DOCSLIB.ORG

"Phytobiomes, the Reason Why Microbiologists and Botanists

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Annual Plant Reviews (2019) 2, 1–34 http://onlinelibrary.wiley.com doi: 10.1002/9781119312994.apr0699 PHYTOBIOMES, THE REASON WHY MICROBIOLOGISTS AND BOTANISTS SHOULD WORK TOGETHER Michelle Snoeijenbos1, Martha Cárdenas1,3, Marcela Guevara-Suarez1,3, Adriana Bernal1, Pedro Jiménez2 and Silvia Restrepo1,3 1Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia 2Facultad de ciencias básicas y aplicadas, Universidad Militar Nueva Granada, Bogotá, Colombia 3Vicerrectoría de Investigaciones, Universidad de los Andes, Bogotá, Colombia Abstract: Phytobiomes consist of plants, their environment, and their associated communities of macro and microorganisms. Within the phytobiome, the micro- biome consists of the microorganisms associated with the plants comprising the endophytes and epiphytes. Endophytes are microorganisms, mainly consisting of bacteria and fungi, which colonise internal plant tissues without causing any dis- ease symptom or tissue damage in different hosts. All these organisms associated to the plant contribute to its fitness. In this article, we revised a total of 103stud- ies containing the terms phytobiomes and microbiomes and endophytes, with the aims of reviewing: (i) the evolution of the term endophyte and the evolution of the endophyte condition; (ii) the current literature on studies considering the endo- phyte community within phytobiomes; and (iii) the literature on the bacteria living in fungal endophytes. In our analyses, we highlighted the biases that have been introduced in the phytobiomes’ studies. For example, the presence of endohyphal bacteria could have contributed to overestimating the number of bacterial endo- phytes in the scientific literature. This is the first article that includes studies that evaluate endophytes that are not considered alone but belonging to a complex interacting community, the phytobiome. Keywords: endohyphal bacteria, endophyte, microbiome, phytobiome Annual Plant Reviews Online, Volume 2. Edited by Jeremy Roberts. © 2019 John Wiley & Sons, Ltd. Published 2019 by John Wiley & Sons, Ltd. 1 M Snoeijenbos et al. 1 Introduction: Plants Are Not Alone: A Continuum of Interactions That Define the Plant Phenotype Most endophytes, mainly bacteria and fungi, colonise internal plant tissues without causing disease symptoms or tissue damage to their hosts (Schulz and Boyle, 2005; Kogel et al., 2006). However, in one of the most influential reviews on endophytes, Schulz and Boyle showed that there is a continuum of phenotypes shown by endophytes within a plant (Schulz and Boyle, 2005). The microorganisms, for their whole – or nearly whole – life cycle can inconspicuously colonise tissues of healthy plants. There are several reports showing that this interaction can be mutualistic and, among other benefits, endophytes are able to protect plants against pathogens (Siegel et al., 1987; Stone et al., 2000). Furthermore, endophytes can also cause disease (Jumpponen, 2001; Sieber, 2002; Schulz and Boyle, 2005). There are multiple studies on endophytes but, to the best of our knowl- edge, there are no reviews published on the study of endophytes when the whole microbial community, the microbiome, or the whole environment and all micro- and macro-organisms living in, on, or around the plant, the phy- tobiome are considered. Prior to 2001, the term microbiome was also in use, mostly to infer a very small ecological niche incorporating plant and animal life. Nowadays, the microbiome is the collection of microorganisms that live on and within the tissues of plants. The microbiome is an important part of the phytobiome, which includes all organisms that could be in association with a given plant. The portion of the microbial community living inside the plant is known as the endophyte community. The phytobiome is now seen as an important partner of the plant, necessary to maintain homeostasis and general health of the plant itself. Thus, for the main sections of this article, we decided to focus on those studies that aimed to characterise the phytobiomes as a whole, but our analyses focused on the endophytic part of the microbiome. A total of 103 research articles on endophytes within plant microbiomes, published in English language peer-reviewed research journals, were located in the litera- ture during September 2018 (the 103 references appear in the section ‘Further Reading’). The articles were found in the online SCOPUS database using the keyword phrases ‘Phytobiome AND Plant microbiome AND Endophytic community’. Our aim in this article is threefold: (i) to very shortly revise the evolution of the term endophyte and the evolution of the endophyte condition, (ii) to review the current literature on studies considering the endophyte commu- nity within phytobiomes, and (iii) to review the literature on the bacteria living in fungal endophytes that are part of phytobiome communities. This last section will discuss important questions, pertinent to all studies con- ducted so far: (i) have we overestimated the plant bacterial endophytes when in fact they were endohyphal bacteria (EHB) of plant endophytes? (ii) Do Annual Plant Reviews Online, Volume 2. Edited by Jeremy Roberts. © 2019 John Wiley & Sons, Ltd. Published 2019 by John Wiley & Sons, Ltd. 2 Phytobiomes these EHB influence the behaviour of the endophytes and the production of their secondary metabolites? 2 Endophyte Definition and Evolution of the Endophytic Lifestyle The term ‘endophyte’ first appeared in scientific publications in the works of the German botanist Anton de Bary during the nineteenth century (de Bary, 1866), and the first isolation of one of these organisms was performed in1904 from Lolium temulentum (Freeman, 1904). Since then, this word has become part of the key terminology in the fields of mycology, phytopathology, and botany but its meaning has changed, adapted and been debated extensively in the last 100 years. De Bary (1866) defined endophytes as ‘organisms occur- ring within plants’ during a time where it was generally believed that healthy and normal growing plants were sterile. Hence, for a long time, the term endophyte was directly related to pathogenicity. Then, along with studies proving the endophytic presence of beneficial or commensal microorganisms in plants (Schneider, 1894), and other studies showing that these organisms could inhabit different plant locations at different phases in their life cycles (Ibáñez et al., 2017), came a redefining of the term. The word began totake on a meaning of plant–microorganism relationship without any pathogenic- ity. More recently, many researchers have defined endophytes as organisms that inhabit plant organs and internal tissues at some point in their life cycle without causing any apparent harm to the plant (Petrini, 1991; Wilson, 1995). Before the development of molecular methods for identification of microor- ganisms, the term ‘endophyte’ referred only to organisms that could be iso- lated and cultivated. Currently, it is widely accepted that fungi and bacteria can be identified without cultivating them and this was duly included in the definition (Rossmann et al., 2017). Although algae, protozoa, amoebas, archaea, and other organisms can infect plant tissues (Trémouillaux-Guiller et al., 2002; Müller and Döring, 2009), the word is mostly used to refer to fungi and bacteria. Since de Bary’s time, so much has been discovered about endophytes that it has been impossible to maintain an exact and stable definition of the word. They are extremely flexible organisms with broad lifestyles. They can becom- mensal, mutualistic, beneficial, or pathogenic and can switch between these lifestyles depending on the phase of their life cycle, the host they are infecting or the environmental conditions in which they are growing (Hardoim et al., 2015), and thus they are considered to represent a continuum of lifestyles (Schulz and Boyle, 2005). As a result of this, the initially strict definition of the term has changed over time, depending on author and research topic, and it will probably continue to change with technological advances. Molecular and Annual Plant Reviews Online, Volume 2. Edited by Jeremy Roberts. © 2019 John Wiley & Sons, Ltd. Published 2019 by John Wiley & Sons, Ltd. 3 M Snoeijenbos et al. genomic approaches to study microorganisms’ lifestyle have redefined the traditional concept of endophytic lifestyle. Alternatives to the traditional def- inition have been proposed, briefly, endophytic microorganisms that have a negative effect on host fitness are named pathogens and those that have a neu- tral or positive effect are considered classical endophytes (Partida-Martinez and Heil, 2011). Currently, researchers are questioning the definition of the word and recommend limiting it to a simple description of habitat, without considerations of pathogenicity or function in plant tissues (Hardoim et al. 2015). 3 Endophytic Lifestyles The most widely accepted hypothesis to explain the occurrence of the endo- phytic lifestyle states that it emerged from a pathogenic ancestor (Schardl and Clay, 1997). This would allow the pathogen to switch to a commensal or a mutualistic lifestyle (Newton et al., 2010; Schulz and Boyle, 2005; Xu et al., 2014). To support this, a previous study showed that a single base mutant in the genome of the plant pathogen Colletotrichum magna caused it to remain inside the plant tissues without causing any symptom (Freeman and Rodriguez, 1993). Nowadays, comparative genomics studies have added evi- dence to that obtained by traditional
Load more

Recommended publications
  • Manipulation of Phytobiome: a New Concept to Control the Plant Disease and Improve the Productivity
    Journal of Bacteriology & Mycology: Open Access Mini Review Open Access Manipulation of phytobiome: a new concept to control the plant disease and improve the productivity Abstract Volume 6 Issue 6 - 2018 Various strategies are currently being developed to improve sustainable agricultural Manoj V Parakhia, Golakiya BA production. Many concepts at present in market to control the plant disease. Most Department of Biotechnology, Junagadh Agricultural University, widely used were chemicals or pesticides. Commercial biological control products India for the use against plant diseases must be highly efficient against the targeted disease. Second concept to control the disease through bio-agents. Many bio-agents available Correspondence: Manoj V Parakhia, Department of in market but not effective as chemical agents so not popularized as compare to Biotechnology, Junagadh Agricultural University, Junagadh, chemical agents. Microbes more diversity found in rhizosphere so rhizosphere is Gujarat, India, Email called house of microbes. Interaction of microbes in rhizosphere will decide the health of plant. It is now widely recognised that plant micro biota provide important Received: June 11, 2018 | Published: November 23, 2018 functions for their host’s performance, and mediate functions like nutrient delivery, fitness, stress tolerance, and pathogen or pest control. Current understanding of plant- microbe interactions is helping to develop microbial products, new applications to improve crop production, and create alternatives to chemicals. Two types of microbes present in rhizosphere culturable and non-culturable. Plant health not depend on only culturable microbes but also depend on non-culturable microbes. it is necessary to study non-culturable microbes. Today new era of microbiology is metagenomics.
    [Show full text]
  • The Untapped Potential of Plant Microbiomes in Agriculture
    The Untapped Potential of Plant Microbiomes in Agriculture Jan E. Leach Colorado State University American Society of Plant Biologists American Phytopathological Society Plant Microbiomes: Assemblages of microbes living in, on and around plants Hirsch & Mauchline, Nature Biotech 2012 Plant microbiomes are components of Phytobiomes: . all organisms living in, on and around plants . microbes . animals . other plants . the Environment Phytobiomes initiative focused on agriculture Plant and their microbiomes are partners for LIFE • Plant microbiomes can influence or be influenced by plants or the plant environment • How can that relationship be tapped to improve crop health, safety, quality and productivity? Quality Health Safety Productivity Nutrition Why now? • Advances in systems-level approaches – High-throughput sequencing – Metagenomics & other ‘-omics technologies – Data sciences (data mining, predictive analytics, …) – Computer science (machine learning, image processing and graphics, …) • Human microbiome discoveries – Conserved patterns despite variation – Strength of longitudinal vs cross-sectional studies – Unexpected impacts on the host – Successful translation to treatments (fecal transplants, probiotics) • International microbiomes attention – OSTP process (NSTC report out SOON!) – Unified Initiative (Science, Nature) • Management strategies in agriculture – Precision Ag – Decision support systems Lessons from the human microbiome When Gut Bacteria Changes Brain Function “…. the microbiome may play a role in regulating how
    [Show full text]
  • Probing the Phytobiome to Advance Agriculture Carolyn Beans, Science Writer
    CORE CONCEPTS CORE CONCEPTS Probing the phytobiome to advance agriculture Carolyn Beans, Science Writer The Colorado potato beetle had Gary Felton stumped. That something else turned out to be bacteria. If he Felton, an entomologist at Pennsylvania State Univer- applied antibiotics, the plants could launch a defense sity, has built his career on revealing how plants defend and inhibit potato beetle larvae growth (1). Bacteria in themselves against voracious insects. Plants often de- the insect’s oral secretions were tricking the plants into tect chemicals in an insect’s oral secretions and respond defending against microbial invaders instead of insect by producing proteins that wreak havoc on insect di- ones. Kill the bacteria and the cover is blown. gestion and nutrient absorption. Myriad factors affect crop health, such as genetics, But the Colorado potato beetle was different. Felton insects, microbes, weather, soil nutrients, weeds, fertilizer, found that oral secretions from its larvae actually pre- tilling. Until recently, scientists typically studied one vented potato and tomato plants from launching a proper variable at a time, says plant pathologist Jan Leach of defense. He tested chemical factors in the secretions that Colorado State University. “When a plant is sitting in the might help the beetle foil the plant, but came up short. field, it’s not just exposed to one pathogen, one tem- “Maybethereissomethingelseherethatwe’ve totally perature, one insect. It’s exposed to everything at once,” overlooked,” he recalls thinking. says Leach. “If we want to understand how plants Bacteria in the oral secretions of Colorado potato beetle larvae can trick potato and tomato plants into defending against microbes instead of the insect pest.
    [Show full text]
  • Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities Terrence H
    Masthead Logo Plant Pathology Presentations and Posters Plant Pathology and Microbiology 3-13-2019 Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities Terrence H. Bell The Pennsylvania State University Gwyn A. Beattie Iowa State University, [email protected] Kurt P. Kowalski U.S. Geological Survey Amy T. Welty Iowa State University, [email protected] et al. Follow this and additional works at: https://lib.dr.iastate.edu/plantpath_conf Part of the Agriculture Commons, Ecology and Evolutionary Biology Commons, and the Plant Sciences Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ plantpath_conf/7. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Conference Proceeding is brought to you for free and open access by the Plant Pathology and Microbiology at Iowa State University Digital Repository. It has been accepted for inclusion in Plant Pathology Presentations and Posters by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities Abstract This white paper presents a series of perspectives on current and future phytobiome management, discussed at the Wild and Tamed Phytobiomes Symposium in University Park, PA, USA, in June 2018. To enhance plant productivity and health, and to translate lab- and greenhouse-based phytobiome research to field applications, the academic community and end-users need to address a variety of scientific, practical, and social challenges. Prior discussion of phytobiomes has focused heavily on plant-associated bacterial and fungal assemblages, but the phytobiomes concept covers all factors that influence plant function.
    [Show full text]
  • Rhizosphere Microbiomes Modulated by Pre-Crops Assisted Plants in Defense Against Plant-Parasitic Nematodes
    fmicb-09-01133 May 31, 2018 Time: 17:22 # 1 ORIGINAL RESEARCH published: 04 June 2018 doi: 10.3389/fmicb.2018.01133 Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes Ahmed Elhady1,2, Shimaa Adss1, Johannes Hallmann1 and Holger Heuer1* 1 Department of Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut – Federal Research Centre for Cultivated Plants, Braunschweig, Germany, 2 Department of Plant Protection, Faculty of Agriculture, Benha University, Benha, Egypt Plant-parasitic nematodes cause considerable damage to crop plants. The rhizosphere microbiome can affect invasion and reproductive success of plant-parasitic nematodes, thus affecting plant damage. In this study, we investigated how the transplanted rhizosphere microbiome from different crops affect plant-parasitic nematodes on soybean or tomato, and whether the plant’s own microbiome from the rhizosphere protects it better than the microbiome from fallow soil. Soybean plants growing in sterilized substrate were inoculated with the microbiome extracted from the rhizosphere of soybean, maize, or tomato. Controls were inoculated with extracts from bulk soil, Edited by: or not inoculated. After the microbiome was established, the root lesion nematode Jesús Mercado-Blanco, Consejo Superior de Investigaciones Pratylenchus penetrans was added. Root invasion of P. penetrans was significantly Científicas (CSIC), Spain reduced on soybean plants inoculated with the microbiome from maize or soybean Reviewed by: compared to tomato or bulk soil, or the uninoculated control. In the analogous Juan Emilio Palomares-Rius, Consejo Superior de Investigaciones experiment with tomato plants inoculated with either P. penetrans or the root knot Científicas (CSIC), Spain nematode Meloidogyne incognita, the rhizosphere microbiomes of maize and tomato Nuria Escudero, reduced root invasion by P.
    [Show full text]
  • BER SFA Categories 1. Foundational Genomics 2. Environmental Genomics 3. Biosystems Design
    SFA Categories – April 2020 BER SFA Categories All Science Focus Areas (SFA) will be identified as belonging to one of the following six (7) SFA categories. 1. Foundational Genomics Foundational genomics supports fundamental systems biology research to achieve a predictive understanding of gene function and regulatory networks at the genome scale. Through interdisciplinary approaches that integrate multiomics data and computational modeling, this research advances towards a comprehensive understanding of genotype-phenotype relationships in microbes and plants relevant to DOE. The results yield an increased range of microorganisms and plants as model systems to expand and complement available microbial and plant species for bioenergy and biotechnology research. These efforts underpin leadership advances in biotechnology crucial for competitiveness in a global market. 2. Environmental Genomics Environmental genomics supports research focused on understanding plants and soil microbial communities and how they impact the cycling and fate of carbon, nutrients, and contaminants in the environment. This research area includes the study of a range of natural and model microbiomes in targeted field environments relevant to BER’s research efforts. With a long history in plant and microbial genomics research coupled with substantial biotechnological and computational capabilities available within the DOE user facilities, BER is well positioned to make transformative contributions in biotechnology and understanding microbiome and phytobiome function. 3. Biosystems Design Biosystems Design develops the fundamental understanding of genome biology needed to design, engineer, and optimize plants, microbes, and biomes for sustainable production of biofuels and bioproducts from renewable sources. By developing novel genome-scale synthetic biology technologies and computer-aided design tools, Biosystems Design accelerates the “design-build- test-learn” cycle to engineer biological systems.
    [Show full text]
  • A Review of the Citrus Greening Research and Development Efforts Supported by the Citrus Research and Development Foundation: Fighting a Ravaging Disease (2018)
    THE NATIONAL ACADEMIES PRESS This PDF is available at http://nap.edu/25026 SHARE A Review of the Citrus Greening Research and Development Efforts Supported by the Citrus Research and Development Foundation: Fighting a Ravaging Disease (2018) DETAILS 288 pages | 6 x 9 | PAPERBACK ISBN 978-0-309-47214-2 | DOI 10.17226/25026 CONTRIBUTORS GET THIS BOOK Committee on a Review of the Citrus Greening Research and Development Efforts Supported by the Citrus Research and Development Foundation: Fighting a Ravaging Disease; Board on Agriculture and Natural Resources; Division on Earth FIND RELATED TITLES and Life Studies; National Academies of Sciences, Engineering, and Medicine SUGGESTED CITATION National Academies of Sciences, Engineering, and Medicine 2018. A Review of the Citrus Greening Research and Development Efforts Supported by the Citrus Research and Development Foundation: Fighting a Ravaging Disease. Washington, DC: The National Academies Press. https://doi.org/10.17226/25026. Visit the National Academies Press at NAP.edu and login or register to get: – Access to free PDF downloads of thousands of scientific reports – 10% off the price of print titles – Email or social media notifications of new titles related to your interests – Special offers and discounts Distribution, posting, or copying of this PDF is strictly prohibited without written permission of the National Academies Press. (Request Permission) Unless otherwise indicated, all materials in this PDF are copyrighted by the National Academy of Sciences. Copyright © National Academy of Sciences. All rights reserved. A Review of the Citrus Greening Research and Development Efforts Supported by the Citrus Research and Fighting... Committee on a Review of the Citrus Greening Research and Development Efforts Supported by the Citrus Research and Development Foundation: Fighting a Ravaging Disease Board on Agriculture and Natural Resources Division on Earth and Life Studies A Consensus Study Report of Copyright National Academy of Sciences.
    [Show full text]
  • Improving Crop Productivity Through a Comprehensive Understanding Of
    Improving crop productivity through a comprehensive understanding of the phytobiome Mejorando la productividad de cultivos a través del conocimiento comprensivo del fitobioma Jan E. Leach Colorado State University XIII IRCLAC Piura National University Piura, Peru May 2018 Phytobiomes are complex systems Phytobiome: • Interactions of the environment and living organisms that influence or are influenced by plants Plant Microbiome: Phytobiome • The dynamic community of microbes associated with plants Phytobiomes: A Roadmap for Research and translation, 2016. (St. Paul, MN: American Phytopathological Society), pp. 15 Phytobiome members in the soil In 1 g soil: *1 billion bacteria *100 million virus *100 thousand fungi & microalgae plpnemweb.ucdavis.edu *10’s of thousands of protozoa *hundreds of nematodes Embracing the complexity of the Phytoboime! It’s a SYSTEM!!! It’s bacteria! Gut bacteria could predict asthma in kids Sarah Williams, SCIENCE Sept 30, 2015 When Gut Bacteria Changes Brain Function ….the microbiome may play a role in regulating how people think and feel. David Kohn The Atlantic June 24, 2015 Wherever You Go, Your Personal Cloud Of Microbes Follows ROB STEIN, NPR SEPTEMBER 22, 2015 8:38 AM ET Grazers & predators: important phytobiome members e.g., Vermamoeba vermiformis attach to Rhizoctonia solani mycelia, consume mycelial contents, and encyst. • What is the net impact of predators & grazers onplpnemweb.ucdavis.edu the microbiome? • Can these be manipulated to enhance plant health, quality 10 µm and productivity? John Long et al. unpubl. Phytobiome members communicate! Leach et al. 2017 Cell How do they communicate? What are the outcomes? It’s complex! Interkingdom communications: Quorum sensing (QS) Leach et al.
    [Show full text]
  • Phytohormone Pathways As Targets of Pathogens to Facilitate Infection
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector Plant Mol Biol (2016) 91:713–725 DOI 10.1007/s11103-016-0452-0 Phytohormone pathways as targets of pathogens to facilitate infection 1,2 1,2 Ka-Wai Ma • Wenbo Ma Received: 2 September 2015 / Accepted: 7 February 2016 / Published online: 15 February 2016 Ó The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Plants are constantly threatened by potential Introduction pathogens. In order to optimize the output of defense against pathogens with distinct lifestyles, plants depend on In order to complete an infection cycle, phytopathogens hormonal networks to fine-tune specific responses and need to enter plant tissues through physical barriers, over- regulate growth-defense tradeoffs. To counteract, patho- come defense responses mounted by the plant immune gens have evolved various strategies to disturb hormonal system, obtain nutrients for proliferation, and eventually be homeostasis and facilitate infection. Many pathogens syn- disseminated to a new host. During the co-evolutionary arms thesize plant hormones; more importantly, toxins and race with plants, successful pathogens evolved virulence effectors are produced to manipulate hormonal crosstalk. factors such as toxins and secreted proteins (aka effectors) to Accumulating evidence has shown that pathogens exert modulate plant physiology (Bender et al. 1999; Torto- extensive effects on plant hormone pathways not only to Alalibo et al. 2009; Dou and Zhou 2012; Dangl et al. 2013). defeat immunity, but also modify habitat structure, opti- A prominent and extensively studied example is the type III mize nutrient acquisition, and facilitate pathogen dissemi- secreted effectors, which are injected by Gram negative nation.
    [Show full text]
  • Gwyn Beattie Buchanan Distinguished Professor of Bacteriology
    Gwyn Beattie Buchanan Distinguished Professor of Bacteriology Chair, American Phytopathological Society Public Policy Board Global Grand Challenge To sustainably feed the world ……. To feed a global population of 9.6 billion in 2050 Need 70% more food (based on calories) 2050 2013 X 1.7 World Summit on Food Security (2013) c Doubling global crop production by 2050 will require ~2.4% increase per year in yields 2.2 1.8 3.0 0.5 2.2 1.0 1.8 1961-1990 1.1 1990-2007 c American Phytopathological Society 2013 Directive to an international group of “thought leaders”: Develop concepts that can contribute to doubling the amount of safe and nutritious food by 2050 Time is right for a systems approach Phytobiomes: Systems in Context Biological and Environmental Context Plants Climate Micro‐ and Macroorganisms Arthropods, Other Viruses Animals and Plants Insects Archaea Arachnids Bacteria Myriapods Amoeba Worms Oomycetes Birds Fungi Rodents Algae Ruminants Nematodes Weeds All of the associated Their environment Soils organisms Phytobiomes: Systems in Context Management Context c Conceptual development of “Phytobiomes” Phytobiome vs. plant microbiome Phytobiomes - plants, their associated organisms, and their environment c Conceptual development of “Phytobiomes” Plant systems vs. Phytobiomes Plant systems focus on a plant and then determine the interactions of that plant with all other components Phytobiomes focus on a plant ecosystem that may involve any number of different types of plants, organisms, and environmental components. use information on all components and their interactions to identify the best plant(s) to grow at a given site in a given period c Achieve sustainable crop productivity through a systems-level understanding of diverse interacting components Origin of the Phytobiomes Roadmap .
    [Show full text]
  • Soil and Global Issues
    Carbon Management and Sequestration Center SOIL AND GLOBAL ISSUES Rattan Lal Carbon Management and Sequestration Center The Ohio State University Columbus, Ohio 1 Carbon Management and Sequestration Center SOIL: THE ESSENCE OF LIFE “Hello there folks. Do you know who or what I am? I am the geomembrane of the Earth. I am your protective filter, your buffer, your mediator of energy, water, and biogeochemical compounds. I am your sustainer of productive life, your ultimate sources of elements, and the habitat for most biota. I am the foundation that supports you, the cradle of your myths, and the dust from which you will return. I am a soil”. Richard Arnold (2005) Senior Soil Scientist 2 Carbon Management and Sequestration Center THE LIVING SOIL Soil is an organic- carbon mediated realm in which solid, liquid, gas and biology all interact from a scale of nanometer to landscape. The weight of live organisms in arable land is 5 t/ha 3 Carbon Management and Sequestration Center THE DIRT "Dirt has no currency in western society, and has little impact on politicians. It comes under the journalist "MEGO" category… My Eyes Glaze Over. Bar a few impressive dust storms, we care little of our soil. We do not relate what we eat in our home, buy in out supermarkets, or drink from our Starbucks to the soil. And yet, without soil, we become thirsty, hungry, and we die. Without soil, we become Mars, with no water, no atmosphere, and only relics of life, with at best distant stargazers trying to figure our the life that could have been." Young and Crawford (2015) 4 SCALING ISSUES IN SOC STOCK ACarbonSSESSMENT Management and Sequestration Center 1 × 109 World 1 × 108 Continent 1 × 106 River Basin 4 1 × 10 Watershed 1 × 103 Landscape 3677 km 2 1 × 10 Soil Scape 100 12,742 km Soil Profile Size (m) -9 5000 × 10 Clod -9 500 × 10 Macroaggregate 250 × 10-9 Microaggregate 2 × 10-10 Clay 1 × 10-10 Molecules 0 5 Carbon Management and Sequestration Center Population Energy use Water use Deforestation CO2 Emissions Land DegradationThe answer lies in soils.
    [Show full text]
  • 910 Metagenome-Assembled Genomes from the Phytobiomes of Three Urban-Farmed Leafy Asian Greens
    www.nature.com/scientificdata OpeN 910 metagenome-assembled Data DeSCriptor genomes from the phytobiomes of three urban-farmed leafy Asian greens Aditya Bandla 1,2, Shruti Pavagadhi 1,3, Ashwin Sridhar Sudarshan 1, Miko Chin Hong Poh3 & Sanjay Swarup 1,2,3,4 ✉ The genome sequences of many microbial species from the phytobiomes of several leafy Asian greens remain unknown. Here, we address this gap by reconstructing 910 prokaryotic draft genomes from 24 leaf, 65 root, 12 soil, and 6 compost metagenomes from the seedling and adult developmental stages of three leafy Asian greens – Brassica rapa var. parachinensis, Brassica oleracea var. alboglabra and Amaranthus spp. – grown in a commercial, soil-based urban farm. Of these, 128 are near-complete (>90% completeness, <5% redundancy), 540 are substantially complete (≥70% completeness, <10%, redundancy), while the rest have a completeness ≥50% and redundancy <10%. The draft genomes together span 292 bacterial and 3 archaeal species, a subset of which are from underrepresented genus- level lineages in public databases. We expect our dataset to facilitate a wide range of comparative studies that seek to understand the diferent functional aspects of vegetable crop phytobiomes and for devising new strategies for microbial cultivation in the future. Background & Summary Microbiomes within the phytobiome1 – the plant, its environment, and its associated communities of organisms – afect nearly all aspects of growth such as development, diferentiation, nutrient acquisition, and tolerance to biotic and abiotic stresses2. Previous studies have greatly expanded our understanding of the diversity and composition of specifc phytobiome-associated microbiomes3–9, but only a few have investigated their genetic underpinnings in a systematic manner10,11.
    [Show full text]