1
|
Wang Z, Liu J, Xu H, Liu J, Zhao Z, Gong X. Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China. Microorganisms 2023; 11:2144. [PMID: 37763988 PMCID: PMC10537389 DOI: 10.3390/microorganisms11092144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.
Collapse
Affiliation(s)
- Zhaochun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
| | - Haiyan Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhiwei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
| |
Collapse
|
2
|
Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Corrigendum: Divergence with gene flow and contrasting population size blur the species boundary in Cycas Sect. Asiorientales, as inferred from morphology and RAD-seq data. Front Plant Sci 2023; 13:1081728. [PMID: 36714688 PMCID: PMC9879732 DOI: 10.3389/fpls.2022.1081728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.824158.].
Collapse
Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
3
|
Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. Front Plant Sci 2022; 13:824158. [PMID: 35615129 PMCID: PMC9125193 DOI: 10.3389/fpls.2022.824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.
Collapse
Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
4
|
Liu J, Lindstrom AJ, Gong X. Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis. BMC Plant Biol 2022; 22:116. [PMID: 35291941 PMCID: PMC8922756 DOI: 10.1186/s12870-022-03491-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections. RESULTS All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny. CONCLUSIONS Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.
Collapse
Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, 20250, Bangsalae, Sattahip, Chonburi, Thailand.
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
5
|
Tao Y, Chen B, Kang M, Liu Y, Wang J. Genome-Wide Evidence for Complex Hybridization and Demographic History in a Group of Cycas From China. Front Genet 2021; 12:717200. [PMID: 34527022 PMCID: PMC8435751 DOI: 10.3389/fgene.2021.717200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022] Open
Abstract
Cycads represent one of the most ancestral living seed plants as well as one of the most threatened plant groups in the world. South China is a major center and potential origin of Cycas, the most rapidly diversified lineage of cycads. However, genomic-wide diversity of Cycas remains poorly understood due to the challenge of generating genomic markers associated with their inherent large genomes. Here, we perform a comprehensive conservation genomic study based on restriction-site associated DNA sequencing (RADseq) data in six representative species of Cycas in South China. Consistently low genetic diversity and strong genetic differentiation were detected across species. Both phylogenetic inference and genetic structure analysis via several methods revealed generally congruent groups among the six Cycas species. The analysis with ADMIXTURE showed low mixing of genetic composition among species, while individuals of C. dolichophylla exhibited substantial genetic admixture with C. bifida, C. changjiangensis, and C. balansae. Furthermore, the results from Treemix, f4-statistic, and ABBA-BABA test were generally consistent and revealed the complex patterns of interspecific gene flow. Relatively strong signals of hybridization were detected between C. dolichophylla and C. szechuanensis, and the ancestor of C. taiwaniana and C. changjiangensis. Distinct patterns of demographic history were inferred for these species by Stairway Plot, and our results suggested that both climate fluctuation and frequent geological activities during the late Pleistocene exerted deep impacts on the population dynamics of these species in South China. Finally, we explore the practical implications of our findings for the development of conservation strategies in Cycas. The present study demonstrates the efficiency of RADseq for conservation genomic studies on non-model species with large and complex genomes. Given the great significance of cycads as a radical transition in the evolution of plant biodiversity, our study provides important insights into the mechanisms of diversification in such recently radiated living fossil taxa.
Collapse
Affiliation(s)
- Yueqi Tao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bin Chen
- Shanghai Chenshan Botanical Garden, Shanghai, China.,Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Yongbo Liu
- State Environment Protection Key Laboratory of Regional Ecological Process and Functional Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
6
|
Zheng Y, Yang Y, Wang M, Hu S, Wu J, Yu Z. Differences in lipid homeostasis and membrane lipid unsaturation confer differential tolerance to low temperatures in two Cycas species. BMC Plant Biol 2021; 21:377. [PMID: 34399687 PMCID: PMC8369737 DOI: 10.1186/s12870-021-03158-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND C. panzhihuaensis is more tolerant to freezing than C. bifida but the mechanisms underlying the different freezing tolerance are unclear. Photosynthesis is one of the most temperature-sensitive processes. Lipids play important roles in membrane structure, signal transduction and energy storage, which are closely related to the stress responses of plants. In this study, the chlorophyll fluorescence parameters and lipid profiles of the two species were characterized to explore the changes in photosynthetic activity and lipid metabolism following low-temperature exposure and subsequent recovery. RESULTS Photosynthetic activity significantly decreased in C. bifida with the decrease of temperatures and reached zero after recovery. Photosynthetic activity, however, was little affected in C. panzhihuaensis. The lipid composition of C. bifida was more affected by cold and freezing treatments than C. panzhihuaensis. Compared with the control, the proportions of all the lipid categories recovered to the original level in C. panzhihuaensis, but the proportions of most lipid categories changed significantly in C. bifida after 3 d of recovery. In particular, the glycerophospholipids and prenol lipids degraded severely during the recovery period of C. bifida. Changes in acyl chain length and double bond index (DBI) occurred in more lipid classes immediately after low-temperature exposure in C. panzhihuaensis compare with those in C. bifida. DBI of the total main membrane lipids of C. panzhihuaensis was significantly higher than that of C. bifida following all temperature treatments. CONCLUSIONS The results of chlorophyll fluorescence parameters confirmed that the freezing tolerance of C. panzhihuaensis was greater than that of C. bifida. The lipid metabolism of the two species had differential responses to low temperatures. The homeostasis and plastic adjustment of lipid metabolism and the higher level of DBI of the main membrane lipids may contribute to the greater tolerance of C. panzhihuaensis to low temperatures.
Collapse
Affiliation(s)
- Yanling Zheng
- Key Laboratory of State Forestry and Grassland Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650233 Yunnan China
| | - Yongqiong Yang
- Administration Bureau of Panzhihua Cycas National Nature Reserve, Panzhihua, 617000 Sichuan China
| | - Meng Wang
- Key Laboratory of State Forestry and Grassland Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650233 Yunnan China
| | - Shijun Hu
- Key Laboratory of State Forestry and Grassland Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650233 Yunnan China
| | - Jianrong Wu
- Key Laboratory of State Forestry and Grassland Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650233 Yunnan China
| | - Zhixiang Yu
- Administration Bureau of Panzhihua Cycas National Nature Reserve, Panzhihua, 617000 Sichuan China
| |
Collapse
|
7
|
Pecundo MH, Chang ACG, Chen T, dela Cruz TEE, Ren H, Li N. Full-Length 16S rRNA and ITS Gene Sequencing Revealed Rich Microbial Flora in Roots of Cycas spp. in China. Evol Bioinform Online 2021; 17:1176934321989713. [PMID: 33613025 PMCID: PMC7868495 DOI: 10.1177/1176934321989713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/30/2020] [Indexed: 11/30/2022] Open
Abstract
Cycads have developed a complex root system categorized either as normal or coralloid roots. Past literatures revealed that a great diversity of key microbes is associated with these roots. This recent study aims to comprehensively determine the diversity and community structure of bacteria and fungi associated with the roots of two Cycas spp. endemic to China, Cycas debaoensis Zhong & Chen and Cycas fairylakea D.Y. Wang using high-throughput amplicon sequencing of the full-length 16S rRNA (V1-V9 hypervariable) and short fragment ITS region. The total DNA from 12 root samples were extracted, amplified, sequenced, and analyzed. Resulting sequences were clustered into 61 bacteria and 2128 fungal OTUs. Analysis of community structure revealed that the coralloid roots were dominated mostly by the nitrogen-fixer Nostocaceae but also contain other non-diazotrophic bacteria. The sequencing of entire 16S rRNA gene identified four different strains of cyanobacteria under the heterocystous genera Nostoc and Desmonostoc. Meanwhile, the top bacterial families in normal roots were Xanthobacteraceae, Burkholderiaceae, and Bacillaceae. Moreover, a diverse fungal community was also found in the roots of cycads and the predominating families were Ophiocordycipitaceae, Nectriaceae, Bionectriaceae, and Trichocomaceae. Our results demonstrated that bacterial diversity in normal roots of C. fairylakea is higher in richness and abundance than C. debaoensis. On the other hand, a slight difference, albeit insignificant, was noted for the diversity of fungi among root types and host species as the number of shared taxa is relatively high (67%). Our results suggested that diverse microbes are present in roots of cycads which potentially interact together to support cycads survival. Our study provided additional knowledge on the microbial diversity and composition in cycads and thus expanding our current knowledge on cycad-microbe association. Our study also considered the possible impact of ex situ conservation on cyanobiont community of cycads.
Collapse
Affiliation(s)
- Melissa H Pecundo
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aimee Caye G Chang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Tao Chen
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Thomas Edison E dela Cruz
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Hai Ren
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Nan Li
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Wang X, Wu W, Jian S. Transcriptome analysis of two radiated Cycas species and the subsequent species delimitation of the Cycas taiwaniana complex. Appl Plant Sci 2019; 7:e11292. [PMID: 31667020 PMCID: PMC6814181 DOI: 10.1002/aps3.11292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Cycas is an important gymnosperm genus, and the most diverse of all cycad genera. The C. taiwaniana complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources. METHODS We characterized the transcriptomes of two closely related and endangered Cycas species endemic to Hainan, China: C. hainanensis and C. changjiangensis. Three single-copy nuclear genes in the C. taiwaniana complex were sequenced based on these transcriptomes, enabling us to evaluate the species boundaries using the multispecies coalescent method implemented in the Bayesian Phylogenetics and Phylogeography program. RESULTS We obtained 68,184 and 81,561 unigenes for C. changjiangensis and C. hainanensis, respectively. We identified six positively selected genes that are mainly involved in stimulus responses, suggesting that environmental adaptation may have played an important role in the relatively recent divergence of these species. The similar K S distribution peaks at 1.0 observed for the paralogs in the two species indicate a common whole-genome duplication event. Our species delimitation analysis indicated that the C. taiwaniana complex consists of three distinct species, which correspond to the previously reported morphological differences. DISCUSSION Our study provides valuable genetic resources for Cycas species and guidance for the taxonomic treatment of the C. taiwaniana complex, as well as new insights into evolution of species within Cycas.
Collapse
Affiliation(s)
- Xin‐Hui Wang
- Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical GardenChinese Academy of SciencesGuangzhou510650People's Republic of China
- University of Chinese Academy of SciencesBeijing100040People's Republic of China
| | - Wei Wu
- Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical GardenChinese Academy of SciencesGuangzhou510650People's Republic of China
| | - Shu‐Guang Jian
- Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical GardenChinese Academy of SciencesGuangzhou510650People's Republic of China
| |
Collapse
|
9
|
Zheng Y, Chiang TY, Huang CL, Gong X. Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm. J Microbiol 2018; 56:337-45. [PMID: 29721831 DOI: 10.1007/s12275-018-7438-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/11/2018] [Accepted: 02/27/2018] [Indexed: 10/17/2022]
Abstract
As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.
Collapse
|
10
|
Spencer ART, Garwood RJ, Rees AR, Raine RJ, Rothwell GW, Hollingworth NTJ, Hilton J. New insights into Mesozoic cycad evolution: an exploration of anatomically preserved Cycadaceae seeds from the Jurassic Oxford Clay biota. PeerJ 2017; 5:e3723. [PMID: 28875075 PMCID: PMC5578371 DOI: 10.7717/peerj.3723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/31/2017] [Indexed: 11/20/2022] Open
Abstract
Most knowledge concerning Mesozoic Era floras has come from compression fossils. This has been augmented in the last 20 years by rarer permineralized material showing cellular preservation. Here, we describe a new genus of anatomically preserved gymnosperm seed from the Callovian-Oxfordian (Jurassic) Oxford Clay Formation (UK), using a combination of traditional sectioning and synchrotron radiation X-ray micro-tomography (SRXMT). Oxfordiana motturii gen. et sp. nov. is large and bilaterally symmetrical. It has prominent external ribs, and has a three-layered integument comprising: a narrow outer layer of thick walled cells; a thick middle parenchymatous layer; and innermost a thin fleshy layer. The integument has a longitudinal interior groove and micropyle, enveloping a nucellus with a small pollen chamber. The large size, bilateral symmetry and integumentary groove demonstrate an affinity for the new species within the cycads. Moreover, the internal groove in extant taxa is an autapomorphy of the genus Cycas, where it facilitates seed germination. Based upon the unique seed germination mechanism shared with living species of the Cycadaceae, we conclude that O. motturii is a member of the stem-group lineage leading to Cycas after the Jurassic divergence of the Cycadaceae from other extant cycads. SRXMT-for the first time successfully applied to fossils already prepared as slides-reveals the distribution of different mineral phases within the fossil, and allows us to evaluate the taphonomy of Oxfordiana. An early pyrite phase replicates the external surfaces of individual cells, a later carbonate component infilling void spaces. The resulting taphonomic model suggests that the relatively small size of the fossils was key to their exceptional preservation, concentrating sulfate-reducing bacteria in a locally closed microenvironment and thus facilitating soft-tissue permineralization.
Collapse
Affiliation(s)
- Alan R T Spencer
- Department of Earth Science and Engineering, Imperial College London, London, UK
| | - Russell J Garwood
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK.,Department of Earth Sciences, The Natural History Museum London, London, UK
| | - Andrew R Rees
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | - Gar W Rothwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
| | - Neville T J Hollingworth
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK.,Science and Technology Facilities Council, Swindon, UK
| | - Jason Hilton
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK.,Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK
| |
Collapse
|
11
|
Zheng Y, Liu J, Feng X, Gong X. The distribution, diversity, and conservation status of Cycas in China. Ecol Evol 2017; 7:3212-3224. [PMID: 28480020 PMCID: PMC5415521 DOI: 10.1002/ece3.2910] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 11/10/2022] Open
Abstract
As ancient gymnosperm and woody plants, cycads have survived through dramatic tectonic activities, climate fluctuation, and environmental variations making them of great significance in studying the origin and evolution of flora biodiversity. However, they are among the most threatened plant groups in the world. The principal aim of this review is to outline the distribution, diversity, and conservation status of Cycas in China and provide suggestions for conservation practices. In this review, we describe the taxonomy, distribution, and conservation status of Cycas in China. By comparing Chinese Cycas species with its relatives worldwide, we then discuss the current genetic diversity, genetic differentiation of Cycas, and try to disentangle the potential effects of Quaternary climate changes and topographical events on Cycas. We review conservation practices from both researchers and practitioners for these rare and endangered species. High genetic diversity at the species level and strong genetic differentiation within Cycas have been observed. Most Cycas species in southwest China have experienced population retreats in contrast to the coastal Cycas's expansion during the Quaternary glaciation. Additionally, human activities and habitat fragmentation have pushed these endangered taxa to the brink of extinction. Although numerous efforts have been made to mitigate threats to Cycas survival, implementation and compliance monitoring in protection zones are currently inadequate. We outline six proposals to strengthen conservation measures for Cycas in China and anticipate that these measures will provide guidelines for further research on population genetics as well as conservation biology of not only cycads but also other endangered species worldwide.
Collapse
Affiliation(s)
- Ying Zheng
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,Key Laboratory of Economic Plants and Biotechnology Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,University of Chinese Academy of Sciences Beijing China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,Key Laboratory of Economic Plants and Biotechnology Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,University of Chinese Academy of Sciences Beijing China
| | - Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,Key Laboratory of Economic Plants and Biotechnology Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,University of Chinese Academy of Sciences Beijing China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China.,Key Laboratory of Economic Plants and Biotechnology Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China
| |
Collapse
|
12
|
Liu J, Zhou W, Gong X. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China. Front Plant Sci 2015; 6:696. [PMID: 26442013 PMCID: PMC4562272 DOI: 10.3389/fpls.2015.00696] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/21/2015] [Indexed: 06/02/2023]
Abstract
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.
Collapse
Affiliation(s)
- Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Wei Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Yunnan Key Laboratory for Wild Plant ResourcesKunming, China
| |
Collapse
|
13
|
Zhang YJ, Cao KF, Sack L, Li N, Wei XM, Goldstein G. Extending the generality of leaf economic design principles in the cycads, an ancient lineage. New Phytol 2015; 206:817-29. [PMID: 25622799 DOI: 10.1111/nph.13274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 12/08/2014] [Indexed: 05/13/2023]
Abstract
Cycads are the most ancient lineage of living seed plants, but the design of their leaves has received little study. We tested whether cycad leaves are governed by the same fundamental design principles previously established for ferns, conifers and angiosperms, and characterized the uniqueness of this relict lineage in foliar trait relationships. Leaf structure, photosynthesis, hydraulics and nutrient composition were studied in 33 cycad species from nine genera and three families growing in two botanical gardens. Cycads varied greatly in leaf structure and physiology. Similarly to other lineages, light-saturated photosynthetic rate per mass (Am ) was related negatively to leaf mass per area and positively to foliar concentrations of chlorophyll, nitrogen (N), phosphorus and iron, but unlike angiosperms, leaf photosynthetic rate was not associated with leaf hydraulic conductance. Cycads had lower photosynthetic N use efficiency and higher photosynthetic performance relative to hydraulic capacity compared with other lineages. These findings extend the relationships shown for foliar traits in angiosperms to the cycads. This functional convergence supports the modern synthetic understanding of leaf design, with common constraints operating across lineages, even as they highlight exceptional aspects of the biology of this key relict lineage.
Collapse
Affiliation(s)
- Yong-Jiang Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | | | | | | | | |
Collapse
|
14
|
Abstract
UNLABELLED • PREMISE OF THE STUDY Reaction wood (RW) in seed plants can induce late and usually secondary changes in organ orientation. Conifers produce compression wood (CW), generated by compression tracheids, which generate a push force. Angiosperms produce tension wood (TW), generated by tension wood fibers (TWF) often described as "gelatinous fibers," which exert a pull force. Usually RW is produced eccentrically, but it can occur concentrically, as in aerial roots of Ficus. However, gymnosperms can produce gelatinous fibers (tension fibers, TF), as in cortical and secondary phloem tissues (Gnetum). TFs are therefore limited neither to wood, xylem, nor angiosperms. Here we demonstrate that TFs in secondary phloem are involved in contraction of roots of cycads and compare them with TFs of Ficus.• METHODS We sectioned root material of cycads at various stages of seedling development using simple staining and histochemical procedures to follow the course of secondary phloem development. Aerial roots of Ficus were compared with the cycad root material.• KEY RESULTS Tension fibers (gelatinous fibers) occur extensively and continuously in the secondary phloem in roots that undergo contraction. Older tissues, but notably the xylem, become distorted by contraction. TFs in cycads correspond in cell wall features to TFs that occur in Ficus, but do not occur in secondary xylem. The individual fibers visibly contract.• CONCLUSIONS Tissue contraction in Cycas and Zamia corresponds to that found in angiosperms and Gnetum and further broadens the scope of the activity of tension tissues. This finding possibly indicates that gelatinous fibers originated at a very early period of seed plant evolution.
Collapse
Affiliation(s)
- P Barry Tomlinson
- Montgomery Botanical Center 11901 Old Cutler Road, Coral Gables, Florida 33156 USA The Kampong of the National Tropical Botanical Garden, 4013 South Douglas Road, Miami, Florida 33133 USA
| | - Tracy M Magellan
- Montgomery Botanical Center 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - M Patrick Griffith
- Montgomery Botanical Center 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| |
Collapse
|