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Goforth M, Cooper MA, Oliver AS, Pinzon J, Skots M, Obergh V, Suslow TV, Flores GE, Huynh S, Parker CT, Mackelprang R, Cooper KK. Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLoS One 2024; 19:e0297453. [PMID: 38625898 PMCID: PMC11020611 DOI: 10.1371/journal.pone.0297453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/04/2024] [Indexed: 04/18/2024] Open
Abstract
Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.
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Affiliation(s)
- Madison Goforth
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Margarethe A. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Andrew S. Oliver
- USDA-ARS Western Human Nutrition Research Center, Davis, California, United States of America
| | - Janneth Pinzon
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Mariya Skots
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Victoria Obergh
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Trevor V. Suslow
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Gilberto E. Flores
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, USDA, Albany, California, United States of America
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, USDA, Albany, California, United States of America
| | - Rachel Mackelprang
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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Kiss T, Šafářová D, Navrátil M, Nečas T. Molecular Characterization of ' Candidatus Phytoplasma prunorum' in the Czech Republic and Susceptibility of Apricot Rootstocks to the Two Most Abundant Haplotypes. Microorganisms 2024; 12:399. [PMID: 38399803 PMCID: PMC10893538 DOI: 10.3390/microorganisms12020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
'Candidatus Phytoplasma prunorum' is one of the most destructive pathogens of Prunus species, where susceptible species render unproductive several years after infection. In epidemiology, the molecular characterization of phytoplasmas is based on sequence analysis of variable nonribosomal genes. In this study aceF, pnp, imp and secY genes were used for characterization of the 'Ca. P. prunorum' genotypes present in the Czech Republic. In total, 56 plant and 33 vector (Cacopsylla pruni) samples positive to 'Ca. P. prunorum' collected in seven localities were used in the study. Based on sequence analysis, four aceF, two pnp, six imp, and three secY genotypes were identified in analyzed samples. The most abundant in both plant and insect samples were the A6, P2, I4, and S2 genotypes. Most of the Czech 'Ca. P. prunorum' haplotypes clustered together in the haplotype network analysis. Next, two isolates representing the two most abundant Czech haplotypes (A6-P2-I4-S2 and A5-P2-I4-S2) were used in the susceptibility test of three apricot rootstock types (St. Julien A, M-VA-1, GF-305). Susceptibility was analyzed by phytoplasma quantification using quantitative real-time PCR and evaluation of symptom manifestation. Based on the results, the influence of the rootstock type on the phytoplasma titer and symptom manifestation was greater than of the phytoplasma isolate, while the year of analysis had no influence on the results. The results also showed that the phytoplasma titer is increasing in plant tissues during the vegetation period.
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Affiliation(s)
- Tomáš Kiss
- Department of Fruit Science, Faculty of Horticulture, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic;
| | - Dana Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic; (D.Š.); (M.N.)
| | - Milan Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic; (D.Š.); (M.N.)
| | - Tomáš Nečas
- Department of Fruit Science, Faculty of Horticulture, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic;
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Guo Y, Zhang H, Bao Y, Tan H, Liu X, Rahman ZU. Distribution characteristics of soil AM fungi community in soft sandstone area. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115193. [PMID: 35550954 DOI: 10.1016/j.jenvman.2022.115193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
To explore the diversity and distribution characteristics of soil arbuscular mycorrhizae fungi (AMF) communities in the soft sandstone area, thirteen arsenic sandstone rock samples were collected from three planting plots (SI, SII and SIII) and one bare control plot (CK), separately. The sampling locations are as follows: the top of the slope (denoted by the number 1), sunny slope (2), shady slope (3) and gully bottom (4). These samples were then tested with an Illumina HiSeq PE250 high-throughput sequencing platform. Experimental results show that the SIII4 sample (from the gully bottom of the SIII plot) has the highest moisture content of 9.1%, while the CK sample in the control plot has lowest moisture content. SI2 has the highest pH of 9.58 and CK has the lowest pH of 8.73. SII1 has the highest available phosphorus (AP) content of 9.61 mg/kg, while SII3 has the lowest AP content of 2.29 mg/kg. Furthermore, SI2 has the highest NH4-N content of 11.24 mg/kg, while SII1 has the lowest NH4-N of 4.09 mg/kg. SII1 has the highest available potassium (AK) content of 48.92 mg/kg and CK has the lowest AK content of 1.82 mg/kg. In the observed-species index reflecting AMF genetic diversity, SI1 differences significantly from SII4 and SIII3 (P < 0.05). In the Shannon index, SI1 is significantly different from SI2, SI3, SI4; SII2 is significantly different from SII3; SI2, SI4, SII1 and SII3 are quite different from CK (P < 0.05). The dominant genera of AMF in these plots include Glomus (17.24%-65.53%), Scutellospora (0.04%-67.38%), Septoglomus (2.83%-43.03%) and Kamienskia (0.64%-46.38%). The dominant genera of AMF vary significantly between sunny slope and shady slope. Positive correlation exists between soil NH4-N and the AM fungal community structure. There are prominent positive correlations exist among genetic diversity index chao1, observed-species, pH and AP (P < 0.05), and obviously negative correlation between observed species and AK (P < 0.05). The research findings on the distribution characteristics of AM fungus community in the arsenic sandstone plot and their relationship with environmental factors can help with arsenic sandstone management in other similar areas.
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Affiliation(s)
- Yangnan Guo
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Life Sciences, Inner Mongolia University, Hohhot, 010018, China; State Key Laboratory of Water Resource Protection and Utilization in Coal Mining, Beijing, 100000, China; China Energy Group, Shendong Coal Group Technology Research Institute, Ordos, 017200, China
| | - Huandi Zhang
- School of Life Sciences, Inner Mongolia University, Hohhot, 010018, China
| | - Yuying Bao
- School of Life Sciences, Inner Mongolia University, Hohhot, 010018, China; State Key Laboratory of Water Resource Protection and Utilization in Coal Mining, Beijing, 100000, China.
| | - Houzhang Tan
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xianghong Liu
- China Coal Research Institute, Beijing, 100013, China
| | - Zia Ur Rahman
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
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Lefèvre E, Gardner CM, Gunsch CK. A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization. FEMS Microbiol Ecol 2020; 96:5850752. [PMID: 32490528 DOI: 10.1093/femsec/fiaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.
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Affiliation(s)
- Emilie Lefèvre
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane street, Sloan 101, Box 642910, Pullman, WA 99164, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
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Tang Y, Dai T, Su Z, Hasegawa K, Tian J, Chen L, Wen D. A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology. MICROBIAL ECOLOGY 2020; 79:342-356. [PMID: 31428833 DOI: 10.1007/s00248-019-01421-8] [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: 01/17/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.
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Affiliation(s)
- Yushi Tang
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Kohei Hasegawa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Massachusetts General Hospital, Harvard Medical School, 125 Nashua Street, Boston, MA, 02115, USA
| | - Jinping Tian
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lujun Chen
- School of Environment, Tsinghua University, Beijing, 100084, China
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314050, Zhejiang, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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