Plants are subjected to diverse biotic and abiotic stresses in life. These can induce changes in transcriptomics and metabolomics, resulting in changes to root and leaf exudates and, in turn, ...altering the plant-associated microbial community. Emerging evidence demonstrates that changes, especially the increased abundance of commensal microbes following stresses, can be beneficial for plant survival and act as a legacy, enhancing offspring fitness. However, outstanding questions remain regarding the microbial role in plant defense, many of which may now be answered utilizing a novel synthetic community approach. In this article, building on our current understanding on stress-induced changes in plant microbiomes, we propose a ‘DefenseBiome’ concept that informs the design and construction of beneficial microbial synthetic communities for improving fundamental understanding of plant–microbial interactions and the development of plant probiotics.
The recent advances in using synthetic communities together with metagenomics and metabolomics has begun to unravel mechanistic understanding of how stressed plants modulate their microbiomes.Stresses change plant transcriptomics and metabolomics below and above ground. Molecules such as flavonoids, coumarins, and other organic compounds have been recognized as plant signals that shape host microbiomes.A crucial regulating role of the interactions between the microbiome and plant immune system in stress tolerance is emerging. Experimental validation of such interactions and determination of how they influence plant fitness should now be prioritized.The plant-associated microbes that increase in abundance by plant stresses, coined the ‘DefenseBiome’, could benefit plant health and be used for designing functionally reliable synthetic communities to improve plant fitness.
Agronomic practices such as crop residue return and additional nutrient supply are recommended to increase soil organic carbon (SOC) in arable farmlands. However, changes in the priming effect (PE) ...on native SOC mineralization in response to integrated inputs of residue and nutrients are not fully known. This knowledge gap along with a lack of understanding of microbial mechanisms hinders the ability to constrain models and to reduce the uncertainty to predict carbon (C) sequestration potential. Using a 13C‐labeled wheat residue, this 126‐day incubation study examined the dominant microbial mechanisms that underpin the PE response to inputs of wheat residue and nutrients (nitrogen, phosphorus and sulfur) in two contrasting soils. The residue input caused positive PE through “co‐metabolism,” supported by increased microbial biomass, C and nitrogen (N) extracellular enzyme activities (EEAs), and gene abundance of certain microbial taxa (Eubacteria, β‐Proteobacteria, Acidobacteria, and Fungi). The residue input could have induced nutrient limitation, causing an increase in the PE via “microbial nutrient mining” of native soil organic matter, as suggested by the low C‐to‐nutrient stoichiometry of EEAs. At the high residue, exogenous nutrient supply (cf. no‐nutrient) initially decreased positive PE by alleviating nutrient mining, which was supported by the low gene abundance of Eubacteria and Fungi. However, after an initial decrease in PE at the high residue with nutrients, the PE increased to the same magnitude as without nutrients over time. This suggests the dominance of “microbial stoichiometry decomposition,” supported by higher microbial biomass and EEAs, while Eubacteria and Fungi increased over time, at the high residue with nutrients cf. no‐nutrient in both soils. Our study provides novel evidence that different microbial mechanisms operate simultaneously depending on organic C and nutrient availability in a residue‐amended soil. Our results have consequences for SOC modeling and integrated nutrient management employed to increase SOC in arable farmlands.
This study examined the dynamics of priming effect (PE), controlled by the interaction of crop residue input and balanced supply of nutrients (N, P, and S), and the underlying mechanisms in relation to microbial community growth and extracellular enzyme activity. The results showed that the “microbial nutrient mining” and “microbial stoichiometry decomposition” mechanisms relating to nutrient availability mainly operated at high residue input. The image presents a conceptualized model based on key findings on the dominant occurrence of microbial mechanisms relating to PE, with implications to underpin soil organic carbon (SOC) modeling and guide integrated residue–nutrient management in croplands for SOC sequestration.
Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness ...advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions.
The first organophosphorus (OP) compound-degrading bacterial strain was isolated from a paddy field in the Philippines in 1973. Since then, several phylogenetically distinct bacteria that can degrade ...OP by co-metabolism, or use OPs as a source of carbon, phosphorus or nitrogen, have been isolated from different parts of the world. There is huge potential for industrial applications of OP-degrading bacteria. Important advances in our understanding of the microbiology, genomics and evolution of OP-degrading bacteria have been made over the past four decades, and are discussed in this review.
Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is ...considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.
Summary
Climate change is increasing global temperatures and the frequency and severity of droughts in many regions. These anthropogenic stresses pose a significant threat to plant performance and ...crop production. The plant‐associated microbiome modulates the impacts of biotic and abiotic stresses on plant fitness. However, climate change‐induced alteration in composition and activities of plant microbiomes can affect host functions. Here, we highlight recent advancements in our understanding of the impact of climate change (warming and drought) on plant–microbiome interactions and on their ecological functions from genome to ecosystem scales. We identify knowledge gaps, propose new concepts and make recommendations for future research directions. It is proposed that in the short term (years to decades), the adaptation of plants to climate change is mainly driven by the plant microbiome, whereas in the long term (century to millennia), the adaptation of plants will be driven equally by eco‐evolutionary interactions between the plant microbiome and its host. A better understanding of the response of the plant and its microbiome interactions to climate change and the ways in which microbiomes can mitigate the negative impacts will better inform predictions of climate change impacts on primary productivity and aid in developing management and policy tools to improve the resilience of plant systems.
A global atlas of the dominant bacteria found in soil Delgado-Baquerizo, Manuel; Oliverio, Angela M; Brewer, Tess E ...
Science (American Association for the Advancement of Science),
01/2018, Volume:
359, Issue:
6373
Journal Article
Peer reviewed
Open access
The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six ...continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a "most wanted" list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.
Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed ...235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide.
Summary
Host microbiomes play a critical role in host fitness and health. Whilst the current 'holobiont' concept framework has greatly expanded eco‐evolutionary and functional understanding of ...host‐microbiome interactions, the important role of biotic interactions and microbial loop (compositional linkage between soil, plant and animal) in shaping host‐microbiome are poorly understood. We proposed an 'eco‐holobiont' concept to fill the knowledge gap.
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