DOCSLIB.ORG

Host and Environmental Determinants of Microbial Community Structure in the Marine

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Host and Environmental Determinants of Microbial Community Structure in the Marine 1 Host and environmental determinants of microbial community structure in the marine 2 phyllosphere 3 4 Margaret A. Vogel1, Olivia U. Mason2, and Thomas E. Miller1 5 6 7 Author Affiliations: 1Department of Biological Science, Florida State University, Tallahassee, 8 FL, 2Department of Earth, Ocean, and Atmospheric Science, Florida State University, 9 Tallahassee, FL 10 11 Corresponding Author: Margaret A. Vogel, Address 319 Stadium Drive, Tallahassee, FL 12 32301, Phone (850) 644-9823, Fax (850) 645-8447, Email [email protected] 13 14 15 16 17 18 19 20 Abstract 21 Although seagrasses are economically and ecologically critical foundation species, little 22 is known about their blade surface microbial communities and how those communities relate to 23 overall seagrass health. 16S rRNA gene sequencing (iTag) was used to examine the microbial 24 community composition and diversity on blade surfaces at five sites along a gradient of 25 freshwater input in the northern Gulf of Mexico. Additionally, seagrass surveys were performed 26 and environmental parameters were measured to characterize host characteristics and the in situ 27 conditions at each site. Results show that Thalassia testudinum (turtle grass) blades host unique 28 microbial communities that are distinct in composition and diversity from the water column. In 29 addition, compositional changes within these blade surface communities correlated with both 30 environmental conditions, including water depth, salinity, and temperature, and host 31 characteristics, including seagrass growth rates and blade nutrient composition. These 32 correlations may indicate that blade surface community composition changes with stressful 33 conditions either as a direct or indirect effect. Additionally, 15 microorganisms from five phyla 34 (Cyanobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, and Chloroflexi) were present in 35 all blade surface samples, even after a large disturbance event (Hurricane Irma), and may 36 represent a core community for T. testudinum. Members of this core community may have 37 ecological importance for determining community structure or in performing key community 38 functions. Studies such as this are the first step to understanding what processes influence the 39 structure of marine phyllosphere communities in order to determine how these blade surface 40 communities relate to their host and to seagrass health as a whole. 41 Key Words 42 Seagrass; Bacteria; Core Communities; Phyllosphere; Microbial Ecology 43 Introduction 44 In recent years, there has been an increasing number of studies on the microbial 45 communities associated with plant hosts, especially of those communities associated with the 46 phyllosphere, or leaf surfaces (Lindow and Leveau 2002, Lindow and Brandl 2003, Vorholt 47 2012, Vandenkoornhuyse et al. 2015). We now know that the phyllosphere is a rich habitat that 48 can host up to 107 microbial cells per cm2 of leaf tissue and that these epiphytic microbial 49 communities can have a variety of relationships with their host plants ranging from beneficial to 50 pathogenic (Vorholt 2012). However, leaf associated microbial communities of aquatic plants, 51 including seagrasses, remain largely unexplored when compared to those of terrestrial plants. 52 Seagrasses are a polyphyletic group of angiosperms that colonized the marine 53 environment ~100 million years ago and currently have about 72 species distributed worldwide 54 (Hemminga and Duarte 2000, Short et al. 2011). Seagrasses can form dense monospecific or 55 mixed species meadows that serve as nurseries, feeding grounds, and habitats for a wide variety 56 of marine species from invertebrates to sea turtles and manatees. These foundation species also 57 support bacteria, algal epiphytes, and their grazers, creating highly productive ecosystems 58 (Zieman and Zieman 1989, Hemminga and Duarte 2000). In addition, seagrasses provide 59 valuable ecosystem services, such as stabilizing sediments and trapping and cycling nutrients 60 (Costanza et al. 1997, Duarte 2002, Barbier et al. 2011) and are important sites for blue carbon 61 sequestration (Fourqurean et al. 2012, Duarte et al. 2013). However, with rising anthropogenic 62 influence, eutrophication and degraded water quality are increasingly becoming threats to these 63 important habitats (Duarte 2002, Orth et al. 2006, Short et al. 2011) with seagrass coverage 64 declining at a rate of 110 km2 yr-1 worldwide since 1980 (Waycott et al. 2009). 65 Although there have been a few recent studies on the microbial communities that occur 66 on seagrass blade surfaces (Meija et al. 2016, Fahimipour et al. 2017, Crump et al. 2018, Ugarelli 67 et al. 2019), the interactions between these communities and the seagrass host remain poorly 68 understood. This is especially true for the tropical seagrass species Thalassia testudinum Banks 69 ex Kӧnig (turtle grass), for which there is only one previously published study that contains 70 information about its blade surface microbial communities (Ugarelli et al. 2019). Thalassia 71 testudinum is an important climax species and can be a dominant component of shallow waters 72 in the Caribbean, Western Atlantic, and Gulf of Mexico. In these areas, it can act as an 73 ecosystem engineer creating dense meadows which likely provide more ecosystem services than 74 other smaller seagrass species (Nordlund et al. 2016). Adding to their importance, tropical 75 seagrass meadows often occur adjacent to other critical habitats for biodiversity, such as coral 76 reefs and mangrove forests, and their presence has been correlated with a two-fold reduction of 77 disease levels in nearby corals (Lamb et al. 2017). 78 In the terrestrial phyllosphere, host-species has been found to be a significant driver of 79 variation in microbial community composition with more variation in leaf-associated 80 communities often occurring across plant-host species rather than within a host species even 81 across large spatial scales (Redford et al. 2010, Finkel et al. 2012, Laforest-Lapointe et al. 82 2016a). For instance, intra-specific variability of the microbial communities on Pinus ponderosa 83 was found to be less than inter-specific variability within and across continents (Redford et al. 84 2010). However, variation also occurs between these leaf-associated communities due to 85 environmental conditions, including precipitation/moisture, temperature, and salt content 86 (Jackson et al. 2006, Finkel et al. 2012, Vorholt et al. 2012, Laforest-Lapointe et al. 2016a, 87 2016b, 2017). In a study of seven tree species, the proportion of Alphaproteobacteria, a dominant 88 class in the natural plant microbiome, was found to decrease along a gradient of urban intensity 89 (Laforest-Lapointe et al. 2017). These compositional shifts can lead to changes in the 90 relationship between these leaf associated microbial communities and their host plant which can 91 ultimately affect host fitness and performance (Lindow and Leveau 2002, Vandenkoornhuyse et 92 al. 2015, Saleem et al. 2017). However, it is unknown how much variation exists within leaf- 93 associated microbial communities in the marine phyllosphere and what roles both biotic and 94 abiotic factors play in determining microbial community structure. 95 Characterizing the variation in blade surface microbial communities on seagrasses is the 96 first step to understanding the relative influence of host and environmental conditions on 97 community structure in the marine phyllosphere, which is essential to elucidating the potential 98 role of these microbial communities as a part of the seagrass holobiont. This study is the first to 99 use 16S rRNA amplicon sequencing (iTag: Illumina platform) to characterize the structure and 100 diversity of the microbial communities associated with T. testudinum blades and to examine 101 whether these microbial communities vary in composition with environmental and host 102 characteristics. 103 104 Methods 105 Sampling Location 106 This study took place in Apalachee Bay in the northern Gulf of Mexico along the Florida 107 Panhandle. The coastline of this area is mostly undeveloped with the St. Marks National Wildlife 108 Refuge occupying the adjacent land area. Five sites (ABT-1 – ABT-5) were established starting 109 near the mouth of the St. Marks River (30.07059°N, 84.16687°W) and extending south in a 110 linear fashinon approximately two miles into the bay (30.04194°N, 84.16634°W). These sites are 111 situated along a gradient of abiotic conditions caused by riverine input with the farthest site from 112 shore located on a shoal. Seagrasses in this region form dense meadows that have mixed species 113 composition. Thalassia testudinum is the dominant species at all study sites, however 114 Syringodium filiforme Kützing (manatee grass) is common along with small amounts of 115 Halodule wrightii Ascherson (shoal grass) and Halophila engelmannii Ascherson (star grass). 116 Microbial Sampling 117 To determine microbial community structure and diversity, samples were taken at all five sites 118 on three separate dates (22-Jul, 20-Aug, and 21-Sep-2016) capturing both spatial and temporal 119 variation. On each date, samples were taken from both the blade surface and water column with 120 all sites visited during a six-hour period. To sample water column communities, 1 liter of 121 seawater was collected from above the seagrass canopy, filtered using a sterile syringe with a 2.7 122 µM pre-filter, and microbial biomass was collected on a 0.22 μM Sterivex™ filter. To capture the 123 blade surface microbial communities, T. testudinum blades from five haphazardly chosen shoots 124 at least one meter apart were removed using sterile forceps at each site. The blade surface 125 microbial communities were then sampled using a sterile swab (PurFlock® Ultra, Puritan 126 Diagnostics, LLC). Microbial sampling was standardized by using the second oldest blade in the 127 shoot and only swabbing healthy tissue free of algal epiphytes. Microbial samples (swabs and 128 Sterivex™ filters) were immediately fixed in RNAlater® and placed on dry ice to be transported 129 to Florida State University where all samples were stored at -80°C until further processing.
Load more

Recommended publications
  • How Can We Define “Optimal Microbiota?”
    REVIEW published: 02 October 2018 doi: 10.3389/fnut.2018.00090 How Can We Define “Optimal Microbiota?”: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture Wakako Ikeda-Ohtsubo 1*, Sylvia Brugman 2, Craig H. Warden 3, Johanna M. J. Rebel 4, Gert Folkerts 5 and Corné M. J. Pieterse 6 1 Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan, 2 Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands, 3 Departments of Pediatrics, Neurobiology Physiology and Behavior, University of California, Davis, Davis, CA, United States, 4 Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands, 5 Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands, 6 Plant–Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of Edited by: studies on the microbiota of animals, fish, and plants of economic importance is rapidly Raquel Hontecillas, expanding and there are increasing expectations that productivity and sustainability Virginia Tech, United States in agricultural management can be improved by microbiota manipulation. However, Reviewed by: Abdel Qawasmeh, optimizing microbiota is still
    [Show full text]
  • Microbial Phyllosphere Populations Are More Complex Than Previously Realized
    Microbial phyllosphere populations are more complex than previously realized Ching-Hong Yang*, David E. Crowley†, James Borneman*, and Noel T. Keen*‡ Departments of *Plant Pathology and †Environmental Sciences, University of California, Riverside, CA 92521 Contributed by Noel T. Keen, December 29, 2000 Phyllosphere microbial communities were evaluated on leaves of including fatty acid methyl ester (FAME), phospholipid fatty field-grown plant species by culture-dependent and -independent acid ester (PLFA), C0t1/2 curve analysis, and denaturing gradient methods. Denaturing gradient gel electrophoresis (DGGE) with 16S gel electrophoresis (DGGE) have also been applied to analyze rDNA primers generally indicated that microbial community struc- microbial communities with or without culturing microbes (15– tures were similar on different individuals of the same plant 19). In virtually all cases, culture-independent methods have species, but unique on different plant species. Phyllosphere bac- revealed more complexity in the microbial populations of par- teria were identified from Citrus sinesis (cv. Valencia) by using ticular ecosystems than culture-based methods. Although cul- DGGE analysis followed by cloning and sequencing of the domi- ture-independent methods have been widely used on samples nant rDNA bands. Of the 17 unique sequences obtained, database from soil, water, and the rhizosphere, they have not been used queries showed only four strains that had been described previ- to examine the phyllosphere (8, 12, 20–26). ously as phyllosphere bacteria. Five of the 17 sequences had 16S In this study, phyllosphere communities on seven different similarities lower than 90% to database entries, suggesting that plant species were evaluated with culture-dependent and -inde- they represent previously undescribed species.
    [Show full text]
  • Engineering the Microbiome for Animal Health and Conservation
    Minireview Engineering the microbiome for animal health and conservation Se Jin Song1 , Douglas C Woodhams2,3, Cameron Martino4, Celeste Allaband5, Andre Mu6,7, Sandrine Javorschi-Miller-Montgomery8,9, Jan S Suchodolski10 and Rob Knight1,8,9,11 1Department of Pediatrics, University of California, San Diego, CA 92093, USA; 2Biology Department, University of Massachusetts Boston, Boston, MA 02125, USA; 3Smithsonian Tropical Research Institute, Panama city 0843-03092, Panama; 4Bioinformatics and Systems Biology Program, University of California, San Diego, CA 92093, USA; 5Biomedical Sciences Graduate Program, University of California, San Diego, CA 92093, USA; 6Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville 3010, Australia; 7Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville 3010, Australia; 8Department of Bioengineering, University of California, San Diego, CA 92093, USA; 9Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA; 10Gastrointestinal Laboratory, Texas A&M University, College Station, TX 77843, USA; 11Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA Corresponding authors: Se Jin Song. Email: [email protected]; Rob Knight. Email: [email protected] Impact statement Abstract Considering the clear effects of microbiota Interest in animal microbiomes as therapeutics is rapidly expanding,
    [Show full text]
  • Shaping the Leaf Microbiota: Plant–Microbe–Microbe Interactions
    applyparastyle "fig//caption/p[1]" parastyle "FigCapt" Journal of Experimental Botany, Vol. 72, No. 1 pp. 36–56, 2021 doi:10.1093/jxb/eraa417 Advance Access Publication 10 September 2020 This paper is available online free of all access charges (see https://academic.oup.com/jxb/pages/openaccess for further details) REVIEW PAPER Shaping the leaf microbiota: plant–microbe–microbe Downloaded from https://academic.oup.com/jxb/article/72/1/36/5903797 by Max-Planck-Institut fur Zuchtungsforschung user on 03 May 2021 interactions Vasvi Chaudhry1,*, , Paul Runge1,2,* Priyamedha Sengupta3,*, Gunther Doehlemann3, , Jane E. Parker2,3 and Eric Kemen1,†, 1 Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Tübingen, Germany 2 Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Köln, Germany 3 Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, Zuelpicher Str. 47a, D-50674 Cologne, Germany * These authors contributed equally to this work. † Correspondence: [email protected] Received 1 May 2020; Editorial decision 2 September 2020; Accepted 7 September 2020 Editor: Stanislav Kopriva, University of Cologne, Germany Abstract The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf’s phys- ical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces Phyllosphere microbe–microbe interactions | that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes.
    [Show full text]
  • Article Mode, Which Adds to a Better and Living Conditions of Microorganisms in the Atmosphere Understanding of the Overall Atmospheric Microbiome
    Biogeosciences, 15, 4205–4214, 2018 https://doi.org/10.5194/bg-15-4205-2018 © Author(s) 2018. This work is distributed under the Creative Commons Attribution 4.0 License. Community composition and seasonal changes of archaea in coarse and fine air particulate matter Jörn Wehking1,2, Daniel A. Pickersgill1,2, Robert M. Bowers3,4, David Teschner1,2, Ulrich Pöschl2, Janine Fröhlich-Nowoisky2, and Viviane R. Després1,2 1Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany 2Max Planck Institute for Chemistry, P.O. Box 3060, 55020 Mainz, Germany 3DOE Joint Genome Institute, Walnut Creek, CA, USA 4University of Colorado, Ecology and Evolutionary Biology, Boulder, CO, USA Correspondence: Viviane R. Després ([email protected]) and Jörn Wehking ([email protected]) Received: 1 December 2017 – Discussion started: 14 December 2017 Revised: 11 June 2018 – Accepted: 15 June 2018 – Published: 11 July 2018 Abstract. Archaea are ubiquitous in terrestrial and marine narchaeaceae, Nitrososphaeraceae, Methanosarcinales, Ther- environments and play an important role in biogeochemical moplasmata, and the genus Nitrosopumilus as the dominating cycles. Although air acts as the primary medium for their taxa. dispersal among different habitats, their diversity and abun- The seasonal dynamics of methanogenic Euryarchaeota dance is not well characterized. The main reason for this point to anthropogenic activities, such as fertilization of agri- lack of insight is that archaea are difficult to culture, seem cultural fields with biogas substrates or manure, as sources of to be low in number in the atmosphere, and have so far been airborne archaea. This study gains a deeper insight into the difficult to detect even with molecular genetic approaches.
    [Show full text]
  • 11 Microbial Communities in the Phyllosphere Johan H.J
    Biology of the Plant Cuticle Edited by Markus Riederer, Caroline Müller Copyright © 2006 by Blackwell Publishing Ltd Biology of the Plant Cuticle Edited by Markus Riederer, Caroline Müller Copyright © 2006 by Blackwell Publishing Ltd 11 Microbial communities in the phyllosphere Johan H.J. Leveau 11.1 Introduction The term phyllosphere was coined by Last (1955) and Ruinen (1956) to describe the plant leaf surface as an environment that is physically, chemically and biologically distinct from the plant leaf itself or the air surrounding it. The term phylloplane has been used also, either instead of or in addition to the term phyllosphere. Its two- dimensional connotation, however, does not do justice to the three dimensions that characterise the phyllosphere from the perspective of many of its microscopic inhab- itants. On a global scale, the phyllosphere is arguably one of the largest biological surfaces colonised by microorganisms. Satellite images have allowed a conservative approximation of 4 × 108 km2 for the earth’s terrestrial surface area covered with foliage (Morris and Kinkel, 2002). It has been estimated that this leaf surface area is home to an astonishing 1026 bacteria (Morris and Kinkel, 2002), which are the most abundant colonisers of cuticular surfaces. Thus, the phyllosphere represents a significant refuge and resource of microorganisms on this planet. Often-used terms in phyllosphere microbiology are epiphyte and epiphytic (Leben, 1965; Hirano and Upper, 1983): here, microbial epiphytes or epiphytic microorganisms, which include bacteria, fungi and yeasts, are defined as being cap- able of surviving and thriving on plant leaf and fruit surfaces. Several excellent reviews on phyllosphere microbiology have appeared so far (Beattie and Lindow, 1995, 1999; Andrews and Harris, 2000; Hirano and Upper, 2000; Lindow and Leveau, 2002; Lindow and Brandl, 2003).
    [Show full text]
  • Environmental and Plant Genetic Factors Influencing Phyllosphere
    University of Warwick institutional repository: http://go.warwick.ac.uk/wrap This paper is made available online in accordance with publisher policies. Please scroll down to view the document itself. Please refer to the repository record for this item and our policy information available from the repository home page for further information. To see the final version of this paper please visit the publisher’s website. Access to the published version may require a subscription. Author(s): Whipps, J.M.; Hand, P.; Pink, D.; Bending, G.D. Article Title: Phyllosphere microbiology with special reference to diversity and plant genotype Year of publication: 2008 Link to published version: http://dx.doi.org/10.1111/j.1365- 2672.2008.03906.x Publisher statement: The definitive version is available at www.blackwell-synergy.com 1 Phyllosphere microbiology with special reference to diversity and plant 2 genotype 3 John M. Whipps, Paul Hand, David Pink and Gary D. Bending 4 Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK 5 6 Summary 7 The phyllosphere represents the habitat provided by the aboveground parts of plants, and on a 8 global scale supports a large and complex microbial community. Microbial interactions in the 9 phyllosphere can affect the fitness of plants in natural communities, the productivity of 10 agricultural crops, and the safety of horticultural produce for human consumption. The 11 structure of phyllosphere communities reflects immigration, survival and growth of microbial 12 colonists, which is influenced by numerous environmental factors in addition to leaf physico- 13 chemical properties. The recent use of culture independent techniques has demonstrated 14 considerable previously unrecognised diversity in phyllosphere bacterial communities.
    [Show full text]
  • Functional Characterization of Microbial Symbiotic Associations by Metaproteomics
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2012 Functional Characterization of Microbial Symbiotic Associations by Metaproteomics Jacque Caprio Young [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Other Genetics and Genomics Commons Recommended Citation Young, Jacque Caprio, "Functional Characterization of Microbial Symbiotic Associations by Metaproteomics. " PhD diss., University of Tennessee, 2012. https://trace.tennessee.edu/utk_graddiss/1595 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Jacque Caprio Young entitled "Functional Characterization of Microbial Symbiotic Associations by Metaproteomics." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Life Sciences. Robert L. Hettich, Major Professor We have read this dissertation and recommend its acceptance: Steven Wilhelm, Kurt Lamour, Mircea Podar, Loren Hauser Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Functional Characterization of Microbial Symbiotic Associations by Metaproteomics A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Jacque Caprio Young December 2012 Copyright © 2012 by Jacque Caprio Young All rights reserved.
    [Show full text]
  • Ecology and Evolution of Plant Microbiomes
    MI73CH04-Raaijmakers ARjats.cls August 13, 2019 9:28 Annual Review of Microbiology Ecology and Evolution of Plant Microbiomes Viviane Cordovez,1 Francisco Dini-Andreote,1 Víctor J. Carrión,1,2 and Jos M. Raaijmakers1,2 1Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; email: [email protected] 2Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands Annu. Rev. Microbiol. 2019. 73:69–88 Keywords First published as a Review in Advance on microbiome assembly, plant domestication, community ecology, May 15, 2019 plant-microbe interaction, microbiome engineering The Annual Review of Microbiology is online at micro.annualreviews.org Abstract https://doi.org/10.1146/annurev-micro-090817- Microorganisms colonizing plant surfaces and internal tissues provide a 062524 number of life-support functions for their host. Despite increasing recog- Copyright © 2019 by Annual Reviews. Annu. Rev. Microbiol. 2019.73:69-88. Downloaded from www.annualreviews.org nition of the vast functional capabilities of the plant microbiome, our un- All rights reserved derstanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of Access provided by Texas A&M University - College Station on 01/10/20. For personal use only. plant genotypic and phenotypic traits as well as allogenic and autogenic fac- tors that shape microbiome composition and functions. We give specific em- phasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial ef- fects on plant growth, development, and health.
    [Show full text]
  • A Brief from the Leaf: Latest Research to Inform Our Understanding of The
    Available online at www.sciencedirect.com ScienceDirect A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome Johan HJ Leveau The plant leaf surface, or phyllosphere, represents a unique and flowers [17,18], pollen [19], fruit [20,21], stalks [22], and challenging microbial biome with a diverse and dynamic bark [23]; not only leaf surface colonizers (known as community of commensal, parasitic, and mutualistic agents of epiphytic, epiphyllous or foliicolous [24,25] microorgan- microscopic proportions. This mini-review offers a digest of isms), but also endophytes that are found within leaf recently published research dedicated to the study of tissues [26,27]; and not only terrestrial, but also sub- phyllosphere microbiota, framed in the context of processes merged plants [28,29]. Here, however, the term and outcomes of microbial community assembly, structure, ‘phyllosphere’ will be used to exclusively refer to aerial and (inter)activity in the phyllosphere, with particular focus on plant leaf surfaces. Such a narrower focus allows this mini- the contributions of environment, plant, and microbe, and on review to 1) highlight the features and challenges unique the potential benefits of interrogating those contributions at to the leaf surface as a microbial biome or habitat, 2) finer resolutions. consider other plant compartments as potential sources and sinks of leaf surface microbes and as connected parts Address of a larger living entity (i.e. the plant) that influences, and Department of Plant Pathology, University of California, Davis, CA is influenced by, leaf surface-associated microbiota, and 3) 95616, USA provoke thinking about the leaf surface itself as consisting of linked but discrete smaller compartments, such as the Corresponding author: Leveau, Johan HJ ([email protected]) phylloplane, that is, leaf surface landscape, and phyllo- telma, that is, leaf surface waterscape [11 ,16].
    [Show full text]
  • Relationships Between Phyllosphere Bacterial Communities and Plant
    Relationships between phyllosphere bacterial SPECIAL FEATURE communities and plant functional traits in a neotropical forest Steven W. Kembela,b,1, Timothy K. O’Connorb,c, Holly K. Arnoldb, Stephen P. Hubbelld,e, S. Joseph Wrightd, and Jessica L. Greenb,f aDépartement des sciences biologiques, Universitédu Québec àMontréal, Montreal, Quebec, Canada H3C 3P8; bInstitute of Ecology and Evolution, University of Oregon, Eugene, OR 97403; cDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; dSmithsonian Tropical Research Institute, Panama 0843-03092, Panama; eDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095; and fSanta Fe Institute, Santa Fe, NM 87501 Edited by Cyrille Violle, Centre National de la Recherche Scientifique, Montpellier, France, and accepted by the Editorial Board January 28, 2014 (received for review November 5, 2012) The phyllosphere—the aerial surfaces of plants, including leaves— taxa but on the entire genomic content of communities of is a ubiquitous global habitat that harbors diverse bacterial com- microbes in different habitats, or “microbiomes” (12). Numerous munities. Phyllosphere bacterial communities have the potential studies of host-associated microbiomes have shown that micro- to influence plant biogeography and ecosystem function through bial biodiversity is a trait (13) that forms part of the extended their influence on the fitness and function of their hosts, but the phenotype of the host organism (4, 14, 15) with important effects host attributes that drive community assembly in the phyllosphere on the health and fitness (16–18) and evolution (19–21) of the are poorly understood. In this study we used high-throughput host.
    [Show full text]
  • Exploring Interactions of Plant Microbiomes Review
    528 Scientia Agricola http://dx.doi.org/10.1590/0103-9016-2014-0195 Review Exploring interactions of plant microbiomes Fernando Dini Andreote*, Thiago Gumiere, Ademir Durrer University of São Paulo/ESALQ – Dept. of Soil Science, C.P. ABSTRACT: A plethora of microbial cells is present in every gram of soil, and microbes are found 09 – 13418-900 – Piracicaba, SP – Brazil. extensively in plant and animal tissues. The mechanisms governed by microorganisms in the *Corresponding author <[email protected]> regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form Edited by: Paulo Cesar Sentelhas distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the “microbial tissue” is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant mi- crobiome, there is substantial evidence that these communities are involved in disease control, enhance nutrient acquisition, and affect stress tolerance. In this review, we first summarize fea- tures of microbial communities that compose the plant microbiome and further present a series of studies describing the underpinning factors that shape the phylogenetic and functional plant- associated communities. We advocate the idea that understanding the mechanisms by which plants select and interact with their microbiomes may have a direct effect on plant development and health, and further lead to the establishment of novel microbiome-driven strategies, that can Received May 30, 2014 cope with the development of a more sustainable agriculture.
    [Show full text]