Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture

Trends in biotechnology, Journal Year: 2020, Volume and Issue: 39(3), P. 244 - 261

Published: Aug. 13, 2020

Mutualistic microbes associated with plants have enormous potential for economical and sustainable agriculture.There are two approaches to plant microbiome engineering: the bottom-up approach that involves isolating, engineering, reintroducing specific microbes, top-down synthetic ecology, using horizontal gene transfer a broad range of hosts in situ then phenotyping microbiome.Recent advances genome engineering tools, meta-omic computational genome-wide functional genomics can improve our ability engineer biocontrol, biofertilization, biostimulation, as well enhanced crop productivity yield.Various devices facilitate evaluation genetically modified before field studies.Robust biosafety, biosecurity, biocontainment strategies need be developed use environment. To support an ever-increasing population, modern agriculture faces numerous challenges pose major threats global food energy security. Plant-associated their many growth-promoting (PGP) traits, helping solve these challenges. However, results been variable, probably because poor colonization. Phytomicrobiome is emerging biology may offer ways alleviate this limitation. This review highlights recent both non-model bacteria microbiomes promote beneficial plant–microbe interactions, evaluate interactions. Biosafety, address environmental concerns also discussed. The United Nations estimates world population will 9.8 billion people by 2050 (https://population.un.org/wpp/). Agricultural must increase estimated 70% meet increasing demand food, feed, fiber, bioenergy (Global Productivity Initiative: https://globalagriculturalproductivity.org/). Because arable acreage unlikely grow [1.Bruinsma J. Crop production natural resource use.in: Bruinsma World Agriculture: Towards 2015/2030: An FAO Perspective. Earthscan Publications, 2003: 127-137Google Scholar], meeting requires achieving higher yields, currently attempted artificial fertilizers pesticides whose manufacture not sustainable. Synthetic nitrogen (N) fertilizer energy-intensive [2.Wang M. Greenhouse Gases, Regulated Emissions, Energy Use Transportation (GREET) Model: Version 1.5. Center Research, Argonne National Laboratory, 1999Google Scholar]. Phosphorous (P) potassium (K) mainly produced from finite mined resources likely depleted within 100 years. Pesticides carcinogenic, developmental, risks restricted [3.Hoppin J.A. LePrevost C.E. human health.in: Coll Wajnberg E. Environmental Pest Management: Challenges Agronomists, Ecologists, Economists Policymakers. Wiley, 2017: 251-273Crossref Google Scholar,4.Upadhayay et al.Impact pesticide exposure health effects.in: Srivastava P.K. Production: Physiological Biochemical Action. 2020: 69-88Crossref More achieve ever-higher yield urgently needed. harbor provide solutions current agricultural Although diverse ecological niches [5.Compant S. al.A on microbiome: functions trends microbial application.J. Adv. Res. 2019; 19: 29-37Crossref PubMed Scopus (0) Scholar,6.Levy A. al.Elucidating bacterial microbiome.Cell Host Microbe. 2018; 24: 475-485Abstract Full Text PDF (15) traits (see Glossary) [7.Shelake R.M. al.Exploration interactions CRISPR era.Microorganisms. 7: 269Crossref (6) Many PGP isolated, some widely accepted biofertilizers, biostimulants, biocontrol agents (www.cropscience.bayer.com/innovations/agriculture-biologicals/a/hidden-helpers-below-ground). applying fields commercial adoption has had limited success [8.Glick B.R. Plant bacteria: mechanisms applications.Scientifica. 2012; 2012963401Crossref Scholar, 9.Thompson I.P. al.Survival, colonization dispersal Pseudomonas fluorescens SBW25 phytosphere grown sugar beet.Nat. Biotechnol. 1995; 13: 1493-1497Crossref (44) 10.Bloch S.E. al.Biological fixation maize: optimizing nitrogenase expression root-associated diazotroph.J. Exp. Bot. 2020; 71: 4591-4603Crossref 11.De Leij F.A. al.Field release wheat: establishment, survival dissemination.Nat. 1488-1492Crossref (32) 12.Jäderlund L. al.Use novel nonantibiotic triple marker cassette monitor high winter wheat field.FEMS Microbiol. Ecol. 2008; 63: 156-168Crossref (13) new excluded more-resilient existing communities [13.Shade al.Fundamentals community resistance resilience.Front. 3: 417Crossref (556) composition shaped over time through complex multilateral environment [14.Haichar F. al.Plant host habitat root exudates shape soil structure.ISME 2: 1221-1230Crossref 15.Hardoim P.R. al.The hidden plants: evolutionary considerations defining functioning endophytes.Microbiol. Mol. Biol. Rev. 2015; 79: 293-320Crossref (733) 16.Reinhold-Hurek B. al.Roots shaping hotspots activity.Annu. Phytopathol. 53: 403-424Crossref 17.Peterson S.B. al.Peptidoglycan Bacillus cereus mediates commensalism rhizosphere Cytophaga-Flavobacterium group.Appl. Environ. 2006; 72: 5421-5427Crossref (29) 18.Hu al.Root exudate metabolites drive plant–soil feedbacks growth defense microbiota.Nat. Commun. 9: 2738Crossref 19.Rodriguez P.A. al.Systems interactions.Mol. Plant. 12: 804-821Abstract 20.Dangl J.L. Jones J.D. pathogens integrated defence responses infection.Nature. 2001; 411: 826-833Crossref (2693) Finding microorganisms sustainably development, nutrition, fitness, disease control, dynamic stressful environments therefore depends developing manage phytomicrobiomes Scholar,15.Hardoim Scholar,21.Lemanceau P. al.Let core microbiota functional.Trends Sci. 2017; 22: 583-595Abstract 22.Niu al.Simplified representative maize roots.Proc. Natl. Acad. U. 114: E2450-E2459Crossref (153) 23.Zgadzaj R. nodule symbiosis Lotus japonicus drives establishment distinctive rhizosphere, root, communities.Proc. 2016; 113: E7996-E8005Crossref (102) 24.Haney C.H. al.Associations confer adaptive advantage plants.Nat. Plants. 115051Crossref Meta-omic studies tools researchers understanding among phytomicrobiomes. Knowledge derived [25.Mitter al.Plant–microbe partnerships 2020.Microb. 635-640Crossref (19) such only effective under conditions extremely complex, heterogeneous, systems. limitations, based increasingly recognized way give advantages [26.Mueller U.G. Sachs Engineering animal health.Trends 23: 606-617Abstract (183) allows laboratory selection according colonize plants, specifically basis how they deliver advantages. Researchers could potentially species locations (e.g., roots, leaves) at different developmental stages various conditions. In addition, consolidated engineered microbiomes. (GMMs) strictly regulated. since first trial evaluating syringae, which was carried out University California experimental plots 1987, academia industry investigated GMMs nearly three decades without notable accidents and/or [10.Bloch Scholar,27.De indigenous populations wheat.Appl. 61: 3443-3453Crossref Scholar,28.Wozniak C.A. al.Regulation FIFRA, FFDCA TSCA.in: McHughen Wozniak Regulation Biotechnology: States Canada. Springer, 2012: 57-94Crossref (7) suggesting might safely used regulations. These successes now motivating further exploration GMM directly environment, US agencies initiated research programs develop methodologies counter, even reverse effects. Several companies investigating sustainability, related strategies, business model Synlogic, Pivot Bio, JOYN NOVOME Biotechnologies, 64-X). near future, efforts prove safe strategy sustainability agriculture. Accordingly, we here strain make more amenable applications, discuss mitigate impacts (Figure 1). Phytomicrobiomes or top-down, illustrated Figure 2. approach, particular species, strains, organs isolated [29.Rodrigues R.R. al.COREMIC: web-tool search niche CORE MICrobiome.PeerJ. 6e4395Crossref (4) Scholar,30.Toju H. al.Core agroecosystems.Nat. 4: 247-257Crossref (152) After being carry desired reassembled (SynComs) [31.Vorholt al.Establishing causality: opportunities research.Cell 142-155Abstract (93) Plants inoculated robustly recolonize hosts. (HGT) introduce into situ. One incorporate mobile genetic elements (MGEs), integrate exogenous genes random subpopulation allow holistic study traits. Another bacteriophage (phage) systems eliminate populations, roles studied. section 2). Most focus established Escherichia coli. discover functions, engineered, but challenging organism-specific nuances hinder universal tools. host-range (BHR) plasmids one [32.Jain Broad plasmids.FEMS Lett. 2013; 348: 87-96Crossref (21) For example, BHR were microbe–microbe mediated quorum-sensing circuits [33.You al.Programmed control cell–cell communication regulated killing.Nature. 2004; 428: 868-871Crossref (477) Scholar,34.Hong S.H. al.Synthetic circuit consortial biofilm formation microfluidic device.Nat. 3613Crossref (108) Scholar] elucidate function secondary metabolite biosynthetic clusters (BGCs) providing plant-benefiting [35.Hennecke Recombinant carrying Rhizobium japonicum.Nature. 1981; 291: 354-355Crossref Scholar,36.Beyeler al.Enhanced indole-3-acetic acid CHA0 affects cucumber, does protection against Pythium rot.FEMS 1999; 28: 225-233Crossref although versatile, selective pressure necessary maintain them. Microbiome conversely, genome-level stably Fortunately, greatly improved. 3 shows useful including phage integrases, integrative conjugative (ICEs), chassis-independent recombinase-assisted (CRAGE), others [37.Ke Yoshikuni Y. Multi-chassis heterologous products.Curr. Opin. 62: 88-97Crossref (2) All single-step integration large DNA constructs >50 kb length, permit stacking multiple System depend target phyla. integrase, ICE, CRAGE commonly Actinobacteria, Firmicutes, Proteobacteria, respectively. Phage integrases catalyze efficient recombination between attachment sites attP–attB) [38.Fogg P.C. al.New applications integrases.J. 2014; 426: 2703-2716Crossref (88) versatile 3A). Streptomyces πC31 system characterization BGCs compatible Actinobacteria [39.Liu al.Rapid cloning meridamycin cluster coli−Streptomyces chromosome vector, pSBAC.J. Nat. Prod. 2009; 389-395Crossref 40.Li stepwise pristinamycin II biosynthesis pristinaespiralis combinatorial metabolic engineering.Metab. Eng. 29: 12-25Crossref (42) 41.Li al.Multiplexed site-specific overproducing bioactive actinomycetes.Metab. 40: 80-92Crossref (37) 42.Myronovskyi al.Generation cluster-free albus chassis strains improved clusters.Metab. 49: 316-324Crossref (39) A Bxb1 intN2 reliable putida [43.Elmore J.R. al.Development efficiency promoter library rapid modification KT2440.Metab. 5: 1-8Crossref commensal Bacteroides [44.Mimee al.Programming bacterium, thetaiotaomicron, sense respond stimuli murine gut microbiota.Cell Syst. 1: 62-71Abstract (128) 45.García-Bayona Comstock L.E. Streamlined manipulation Parabacteroides isolates microbiota.MBio. 10e01762-19Crossref 46.Wang al.Characterization mobilizable transposon, NBU2, carries lincomycin gene.J. Bacteriol. 2000; 182: 3559-3571Crossref (61) require native site each introduced [47.Dafhnis-Calas al.Iterative vivo assembly transgenes combining activities φC31 integrase Cre recombinase.Nucleic Acids 2005; 33: e189Crossref With systems, vector backbone remains scar Mini-Tn7 another promising transposon-based tool [48.Choi K.H. Tn 7-based broad-range system.Nat. Methods. 443-448Crossref 49.Kumar al.Mini-Tn7 vectors single copy Acinetobacter baumannii.J. 2010; 82: 296-300Crossref 50.LoVullo E.D. al.Single-copy chromosomal Francisella tularensis.Microbiology. 155: 1152-1163Crossref (48) mini-Tn7 relatively small [51.Roos K. al.Multicopy transposons selected Salmonella vaccine strain.Microb. 8: 177-187Crossref ICEs group MGEs via propagate replication 3B). They encode conjugation mediate intercellular [52.Johnson C.M. Grossman A.D. Integrative (ICEs): what do work.Annu. Genet. 577-601Crossref (168) autonomous [53.Lee al.Autonomous plasmid-like transposon.Mol. 75: 268-279Crossref Some conserved prfC, tRNA genes) range, evolved seamless mechanism 5′ end prevent disruption [54.Touchon accommodation domestication elements.Curr. 22-29Crossref (26) Scholar,55.Botelho al.Antibiotic aeruginosa – mechanisms, epidemiology evolution.Drug Resist. Updat. 44100640Crossref Other less AT-rich regions), fitness disrupting physiologically important [56.Wozniak R.A. Waldor M.K. elements: mosaic enabling lateral flow.Nat. 552-563Crossref (438) Genes encoding machinery, transposases identified incorporated domesticated mating partners, coli subtilis Scholar,57.Inda M.E. al.Emerging frontiers engineering.Trends Immunol. 952-973Abstract Scholar,58.Brophy al.Engineered inducible undomesticated bacteria.Nat. 1043-1053Crossref (40) [59.Cury al.Integrative hosts: composition, distribution organization.Nucleic 45: 8943-8956Crossref (27) recipients usually limited, drops exponentially construct size increases [58.Brophy colleagues recently CRAGE, technology enables highly accurate large, biological chromosomes 3C) [60.Wang G. al.CRAGE activation 2498-2510Crossref (16) process begins landing pad (LP) containing P1 recombinase flanked mutually exclusive loxP sites. Constructs pathways assembled accessory vectors. As proof concept, 25 γ-Proteobacteria 11 genera integrating unified LP enabled BGCs. substantially increased successful BGC harnessing regulatory physiological diversity species. extended 40 α-, β-, several Actinobacteria. CRAGE's versatility makes it microbe genomes characterizing pathway Overcoming restriction/modification common problem Unique protect them foreign DNA, limiting transformation. Riley overcame limitation evade immune Clostridium thermocellum [61.Riley L.A. al.Rational development transformation ATCC 27405 complete methylome analysis evasion restriction-modification systems.J. Ind. 46: 1435-1443Crossref corresponding methyltransferases cloned mimic C. methylome. Plasmids propagated efficiently transformed thermocellum. rhizobacteria, throughput dozen once. thousands associate natively SynComs rapidly diluted resilient pre-existing [62.Mallon impact failure: unsuccessful invasions steer away invader's niche.ISME 728-741Crossref Scholar,63.Costello E.K. application theory toward microbiome.Science. 336: 1255-1262Crossref (701) knowledge microbiomes, robust plants. frontier offers alternative recode metagenome build instead modifying enable introduction deletion minimal context [64.Sheth R.U. al.Manipulating 32: 189-200Abstract (87) Bacterial members undergo abundant HGT [65.Kommineni al.Bacteriocin augments competition enterococci mammalian gastrointestinal tract.Nature. 526: 719-722Crossref (173) MGEs, redesigned studies, conjugal donor transiently transferred across phyla those [66.Klümper al.Broad invade unexpectedly fraction community.ISME 934-945Crossref Scholar,67.Musovic al.Long-term manure plasmid uptake.Environ. Rep. 6: 125-130Crossref Based ICE subtilis, Brophy coworkers created miniaturized (mini-ICEBs1) delivery wide Firmicutes collected humans soil, variable (10−1 10−7 conjugations per donor) 3D) demonstrated (XPORT) 10 synthetically defined consortium situ, there four six s

Language: Английский

---

Plant-soil-microbes: A tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices

Environmental Research, Journal Year: 2022, Volume and Issue: 214, P. 113821 - 113821

Published: July 8, 2022

Language: Английский

---

Foliar application of nanoparticles: mechanisms of absorption, transfer, and multiple impacts

Environmental Science Nano, Journal Year: 2021, Volume and Issue: 8(5), P. 1196 - 1210

Published: Jan. 1, 2021

Foliar spray of NPs is more effective than root/soil application, but potential human exposure and plant toxicity should be addressed.

Language: Английский

---

Biofertilizers and Biocontrol Agents for Agriculture: How to Identify and Develop New Potent Microbial Strains and Traits

Microorganisms, Journal Year: 2021, Volume and Issue: 9(4), P. 817 - 817

Published: April 13, 2021

Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria fungi capable of providing beneficial outcomes in crop plant growth health, have been developed for several decades. Currently we a selection strains available as products agriculture, predominantly based on plant-growth-promoting rhizobacteria (PGPR), soil, epiphytic, mycorrhizal fungi, each having specific challenges their production use, with the main one being inconsistency field performance. With growing global concern about pollution, greenhouse gas accumulation, increased need plant-based foods, demand biofertilizers agents is expected to grow. What prospects finding solutions existing tools? The inconsistent performance could be overcome by using combinations different types microbial strains, consisting various members full microbiome. However, thorough understanding microbiological tool, communities, mechanisms action must precede product development. In this review, offer brief overview tools consider techniques approaches that can produce information new traits biofertilizer strains. We also discuss innovative ideas how where identify efficient strain family.

Language: Английский

---

Interaction between arbuscular mycorrhizal fungi and Bacillus spp. in soil enhancing growth of crop plants

Fungal Biology and Biotechnology, Journal Year: 2019, Volume and Issue: 6(1)

Published: Nov. 28, 2019

Abstract Soil microorganisms play an important role in enhancing soil fertility and plant health. Arbuscular mycorrhizal fungi growth promoting rhizobacteria form a key component of the microbial population. symbiotic association with most cultivated crop plants they help phosphorus nutrition protecting them against biotic abiotic stresses. Many species Bacillus occurring are also known to promote through phosphate solubilization, phytohormone production protection Synergistic interaction between AMF spp. compared single inoculation either has been reported. This is because enhanced nutrient uptake, pathogens alleviation stresses (water, salinity heavy metal) dual or alone.

Language: Английский

---

Salinity Stress in Potato: Understanding Physiological, Biochemical and Molecular Responses

Life, Journal Year: 2021, Volume and Issue: 11(6), P. 545 - 545

Published: June 10, 2021

Among abiotic stresses, salinity is a major global threat to agriculture, causing severe damage crop production and productivity. Potato (Solanum tuberosum) regarded as future food by FAO ensure security, which severely affected salinity. The growth of the potato plant inhibited under salt stress due osmotic stress-induced ion toxicity. Salinity-mediated leads physiological changes in plant, including nutrient imbalance, impairment detoxifying reactive oxygen species (ROS), membrane damage, reduced photosynthetic activities. Several biochemical phenomena, such maintenance water status, transpiration, respiration, use efficiency, hormonal balance, leaf area, germination, antioxidants are adversely affected. ROS increased plasma permeability extravasations substances, causes imbalance plasmolysis. However, plants cope with mediated oxidative conditions enhancing both enzymatic non-enzymatic antioxidant osmoprotectants, proline, polyols (sorbitol, mannitol, xylitol, lactitol, maltitol), quaternary ammonium compound (glycine betaine) synthesized overcome adverse effect response tolerance include complex multifaceted mechanisms that controlled multiple proteins their interactions. This review aims redraw attention researchers explore current physiological, molecular responses subsequently develop potential mitigation strategies against potatoes.

Language: Английский

---

CRISPR/Cas9-Mediated Generation of Pathogen-Resistant Tomato against Tomato Yellow Leaf Curl Virus and Powdery Mildew

International Journal of Molecular Sciences, Journal Year: 2021, Volume and Issue: 22(4), P. 1878 - 1878

Published: Feb. 13, 2021

Tomato is one of the major vegetable crops consumed worldwide. yellow leaf curl virus (TYLCV) and fungal Oidium sp. are devastating pathogens causing disease powdery mildew. Such viral reduce tomato crop yields cause substantial economic losses every year. Several commercial varieties include Ty-5 (SlPelo) Mildew resistance locus o 1 (SlMlo1) that carries susceptibility (S-gene) factors for TYLCV mildew, respectively. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) a valuable genome editing tool to develop disease-resistant varieties. In this regard, targeting encoded by host plant instead promising approach achieve pathogen without need stable inheritance CRISPR components. study, CRISPR/Cas9 system was employed target SlPelo SlMlo1 trait introgression in elite cultivar BN-86 confer host-mediated immunity against pathogens. SlPelo-knockout lines were successfully generated, carrying biallelic indel mutations. assays mutant confirmed suppressed accumulation restricted spread non-inoculated parts. Generated knockout showed complete mildew fungus. Overall, our results demonstrate efficiency introduce targeted mutagenesis rapid development pathogen-resistant tomato.

Language: Английский

---

The Role of Synthetic Microbial Communities (SynCom) in Sustainable Agriculture

Frontiers in Agronomy, Journal Year: 2022, Volume and Issue: 4

Published: June 30, 2022

Modern agriculture faces several challenges due to climate change, limited resources, and land degradation. Plant-associated soil microbes harbor beneficial plant growth-promoting (PGP) traits that can be used address some of these challenges. These are often formulated as inoculants for many crops. However, inconsistent productivity a problem since the performance individual inoculants/microbes vary with environmental conditions. Over past decade, ability utilize Next Generation Sequencing (NGS) approaches has led an explosion information regarding associated microbiomes. Although this type work been predominantly sequence-based descriptive in nature, increasingly it is moving towards microbiome functionality. The synthetic microbial communities (SynCom) approach emerging technique involves co-culturing multiple taxa under well-defined conditions mimic structure function microbiome. SynCom hopes increase community stability through synergistic interactions between its members. This review will focus on plant-soil-microbiome how they have potential improve crop production. Current formulation discussed, practical application considered.

Language: Английский

---

Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives

Plant Communications, Journal Year: 2022, Volume and Issue: 3(6), P. 100417 - 100417

Published: Aug. 3, 2022

Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one the major abiotic stresses that severely affect crop health production. Plant responses involve multiple processes operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, post-translational changes. Consequently, tolerance are polygenic traits influenced genome-environment interactions. One ideal solutions these challenges development high-yielding varieties with enhanced tolerance, together improved practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied elucidate how plants deal saline environments. this work, we aim portray combined use CRISPR-based genome engineering tools modern genomic-assisted breeding approaches gaining momentum identifying genetic determinants complex for improvement. This review provides synopsis at morphological, physiological, molecular levels. We also highlight recent advances their understanding multi-level nature adaptations stress. Integrating CRISPR factors regulate stress-response pathways introgression beneficial develop stress-resilient crops.

Language: Английский

---

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

Molecular Plant, Journal Year: 2020, Volume and Issue: 14(1), P. 127 - 150

Published: Nov. 3, 2020

The central dogma (CD) of molecular biology is the transfer genetic information from DNA to RNA protein. Major CD processes governing flow include cell cycle, replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. are tightly regulated in plants maintain integrity throughout life cycle pass materials next generation. Engineering various involved gene regulation will accelerate crop improvement feed growing world population. CRISPR technology enables programmable editing alter DNA, RNA, or protein, which would have been impossible past. Here, an overview recent advancements tool development CRISPR-based modulations that expedite basic applied plant research provided. Furthermore, applications major thriving areas research, such as discovery (allele mining cryptic activation), introgression (de novo domestication haploid induction), application desired traits beneficial farmers consumers (biotic/abiotic stress-resilient crops, factories, delayed senescence), described. Finally, global regulatory policies, challenges, prospects for CRISPR-mediated discussed.

Language: Английский

---