Soil microbiome engineering for sustainability in a changing environment

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(12), P. 1716 - 1728

Published: Oct. 30, 2023

Language: Английский

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Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 923, P. 171332 - 171332

Published: March 5, 2024

Language: Английский

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Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral‐associated organic matter

New Phytologist, Journal Year: 2024, Volume and Issue: 242(4), P. 1661 - 1675

Published: Feb. 15, 2024

Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, precursor of organic matter (SOM), and driver microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we

Language: Английский

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Hyphosphere microbiome of arbuscular mycorrhizal fungi: a realm of unknowns

Biology and Fertility of Soils, Journal Year: 2022, Volume and Issue: 59(1), P. 17 - 34

Published: Nov. 28, 2022

Language: Английский

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HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: Nov. 25, 2022

Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive this goal, Stable-isotope probing-SIP-remains among most comprehensive studying whole communities in situ. In DNA-SIP, actively growing microorganisms take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions sequenced. However, SIP relatively low throughput requires significant hands-on labor. We designed tested semi-automated, high-throughput (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon metagenomics experiments. applied soil microhabitat ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships plant species play roles terrestrial nutrient carbon cycling.

Language: Английский

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Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(11), P. 1809 - 1822

Published: Sept. 28, 2023

Language: Английский

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Can arbuscular mycorrhizal fungi and rhizobacteria facilitate 33P uptake in maize plants under water stress?

Microbiological Research, Journal Year: 2023, Volume and Issue: 271, P. 127350 - 127350

Published: March 5, 2023

Language: Английский

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Synthetic microbial communities: Sandbox and blueprint for soil health enhancement

iMeta, Journal Year: 2024, Volume and Issue: 3(1)

Published: Feb. 1, 2024

We summarize here the use of SynComs in improving various dimensions soil health, including fertility, pollutant removal, soil-borne disease suppression, and resilience; as well a set useful guidelines to assess understand principles for designing enhance health. Finally, we discuss next stages applications, highly diverse multikingdom targeting several functions simultaneously. In nature, microorganisms do not act individuals but rather interact communicate with one another dynamically changing microbial community, they are essential maintaining Earth's biosphere survival plants animals contribute nearly all biogeochemical cycles on earth. However, studying populations directly their natural environment poses significant challenges due vast population size complex interaction network. This difficulty hampers our ability predict behavior communities thereby limiting understanding functionality environmental systems developing utilizing resources. Further, inherent complexity microbiota makes it immensely challenging establish causality and, subsequently, dissect mechanisms. One emerging strategy tackle aforementioned challenge is simplified, synthetic (SynComs). artificial combinations two or more distinct cultured well-defined taxonomic status specific functional characteristics. Compared individual organisms, functionally redundant which implies exhibit reduced metabolic burden division labor, exchange resources, possess expanded capabilities relative monocultures, constantly (chemically physically), hence better resist perturbations invasions by other species such [1]. Moreover, maintain key features because defined have been increasingly used model system study functional, ecological, structural concepts native microbiota. Construction application demonstrated different contexts, human marine bacteria–plankton interaction, following sections, review how broad potential field health improvement, fertility restoration, bioremediation, resilience enhancement (Figure 1). Intensive agriculture has caused variety issues exhaustion organic matter nutrient reserves, resulting degradation. At present, one-third global land surfaces degraded some extent, 24 billion metric tons fertile lost every year [2]. Driven role crop productivity, applications restore studied. The can through structure, cycling, bioavailability 1A). Microorganisms an important determinant both aggregate formation stabilization this effect consistent across soils. main drivers production extracellular polymeric substances (EPS) bacteria fungi, combine particles together importance synergetic interspecific interactions EPS suggests that maximizing may improve structure. Application revealed biotic formation. For instance, Pseudomonas fluorescens Stenotrophomonas maltophilia isolated from Agaricus lilaceps fruiting body binds than Bacillus sp. outside inside fairy ring [3]. Additionally, fungal activity alter nature extent availability pore spaces habitat surrounding microbes. Furthermore, recent work studied effects trophic aggregation building simple community included protist bacteria/fungus. They found Acanthamoeba castellanii increased aggregates decreased stability, authors attributed changes bacterial mucilage [4]. Soil involved cycle plant nutrients encountered soil. Several instance solubilize phosphorus (P) microelements iron (Fe) zinc (Zn) matrix, mineralize nitrogen (N) material pool even fix air. showed N2-fixing, P-solubilizing, K-solubilizing, indole-3-acetic acid (IAA)-producing significantly increase content available N, P, K soil, combination these growth-promoting effectively improved N/P/K uptake growth [5]. pollution, pesticide residues, heavy metals, petroleum hydrocarbons, microplastics, serious threat quality. naturally degrade pollutants, property often implemented bioremediation strategies. applied bioaugmentation strategies, goal invading microbiome harboring contaminant 1B). Given high contaminants, single strains be sufficient achieve "removal efficiency," case linuron [6]. Variovorax strain WDL1 could via using carbon, nitrogen, energy sources directly. While Delftia acidovorans WDL34 WDL5 were able linuron, intermediate linuron's When was mixed cannot source SynCom, degradation rate dramatically interactions. reductionist approaches resident micropollutant 2,6-Dichlorobenzamide cooperating degrading Aminobacter MSH1. opens door assisting coinoculation "helper" originating and/or already adapted target [7]. Specific microbes rhizobacteria (PGPR) indirect positive impacts removal contaminants (phytoremediation). composed PGPR accumulation stimulating growth, manipulated efficacy phytoremediation. inoculation contaminated soils Arbuscular mycorrhiza Aspergillus terreus at vegetation reintroduction only enhanced extraction metals polluted also enabled establishment [8]. Plant diseases pathogens major food security currently require massive yields. Many studies rhizosphere composition function, especially among microbes, between microbe very suppression. By SynComs, progresses made revealing relationship resistance pathogen invasion, exploring microbiota-plant suppression 1C). Soil-borne affected determined either within rhizosphere. A large number inferred co-occurrence networks profiling metagenomic data suggested associations (either positive, neutral, negative) linked immunity. correlative approach fails reveal causal mechanisms affect each other, pathogens. purposes, test under laboratory conditions, strain–strain infection. Durán colleagues combined metagenomics show negative prokaryotic eukaryotic root members critical host maintenance host-microbiota balance [9]. conclusion, patterns omics-based actual SynComs-based elucidate There numerous physiology, immune participates defense against pathogens, identify microbe-associated molecular pattern-recognition receptors, thus affecting colonization beneficial Although plant-rhizosphere mainly focused single-model microorganisms, researchers recently began pay attention It worth pointing out Lebeis first employed SynCom 38 explore immunity assembly communities. signal-salicylic modulated families [10]. Castrillo et al. P-starvation, 35 activities P stress response genes PSR PHR1, coordinating nutrition [11]. These suggest present opportunities rational design aimed suppressing disease. With resilience, refer preserve its stressors, multispecies prevent substantial alterations average function perturbations. environment, unlikely perform multiple desired functions, stabilizing biodiversity emerge consequence redundancy when vary niche sensitivity stressors. Therefore, plays plant-soil abiotic stresses. help driving microbe–microbe interactions, plant–microbe 1D). Microbe–microbe play roles almost processes occurring Earth, stresses Recently, fungi shown facilitate dry [12], therefore investigating coinoculations drought interest. exopolysaccharides produced array like bacteria, cyanobacteria, microalgae, yeasts, impart wide range Such quorum sensing, supporting saline halophilic remediate status, matter, pH, electrical conductivity, deposition ionic salts [13]. Microbiomes alleviation increasing water nutrients, reducing oxidative stress, decreasing metal toxicity, producing hormones, regulating signaling pathways plants. Nearly lead reactive oxygen plants, associated release catalase, peroxidase, enzymes reduce damage [14]. combining five desert promote tomato nonsterile conditions. salt tolerance expression stress-related shoots [15]. microbe–plant [16]. technically apply there still many overcome before precisely construct designed allow translation scientific findings real-world improvements. involves deliberate microorganism treatment relates invasion process, is, requires alien particular while performing functionality. Whether manages successfully invade depends factors, structure locally community. deep mechanistic comprehension relevant take place during into microbiome, influence physical chemical properties ecological form principle efficient 2). core functions. Like define keystone central organizing (such degradation, resilience). related need targeted pollutant, P-solubilizing necessary bioavailability. culture-dependent method track abundance strain, Niu investigated played assembly. E. cloacae led complete loss function. result keynote ecosystem [17]. support species, proliferation colonize called species. process will higher probability success "helpers" provide invader invader's fitness so niches occupied others colonized improves efficiency 2A). Species diversity affects most generally accepted richness 2B). chance include strains, providing bioavailability, nutrition, hormonal any isolate. As usually kind SnyCom contain achieving efficiency. occupy pressures [18], survive environments should noted always beneficial. Under limited-resource aggravate risk resource competition decline overall biomass Interactions 2C). Positive same level public goods cross-feeding, where benefit presence other. Negative direct interference suppress antagonism. ways. resistance, competitive less prone if efficiently utilize consume resources would otherwise competing inhibit toxic metabolites, facilitative utilized Conversely, cooperative seems fertility. removed synergy. Cooperation addition level, organisms levels, predation parasitism, considered SynComs. enable precise control over manipulations dropouts gene knockouts, typically low (<20 strains), biology native-scale [19]. develop clear compositions further investigate principles. possible validate correlations (e.g., >100 assessing metabolism genome sequencing isolate intrinsic enhancing [20]. interesting moving toward realistic complexity, containing phages, protozoa) factors availability) dynamics Because screening candidates crucial step design, focus based SynCom. reliable predictive linking established, combines theory, basic experimental data, engineering development strategies design-build-test-learning cycle), machine learning algorithms Zhong Wei provided direction guidance throughout preparation manuscript. Mei Li wrote original draft. Jie Hu drawings Li, Hu, Wei, Alexandre Jousset, Thomas Pommier, Xiangyang Yu, Yangchun Xu, Qirong Shen reviewed revisions All read approved final financially supported National Natural Science Foundation China (42207156 42325704), Key Research Development Program (2021YFD1900100), Fundamental Funds Central Universities (KYT2023001). apologize being cite additional owing space limitations. declare no conflict paper does generate new data. Supplementary materials (graphical abstract, slides, videos, Chinese translated version updated materials) online DOI iMeta http://www.imeta.science/.

Language: Английский

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Enhancing consistency in arbuscular mycorrhizal trait-based research to improve predictions of function

Mycorrhiza, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 26, 2025

Language: Английский

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Selenium-induced rhizosphere microorganisms endow salt-sensitive soybeans with salt tolerance

Environmental Research, Journal Year: 2023, Volume and Issue: 236, P. 116827 - 116827

Published: Aug. 4, 2023

Language: Английский

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