Rhizosphere Colonization Determinants by Plant Growth-Promoting Rhizobacteria (PGPR)

Biology, Journal Year: 2021, Volume and Issue: 10(6), P. 475 - 475

Published: May 27, 2021

The application of plant growth-promoting rhizobacteria (PGPR) in the field has been hampered by a number gaps knowledge mechanisms that improve growth, health, and production. These include (i) ability PGPR to colonize rhizosphere plants (ii) bacterial strains thrive under different environmental conditions. In this review, strategies host are summarized advantages having highly competitive discussed. Some exhibited recognition chemical signals nutrients from root exudates, antioxidant activities, biofilm production, motility, as well efficient evasion suppression immune system. Moreover, many contain secretion systems produce antimicrobial compounds, such antibiotics, volatile organic lytic enzymes enable them restrict growth potentially phytopathogenic microorganisms. Finally, compete successfully should be considered development bioinoculants.

Language: Английский

---

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

Journal of Environmental Management, Journal Year: 2020, Volume and Issue: 273, P. 111118 - 111118

Published: Aug. 1, 2020

Language: Английский

---

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

---

The plant endosphere world – bacterial life within plants

Environmental Microbiology, Journal Year: 2020, Volume and Issue: 23(4), P. 1812 - 1829

Published: Sept. 21, 2020

Summary The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the interior at least part of their lifetime are termed endophytes. Their functions range from mutualism to pathogenicity. All organs tissues generally bacterial endophytes diversity composition depend on plant, organ its physiological conditions, growth stage as well environment. Plant‐associated in particular endophytes, have lately received high attention, because increasing awareness importance host‐associated microbiota for functioning performance host. Some endophyte known mostly lab assays, genome prediction few metagenome analyses; however, we limited understanding planta activities, particularly considering micro‐environments dynamics conditions. In our review, present recent findings environments, conditions colonization. Furthermore, discuss functions, interaction between plants methodological limitations research. We also provide an outlook needs future research improve role colonizing traits ecosystem functioning.

Language: Английский

---

Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies

Frontiers in Sustainable Food Systems, Journal Year: 2021, Volume and Issue: 5

Published: Feb. 19, 2021

Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by plant-associated microorganisms presents promising strategy reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition either mobilizing or increasing nutrient availability soils. Various microbial taxa including beneficial bacteria fungi currently used biofertilizers, they successfully colonize the rhizosphere, rhizoplane root interior. Despite their great potential improve fertility, biofertilizers have yet replace conventional chemical fertilizers commercial agriculture. last 10 years, multi-omics studies made significant step forward understanding drivers, roles, processes, mechanisms microbiome. However, translating knowledge microbiome functions order capitalize agroecosystems still remains challenge. Here, we address key factors limiting successful field applications suggest solutions based emerging strategies for product development. Finally, discuss importance biosafety guidelines propose new avenues research biofertilizer

Language: Английский

---

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

The ISME Journal, Journal Year: 2021, Volume and Issue: 16(3), P. 774 - 787

Published: Sept. 30, 2021

Language: Английский

---

The root microbiome: Community assembly and its contributions to plant fitness

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 64(2), P. 230 - 243

Published: Jan. 14, 2022

The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, commensals. Here we focus on recent advances study commensal which is major research object microbiome-related researches. With rapid development new technologies, plant-commensal interactions can be explored unprecedented breadth depth. Both soil environment host plant drive assembly. bulk seed bank potential commensals, plants use exudates immune responses build healthy microbial communities from available microbes. extends functional system by participating variety processes, including nutrient absorption, growth promotion, resistance biotic abiotic stresses. Plants their microbiomes have evolved adaptation strategies over time. However, there still huge gap our understanding regulatory mechanisms interactions. In this review, summarize assembly effects these development, look at prospects for promoting sustainable agricultural through microbiome.

Language: Английский

---

Revisiting Plant–Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: Dec. 21, 2020

The present scenario of agricultural sector is dependent hugely on the use chemical-based fertilizers and pesticides that impact nutritional quality, health status, productivity crops. Moreover, continuous release these chemical inputs causes toxic compounds such as metals to accumulate in soil move plants with prolonged exposure, which ultimately human health. Hence, it becomes necessary bring out alternatives pesticides/fertilizers for improvement outputs. rhizosphere plant an important niche abundant microorganisms residing it. They possess properties growth promotion, disease suppression, removal compounds, assimilating nutrients plants. Utilizing beneficial microbes crop presents efficient way modulate yield by maintaining healthy status quality through bioformulations. To understand microbial formulation compositions, essential processes going well their concrete identification better utilization diversity growth–promoting bacteria arbuscular mycorrhizal fungi. this background, review article highlights microbiome aboveground belowground, importance inoculants various species, subsequent interactive mechanisms sustainable agriculture.

Language: Английский

---

Enabling sustainable agriculture through understanding and enhancement of microbiomes

New Phytologist, Journal Year: 2021, Volume and Issue: 230(6), P. 2129 - 2147

Published: March 4, 2021

Summary Harnessing plant‐associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment microbes, occurring both above below ground, drive recognition, recruitment colonization resulting in activation downstream host responses functionality. Dissecting these complex by integrating multiomic approaches, high‐throughput culturing, computational synthetic biology advances is providing deeper understanding structure function native microbial communities. Such insights are paving way towards development products as well engineered with communities capable delivering agronomic solutions. While there a market microbial‐based solutions improve crop productivity, challenges commercialization remain. The continued translation microbiome knowledge into real‐world scenarios will require concerted transdisciplinary research, cross‐training next generation scientists, targeted educational efforts prime growers general public successful adoption innovative technologies.

Language: Английский

---

Arbuscular mycorrhizal fungi and its major role in plant growth, zinc nutrition, phosphorous regulation and phytoremediation

Symbiosis, Journal Year: 2021, Volume and Issue: 84(1), P. 19 - 37

Published: April 12, 2021

Language: Английский

---