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Jiang J, Hu X, Ji X, Chen H. High throughput sequencing technology facility research of genomic modification crop cultivation influencing soil microbe. FRONTIERS IN PLANT SCIENCE 2023; 14:1208111. [PMID: 37324715 PMCID: PMC10264764 DOI: 10.3389/fpls.2023.1208111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023]
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Kasanke CP, Zhao Q, Alfaro T, Walter CA, Hobbie SE, Cheeke TE, Hofmockel KS. Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands. Mol Ecol 2023; 32:1133-1148. [PMID: 36516408 DOI: 10.1111/mec.16823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. To evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.
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Affiliation(s)
- Christopher P Kasanke
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Qian Zhao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Trinidad Alfaro
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Tanya E Cheeke
- Department of Biological Sciences, Washington State University, Richland, Washington, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.,Department of Agronomy, Iowa State University, Ames, Iowa, USA
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Zheng Y, Lv GB, Chen K, Yu Q, Niu B, Jiang J, Liu G. Impact of PaGLK transgenic poplar on microbial community and soil enzyme activity in rhizosphere soil. Front Bioeng Biotechnol 2022; 10:965209. [PMID: 35942008 PMCID: PMC9355801 DOI: 10.3389/fbioe.2022.965209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022] Open
Abstract
Rhizosphere microorganisms are essential parts in maintaining soil ecological functions. Reforestation using genetically modified trees might have great potential to enhance tree production in biotic and abiotic stress, however, their long-term impact on rhizosphere microorganisms is scant. In this study, we studied soil enzyme activities and composition of rhizosphere microorganisms in 2-year-old transgenic PaGLK overexpression (OE), repressed expression (RE) and wild-type (WT) poplar (P. alba × P.berlinensis). The root exudates of PaGLK transgenic poplar (P.alba × P. berlinensis) were analyzed by liquid chromatography-mass spectrometry (LC-MS). The results showed that there were significant difference for soil sucrase, urease, catalase, neutral protease and cellulase between the transgenic and WT lines at different growth periods. Alpha diversity analysis showed that bacterial community abundance and diversity for RE lines were significantly lower than WT (p < 0.05), while RE lines for fungi were significantly higher than WT lines. At the genus level, Burkholderia was the dominant group of rhizosphere bacterial community, and the relative abundance for RE was significantly higher than WT. Tomentella was the dominant group for fungi community. Serendipita for RE was significantly higher than WT and OE. Main metabolite contents of (S)-ACPA, geniposidic acid, agnuside, hydroquinone and pyranocoumarins were significantly different among transgenic lines. These results suggest that transgenic activities have effects on root exudates, rhizosphere soil enzyme activities and soil microbial community composition, but long term effects need to be further investigated.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Haerbin, HL, China
| | - Guan Bin Lv
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Haerbin, HL, China
| | - Kun Chen
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Haerbin, HL, China
| | - Qibin Yu
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Haerbin, HL, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Haerbin, HL, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Haerbin, HL, China
- *Correspondence: Guifeng Liu,
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Tóthné Bogdányi F, Boziné Pullai K, Doshi P, Erdős E, Gilián LD, Lajos K, Leonetti P, Nagy PI, Pantaleo V, Petrikovszki R, Sera B, Seres A, Simon B, Tóth F. Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review. Microorganisms 2021; 9:2130. [PMID: 34683451 PMCID: PMC8538326 DOI: 10.3390/microorganisms9102130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022] Open
Abstract
The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.
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Affiliation(s)
| | - Krisztina Boziné Pullai
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (K.B.P.); (R.P.)
| | - Pratik Doshi
- ImMuniPot Independent Research Group, H-2100 Gödöllő, Hungary
| | - Eszter Erdős
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (E.E.); (K.L.)
| | - Lilla Diána Gilián
- Szent István Campus Dormitories, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary;
| | - Károly Lajos
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (E.E.); (K.L.)
| | - Paola Leonetti
- Bari Unit, Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection of the CNR, 70126 Bari, Italy; (P.L.); (V.P.)
| | - Péter István Nagy
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Vitantonio Pantaleo
- Bari Unit, Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection of the CNR, 70126 Bari, Italy; (P.L.); (V.P.)
| | - Renáta Petrikovszki
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (K.B.P.); (R.P.)
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Bozena Sera
- Department of Environmental Ecology and Landscape Management, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia;
| | - Anikó Seres
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Barbara Simon
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary;
| | - Ferenc Tóth
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
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Wang L, Wang X, Gao F, Lv C, Li L, Han T, Chen F. AMF Inoculation Can Enhance Yield of Transgenic Bt Maize and Its Control Efficiency Against Mythimna separata Especially Under Elevated CO 2. FRONTIERS IN PLANT SCIENCE 2021; 12:655060. [PMID: 34168665 PMCID: PMC8217876 DOI: 10.3389/fpls.2021.655060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
The promotion and application of transgenic Bt crops provides an approach for the prevention and control of target lepidopteran pests and effectively relieves the environmental pressure caused by the massive usage of chemical pesticides in fields. However, studies have shown that Bt crops will face a new risk due to a decrease in exogenous toxin content under elevated carbon dioxide (CO2) concentration, thus negatively affecting the ecological sustainability of Bt crops. Arbuscular mycorrhizal fungi (AMF) are important beneficial microorganisms that can effectively improve the nutrient status of host plants and are expected to relieve the ecological risk of Bt crops under increasing CO2 due to global climate change. In this study, the Bt maize and its parental line of non-transgenic Bt maize were selected and inoculated with a species of AMF (Funneliformis caledonium, synonyms: Glomus caledonium), in order to study the secondary defensive chemicals and yield of maize, and to explore the effects of F. caledonium inoculation on the growth, development, and reproduction of the pest Mythimna separata fed on Bt maize and non-Bt maize under ambient carbon dioxide concentration (aCO2) and elevated carbon dioxide concentration (eCO2). The results showed that eCO2 increased the AM fungal colonization, maize yield, and foliar contents of jasmonic acid (JA) and salicylic acid (SA), but decreased foliar Bt toxin content and Bt gene expression in Bt maize leaves. F. caledonium inoculation increased maize yield, foliar JA, SA contents, Bt toxin contents, and Bt gene expression in Bt maize leaves, and positively improved the growth, development, reproduction, and food utilization of the M. separata fed on non-Bt maize. However, F. caledonium inoculation was unfavorable for the fitness of M. separata fed on Bt maize, and the effect was intensified when combined with eCO2. It is indicated that F. caledonium inoculation had adverse effects on the production of non-Bt maize due to the high potential risk of population occurrence of M. separata, while it was just the opposite for Bt maize. Therefore, this study confirms that the AMF can increase the yield and promote the expression levels of its endogenous (JA, SA) and exogenous (Bt toxin) secondary defense substances of Bt maize under eCO2, and finally can enhance the insect resistance capacity of Bt crops, which will help ensure the sustainable utilization and safety of Bt crops under climate change.
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Affiliation(s)
- Long Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Department of Landscape Architecture, College of Biological and Agricultural Engineering, Weifang University, Weifang, China
| | - Xiaohui Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Fanqi Gao
- Jinshanbao Experimental Class, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Changning Lv
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Likun Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Tong Han
- Department of Phytology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fajun Chen
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Brown AJ, Newhouse AE, Powell WA, Parry D. Comparative efficacy of gypsy moth (Lepidoptera: Erebidae) entomopathogens on transgenic blight-tolerant and wild-type American, Chinese, and hybrid chestnuts (Fagales: Fagaceae). INSECT SCIENCE 2020; 27:1067-1078. [PMID: 31339228 DOI: 10.1111/1744-7917.12713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
American chestnut (Castanea dentata [Marsh.] Borkh.) was once the dominant hardwood species in Eastern North America before an exotic fungal pathogen, Cryphonectria parasitica (Murrill) Barr, functionally eliminated it across its range. One promising approach toward restoring American chestnut to natural forests is development of blight-tolerant trees using genetic transformation. However, transformation and related processes can result in unexpected and unintended phenotypic changes, potentially altering ecological interactions. To assess unintended tritrophic impacts of transgenic American chestnut on plant-herbivore interactions, gypsy moth (Lymantria dispar L.) caterpillars were fed leaf disks excised from two transgenic events, Darling 54 and Darling 58, and four control American chestnut lines. Leaf disks were previously treated with an LD50 dose of either the species-specific Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) or the generalist pathogen Bacillus thuringiensis subsp. kurstaki (Btk). Mortality was quantified and compared to water blank controls. Tree genotype had a strong effect on the efficacies of both pathogens. Larval mortality from Btk-treated foliage from only one transgenic event, Darling 54, differed from its isogenic progenitor, Ellis 1, but was similar to an unrelated wild-type American chestnut control. LdMNPV efficacy was unaffected by genetic transformation. Results suggest that although genetic modification of trees may affect interactions with other nontarget organisms, this may be due to insertion effects, and variation among different genotypes (whether transgenic or wild-type) imparts a greater change in response than transgene presence.
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Affiliation(s)
- Aaron J Brown
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Andrew E Newhouse
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - William A Powell
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Dylan Parry
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
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Walters KE, Martiny JBH. Alpha-, beta-, and gamma-diversity of bacteria varies across habitats. PLoS One 2020; 15:e0233872. [PMID: 32966309 PMCID: PMC7510982 DOI: 10.1371/journal.pone.0233872] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
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Affiliation(s)
- Kendra E. Walters
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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Londoño DMM, Meyer E, da Silva KJ, Hernández AG, de Armas RD, Soares LM, Stürmer SL, Nodari RO, Soares CRFS, Lovato PE. Root colonization and arbuscular mycorrhizal fungal community composition in a genetically modified maize, its non-modified isoline, and a landrace. MYCORRHIZA 2020; 30:611-621. [PMID: 32556837 DOI: 10.1007/s00572-020-00969-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
The use of genetically modified (GM) plants has increased in recent decades, but there are uncertainties about their effects on soil microbial communities. Aiming to quantify root colonization and characterize arbuscular mycorrhizal fungi (AMF) communities associated with roots and rhizosphere soil of different maize genotypes, a field trial was carried out in Southern Brazil with three maize genotypes as follows: a GM hybrid (DKB 240 VTPRO), its non-modified isoline (DKB 240), and a landrace (Pixurum). Soil samples were collected to evaluate the occurrence of AMF during the growth of corn genotypes at sowing and V3 (vegetative), R1 (flowering), and R3 (grain formation) stages of the crop. The occurrence of AMF was determined by the morphological identification of spores, and by analyzing AMF community composition in soil and roots of maize, using PCR-DGGE. The GM genotype of maize promoted lower mycorrhizal colonization in the vegetative stage and had lower sporulation at grain development than the conventional hybrid and the landrace maize. Twenty AMF morphotypes were identified and 13 were associated with all maize genotypes. The genera Acaulospora, Glomus, and Dentiscutata had the largest numbers of species. There were no differences in AMF community composition due to maize genotypes or genetic modification, but crop phenological stages affected AMF communities associated with maize roots.
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Affiliation(s)
- Diana Marcela Morales Londoño
- Departamento de Engenharia Rural, Centro de Ciências Agrarias, Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, CEP: 88034-001, Brazil
| | - Edenilson Meyer
- Departamento de Engenharia Rural, Centro de Ciências Agrarias, Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, CEP: 88034-001, Brazil
| | - Kelly Justin da Silva
- Centro Universitário Católica de Santa Catarina - Joinville, Campus Joinville. Rua Visconde de Taunay 427, Joinville, Santa Catarina, CEP 89203-005, Brazil
| | - Anabel González Hernández
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina. Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Rafael Dutra de Armas
- Centro Universitário Católica de Santa Catarina - Joinville, Campus Joinville. Rua Visconde de Taunay 427, Joinville, Santa Catarina, CEP 89203-005, Brazil
| | - Luis Macedo Soares
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina. Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Sidney Luiz Stürmer
- Departamento de Ciencias Naturais, Centro de Ciencias Exatas e Naturais, Fundação Universidade Regional de Blumenau. Rua Antonio da Veiga, 140, Centro, Blumenau, Santa Catarina, CEP 89030-903, Brazil
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Centro de Ciências Agrárias Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Bloco B, Itacorubi, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Cláudio Roberto Fonsêca Sousa Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina. Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Paulo Emilio Lovato
- Departamento de Engenharia Rural, Centro de Ciências Agrarias, Universidade Federal de Santa Catarina. Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, CEP: 88034-001, Brazil.
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A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer. Biotechniques 2019; 68:72-78. [PMID: 31849245 DOI: 10.2144/btn-2019-0072] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches and the ability to identify a broad diversity of fungal taxa. To assess capabilities, three fungal mock communities were sequenced, each of which had varying ratios of 16 taxa. The data were processed through our selected pipeline. The MinION recovered all mock community members, when mixed at equal ratios. When a taxon was represented at a lower ratio, it was not recovered or decreased in relative abundance. Despite high error rates, highly accurate consensus sequences can be derived. This methodological approach identified all mock community taxa, demonstrating the MinION can be used as a practical alternative to profile fungal communities.
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Szoboszlay M, Näther A, Mullins E, Tebbe CC. Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions. PLoS One 2019; 14:e0222737. [PMID: 31846458 PMCID: PMC6917299 DOI: 10.1371/journal.pone.0222737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
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Affiliation(s)
- Márton Szoboszlay
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
| | - Astrid Näther
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
| | - Ewen Mullins
- Teagasc, Agriculture and Food Development Authority, Dept. Crop Science, Oak Park, Carlow, Ireland
| | - Christoph C. Tebbe
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
- * E-mail:
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Pan J, Lv X, Jin D, Bai Z, Qi H, Zhang H, Zhuang G. Developmental stage has a greater effect than Cry1Ac expression in transgenic cotton on the phyllosphere mycobiome. Can J Microbiol 2019; 65:116-125. [DOI: 10.1139/cjm-2018-0309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transgenic Bt cotton is widely cultivated, yet its impact on the phyllosphere mycobiome is poorly understood. Hence, the objective of this study was to investigate the effects resulting from the planting of Bt cotton on fungal diversity composition. The α diversity for the Bt cotton line SGK321 was lower than that of control plants at the budding stage and the blossoming and boll-forming stage, while an obvious increase in diversity for Bt cotton XP188 was observed at the same stage. The Cry1Ac levels were higher at the seedling stage than at the budding stage and the blossoming and boll-forming stage. There was no direct relationship between the expression of the Bt protein and variation in the fungal community for Bt cotton. However, PCoA and PCA results indicated that community structure differed among developmental stages. These results indicated that developmental stage rather than Cry1Ac expression was the key factor shaping the phyllosphere mycobiome in transgenic cotton.
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Affiliation(s)
- Jiangang Pan
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou 014010, P.R. China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- College of Resource and Environmental Science, University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xin Lv
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Decai Jin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Hongyan Qi
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Hongxun Zhang
- College of Resource and Environmental Science, University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
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12
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Zeng H, Zhong W, Tan F, Shu Y, Feng Y, Wang J. The Influence of Bt Maize Cultivation on Communities of Arbuscular Mycorrhizal Fungi Revealed by MiSeq Sequencing. Front Microbiol 2019; 9:3275. [PMID: 30687266 PMCID: PMC6334669 DOI: 10.3389/fmicb.2018.03275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/17/2018] [Indexed: 11/13/2022] Open
Abstract
The cultivation of transgenic Bacillus thuringiensis (Bt) has received worldwide attention since Bt crops were first released. Its ecological risks on arbuscular mycorrhizal fungi (AMF) have been widely studied. In this study, after cultivation for five seasons, the AMF diversity and community composition of two Bt maize varieties, 5422Bt1 (event Bt11) and 5422CBCL (event MO10), which both express Cry1Ab protein, and their isoline non-Bt maize 5422, as well as Bt straw after cultivation had been returned to subsequent conventional maize variety, were analyzed using Illumina MiSeq sequencing. A total of 263 OTUs (operational taxonomic units) from 511,847 sequenced affiliated with the AMF which belonged to Mucoromycota phylum Glomeromycotina subphylum were obtained. No significant difference was detected in the AMF diversity and richness (Shannon, Simpson, ACE, and Chao 1 indices) and community composition in rhizosphere soils and roots between Bt and non-Bt treatment revealed by NMDS (non-metric multidimensional scaling) and NPMANOVA (non-parametric multivariate analysis). Moreover, Glomus was the most dominant genus in all samples. Although there was no significant difference in the AMF community in roots and rhizosphere soils between the Bt and non-Bt maize treatments, total phosphorus (TP), total nitrogen (TN), organic carbon (OC), and pH were driving factors affecting the AMF community, and their composition varied between rhizosphere soils and roots during the maturity period of the fifth season. Compared to our previous study, the results were identical. In conclusion, no significant difference was observed between the Bt and non-Bt treatments, and the Illumina MiSeq method had higher throughput and higher quality read cover, which gave us comprehensive insight into AMF communities in agro-ecosystems.
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Affiliation(s)
- Huilan Zeng
- Department of Horticulture, College of Life Science and Environmental Resources, Yichun University, Yichun, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Wang Zhong
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Fengxiao Tan
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Yinghua Shu
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Yuanjiao Feng
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jianwu Wang
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
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13
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Berruti A, Bianciotto V, Lumini E. Seasonal variation in winter wheat field soil arbuscular mycorrhizal fungus communities after non-mycorrhizal crop cultivation. MYCORRHIZA 2018; 28:535-548. [PMID: 29931405 DOI: 10.1007/s00572-018-0845-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Intensive farming practices that implement deep and frequent tillage, high input inorganic fertilization, cultivation with non-host species, and pesticide use are widely reported to be detrimental for arbuscular mycorrhizal fungi (AMF), which are one of the most important plant biofertilizers. The effect of the reduction of agricultural input on AMF community dynamics following conversion from conventional non-mycorrhizal to lower input mycorrhizal crop cultivation has not yet been fully elucidated. We investigated the effect of the reduction of agricultural input, rotation, and season on AMF communities in winter wheat field soil after conversion from long-term (more than 20 years) non-mycorrhizal (sugar beet) crop cultivation. We described AMF communities from bulk soil samples by specifically targeting the 18S ribosomal gene using a combination of AMF specific primers and 454 pyrosequencing. No effect was found after 3 years' reduction of agricultural input, and only marginal effects were due to rotation with specific crops preceding winter wheat. Instead, season and year of sampling had the most appreciable influence on the AMF community. We suggest that, after conversion from long-term non-mycorrhizal to mycorrhizal crop cultivation, AMF diversity is low if compared to similar agroecosystems. Seasonal and successional dynamics play an important role as determinants of community structure.
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Affiliation(s)
- Andrea Berruti
- Institute for Sustainable Plant Protection -Turin unit, National Research Council, Viale Mattioli 25, 10125, Torino, Italy
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection -Turin unit, National Research Council, Viale Mattioli 25, 10125, Torino, Italy
| | - Erica Lumini
- Institute for Sustainable Plant Protection -Turin unit, National Research Council, Viale Mattioli 25, 10125, Torino, Italy.
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Newhouse AE, Oakes AD, Pilkey HC, Roden HE, Horton TR, Powell WA. Transgenic American Chestnuts Do Not Inhibit Germination of Native Seeds or Colonization of Mycorrhizal Fungi. FRONTIERS IN PLANT SCIENCE 2018; 9:1046. [PMID: 30073011 PMCID: PMC6060562 DOI: 10.3389/fpls.2018.01046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/27/2018] [Indexed: 05/29/2023]
Abstract
The American chestnut (Castanea dentata) was once an integral part of eastern United States deciduous forests, with many environmental, economic, and social values. This ended with the introduction of an invasive fungal pathogen that wiped out over three billion trees. Transgenic American chestnuts expressing a gene for oxalate oxidase successfully tolerate infections by this blight fungus, but potential non-target environmental effects should be evaluated before new restoration material is released. Two greenhouse bioassays evaluated belowground interactions between transgenic American chestnuts and neighboring organisms found in their native ecosystems. Potential allelopathy was tested by germinating several types of seeds, all native to American chestnut habitats, in the presence of chestnut leaf litter. Germination was not significantly different in terms of number of seeds germinated or total biomass of germinated seedlings in transgenic and non-transgenic leaf litter. Separately, ectomycorrhizal associations were observed on transgenic and non-transgenic American chestnut roots using field soil inoculum. Root tip colonization was consistently high (>90% colonization) on all plants and not significantly different between any tree types. These observations on mycorrhizal fungi complement previous studies performed on older transgenic lines which expressed oxalate oxidase at lower levels. Along with other environmental impact comparisons, these conclusions provide further evidence that transgenic American chestnuts are not functionally different with regard to ecosystem interactions than non-transgenic American chestnuts.
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Affiliation(s)
| | | | | | | | | | - William A. Powell
- Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY, United States
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15
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Curd EE, Martiny JBH, Li H, Smith TB. Bacterial diversity is positively correlated with soil heterogeneity. Ecosphere 2018. [DOI: 10.1002/ecs2.2079] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Emily E. Curd
- Department of Ecology and Evolutionary Biology University of California Los Angeles 612 Charles E. Young Drive South, Box 957246 Los Angeles California 90095 USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology University of California Irvine 321 Steinhaus Hall Irvine California 92697 USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology Crump Institute for Molecular Imaging David Geffen School of Medicine University of California Los Angeles 650 Charles E. Young Drive South Los Angeles California 90095 USA
- DOE Institute University of California Los Angeles 611 Charles E. Young Drive East Los Angeles California 90095 USA
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology University of California Los Angeles 612 Charles E. Young Drive South, Box 957246 Los Angeles California 90095 USA
- Center for Tropical Research University of California Los Angeles LaKretz Hall, 619 Charles E. Young Drive East, #300 Los Angeles California 90095 USA
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16
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Johansen RB, Johnston P, Mieczkowski P, Perry GL, Robeson MS, Burns BR, Vilgalys R. A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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