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Kang L, Luo W, Dai Q, Zhou H, Wei W, Tang J, Han H, Yuan Y, Long J, Zhang Z, Hong M. Giant pandas' staple food bamboo phyllosphere fungal community and its influencing factors. Front Microbiol 2022; 13:1009588. [PMID: 36246256 PMCID: PMC9561849 DOI: 10.3389/fmicb.2022.1009588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
Giant pandas have developed a series of foraging strategies to adapt to their special bamboo diets. Although bamboo is an important food resource for giant pandas in Liziping National Nature Reserve (Liziping NR), China, there are relatively few studies on their phyllosphere fungal community and its influencing factors. Herein, we used ITS1 amplification and metagenomic sequencing to analyze the phyllosphere fungi diversity and functions (KEGG, CAZyme, and antibiotic resistance gene) and explore the influencing factors for the three giant pandas foraging bamboo species (Arundinaria spanostachya, AS; Yushania lineolate, YL; and Fargesia ferax, FF) over different seasons (spring vs. autumn) in Liziping NR, China. We found that Ascomycota and Basidiomycota were the most dominant phyla in the bamboo phyllosphere. The alpha diversity (e.g., the Sobs index and Shannon index) was relatively higher in autumn samples than in spring samples, and the community structure differed significantly between the three bamboo species in spring and autumn. Some biotic and abiotic variables (e.g., the elevation and mean base diameter of bamboo) significantly influenced the abundance, diversity, and community structure of the bamboo phyllosphere fungal community. Moreover, the functional analysis showed the differences in the glycoside hydrolase community and antibiotic resistance gene (ARG) profile between spring and autumn samples. Co-occurrence network modeling suggested that AS phyllosphere fungal communities in autumn employed a much more complex network than that in spring, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was high and closely correlated with other ARGs. These results indicate that fungal community's abundance, diversity, and community structure are mainly affected by the season, host species, and elevation. The season and host species are major factors affecting the biological functions (KEGG and CAZyme), ARGs, and interactions between sympatric bacterial and fungal communities in bamboo phyllosphere. This integrated study can provide a reference basis for the seasonal management of bamboo resources foraged by wild giant pandas, and predict the risk of antibiotic resistance in bamboo phyllosphere fungal flora in Liziping NR (Xiaoxiangling mountains), China.
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Affiliation(s)
- Liwen Kang
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Wei Luo
- Liziping National Nature Reserve Administration, Ya’an, China
| | - Qinglong Dai
- Liziping National Nature Reserve Administration, Ya’an, China
| | - Hong Zhou
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Wei Wei
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Junfeng Tang
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Han Han
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yuan Yuan
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Juejie Long
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Zejun Zhang
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Mingsheng Hong
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
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Dale JCM, Newman JA. A First Draft of the Core Fungal Microbiome of Schedonorus arundinaceus with and without Its Fungal Mutualist Epichloë coenophiala. J Fungi (Basel) 2022; 8:jof8101026. [PMID: 36294590 PMCID: PMC9605371 DOI: 10.3390/jof8101026] [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: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022] Open
Abstract
Tall fescue (Schedonorus arundinaceus) is a cool-season grass which is commonly infected with the fungal endophyte Epichloë coenophiala. Although the relationship between tall fescue and E. coenophiala is well-studied, less is known about its broader fungal communities. We used next-generation sequencing of the ITS2 region to describe the complete foliar fungal microbiomes in a set of field-grown tall fescue plants over two years, and whether these fungal communities were affected by the presence of Epichloë. We used the Georgia 5 cultivar of tall fescue, grown in the field for six years prior to sampling. Plants were either uninfected with E. coenophiala, or they were infected with one of two E. coenophiala strains: The common toxic strain or the AR542 strain (sold commerically as MaxQ). We observed 3487 amplicon sequence variants (ASVs) across all plants and identified 43 ASVs which may make up a potential core microbiome. Fungal communities did not differ strongly between Epichloë treatments, but did show a great deal of variation between the two years. Plant fitness also changed over time but was not influenced by E. coenophiala infection.
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Affiliation(s)
- Jenna C. M. Dale
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
| | - Jonathan A. Newman
- Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
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Dea HI, Urban A, Kazarina A, Houseman GR, Thomas SG, Loecke T, Greer MJ, Platt TG, Lee S, Jumpponen A. Precipitation, Not Land Use, Primarily Determines the Composition of Both Plant and Phyllosphere Fungal Communities. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:805225. [PMID: 37746168 PMCID: PMC10512219 DOI: 10.3389/ffunb.2022.805225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 06/10/2022] [Indexed: 09/26/2023]
Abstract
Plant communities and fungi inhabiting their phyllospheres change along precipitation gradients and often respond to changes in land use. Many studies have focused on the changes in foliar fungal communities on specific plant species, however, few have addressed the association between whole plant communities and their phyllosphere fungi. We sampled plant communities and associated phyllosphere fungal communities in native prairie remnants and post-agricultural sites across the steep precipitation gradient in the central plains in Kansas, USA. Plant community cover data and MiSeq ITS2 metabarcode data of the phyllosphere fungal communities indicated that both plant and fungal community composition respond strongly to mean annual precipitation (MAP), but less so to land use (native prairie remnants vs. post-agricultural sites). However, plant and fungal diversity were greater in the native remnant prairies than in post-agricultural sites. Overall, both plant and fungal diversity increased with MAP and the communities in the arid and mesic parts of the gradient were distinct. Analyses of the linkages between plant and fungal communities (Mantel and Procrustes tests) identified strong correlations between the composition of the two. However, despite the strong correlations, regression models with plant richness, diversity, or composition (ordination axis scores) and land use as explanatory variables for fungal diversity and evenness did not improve the models compared to those with precipitation and land use (ΔAIC < 2), even though the explanatory power of some plant variables was greater than that of MAP as measured by R2. Indicator taxon analyses suggest that grass species are the primary taxa that differ in the plant communities. Similar analyses of the phyllosphere fungi indicated that many plant pathogens are disproportionately abundant either in the arid or mesic environments. Although decoupling the drivers of fungal communities and their composition - whether abiotic or host-dependent - remains a challenge, our study highlights the distinct community responses to precipitation and the tight tracking of the plant communities by their associated fungal symbionts.
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Affiliation(s)
- Hannah I. Dea
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Abigail Urban
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Gregory R. Houseman
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Samantha G. Thomas
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, United States
| | - Terry Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, United States
- Environmental Studies Program, University of Kansas, Lawrence, KS, United States
| | - Mitchell J. Greer
- Department of Agriculture and Nutrition Science, Southern Utah University, Cedar City, UT, United States
| | - Thomas G. Platt
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Sonny Lee
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, United States
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O'Brien AM, Ginnan NA, Rebolleda-Gómez M, Wagner MR. Microbial effects on plant phenology and fitness. AMERICAN JOURNAL OF BOTANY 2021; 108:1824-1837. [PMID: 34655479 DOI: 10.1002/ajb2.1743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Plant development and the timing of developmental events (phenology) are tightly coupled with plant fitness. A variety of internal and external factors determine the timing and fitness consequences of these life-history transitions. Microbes interact with plants throughout their life history and impact host phenology. This review summarizes current mechanistic and theoretical knowledge surrounding microbe-driven changes in plant phenology. Overall, there are examples of microbes impacting every phenological transition. While most studies have focused on flowering time, microbial effects remain important for host survival and fitness across all phenological phases. Microbe-mediated changes in nutrient acquisition and phytohormone signaling can release plants from stressful conditions and alter plant stress responses inducing shifts in developmental events. The frequency and direction of phenological effects appear to be partly determined by the lifestyle and the underlying nature of a plant-microbe interaction (i.e., mutualistic or pathogenic), in addition to the taxonomic group of the microbe (fungi vs. bacteria). Finally, we highlight biases, gaps in knowledge, and future directions. This biotic source of plasticity for plant adaptation will serve an important role in sustaining plant biodiversity and managing agriculture under the pressures of climate change.
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Affiliation(s)
- Anna M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nichole A Ginnan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, CA, USA
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, USA
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Bernard J, Wall CB, Costantini MS, Rollins RL, Atkins ML, Cabrera FP, Cetraro ND, Feliciano CKJ, Greene AL, Kitamura PK, Olmedo-Velarde A, Sirimalwatta VNS, Sung HW, Thompson LPM, Vu HT, Wilhite CJ, Amend AS. Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. THE ISME JOURNAL 2021; 15:999-1009. [PMID: 33188299 PMCID: PMC8115680 DOI: 10.1038/s41396-020-00826-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep, but short, environmental gradient within a single Hawaiian watershed. At each location, we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. The composition of bacterial communities is better explained by microhabitat, while location better predicted compositional variance for fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacterial composition. Additionally, the rates of fungal community compositional dissimilarity along the gradient differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings indicate that both environmental context and microhabitat contribute to microbial compositional variance in our study, but that these contributions are influenced by the domain of microbe and the specific microhabitat in question, suggesting a complicated and potentially interacting dynamic.
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Affiliation(s)
- Jared Bernard
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Christopher B. Wall
- grid.410445.00000 0001 2188 0957Hawai’i Institute of Marine Biology, University of Hawai’i–Mānoa, 46-007 Lilipuna Road, Kāneʻohe, HI 96744 USA ,grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Maria S. Costantini
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Randi L. Rollins
- grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA ,grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Melissa L. Atkins
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Feresa P. Cabrera
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Nicolas D. Cetraro
- grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Christian K. J. Feliciano
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Austin L. Greene
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Philip K. Kitamura
- grid.410445.00000 0001 2188 0957Department of Natural Resources and Environmental Management, University of Hawai’i–Mānoa, 1910 East-West Road, Honolulu, HI 96822 USA
| | - Alejandro Olmedo-Velarde
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Vithanage N. S. Sirimalwatta
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Helen W. Sung
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Leah P. M. Thompson
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Huong T. Vu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawai’i–Mānoa, 1955 East-West Road, Honolulu, HI 96822 USA
| | - Chad J. Wilhite
- grid.410445.00000 0001 2188 0957Department of Natural Resources and Environmental Management, University of Hawai’i–Mānoa, 1910 East-West Road, Honolulu, HI 96822 USA
| | - Anthony S. Amend
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
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