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Tang Q, Moeskjær S, Cotton A, Dai W, Wang X, Yan X, Daniell TJ. Organic fertilization reduces nitrous oxide emission by altering nitrogen cycling microbial guilds favouring complete denitrification at soil aggregate scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174178. [PMID: 38917905 DOI: 10.1016/j.scitotenv.2024.174178] [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: 03/05/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Agricultural management practices can induce changes in soil aggregation structure that alter the microbial nitrous oxide (N2O) production and reduction processes occurring at the microscale, leading to large-scale consequences for N2O emissions. However, the mechanistic understanding of how organic fertilization affects these context-dependent small-scale N2O emissions and associated key nitrogen (N) cycling microbial communities is lacking. Here, denitrification gas (N2O, N2) and potential denitrification capacity N2O/(N2O + N2) were assessed by automated gas chromatography in different soil aggregates (>2 mm, 2-0.25 and <0.25 mm), while associated microbial communities were assessed by sequencing and qPCR of N2O-producing (nirK and nirS) and reducing (nosZ clade I and II) genes. The results indicated that organic fertilization reduced N2O emissions by enhancing the conversion of N2O to N2 in all aggregate sizes. Moreover, potential N2O production and reduction hotspots occurred in smaller soil aggregates, with the degree depending on organic fertilizer type and application rate. Further, significantly higher abundance and diversity of nosZ clades relative to nirK and nirS revealed complete denitrification promoted through selection of denitrifying communities at microscales favouring N2O reduction. Communities associated with high and low emission treatments form modules with specific sequence types which may be diagnostic of emission levels. Taken together, these findings suggest that organic fertilizers reduced N2O emissions through influencing soil factors and patterns of niche partitioning between N2O-producing and reducing communities within soil aggregates, and selection for communities that overall are more likely to consume than emit N2O. These findings are helpful in strengthening the ability to predict N2O emissions from agricultural soils under organic fertilization as well as contributing to the development of net-zero carbon strategies for sustainable agriculture.
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Affiliation(s)
- Quan Tang
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Sara Moeskjær
- Microbiology to Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Anne Cotton
- Microbiology to Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Department of Earth and Environmental Sciences, The University of Manchester, Williamson Building, Manchester M13 9PY, UK; Manchester Institute of Biotechnology, The University of Manchester, John Garside Building, 131 Princess Street, Manchester M1 7DN, UK
| | - Wenxia Dai
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Xiaozhi Wang
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Tim J Daniell
- Microbiology to Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK.
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2
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Li W, Shi R, Yuan L, Lan X, Feng D, Chen H. Effect of short-term warming and drought on the methanogenic communities in degraded peatlands in Zoige Plateau. Front Microbiol 2022; 13:880300. [PMID: 36386660 PMCID: PMC9650419 DOI: 10.3389/fmicb.2022.880300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Peatlands in Qinghai-Tibetan are degrading with climate change and human activities. Peatland degradation and climate change affect methane emissions. Methanogens are key functional microbes during methane production; however, knowledge of methanogens in degraded peatlands is lacking. Here, we investigated the effects of short-term (1 year) warming (OTC), drought (20%), and their combination on methanogens in the degraded peatlands on the Zoige Plateau of China via qPCR and clone library analysis. The results showed that Methanomicrobiales and Methanobacteriales were predominant in all the treatments. Non-metric multidimensional scaling (NMDS) and PERMANOVA analyses showed that the methanogenic community structure among the climate change treatments was not significantly different. The relative abundance of methanogen communities showed insignificant variation among the climate change treatments. The copy number and Shannon diversity of methanogens were significantly different within the climate change treatments, and drought significantly decreased the copy number of methanogens when compared to the control. The Redundancy analysis (RDA) results and correlation analysis showed that the environmental variables measured had no significant effect on methanogenic community structure and Shannon diversity. These results indicate that methanogens are insensitive to short-term climate change in degraded peatlands. This study provides insight into methane emissions from the Zoige Plateau peatlands by focusing on the possible responses of the methanogens to climate-driven changes.
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Affiliation(s)
- Wei Li
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Kunming, China
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Rui Shi
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Lingchen Yuan
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Xianli Lan
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Defeng Feng
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, China
- *Correspondence: Defeng Feng,
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Huai Chen,
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3
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Li J, Meng B, Yang X, Cui N, Zhao T, Chai H, Zhang T, Sun W. Suppression of AMF accelerates N2O emission by altering soil bacterial community and genes abundance under varied precipitation conditions in a semiarid grassland. Front Microbiol 2022; 13:961969. [PMID: 36003936 PMCID: PMC9393504 DOI: 10.3389/fmicb.2022.961969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrous oxide (N2O) is one of the most important greenhouse gases contributing to global climate warming. Recently, studies have shown that arbuscular mycorrhizal fungi (AMF) could reduce N2O emissions in terrestrial ecosystems; however, the microbial mechanisms of how AMF reduces N2O emissions under climate change are still not well understood. We tested the influence of AMF on N2O emissions by setting up a gradient of precipitation intensity (+50%, +30%, ambient (0%), −30%, −50%, and −70%) and manipulating the presence or exclusion of AMF hyphae in a semiarid grassland located in northeast China. Our results showed that N2O fluxes dramatically declined with the decrease in precipitation gradient during the peak growing season (June–August) in both 2019 and 2020. There was a significantly positive correlation between soil water content and N2O fluxes. Interestingly, N2O fluxes significantly decreased when AMF were present compared to when they were absent under all precipitation conditions. The contribution of AMF to mitigate N2O emission increased gradually with decreasing precipitation magnitudes, but no contribution in the severe drought (−70%). AMF significantly reduced the soil’s available nitrogen concentration and altered the composition of the soil bacteria community including those associated with N2O production. Hyphal length density was negatively correlated with the copy numbers of key genes for N2O production (nirK and nirS) and positively correlated with the copy numbers of key genes for N2O consumption (nosZ). Our results highlight that AMF would reduce the soil N2O emission under precipitation variability in a temperate grassland except for extreme drought.
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Affiliation(s)
- Junqin Li
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Bo Meng
- Institute of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Xuechen Yang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Nan Cui
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Tianhang Zhao
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Hua Chai
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Tao Zhang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
- *Correspondence: Tao Zhang,
| | - Wei Sun
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, China
- Wei Sun,
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Mwafulirwa L, Paterson E, Cairns JE, Daniell TJ, Thierfelder C, Baggs EM. Genotypic variation in maize (Zea mays) influences rates of soil organic matter mineralization and gross nitrification. THE NEW PHYTOLOGIST 2021; 231:2015-2028. [PMID: 34096623 DOI: 10.1111/nph.17537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Agricultural management practices that increase soil organic matter (SOM), such as no-tillage (NT) with crop residue retention, together with crop varieties best able to source nutrients from SOM, may help reverse soil degradation and improve soil nutrient supply and uptake by plants in low-input environments of tropical and subtropical areas. Here, we screened germplasm representing genetic diversity within tropical maize breeding programmes in relation to shaping SOM mineralization. Then we assessed effects of contrasting genotypes on nitrification rates, and genotype-by-management history interactions on these rates. SOM-C mineralization and gross nitrification rates varied under different maize genotypes. Cumulative SOM-C mineralization increased with root diameter but decreased with increasing root length. Strong influences of management history and interaction of maize genotype-by-management history on nitrification were observed. Overall, nitrification rates were higher in NT soil with residue retention. We propose that there is potential to exploit genotypic variation in traits associated with SOM mineralization and nitrification within breeding programmes. Root diameter and length could be used as proxies for root-soil interactions driving these processes. Development of maize varieties with enhanced ability to mineralize SOM combined with NT and residue retention to build/replenish SOM could be key to sustainable production.
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Affiliation(s)
- Lumbani Mwafulirwa
- Global Academy of Agriculture and Food Security, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eric Paterson
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - Jill E Cairns
- International Maize and Wheat Improvement Centre (CIMMYT), 12.5 KM Peg, Mazowe Road, Mount Pleasant, Harare, MP 163, Zimbabwe
| | - Tim J Daniell
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Christian Thierfelder
- International Maize and Wheat Improvement Centre (CIMMYT), 12.5 KM Peg, Mazowe Road, Mount Pleasant, Harare, MP 163, Zimbabwe
| | - Elizabeth M Baggs
- Global Academy of Agriculture and Food Security, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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Gui H, Gao Y, Wang Z, Shi L, Yan K, Xu J. Arbuscular mycorrhizal fungi potentially regulate N 2O emissions from agricultural soils via altered expression of denitrification genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145133. [PMID: 33610977 DOI: 10.1016/j.scitotenv.2021.145133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 05/20/2023]
Abstract
Agricultural soils are an important source of nitrous oxide (N2O), a potent greenhouse gas involved in the destruction of the protective ozone layer that contributes to global warming. During N2O production, soil microorganisms play important driving and regulating roles. A few recent studies have revealed the potential effects of arbuscular mycorrhizal fungi (AMF), a widely distributed soil fungi, on controlling N2O emissions. However, how AMF regulate N2O production from soils remains poorly understood. To address the knowledge gap, we manipulated two independent soil environments, which were either allowed (AM) or prevented (NM) access by AMF hyphae in a microcosm experiment (n = 5). Soil physicochemical properties, N2O flux, the diversity of bacterial communities, and the abundance of key genes responsible for N2O production were assessed in both treatments over three months. Results showed that the presence of AMF significantly decreased N2O emissions from agricultural soils in the 1st month, and the abundance of key genes responsible for denitrification (nirK and nosZ) significantly decreased in AM treatments, indicating that the regulation of N2O emissions is transmitted by AMF-induced changes in the denitrification process. A structural equation model further revealed that AMF indirectly influenced N2O emissions by altering the abundance of N metabolism-related genes, rather than by altering soil chemical properties or the diversity of bacterial communities. Thus, we proposed a possible mechanism by which AMF can regulate denitrification activities and therefore N2O emissions from agricultural soils.
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Affiliation(s)
- Heng Gui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ying Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhenghong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lingling Shi
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Kai Yan
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China.
| | - Jianchu Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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6
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Lee J, Kim HS, Jo HY, Kwon MJ. Revisiting soil bacterial counting methods: Optimal soil storage and pretreatment methods and comparison of culture-dependent and -independent methods. PLoS One 2021; 16:e0246142. [PMID: 33566842 PMCID: PMC7875414 DOI: 10.1371/journal.pone.0246142] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Although a number of different methods have been used to quantify soil bacteria, identifying the optimal method(s) for soil bacterial abundance is still in question. No single method exists for undertaking an absolute microbial count using culture-dependent methods (CDMs) or even culture-independent methods (CIMs). This study investigated soil storage and pretreatment methods for optimal bacterial counts. Appropriate storage temperature (4°C) and optimal pretreatment methods (sonication time for 3 min and centrifugation at 1400 g) were necessary to preserve bacterial cell viability and eliminate interference from soil particles. To better estimate soil bacterial numbers under various cellular state and respiration, this study also evaluated three CDMs (i.e., colony forming unit, spotting, and most probable number (MPN) and three CIMs (i.e., flow cytometry (FCM), epifluorescence microscopy (EM) count, and DNA quantitation). Each counting method was tested using 72 soil samples collected from a local arable farm site at three different depths (i.e., 10-20, 90-100, and 180-190 cm). Among all CDMs, MPN was found to be rapid, simple, and reliable. However, the number of bacteria quantified by MPN was 1-2 orders lower than that quantified by CIMs, likely due to the inability of MPN to count anaerobic bacteria. The DNA quantitation method appeared to overestimate soil bacterial numbers, which may be attributed to DNA from dead bacteria and free DNA in the soil matrix. FCM was found to be ineffective in counting soil bacteria as it was difficult to separate the bacterial cells from the soil particles. Dyes used in FCM stained the bacterial DNA and clay particles. The EM count was deemed a highly effective method as it provided information on soil mineral particles, live bacteria, and dead bacteria; however, it was a time-consuming and labor-intensive process. Combining both types of methods was considered the best approach to acquire better information on the characteristics of indigenous soil microorganisms (aerobic versus anaerobic, live versus dead).
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Affiliation(s)
- Jeonggil Lee
- KU-KIST Green School, Korea University, Seoul, Republic of Korea
| | - Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul, Republic of Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul, Republic of Korea
| | - Man Jae Kwon
- KU-KIST Green School, Korea University, Seoul, Republic of Korea
- Department of Earth and Environmental Sciences, Korea University, Seoul, Republic of Korea
- * E-mail:
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7
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Anoshkin K, Vasilyev I, Karandasheva K, Shugay M, Kudryavtseva V, Egorov A, Gurevich L, Mironova A, Serikov A, Kutsev S, Strelnikov V. New Regions With Molecular Alterations in a Rare Case of Insulinomatosis: Case Report With Literature Review. Front Endocrinol (Lausanne) 2021; 12:760154. [PMID: 34737724 PMCID: PMC8563021 DOI: 10.3389/fendo.2021.760154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Insulinomatosis is characterized by monohormonality of multiple macro-tumors and micro-tumors that arise synchronously and metachronously in all regions of the pancreas, and often recurring hypoglycemia. One of the main characteristics of insulinomatosis is the presence of insulin-expressing monohormonal endocrine cell clusters that are exclusively composed of proliferating insulin-positive cells, are less than 1 mm in size, and show solid islet-like structure. It is presumed that insulinomatosis affects the entire population of β-cells. With regards to molecular genetics, this phenomenon is not related to mutation in MEN1 gene and is more similar to sporadic benign insulinomas, however, at the moment molecular genetics of this disease remains poorly investigated. NGS sequencing was performed with a panel of 409 cancer-related genes. Results of sequencing were analyzed by bioinformatic algorithms for detecting point mutations and copy number variations. DNA copy number variations were detected that harbor a large number of genes in insulinoma and fewer genes in micro-tumors. qPCR was used to confirm copy number variations at ATRX, FOXL2, IRS2 and CEBPA genes. Copy number alterations involving FOXL2, IRS2, CEBPA and ATRX genes were observed in insulinoma as well as in micro-tumors samples, suggesting that alterations of these genes may promote malignization in the β-cells population.
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Affiliation(s)
- Kirill Anoshkin
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ivan Vasilyev
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Valeriya Kudryavtseva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Egorov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Larisa Gurevich
- Morphological Department of Oncology, M.F. Vladimirsky Moscow Regional Research and Clinical Institute, Moscow, Russia
| | - Anna Mironova
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey Serikov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergei Kutsev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Vladimir Strelnikov
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
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Pei Y, Mamtimin T, Ji J, Khan A, Kakade A, Zhou T, Yu Z, Zain H, Yang W, Ling Z, Zhang W, Zhang Y, Li X. The guanidine thiocyanate-high EDTA method for total microbial RNA extraction from severely heavy metal-contaminated soils. Microb Biotechnol 2020; 14:465-478. [PMID: 32578381 PMCID: PMC7936289 DOI: 10.1111/1751-7915.13615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular analyses relying on RNA, as a direct way to unravel active microbes and their functional genes, have received increasing attention from environmental researchers recently. However, extracting sufficient and high‐quality total microbial RNA from seriously heavy metal‐contaminated soils is still a challenge. In this study, the guanidine thiocyanate‐high EDTA (GTHE) method was established and optimized for recovering high quantity and quality of RNA from long‐term heavy metal‐contaminated soils. Due to the low microbial biomass in the soils, we combined multiple strong denaturants and intense mechanical lysis to break cells for increasing RNA yields. To minimize RNAase and heavy metals interference on RNA integrity, the concentrations of guanidine thiocyanate and EDTA were increased from 0.5 to 0.625 ml g−1 soil and 10 to 100 mM, respectively. This optimized GTHE method was applied to seven severely contaminated soils, and the RNA recovery efficiencies were 2.80 ~ 59.41 μg g−1 soil. The total microbial RNA of non‐Cr(VI) (NT) and Cr(VI)‐treated (CT) samples was utilized for molecular analyses. The result of qRT‐PCR demonstrated that the expressions of two tested genes, chrA and yieF, were respectively upregulated 4.12‐ and 62.43‐fold after Cr(VI) treatment. The total microbial RNA extracted from NT and CT samples, respectively, reached to 26.70 μg and 30.75 μg, which were much higher than the required amount (5 μg) for metatranscriptomic library construction. Besides, ratios of mRNA read were more than 86%, which indicated the high‐quality libraries constructed for metatranscriptomic analysis. In summary, the GTHE method is useful to study microbes of contaminated habitats.
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Affiliation(s)
- Yaxin Pei
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Tursunay Mamtimin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Jing Ji
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Aman Khan
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Apurva Kakade
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Tuoyu Zhou
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Zhengsheng Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Hajira Zain
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Wenzhi Yang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Zhenmin Ling
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Xiangkai Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
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9
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Rebel P, Poblete-Echeverría C, van Zyl JG, Wessels JPB, Coetzer C, McLeod A. Determining Mancozeb Deposition Benchmark Values on Apple Leaves for the Management of Venturia inaequalis. PLANT DISEASE 2020; 104:168-178. [PMID: 31697224 DOI: 10.1094/pdis-04-19-0873-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Apple scab, caused by Venturia inaequalis, is the most common fruit and foliar disease in commercial apple production worldwide. Early in the production season, preventative contact fungicide sprays are essential for protecting highly susceptible continuously unfolding and expanding young leaves. In South Africa, mancozeb is a key contact fungicide used for controlling apple scab early in the season. The current study developed deposition benchmarks indicative of the biological efficacy of mancozeb against apple scab, using a laboratory-based apple seedling model system. The model system employed a yellow fluorescent pigment that is known to be an effective tracer of mancozeb deposition. A concentration range of mancozeb (0.15 to 1 times the registered dosage) and fluorescent pigment concentrations was sprayed onto seedling leaves, which yielded various fluorescent particle coverage (FPC%) levels. Modeling of the FPC% values versus percent disease control yielded different benchmark values when disease quantification was conducted using two different methods. Thermal infrared imaging (TIRI) disease quantification resulted in a benchmark model where 0.40%, 0.79%, and 1.35 FPC% yielded 50, 75, and 90% apple scab control, respectively. These FPC% values were higher than the benchmarks (0.10, 0.20, and 0.34 FPC%, respectively) obtained with quantitative real-time PCR (qPCR) disease quantification. The qPCR benchmark model is recommended as a guideline for evaluating the efficacy of mancozeb sprays on leaves in apple orchards since the TIRI benchmark model underestimated disease control. The TIRI benchmark model yielded 68% disease control at the lowest mancozeb dosage, yet no visible lesion developed at this dosage. Both benchmark models showed that mancozeb yielded high levels of disease control at very low concentrations; for the qPCR benchmark model the FPC% value of the FPC90 (90% control) corresponded to 0.15 times that of the registered mancozeb concentration in South Africa, i.e., 85% lower than the registered dosage.
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Affiliation(s)
- P Rebel
- Department of Plant Pathology, Stellenbosch University, Matieland, 7600, South Africa
| | - C Poblete-Echeverría
- Department of Viticulture and Oenology, Stellenbosch University, 7600, South Africa
| | | | | | - C Coetzer
- Department of Plant Pathology, Stellenbosch University, Matieland, 7600, South Africa
| | - A McLeod
- Department of Plant Pathology, Stellenbosch University, Matieland, 7600, South Africa
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10
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Huang D, Yan G, Gudmestad NC, Whitworth J. Assessment of Factors Associated with Molecular Quantification of Stubby Root Nematode Paratrichodorus allius from Field Soil DNA. PLANT DISEASE 2019; 103:3265-3273. [PMID: 31596692 DOI: 10.1094/pdis-12-18-2240-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Factors relating to SYBR Green-based quantitative real-time PCR (qPCR) quantification of stubby root nematode Paratrichodorus allius using soil DNA were evaluated in this study. Soils used were loamy sand from potato fields in North Dakota and Idaho. Results showed that the largest nematode individuals (body length >720 µm) produced significant lower Cq values than the smallest individuals (<359 µm), indicating more total DNA amount in the largest nematodes. Soil pre-treatments showed that autoclaved field soil had significantly reduced DNA amount and quality. The air- or oven-dried soil yielded a lower amount of DNA with similar purity, compared with natural field soil. PCR inhibitors were detected in soil DNA substrates targeting pBluescript II SK(+)-plasmid DNA. Al(NH4)(SO4)2 treatment during DNA preparation significantly reduced the inhibitors compared with post-treatment of soil DNA with polyvinylpolypyrrolidone column. The effect of PCR inhibitors on qPCR was suppressed by bovine serum albumin. Quantification results did not significantly change when increasing the number of DNA extractions from three to six per soil sample when soil grinding and grid sampling strategies were used. Two standard curves, generated from serial dilutions of plasmid DNA containing P. allius ITS1 rDNA and soil DNA containing known nematode numbers, produced similar correlations between Cq values and amount of targets. The targets in soil DNA quantified by qPCR using either standard curve correlated well with microscopic observations using both artificially and naturally infested field soils. This is the first study for assessing various factors that may affect qPCR quantification of stubby root nematodes. Results will be useful during the setup or optimization of qPCR-based quantification of plant-parasitic nematodes from soil DNA.
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Affiliation(s)
- Danqiong Huang
- North Dakota State University, Department of Plant Pathology, Fargo, ND 58102, U.S.A
| | - Guiping Yan
- North Dakota State University, Department of Plant Pathology, Fargo, ND 58102, U.S.A
| | - Neil C Gudmestad
- North Dakota State University, Department of Plant Pathology, Fargo, ND 58102, U.S.A
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11
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Mallik I, Fulladolsa AC, Yellareddygari SKR, Bittara FG, Charkowski AO, Gudmestad NC. Detection and Quantification of Spongospora subterranea Sporosori in Soil by Quantitative Real-Time PCR. PLANT DISEASE 2019; 103:3189-3198. [PMID: 31613190 DOI: 10.1094/pdis-05-19-1092-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Powdery scab on potato tubers is caused by the obligate soilborne biotroph Spongospora subterranea and is known to cause substantial losses in potato production. The pathogen also infects roots of susceptible hosts, forming galls which can negatively affect root function. S. subterranea is also the vector of Potato mop-top virus, which causes a tuber necrosis disease that can, depending on temperature and cultivar, render potato tubers unmarketable. In this study, we adapted a published protocol to develop a sensitive and robust quantitative real-time PCR (qPCR) assay using specific primers and probes for detecting and quantifying S. subterranea sporosori in soil types that differ in physical properties, including organic matter content and soil pH. For the first time, an external control was utilized and applied directly to the soil prior to DNA extraction, which facilitated normalization of S. subterranea sporosori soil levels from sample to sample. The duplex qPCR protocol was demonstrated to be highly sensitive, capable of detecting and quantifying as few as 1 sporosorus/g of soil, with consistently high qPCR efficiency and the coefficient of determination (R2) values ranging from 94 to 99% and 0.98 to 0.99, respectively. The protocol was successfully implemented in enumerating S. subterranea sporosori in naturally infested field soil collected from several states and in artificial potting mixes with high organic matter content ranging from 64 to 71%. The qPCR method developed can be useful for potato growers to avoid agricultural soils highly infested with S. subterranea and in the development of risk assessment models in the future that incorporate cultivar susceptibility to powdery scab and soil infestation levels.
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Affiliation(s)
- Ipsita Mallik
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Ana Cristina Fulladolsa
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523
| | | | - Francisco G Bittara
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Amy O Charkowski
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523
| | - Neil C Gudmestad
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
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12
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Herold MB, Giles ME, Alexander CJ, Baggs EM, Daniell TJ. Variable response of nirK and nirS containing denitrifier communities to long-term pH manipulation and cultivation. FEMS Microbiol Lett 2019; 365:4875922. [PMID: 29471521 DOI: 10.1093/femsle/fny035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/16/2018] [Indexed: 11/14/2022] Open
Abstract
Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH-adjusted soils (ranging from pH 4.2 to 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH, while cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.
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Affiliation(s)
- Miriam B Herold
- Ecological Sciences, The James Hutton Institute, Dundee, Perth and Kinross, DD2 5DA, UK.,Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Madeline E Giles
- Ecological Sciences, The James Hutton Institute, Dundee, Perth and Kinross, DD2 5DA, UK
| | - Colin J Alexander
- Biomathematics and Statistics Scotland, Dundee, Perth and Kinross, DD2 5DA, UK
| | - Elizabeth M Baggs
- The Royal (Dick) School of Veterinary Studies, Easter Bush Campus, Midlothian EH25 9RG University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Tim J Daniell
- Ecological Sciences, The James Hutton Institute, Dundee, Perth and Kinross, DD2 5DA, UK.,Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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13
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Van der Heyden H, Wallon T, Lévesque CA, Carisse O. Detection and Quantification of Pythium tracheiphilum in Soil by Multiplex Real-Time qPCR. PLANT DISEASE 2019; 103:475-483. [PMID: 30657427 DOI: 10.1094/pdis-03-18-0419-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Canada, head lettuce (Lactuca sativa capitata) is extensively produced in the muck soils of southwestern Québec. However, yields are increasingly affected by various soilborne pathogens, including Pythium spp., which cause wilt and damping off. In a survey conducted in Québec muck soils in 2010 and 2011, Pythium tracheiphilum Matta was identified as the predominant Pythium sp. in the root of head lettuce showing Pythium stunt symptoms. Therefore, to improve risk assessment and help further understanding of disease epidemiology, a specific and sensitive real-time quantitative polymerase chain reaction (qPCR) assay based on TaqMan-minor groove binder (MGB) technology was developed for P. tracheiphilum. The PCR primers along with a TaqMan-MGB probe were designed from the ribosomal internal transcribed spacer 2 region. A 100-bp product was amplified by PCR from all P. tracheiphilum isolates tested while no PCR product was obtained from 38 other Pythium spp. or from a selection of additional lettuce pathogens tested. In addition to P. tracheiphilum, the assay was multiplexed with an internal control allowing for the individual validation of each PCR. In artificially infested soils, the sensitivity of the qPCR assay was established as 10 oospores/g of dry soil. P. tracheiphilum was not detected in soils in which lettuce has never been grown; however, inoculum ranged from 0 to more than 200,000 oospores/g of dry soil in commercial lettuce fields. Also, disease incidence was positively correlated with inoculum concentration (r = 0.764). The results suggest that inoculum concentration should be considered when making Pythium stunt management decisions. The developed qPCR assay will facilitate reliable detection and quantification of P. tracheiphilum from field soil.
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Affiliation(s)
| | - Thérèse Wallon
- 1 Compagnie de recherche Phytodata, Sherrington, QC J0L 2N0, Canada
| | - C André Lévesque
- 2 Ottawa Research and Development Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; and
| | - Odile Carisse
- 3 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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14
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Buonicontro DS, Roberts DM, Oliveira CMG, Blok VC, Neilson R, Oliveira RDDL. A Rapid Diagnostic for Detection of Aphelenchoides besseyi and A. fujianensis Based on Real-Time PCR. PLANT DISEASE 2018; 102:519-526. [PMID: 30673493 DOI: 10.1094/pdis-08-17-1160-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Aphelenchoides besseyi and A. fujianensis have been frequently found in mixed populations associated with forage grass seed in Brazil. The morphological similarity between both species has previously led A. fujianensis to be erroneously identified as A. besseyi. A. besseyi is a quarantine pest in many countries that import Brazilian forage seed; however, there is no current evidence suggesting that A. fujianensis is a plant-parasitic species. Two real-time polymerase chain reaction (qPCR) diagnostics were developed to detect each species and an operational envelope was established. A set of primers and hydrolysis probes for each species was designed targeting the large subunit (LSU) region. To assess their specificity, primers and probes sets were tested with samples of nontarget Aphelenchoides and Paraphelenchus sp. also frequently associated with forage seed. Experiments using dilutions of purified plasmid standards underpinned the sensitivity of the qPCR assays, which detected as few as 10 copies of target nematode ribosomal DNA. Thus, the developed diagnostics were sufficiently sensitive to detect DNA extracted from a fragment of a single target nematode. There was a positive correlation between copy number of the target species and nematode abundance, suggesting the potential of this method for quantification. Evidence of intra-individual variability among cloned sequences of the LSU region in a single A. besseyi population is also reported.
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Affiliation(s)
- Dalila Sêni Buonicontro
- Viçosa Federal University, Department of Plant Pathology, Laboratory of Nematology, 36570-900, Viçosa, MG, Brazil
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15
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Meynet P, Head IM, Werner D, Davenport RJ. Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders. FEMS Microbiol Ecol 2015; 91:fiv049. [PMID: 25944871 PMCID: PMC4462182 DOI: 10.1093/femsec/fiv049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2015] [Indexed: 11/30/2022] Open
Abstract
Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon-degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimized, following MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments). Comparison of the qPCR quantification of dioxygenases in spiked sediment samples and in pure cultures demonstrated an underestimation of the Ct value, and the requirement for a correction factor at gene abundances below 108 gene copies per g of sediment. Externally validated qPCR provides a valuable tool to monitor aromatic hydrocarbon degrader population abundances at contaminated sites. Our study aimed to re-evaluate the phylogeny of Rieske non-heme iron dioxygenases using only retrieved primary nucleic acid sequences for the development of quantitative real-time PCR primers.
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Affiliation(s)
- Paola Meynet
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
| | - David Werner
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
| | - Russell J Davenport
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
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16
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Survival of a novel endophytic fungus Phomopsis liquidambari B3 in the indole-contaminated soil detected by real-time PCR and its effects on the indigenous microbial community. Microbiol Res 2014; 169:881-7. [DOI: 10.1016/j.micres.2014.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/21/2014] [Accepted: 05/28/2014] [Indexed: 11/22/2022]
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17
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Hoffmann M, Coy MR, Kingdom Gibbard HN, Pelz-Stelinski KS. Wolbachia infection density in populations of the Asian citrus psyllid (Hemiptera: Liviidae). ENVIRONMENTAL ENTOMOLOGY 2014; 43:1215-22. [PMID: 25259690 DOI: 10.1603/en14193] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The symbiotic relationships between bacteria of the genus Wolbachia (order Rickettsiales) and their arthropod hosts are diverse and can range from mutualism to parasitism. Whereas effects of Wolbachia on host biology are well investigated, little is known about diversity and abundance of Wolbachia in their natural hosts. The phloem-feeding Asian citrus psyllid, Diaphorina citri (Kuwayama) (Hemiptera: Liviidae), is naturally infected with Wolbachia (wDi). In the current study, we calculated the within-host density of Wolbachia in Florida D. citri populations using quantitative polymerase chain reaction for detection of the Wolbachia outer surface protein gene, wsp. Gene quantities were normalized to the D. citri wingless gene (Wg) to estimate Wolbachia abundance in individual D. citri. Using this method, significant geographic differences in Wolbachia densities were detected among Florida D. citri populations, with higher infection levels occurring in male versus female hosts.
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Affiliation(s)
- M Hoffmann
- Department of Entomology and Nematology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA
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18
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Zhai L, Yu Q, Bie X, Lu Z, Lv F, Zhang C, Kong X, Zhao H. Development of a PCR test system for specific detection of Salmonella Paratyphi B in foods. FEMS Microbiol Lett 2014; 355:83-9. [PMID: 24725227 DOI: 10.1111/1574-6968.12443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/10/2014] [Accepted: 04/10/2014] [Indexed: 01/02/2023] Open
Abstract
Salmonella enterica serotype Paratyphi B is a globally distributed human-specific pathogen causing paratyphoid fever. The aim of this study was to develop a rapid and reliable polymerase chain reaction (PCR) assay for its detection in food. The SPAB_01124 gene was found to be unique to S. Paratyphi B using comparative genomics. Primers for fragments of the SPAB_01124 gene and the Salmonella-specific invA gene were used in combination to establish a multiplex PCR assay that showed 100% specificity across 45 Salmonella strains (representing 34 serotypes) and 18 non-Salmonella strains. The detection limit was 2.2 CFU mL(-1) of S. Paratyphi B after 12-h enrichment in pure culture. It was shown that co-culture with S. Typhimurium or Escherichia coli up to concentrations of 3.6 × 10(5) CFU and 3.3 × 10(4) CFU, respectively, did not interfere with PCR detection of S. Paratyphi B. In artificially contaminated milk, the assay could detect as few as 62 CFU mL(-1) after 8 h of enrichment. In conclusion, comparative genomics was found to be an efficient approach to the mining of pathogen-specific target genes, and the PCR assay that was developed from this provided a rapid, specific, and sensitive method for detection of S. Paratyphi B.
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Affiliation(s)
- Ligong Zhai
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing, China
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19
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Zhai L, Kong X, Lu Z, Lv F, Zhang C, Bie X. Detection of Salmonella enterica serovar Dublin by polymerase chain reaction in multiplex format. J Microbiol Methods 2014; 100:52-7. [DOI: 10.1016/j.mimet.2014.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 11/28/2022]
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20
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Hou LB, Yanagisawa Y, Yachi S, Kaneko N, Nakamori T. Biomass estimation of the terrestrial ecotoxicological species Folsomia candida (Collembola) using a real-time polymerase chain reaction. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 101:59-63. [PMID: 24507127 DOI: 10.1016/j.ecoenv.2013.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 06/03/2023]
Abstract
The abundance and growth of the Folsomia candida soil arthropod have been widely used to assess the environmental impact of a range of soil pollutants, and increasing concerns about environmental pollution require advanced and rapid methods to estimate ecological toxicity. Here, we developed a quantitative polymerase chain reaction (qPCR)-based assay for determining the biomass of F. candida. Prior to DNA extraction, an appropriate amount of an artificial sequence was spiked into the test samples, allowing us to assess the extraction efficiency used for normalisation. We designed primers based on the sequencing information of the nuclear RNA polymerase II (Pol II) and mitochondrial cytochrome c oxidase subunit I (mtCOI) genes of F. candida. Assays were performed on samples containing a different number of individuals at the same body length (individually same biomass; same age) and samples containing the same number of individuals at a different body length (individually different biomass; different age). Biomass was estimated from the body lengths of collembolan samples. For both genes, DNA quantity showed a significant linear relationship between increased collembolan numbers and the estimated biomass; DNA quantity in different ages of collembolans showed a significant correlation with body length and a linear relationship with the estimated biomass. We believe that this rapid and accurate technique could be used to detect and quantify soil animals and thus would improve ecotoxicological testing.
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Affiliation(s)
- Li-Bo Hou
- Laboratory of Soil Ecology, Graduate School of Environment and Information Sciences, Yokohama National University, Japan.
| | - Yukinari Yanagisawa
- Laboratory of Soil Ecology, Graduate School of Environment and Information Sciences, Yokohama National University, Japan
| | - Shunji Yachi
- National Institute for Agro-Environmental Sciences Organo-Chemicals Division, Japan
| | - Nobuhiro Kaneko
- Laboratory of Soil Ecology, Graduate School of Environment and Information Sciences, Yokohama National University, Japan
| | - Taizo Nakamori
- Laboratory of Soil Ecology, Graduate School of Environment and Information Sciences, Yokohama National University, Japan
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21
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Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil. ISME JOURNAL 2013; 8:1336-45. [PMID: 24351937 DOI: 10.1038/ismej.2013.224] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 11/08/2022]
Abstract
N2O is a potent greenhouse gas involved in the destruction of the protective ozone layer in the stratosphere and contributing to global warming. The ecological processes regulating its emissions from soil are still poorly understood. Here, we show that the presence of arbuscular mycorrhizal fungi (AMF), a dominant group of soil fungi, which form symbiotic associations with the majority of land plants and which influence a range of important ecosystem functions, can induce a reduction in N2O emissions from soil. To test for a functional relationship between AMF and N2O emissions, we manipulated the abundance of AMF in two independent greenhouse experiments using two different approaches (sterilized and re-inoculated soil and non-mycorrhizal tomato mutants) and two different soils. N2O emissions were increased by 42 and 33% in microcosms with reduced AMF abundance compared to microcosms with a well-established AMF community, suggesting that AMF regulate N2O emissions. This could partly be explained by increased N immobilization into microbial or plant biomass, reduced concentrations of mineral soil N as a substrate for N2O emission and altered water relations. Moreover, the abundance of key genes responsible for N2O production (nirK) was negatively and for N2O consumption (nosZ) positively correlated to AMF abundance, indicating that the regulation of N2O emissions is transmitted by AMF-induced changes in the soil microbial community. Our results suggest that the disruption of the AMF symbiosis through intensification of agricultural practices may further contribute to increased N2O emissions.
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22
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Bodelier PLE, Meima-Franke M, Hordijk CA, Steenbergh AK, Hefting MM, Bodrossy L, von Bergen M, Seifert J. Microbial minorities modulate methane consumption through niche partitioning. ISME JOURNAL 2013; 7:2214-28. [PMID: 23788331 DOI: 10.1038/ismej.2013.99] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/03/2013] [Accepted: 05/17/2013] [Indexed: 01/12/2023]
Abstract
Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.
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Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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23
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Quantification of rice brown leaf spot through Taqman real-time PCR specific to the unigene encoding Cochliobolus miyabeanus SCYTALONE DEHYDRATASE1 involved in fungal melanin biosynthesis. J Microbiol 2012; 50:947-54. [PMID: 23274981 DOI: 10.1007/s12275-012-2538-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 10/25/2012] [Indexed: 10/27/2022]
Abstract
Rice brown leaf spot is a major disease in the rice paddy field. The causal agent Cochliobolus miyabeanus is an ascomycete fungus and a representative necrotrophic pathogen in the investigation of rice-microbe interactions. The aims of this research were to identify a quantitative evaluation method to determine the amount of C. miyabeanus proliferation in planta and determine the method's sensitivity. Real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to CmSCD1, a C. miyabeanus unigene encoding SCYTALONE DEHYDRATASE, which is involved in fungal melanin biosynthesis. Comparative analysis of the nucleotide sequences of CmSCD1 from Korean strains with those from the Japanese and Taiwanese strains revealed some sequence differences. Based on the crossing point (CP) values from Taqman real-time PCR containing a series of increasing concentrations of cloned amplicon or fungal genomic DNA, linear regressions with a high level of reliability (R(2)>0.997) were constructed. This system was able to estimate fungal genomic DNA at the picogram level. The reliability of this equation was further confirmed using DNA samples from both resistant and susceptible cultivars infected with C. miyabeanus. In summary, our quantitative system is a powerful alternative in brown leaf spot forecasting and in the consistent evaluation of disease progression.
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Giles M, Morley N, Baggs EM, Daniell TJ. Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production. Front Microbiol 2012; 3:407. [PMID: 23264770 PMCID: PMC3524552 DOI: 10.3389/fmicb.2012.00407] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 11/12/2012] [Indexed: 11/13/2022] Open
Abstract
The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.
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Affiliation(s)
- Madeline Giles
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen Aberdeen, UK ; Ecological Sciences, The James Hutton Institute Dundee, UK
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