubated under 400, 500 and 600 μmol mol(-1) CO(2) concentration at 25°C, 35°C and 45°C for 2 months. Elevated CO(2) significantly increased the mean microbial biomass carbon (MBC) content, across the soils, over control by 6.2%, 38.0% and 49.2% at 400, 500 and 600 μmol mol(-1) CO(2) concentration, respectively. Soil enzyme activities (fluorescein diacetate hydrolase, dehydrogenase, β-glucosidase, urease, alkaline and acid phosphatases) also increased significantly ranging from 1.3% (urease) to 53.2% (alkaline phosphatase) under high CO(2) in the soils studied. Both MBC and soil enzyme activities were further stimulated at high temperatures suggesting elevated CO(2) and high temperature interaction accelerated the general turnover of the organic C fractions of the soil and through increase in microbially mediated processes.
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Affiliation(s)
- Suvendu Das
- Division of Crop Production, Central Rice Research Institute, Cuttack, 753006, Orissa, India.
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NEWBOUND MARK, BENNETT LAURENT, TIBBITS JOSQUIN, KASEL SABINE. Soil chemical properties, rather than landscape context, influence woodland fungal communities along an urban-rural gradient. AUSTRAL ECOL 2011. [DOI: 10.1111/j.1442-9993.2011.02269.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Nelson DM, Cann IKO, Mackie RI. Response of archaeal communities in the rhizosphere of maize and soybean to elevated atmospheric CO2 concentrations. PLoS One 2010; 5:e15897. [PMID: 21209969 PMCID: PMC3012111 DOI: 10.1371/journal.pone.0015897] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 11/29/2010] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Archaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO(2)]) will influence the structure and function of soil archaeal communities. METHODOLOGY/PRINCIPAL FINDINGS We measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (∼385 ppm) and elevated (550 ppm) [CO(2)] in a replicated and field-based study. There was no influence of elevated [CO(2)] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C(4) plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C(3) plant, at elevated [CO(2)], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO(2)] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO(2)] for soybean. CONCLUSION Plant-driven shifts in soil biogeochemical processes in response to elevated [CO(2)] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO(2)] in the absence of drought.
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Affiliation(s)
- David M Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland, United States of America.
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25
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Mohamed DJ, Martiny JBH. Patterns of fungal diversity and composition along a salinity gradient. ISME JOURNAL 2010; 5:379-88. [PMID: 20882058 DOI: 10.1038/ismej.2010.137] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes--a salt, brackish and freshwater marsh--in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution.
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Affiliation(s)
- Devon J Mohamed
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
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The spatial factor, rather than elevated CO₂, controls the soil bacterial community in a temperate Forest Ecosystem. Appl Environ Microbiol 2010; 76:7429-36. [PMID: 20851972 DOI: 10.1128/aem.00831-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The global atmospheric carbon dioxide (CO₂) concentration is expected to increase continuously over the next century. However, little is known about the responses of soil bacterial communities to elevated CO₂ in terrestrial ecosystems. This study aimed to partition the relative influences of CO₂, nitrogen (N), and the spatial factor (different sampling plots) on soil bacterial communities at the free-air CO₂ enrichment research site in Duke Forest, North Carolina, by two independent techniques: an entirely sequencing-based approach and denaturing gradient gel electrophoresis. Multivariate regression tree analysis demonstrated that the spatial factor could explain more than 70% of the variation in soil bacterial diversity and 20% of the variation in community structure, while CO₂ or N treatment explains less than 3% of the variation. For the effects of soil environmental heterogeneity, the diversity estimates were distinguished mainly by the total soil N and C/N ratio. Bacterial diversity estimates were positively correlated with total soil N and negatively correlated with C/N ratio. There was no correlation between the overall bacterial community structures and the soil properties investigated. This study contributes to the information about the effects of elevated CO₂ and soil fertility on soil bacterial communities and the environmental factors shaping the distribution patterns of bacterial community diversity and structure in temperate forest soils.
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Edel-Hermann V, Dreumont C, Pérez-Piqueres A, Steinberg C. Terminal restriction fragment length polymorphism analysis of ribosomal RNA genes to assess changes in fungal community structure in soils. FEMS Microbiol Ecol 2009; 47:397-404. [PMID: 19712328 DOI: 10.1016/s0168-6496(04)00002-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Monitoring the structure and dynamics of fungal communities in soils under agricultural and environmental disturbances is currently a challenge. In this study, a terminal restriction fragment length polymorphism (T-RFLP) fingerprinting method was developed for the rapid comparison of fungal community structures. The terminal restriction fragment polymorphism of different regions of the small-subunit (SSU) ribosomal RNA (rRNA) gene was simulated by sequence comparison using 10 restriction enzymes, and analyzed among three different soils using fungal-specific primers. Polymerase chain reaction amplification of the 3' end of the SSU rRNA gene with the primer nu-SSU-0817-5' and with the fluorescently labelled primer nu-SSU-1536-3', and digestion of the amplicons with AluI and MboI were found to be optimal and were used in a standardized T-RFLP procedure. Both the number and the intensity of terminal restriction fragments detected by capillary gel electrophoresis were integrated in correspondence analyses. Three soils with contrasting physicochemical properties were differentiated according to the structure of their fungal communities. Assessment of the impact on the fungal community structure of the amendment of two soils with compost or manure confirmed the reproducibility and the sensitivity of the method. Shifts in the community structure were detected between non-amended and amended soil samples. In both soils, the shift differed with the organic amendment applied. In addition, the fungal community structures of the two soils were affected in a different way by the same organic amendment. The fingerprinting method provides a rapid tool to investigate the effect of various perturbations on the fungal communities in soils.
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28
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Lim M, Adams JDW, Wilcox M, Finan P, Sagar P, Burke D. An assessment of bacterial dysbiosis in pouchitis using terminal restriction fragment length polymorphisms of 16S ribosomal DNA from pouch effluent microbiota. Dis Colon Rectum 2009; 52:1492-500. [PMID: 19617766 DOI: 10.1007/dcr.0b013e3181a7b77a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE Previous studies on dysbiosis and pouchitis using conventional culture techniques have been disappointing because of inherent limitations associated with the technique. This study was designed to use terminal restriction fragment length polymorphism to evaluate patients with and without pouchitis. METHODS Bacterial microbiota in 20 pouch patients (15 healthy and 5 with inflamed) were studied. DNA was extracted from feces, and polymerase chain reaction was performed using primers (V6-V8 region) that were modified at the 5' end with cyanine dyes. Amplicons were digested with merozoite surface protein-1 enzyme. The restricted fragments were analyzed by capillary electrophoresis, and the electrophenograms were studied. Electrophenograms provide information about operational taxonomic units, which correspond to specific organisms. Principal component analysis was performed to identify dominant and important operational taxonomic units in the 20 patients. Bacterial diversity and counts of these operational taxonomic units were compared in the two groups of patients. RESULTS Total bacterial diversity in patients with pouchitis was similar to that in patients with healthy pouches (16 (11-20) vs. 12 (9-13), P = 0.279). Using principal component analysis, 29 operational taxonomic units were found to be important. Bacterial counts of seven dominant organisms (operational taxonomic unit 79 (enterococci), 85 (Pantoea), 88 (Enterobacteriaceae), 90 (eubacteria), 91 (Pseudomonas), 146 (clostridia), and 148 (bacilli)) were similar in patients with pouchitis and those with a healthy pouch (P > 0.05). Seventeen (operational taxonomic unit 73 (Leptospira), 93 (Pseudoalteromonas), 96, 100 (Desulfosporosinus), 114, 121, 134, 137, 141 (Microcystis), 159, 174 (Methylobacter), 193 (uncultured proteobacteria), 232, 376, 381, 414, and 465) of the remaining 22 nondominant organisms were seen exclusively in patients with pouchitis. The majority of these organisms were novel. CONCLUSION Terminal restriction fragment length polymorphism can be used to identify candidate organisms that may be associated with pouchitis.
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Affiliation(s)
- Michael Lim
- John Goligher Colorectal Unit, The General Infirmary at Leeds, Leeds, United Kingdom
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29
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Comparison of molecular fingerprinting methods for analysis of soil microbial community structure. Ecol Res 2009. [DOI: 10.1007/s11284-009-0602-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Characterization of fungal soil communities by F-RISA and arbuscular mycorrhizal fungi fromAraucaria angustifolia forest soils after replanting and wildfire disturbances. Symbiosis 2009. [DOI: 10.1007/bf03179995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Haase S, Rothe A, Kania A, Wasaki J, Römheld V, Engels C, Kandeler E, Neumann G. Responses to iron limitation in Hordeum vulgare L. as affected by the atmospheric CO2 concentration. JOURNAL OF ENVIRONMENTAL QUALITY 2008; 37:1254-1262. [PMID: 18453445 DOI: 10.2134/jeq2006.0136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Elevated atmospheric CO2 treatments stimulated biomass production in Fe-sufficient and Fe-deficient barley plants, both in hydroponics and in soil culture. Root/shoot biomass ratio was increased in severely Fe-deficient plants grown in hydroponics but not under moderate Fe limitation in soil culture. Significantly increased biomass production in high CO2 treatments, even under severe Fe deficiency in hydroponic culture, indicates an improved internal Fe utilization. Iron deficiency-induced secretion of PS in 0.5 to 2.5 cm sub-apical root zones was increased by 74% in response to elevated CO2 treatments of barley plants in hydroponics but no PS were detectable in root exudates collected from soil-grown plants. This may be attributed to suppression of PS release by internal Fe concentrations above the critical level for Fe deficiency, determined at final harvest for soil-grown barley plants, even without additional Fe supply. However, extremely low concentrations of easily plant-available Fe in the investigated soil and low Fe seed reserves suggest a contribution of PS-mediated Fe mobilization from sparingly soluble Fe sources to Fe acquisition of the soil-grown barley plants during the preceding culture period. Higher Fe contents in shoots (+52%) of plants grown in soil culture without Fe supply under elevated atmospheric CO2 concentrations may indicate an increased efficiency for Fe acquisition. No significant influence on diversity and function of rhizosphere-bacterial communities was detectable in the outer rhizosphere soil (0-3 mm distance from the root surface) by DGGE of 16S rRNA gene fragments and analysis of marker enzyme activities for C-, N-, and P-cycles.
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Affiliation(s)
- S Haase
- Inst. of Soil Science, Univ. of Hohenheim, 70599 Stuttgart, Germany
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The effect of experimental warming on the root-associated fungal community of Salix arctica. ISME JOURNAL 2007; 2:105-14. [DOI: 10.1038/ismej.2007.89] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zinger L, Gury J, Alibeu O, Rioux D, Gielly L, Sage L, Pompanon F, Geremia RA. CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies. J Microbiol Methods 2007; 72:42-53. [PMID: 18054096 DOI: 10.1016/j.mimet.2007.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 10/12/2007] [Accepted: 10/12/2007] [Indexed: 11/18/2022]
Abstract
Fungal communities are key components of soil, but the study of their ecological significance is limited by a lack of appropriated methods. For instance, the assessment of fungi occurrence and spatio-temporal variation in soil requires the analysis of a large number of samples. The molecular signature methods provide a useful tool to monitor these microbial communities and can be easily adapted to capillary electrophoresis (CE) allowing high-throughput studies. Here we assess the suitability of CE-FLA (Fragment Length Polymorphism, denaturing conditions) and CE-SSCP (Single-Stranded Conformation Polymorphism, native conditions) applied to environmental studies since they require a short molecular marker and no post-PCR treatments. We amplified the ITS1 region from 22 fungal strains isolated from an alpine ecosystem and from total genomic DNA of alpine and infiltration basin soils. The CE-FLA and CE-SSCP separated 17 and 15 peaks respectively from a mixture of 19 strains. For the alpine soil-metagenomic DNA, the FLA displayed more peaks than the SSCP and the converse result was found for infiltration basin sediments. We concluded that CE-FLA and CE-SSCP of ITS1 region provided complementary information. In order to improve CE-SSCP sensitivity, we tested its resolution according to migration temperature and found 32 degrees C to be optimal. Because of their simplicity, quickness and reproducibility, we found that these two methods were promising for high-throughput studies of soil fungal communities.
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Affiliation(s)
- Lucie Zinger
- Laboratoire d'Ecologie Alpine UMR 5553 UJF/CNRS, Grenoble Cedex 9, France
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Nocker A, Lepo JE, Martin LL, Snyder RA. Genotypic microbial community profiling: a critical technical review. MICROBIAL ECOLOGY 2007; 54:532-42. [PMID: 17351811 DOI: 10.1007/s00248-007-9236-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 10/23/2006] [Accepted: 11/23/2006] [Indexed: 05/04/2023]
Abstract
Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
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Affiliation(s)
- Andreas Nocker
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514, USA
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Nocker A, Burr M, Camper AK. Genotypic microbial community profiling: a critical technical review. MICROBIAL ECOLOGY 2007; 54:276-89. [PMID: 17345133 DOI: 10.1007/s00248-006-9199-5] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 11/27/2006] [Accepted: 12/12/2006] [Indexed: 05/14/2023]
Abstract
Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
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Affiliation(s)
- Andreas Nocker
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980, USA.
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36
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Manter DK, Vivanco JM. Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J Microbiol Methods 2007; 71:7-14. [PMID: 17683818 DOI: 10.1016/j.mimet.2007.06.016] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 06/25/2007] [Accepted: 06/25/2007] [Indexed: 11/28/2022]
Abstract
Molecular-based approaches to assess microbial biomass and diversity from soil and other ecosystems are rapidly becoming the standard methodology for analysis. While these techniques are advantageous, because they do not rely on the need to culture organisms, each technique may have its own biases and/or limitations when used to assess fungal diversity from mixed-template samples. In this study, we analyzed PCR specificity and efficiency of the ITS primers (ITS1F and ITS4) in a series of single- and mixed-template samples using a combined quantitative PCR-length heterogeneity analysis (LH-qPCR) approach. As expected, these primers successfully amplified all higher fungal species tested (10 ascomycetes, 6 basidiomycetes, and 4 zygomycetes) and no members of the oomycetes. Based on our results, and a search of the GenBank database, amplicons of the ITS1F and ITS4 primer set exhibit considerable variability (420 to 825 bp), but due to similarities in amplicon sizes of some fungal species, actual species diversity in environmental samples may be underestimated approximately two-fold. The addition of an initial qPCR step allowed for the accurate quantitation of total fungal DNA in mixed-template samples over five orders of magnitude (10(-)(1) to 10(3) pg microl(-)(1)). PCR biases between individuals in mixed-templates rendered it impossible to determine the absolute quantity of any individual within a population from its individual peak height. However, relative changes in individuals within a mixed-template sample could be determined due to a constant proportionality between peak heights and starting template concentration. Variability associated with the individual steps of the LH-qPCR analysis was also determined from environmental samples.
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Affiliation(s)
- Daniel K Manter
- USDA-ARS, Soil-Plant-Nutrient Research Unit, Ft. Collins, CO, United States.
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Abstract
Ectomycorrhizal (ECM) fungi form mutualistic symbioses with many tree species and are regarded as key organisms in nutrient and carbon cycles in forest ecosystems. Our appreciation of their roles in these processes is hampered by a lack of understanding of their soil-borne mycelial systems. These mycelia represent the vegetative thalli of ECM fungi that link carbon-yielding tree roots with soil nutrients, yet we remain largely ignorant of their distribution, dynamics and activities in forest soils. In this review we consider information derived from investigations of fruiting bodies, ECM root tips and laboratory-based microcosm studies, and conclude that these provide only limited insights into soil-borne ECM mycelial communities. Recent advances in understanding soil-borne mycelia of ECM fungi have arisen from the combined use of molecular technologies and novel field experimentation. These approaches have the potential to provide unprecedented insights into the functioning of ECM mycelia at the ecosystem level, particularly in the context of land-use changes and global climate change.
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Dickie IA, FitzJohn RG. Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review. MYCORRHIZA 2007; 17:259-270. [PMID: 17429700 DOI: 10.1007/s00572-007-0129-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2007] [Accepted: 03/23/2007] [Indexed: 05/13/2023]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) is an increasingly widely used technique in mycorrhizal ecology. In this paper, we review the technique as it is used to identify species of mycorrhizal fungi and distinguish two different versions of the technique: peak-profile T-RFLP (the original version) and database T-RFLP. We define database T-RFLP as the use of T-RFLP to identify individual species within samples by comparison of unknown data with a database of known T-RFLP patterns. This application of T-RFLP avoids some of the pitfalls of peak-profile T-RFLP and allows T-RFLP to be applied to polyphyletic functional groups such as ectomycorrhizal fungi. The identification of species using database T-RFLP is subject to several sources of potential error, including (1) random erroneous matches of peaks to species, (2) shared T-RFLP profiles across species, and (3) multiple T-RFLP profiles within a species. A mathematical approximation of the risk of the first type of error as a function of experimental parameters is discussed. Although potentially less accurate than some other methods such as clone libraries, the high throughput of database T-RFLP permits much greater replication and may, therefore, be preferable for many ecological questions, particularly when combined with other techniques such as cloning.
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Affiliation(s)
- I A Dickie
- Landcare Research, P.O. Box 40, Lincoln, 7640, New Zealand.
| | - R G FitzJohn
- Landcare Research, P.O. Box 40, Lincoln, 7640, New Zealand
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Anderson IC, Bastias BA, Genney DR, Parkin PI, Cairney JWG. Basidiomycete fungal communities in Australian sclerophyll forest soil are altered by repeated prescribed burning. ACTA ACUST UNITED AC 2007; 111:482-6. [PMID: 17512711 DOI: 10.1016/j.mycres.2007.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 01/08/2007] [Accepted: 02/09/2007] [Indexed: 11/27/2022]
Abstract
Soil basidiomycetes play key roles in forest nutrient and carbon cycling processes, yet the diversity and structure of below ground basidiomycete communities remain poorly understood. Prescribed burning is a commonly used forest management practice and there is evidence that single fire events can have an impact on soil fungal communities but little is known about the effects of repeated prescribed burning. We have used internal transcribed spacer (ITS) terminal restriction fragment length polymorphism (T-RFLP) analysis to investigate the impacts of repeated prescribed burning every two or four years over a period of 30 years on soil basidiomycete communities in an Australian wet sclerophyll forest. Detrended correspondence analysis of ITS T-RFLP profiles separated basidiomycete communities in unburned control plots from those in burned plots, with those burned every two years being the most different from controls. Burning had no effect on basidiomycete species richness, thus these differences appear to be due to changes in community structure. Basidiomycete communities in the unburned control plots were vertically stratified in the upper 20 cm of soil, but no evidence was found for stratification in the burned plots, suggesting that repeated prescribed burning results in more uniform basidiomycete communities. Overall, the results demonstrate that repeated prescribed burning alters soil basidiomycete communities, with the effect being greater with more frequent burning.
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Affiliation(s)
- Ian C Anderson
- The Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, UK.
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40
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Carney KM, Hungate BA, Drake BG, Megonigal JP. Altered soil microbial community at elevated CO(2) leads to loss of soil carbon. Proc Natl Acad Sci U S A 2007; 104:4990-5. [PMID: 17360374 PMCID: PMC1820881 DOI: 10.1073/pnas.0610045104] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Indexed: 11/18/2022] Open
Abstract
Increased carbon storage in ecosystems due to elevated CO(2) may help stabilize atmospheric CO(2) concentrations and slow global warming. Many field studies have found that elevated CO(2) leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO(2) doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting approximately 52% of the additional carbon that had accumulated at elevated CO(2) in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO(2) had higher relative abundances of fungi and higher activities of a soil carbon-degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO(2). The isotopic composition of microbial fatty acids confirmed that elevated CO(2) increased microbial utilization of soil organic matter. These results show how elevated CO(2), by altering soil microbial communities, can cause a potential carbon sink to become a carbon source.
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Affiliation(s)
- Karen M. Carney
- *Smithsonian Environmental Research Center, P.O. Box 28, Edgewater, MD 21037; and
| | - Bruce A. Hungate
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, P.O. Box 5640, Flagstaff, AZ 86011
| | - Bert G. Drake
- *Smithsonian Environmental Research Center, P.O. Box 28, Edgewater, MD 21037; and
| | - J. Patrick Megonigal
- *Smithsonian Environmental Research Center, P.O. Box 28, Edgewater, MD 21037; and
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41
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Zepp RG, Erickson DJ, Paul ND, Sulzberger B. Interactive effects of solar UV radiation and climate change on biogeochemical cycling. Photochem Photobiol Sci 2007; 6:286-300. [PMID: 17344963 DOI: 10.1039/b700021a] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This report assesses research on the interactions of UV radiation (280-400 nm) and global climate change with global biogeochemical cycles at the Earth's surface. The effects of UV-B (280-315 nm), which are dependent on the stratospheric ozone layer, on biogeochemical cycles are often linked to concurrent exposure to UV-A radiation (315-400 nm), which is influenced by global climate change. These interactions involving UV radiation (the combination of UV-B and UV-A) are central to the prediction and evaluation of future Earth environmental conditions. There is increasing evidence that elevated UV-B radiation has significant effects on the terrestrial biosphere with implications for the cycling of carbon, nitrogen and other elements. The cycling of carbon and inorganic nutrients such as nitrogen can be affected by UV-B-mediated changes in communities of soil organisms, probably due to the effects of UV-B radiation on plant root exudation and/or the chemistry of dead plant material falling to the soil. In arid environments direct photodegradation can play a major role in the decay of plant litter, and UV-B radiation is responsible for a significant part of this photodegradation. UV-B radiation strongly influences aquatic carbon, nitrogen, sulfur and metals cycling that affect a wide range of life processes. UV-B radiation changes the biological availability of dissolved organic matter to microorganisms, and accelerates its transformation into dissolved inorganic carbon and nitrogen, including carbon dioxide and ammonium. The coloured part of dissolved organic matter (CDOM) controls the penetration of UV radiation into water bodies, but CDOM is also photodegraded by solar UV radiation. Changes in CDOM influence the penetration of UV radiation into water bodies with major consequences for aquatic biogeochemical processes. Changes in aquatic primary productivity and decomposition due to climate-related changes in circulation and nutrient supply occur concurrently with exposure to increased UV-B radiation, and have synergistic effects on the penetration of light into aquatic ecosystems. Future changes in climate will enhance stratification of lakes and the ocean, which will intensify photodegradation of CDOM by UV radiation. The resultant increase in the transparency of water bodies may increase UV-B effects on aquatic biogeochemistry in the surface layer. Changing solar UV radiation and climate also interact to influence exchanges of trace gases, such as halocarbons (e.g., methyl bromide) which influence ozone depletion, and sulfur gases (e.g., dimethylsulfide) that oxidize to produce sulfate aerosols that cool the marine atmosphere. UV radiation affects the biological availability of iron, copper and other trace metals in aquatic environments thus potentially affecting metal toxicity and the growth of phytoplankton and other microorganisms that are involved in carbon and nitrogen cycling. Future changes in ecosystem distribution due to alterations in the physical and chemical climate interact with ozone-modulated changes in UV-B radiation. These interactions between the effects of climate change and UV-B radiation on biogeochemical cycles in terrestrial and aquatic systems may partially offset the beneficial effects of an ozone recovery.
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Affiliation(s)
- R G Zepp
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, 960 College Station Road, Athens, Georgia 30605-2700, USA
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Schwarzenbach K, Enkerli J, Widmer F. Objective criteria to assess representativity of soil fungal community profiles. J Microbiol Methods 2007; 68:358-66. [PMID: 17084474 DOI: 10.1016/j.mimet.2006.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Revised: 09/18/2006] [Accepted: 09/18/2006] [Indexed: 11/27/2022]
Abstract
Soil fungal community structures are often highly heterogeneous even among samples taken from small field plots. Sample pooling is widely used in order to overcome this heterogeneity, however, no objective criteria have yet been defined on how to determine the number of samples to be pooled for representatively profiling a field plot. In the present study PCR/RFLP and T-RFLP analysis of fungal 18S rDNA in ten soil samples obtained from a grassland plot of 400 m(2) also revealed this known heterogeneity in fungal community structures. Based on these data a three-step approach to assess representativity of fungal community profiles was established. First, soil DNA quantities needed for robust community profiling were determined. Second, profiles of single or multiple samples were theoretically averaged to test for statistically significant clustering in order to determine the minimal number of samples to be pooled to achieve representativity. Third, DNA extracts of single or multiple samples were pooled prior to profiling in order to test for statistically significant clustering. Analyses revealed robust profiles for 50 ng soil DNA but not for 5 ng. Averaged T-RFLP profiles from five or more soil samples and experimental T-RFLP profiles from pools of seven or more samples formed one significant branch. Theoretical averaging and experimental pooling revealed that five to seven samples have to be pooled for robustly representing the field plot. Our results demonstrate that representativity of soil fungal community profiles can objectively be determined for a field plot with only little deviation between theoretical and experimental approaches. This three-step approach will be of assistance for designing sampling and pooling strategies for comparative analyses of soil fungal communities in ecological studies.
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Affiliation(s)
- Kaspar Schwarzenbach
- Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
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Saito A, Ikeda S, Ezura H, Minamisawa K. Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.93] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Asami Saito
- Graduate School of Life Sciences, Tohoku University
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University
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Lagomarsino A, Moscatelli MC, De Angelis P, Grego S. Labile substrates quality as the main driving force of microbial mineralization activity in a poplar plantation soil under elevated CO2 and nitrogen fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2006; 372:256-65. [PMID: 17023027 DOI: 10.1016/j.scitotenv.2006.08.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 08/16/2006] [Accepted: 08/16/2006] [Indexed: 05/12/2023]
Abstract
Soil carbon (C) long term storage is influenced by the balance among ecosystem net primary productivity (NPP), the rate of delivery of new organic matter to soil pools and the decomposition of soil organic matter (SOM). The increase of NPP under elevated CO(2) can result in a greater production and higher turnover of fine roots or root exudation and, in turn, in an increase of labile C belowground. The aim of this work was to detect if changes in labile C substrates influenced the organic C storage in soils, verifying (i) whether treatments with elevated CO(2) and N fertilization induced changes in the amount and quality of labile C pools and in microbial C immobilization and (ii) whether these changes provoked modifications in the microbial C mineralization activity, and therefore changes in soil C losses. The effect of elevated CO(2) was a significant increase in both seasons (June and October 2004), of all labile C fractions: microbial biomass C (MBC), K(2)SO(4) extractable C (ExC), and water soluble C (WSC). The C/N ratio of the microbial biomass and of the K(2)SO(4) extractable SOM presented a seasonal fluctuation showing higher values in June, whereas the elevated CO(2) increased significantly the C/N ratio of these fractions independent of the season and the N addition, indicating a lower quality of labile SOM. Microbial respiration was more than doubled in October compared to June, confirming that changes in substrate quality and nutrient availability, occurring in the plantation at the beginning and at the end of the vegetative period, influenced the microbial activity in the bulk soil. Furthermore, the microbial respiration response to N fertilization was dependent on the season, with an opposite effect between June and October. The kinetic parameters calculated according to the first-order equation C(m)=C(0)(1-e(-kt)) were unaffected by elevated CO(2) treatment, except C(0)k and MR(basal), that showed a significant reduction, ascribable to (i) a lower quality of labile pools, and (ii) a more efficient microbial biomass in the use of available substrates. The C surplus found in elevated CO(2) soils was indeed immobilized and used for microbial growth, thus excluding a priming effect mechanism of elevated CO(2) on SOM decomposition.
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Affiliation(s)
- A Lagomarsino
- Department of Agrobiology and Agrochemistry, University of Tuscia, VITERBO, Italy.
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45
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Angeloni NL, Jankowski KJ, Tuchman NC, Kelly JJ. Effects of an invasive cattail species (TyphaÃglauca) on sediment nitrogen and microbial community composition in a freshwater wetland. FEMS Microbiol Lett 2006; 263:86-92. [PMID: 16958855 DOI: 10.1111/j.1574-6968.2006.00409.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sediments from Cheboygan Marsh, a coastal freshwater wetland on Lake Huron that has been invaded by an emergent exotic plant, Typhaxglauca, were examined to assess the effects of invasion on wetland nutrient levels and sediment microbial communities. Comparison of invaded and uninvaded zones of the marsh indicated that the invaded zone showed significantly lower plant diversity, as well as significantly higher aboveground plant biomass and soil organic matter. The sediments in the invaded zone also showed dramatically higher concentrations of soluble nutrients, including greater than 10-fold higher soluble ammonium, nitrate, and phosphate, which suggests that Typhaxglauca invasion may be impacting the wetland's ability to remove nutrients. Terminal restriction fragment length polymorphism analyses revealed significant differences in the composition of total bacterial communities (based on 16S-rRNA genes) and denitrifier communities (based on nirS genes) between invaded and uninvaded zones. This shift in denitrifiers in the sediments may be ecologically significant due to the critical role that denitrifying bacteria play in removal of nitrogen by wetlands.
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Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K. Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 2006; 56:236-49. [PMID: 16629753 DOI: 10.1111/j.1574-6941.2005.00026.x] [Citation(s) in RCA: 317] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The bacterial and fungal rhizosphere communities of strawberry (Fragaria ananassa Duch.) and oilseed rape (Brassica napus L.) were analysed using molecular fingerprints. We aimed to determine to what extent the structure of different microbial groups in the rhizosphere is influenced by plant species and sampling site. Total community DNA was extracted from bulk and rhizosphere soil taken from three sites in Germany in two consecutive years. Bacterial, fungal and group-specific (Alphaproteobacteria, Betaproteobacteria and Actinobacteria) primers were used to PCR-amplify 16S rRNA and 18S rRNA gene fragments from community DNA prior to denaturing gradient gel electrophoresis (DGGE) analysis. Bacterial fingerprints of soil DNA revealed a high number of equally abundant faint bands, while rhizosphere fingerprints displayed a higher proportion of dominant bands and reduced richness, suggesting selection of bacterial populations in this environment. Plant specificity was detected in the rhizosphere by bacterial and group-specific DGGE profiles. Different bulk soil community fingerprints were revealed for each sampling site. The plant species was a determinant factor in shaping similar actinobacterial communities in the strawberry rhizosphere from different sites in both years. Higher heterogeneity of DGGE profiles within soil and rhizosphere replicates was observed for the fungi. Plant-specific composition of fungal communities in the rhizosphere could also be detected, but not in all cases. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Rostock site revealed that Streptomyces sp. and Rhizobium sp. were among the dominant ribotypes in the strawberry rhizosphere, while sequences from Arthrobacter sp. corresponded to dominant bands from oilseed rape bacterial fingerprints.
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Affiliation(s)
- Rodrigo Costa
- Federal Biological Research Centre for Agriculture and Forestry, Braunschweig, Germany
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47
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Burke DJ, Martin KJ, Rygiewicz PT, Topa MA. Relative abundance of ectomycorrhizas in a managed loblolly pine (Pinus taeda) genetics plantation as determined through terminal restriction fragment length polymorphism profiles. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-046] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We examined the relationship between relative abundance of ectomycorrhizas in soil cores determined using morphotype tip counts and terminal restriction fragment length polymorphism (TRFLP) analysis. Root tips were harvested from a total of 120 soil cores collected from six family plots in a loblolly pine ( Pinus taeda L.) genetics plantation. Tips from each soil core were morphotyped based on physical characteristics, identified through TRFLP and sequence analysis, then pooled to reconstruct the ectomycorrhizal community within that core. The identity and relative abundance of specific ectomycorrhizas in each reconstructed community was then determined using TRFLP analysis of the internal transcribed spacer of the rRNA gene. Using TRFLP, we were able to detect 34 ectomycorrhizal phylotypes colonizing roots of loblolly pine. TRFLP peak area was an accurate approximation of the relative number of tips of each ectomycorrhizal type within a soil core. Relative abundance of each ectomycorrhiza as determined by TRFLP was used to describe their distribution in the pine plantation. Although there were no differences found in ectomycorrhizal richness and evenness among the six family plots, the two fertilized plots had generally lower levels of ectomycorrhizal richness and evenness as indicated by rank abundance curves. Our results suggest that TRFLP is a useful tool for describing the occurrence and distribution of ectomycorrhizas in environmental samples.
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Affiliation(s)
- David J. Burke
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
- USEPA National Health and Environmental Effects Research Laboratory, 200 S.W. 35th Street, Corvallis, OR 97333, USA
| | - Kendall J. Martin
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
- USEPA National Health and Environmental Effects Research Laboratory, 200 S.W. 35th Street, Corvallis, OR 97333, USA
| | - Paul T. Rygiewicz
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
- USEPA National Health and Environmental Effects Research Laboratory, 200 S.W. 35th Street, Corvallis, OR 97333, USA
| | - Mary A. Topa
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
- USEPA National Health and Environmental Effects Research Laboratory, 200 S.W. 35th Street, Corvallis, OR 97333, USA
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48
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49
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Avis PG, Dickie IA, Mueller GM. A ‘dirty’ business: testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi. Mol Ecol 2006; 15:873-82. [PMID: 16499709 DOI: 10.1111/j.1365-294x.2005.02842.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Terminal restriction fragment length polymorphism (TRFLP) is an increasingly popular method in molecular ecology. However, several key limitations of this method have not been fully examined especially when used to study fungi. We investigated the impact of spore contamination, intracollection ribosomal DNA internal transcribed spacer (ITS) region variation, and conserved restriction enzyme recognition loci on the results produced by TRFLP to characterize soil fungal communities. We find that (i) the potential for nontarget structures such as spores to contribute DNA to target sample extractions is high; (ii) multiple fragments (i.e. 'extra peaks') per PCR primer-restriction enzyme combination can be detected that are caused by restriction enzyme inefficiency and intracollection ribosomal DNA ITS variation; and (iii) restriction enzyme digestion in conserved vs. variable gene regions leads to different characterizations of community diversity. Based on these results, we suggest that studies employing TRFLP need to include information from known, identified fungi from sites within which studies take place and not to rely only on TRFLP profiles as a short cut to fungal community description.
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Affiliation(s)
- Peter G Avis
- Department of Botany, The Field Museum, Chicago, IL 60605-2496, USA.
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Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural Gene Markers. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/3-540-29449-x_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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