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Gibson E, Zimmerman NB. Urban biogeography of fungal endophytes across San Francisco. PeerJ 2023; 11:e15454. [PMID: 37547726 PMCID: PMC10399560 DOI: 10.7717/peerj.15454] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/03/2023] [Indexed: 08/08/2023] Open
Abstract
In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.
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Affiliation(s)
- Emma Gibson
- Department of Biology, University of San Francisco, San Francisco, CA, United States of America
| | - Naupaka B. Zimmerman
- Department of Biology, University of San Francisco, San Francisco, CA, United States of America
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2
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Hadi M, Stacy EA. An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex. Appl Plant Sci 2023; 11:e11518. [PMID: 37342165 PMCID: PMC10278935 DOI: 10.1002/aps3.11518] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 06/22/2023]
Abstract
Premise The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse Metrosideros taxa representing a broad range of leaf toughness, pubescence, and secondary metabolites. Methods and Results We tested popular RNA isolation kits and protocols that were effective on other recalcitrant trees, including a broad range of optimization and purification steps. We optimized a protocol involving two silica-membrane column-based kits that yielded high-quantity RNA with an RNA integrity number >7 and without DNA contamination. All RNA samples were used successfully in a follow-on RNA-Seq experiment. Conclusions We present an optimized high-throughput RNA extraction protocol that yielded high-quality and high-quantity RNA from three contrasting leaf phenotypes within a hyperdiverse woody species complex.
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Affiliation(s)
- Maryam Hadi
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevada89154USA
| | - Elizabeth A. Stacy
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevada89154USA
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Choi JY, Dai X, Alam O, Peng JZ, Rughani P, Hickey S, Harrington E, Juul S, Ayroles JF, Purugganan MD, Stacy EA. Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands. Proc Natl Acad Sci U S A 2021; 118:e2023801118. [PMID: 34497122 PMCID: PMC8449318 DOI: 10.1073/pnas.2023801118] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2021] [Indexed: 01/05/2023] Open
Abstract
Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003;
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Inc., New York, NY 10013
| | - Ornob Alam
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Julie Z Peng
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | | | - Scott Hickey
- Oxford Nanopore Technologies Inc., San Francisco, CA 94501
| | | | - Sissel Juul
- Oxford Nanopore Technologies Inc., New York, NY 10013
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89119;
- College of Agriculture, Forestry, and Natural Resource Management, University of Hawaii Hilo, Hilo, HI 96720
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4
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Abstract
A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Michael Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
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Wolkis D, Deans S. Picking from the Past in Preparation for a Pest: Seed Banks Outperform Herbaria as Sources of Preserved 'Ōhi'a Seed. Biopreserv Biobank 2019; 17:583-590. [PMID: 31429591 DOI: 10.1089/bio.2019.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Seed banks serve the purpose of maintaining germplasm for ex situ species preservation. Herbarium vouchers may be a viable source of unique and/or additional seeds for restoration as they can sometimes be from larger and more representative populations compared with seed banks. Rapid 'ōhi'a death (ROD) has emerged as a serious threat against Hawaii's most iconic and foundational forest tree (Metrosideros spp.), and seed banking has been identified as an important strategy in preserving the genetic diversity of 'ōhi'a. With respect to 'ōhi'a we ask the following: (1) what is the long-term viability of 'ōhi'a seeds stored in herbarium conditions, (2) how do herbarium curation practices affect seed viability, and (3) how long do seeds survive using conventional storage methods? We placed fresh 'ōhi'a seeds in a herbarium dryer (57°C/5% relative humidity) for 5 days, freezer (-18°C/95% RH) for 2 weeks, and dryer then freezer, and compared against fresh control seeds. Seeds were harvested from a chronosequence of herbarium specimens, withdrawn from conventional storage conditions up to 3.75 and 6.5 years before experiments began, and germination assessed. There was no difference in the proportion germinated among treatments and control testing for herbarium entry (p = 0.56). Although no seeds from herbarium specimens germinated, freshly collected dried and frozen seeds germinated at a level equivalent to the control (p = 0.76). For seeds stored using conventional storage methods at 3.75 and 6.5 years, germination was equivalent to freshly harvested seeds. This suggests that seeds can survive the extreme climate conditions necessary to enter herbaria, but lose viability after storage at ambient conditions in 4 years or less. Although 'ōhi'a seeds may be plentiful in herbaria, we recommend using seeds deposited into seed banks using conventional storage methods for orthodox seeds for postdisturbance restoration, and to combat ROD.
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Affiliation(s)
- Dustin Wolkis
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaii
| | - Susan Deans
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaii.,Department of Plant Science, Chicago Botanic Garden, Glencoe, Illinois.,Plant Biology and Conservation, Northwestern University, Evanston, Illinois
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6
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Stacy EA, Paritosh B, Johnson MA, Price DK. Incipient ecological speciation between successional varieties of a dominant tree involves intrinsic postzygotic isolating barriers. Ecol Evol 2017; 7:2501-2512. [PMID: 28428842 PMCID: PMC5395442 DOI: 10.1002/ece3.2867] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 12/08/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 01/18/2023] Open
Abstract
Whereas disruptive selection imposed by heterogeneous environments can lead to the evolution of extrinsic isolating barriers between diverging populations, the evolution of intrinsic postzygotic barriers through divergent selection is less certain. Long-lived species such as trees may be especially slow to evolve intrinsic isolating barriers. We examined postpollination reproductive isolating barriers below the species boundary, in an ephemeral hybrid zone between two successional varieties of the landscape-dominant Hawaiian tree, Metrosideros polymorpha, on volcanically active Hawai'i Island. These archipelago-wide sympatric varieties show the weakest neutral genetic divergence of any taxon pair on Hawai'i Island but significant morphological and ecological differentiation consistent with adaptation to new and old lava flows. Cross-fertility between varieties was high and included heterosis of F1 hybrids at the seed germination stage, consistent with a substantial genetic load apparent within varieties through low self-fertility and a lack of self-pollen discrimination. However, a partial, but significant, barrier was observed in the form of reduced female and male fertility of hybrids, especially backcross hybrids, consistent with the accumulation of genetic incompatibilities between varieties. These results suggest that partial intrinsic postzygotic barriers can arise through disruptive selection acting on large, hybridizing populations of a long-lived species.
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Affiliation(s)
- Elizabeth A Stacy
- Department of Biology University of Hawai'i Hilo Hilo HI USA.,Tropical Conservation Biology and Environmental Science Graduate Program University of Hawai'i Hilo Hilo HI USA.,Present address: School of Life Sciences University of Nevada, Las Vegas 4505 S Maryland Pkwy Las Vegas NV 89154 USA
| | - Bhama Paritosh
- Department of Biology University of Hawai'i Hilo Hilo HI USA
| | - Melissa A Johnson
- Tropical Conservation Biology and Environmental Science Graduate Program University of Hawai'i Hilo Hilo HI USA.,Present address: Department of Botany Claremont Graduate University, Rancho Santa Ana Botanic Garden 1500 N. College Ave. Claremont CA 91711 USA
| | - Donald K Price
- Department of Biology University of Hawai'i Hilo Hilo HI USA.,Tropical Conservation Biology and Environmental Science Graduate Program University of Hawai'i Hilo Hilo HI USA.,Present address: School of Life Sciences University of Nevada, Las Vegas 4505 S Maryland Pkwy Las Vegas NV 89154 USA
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Izuno A, Hatakeyama M, Nishiyama T, Tamaki I, Shimizu-Inatsugi R, Sasaki R, Shimizu KK, Isagi Y. Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations. J Plant Res 2016; 129:727-736. [PMID: 27052216 DOI: 10.1007/s10265-016-0822-3] [Citation(s) in RCA: 10] [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: 01/12/2016] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.
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Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ryuta Sasaki
- Organization of Frontier Science and Innovation, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Stacy EA. Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae. Appl Plant Sci 2014; 2:apps1400049. [PMID: 25309837 PMCID: PMC4189496 DOI: 10.3732/apps.1400049] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/13/2014] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY Primers were developed to amplify low-copy nuclear genes in Hawaiian Metrosideros (Myrtaceae). • METHODS AND RESULTS Data from a pooled 454 Titanium run of the partial transcriptomes of four Metrosideros taxa were used to identify the loci of interest. Ten exon-primed intron-crossing (EPIC) markers were amplified and sequenced directly with success in Metrosideros, as well as in a representative selection of Myrtaceae, including Syzygium, Psidium, and Melaleuca for most of the markers. The loci amplified ranged between 500 and 1100 bp, and up to 117 polymorphic sites were observed within an individual gene alignment. Two introns contained microsatellites in some of the species. • CONCLUSIONS These novel primer pairs should be useful for phylogenetic analysis and population genetics of a broad range of Myrtaceae, particularly the diverse fleshy-fruited tribes Syzygieae and Myrteae.
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Affiliation(s)
- Yohan Pillon
- Tropical Conservation Biology and Environmental Science Program, University of Hawai‘i at Hilo, 200 West Kawili Street, Hilo, Hawai‘i 96720 USA
| | - Jennifer Johansen
- Tropical Conservation Biology and Environmental Science Program, University of Hawai‘i at Hilo, 200 West Kawili Street, Hilo, Hawai‘i 96720 USA
| | - Tomoko Sakishima
- Tropical Conservation Biology and Environmental Science Program, University of Hawai‘i at Hilo, 200 West Kawili Street, Hilo, Hawai‘i 96720 USA
| | - Srikar Chamala
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610 USA
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610 USA
| | - Elizabeth A. Stacy
- Tropical Conservation Biology and Environmental Science Program, University of Hawai‘i at Hilo, 200 West Kawili Street, Hilo, Hawai‘i 96720 USA
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