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Insights into the taxonomic and functional characterization of agricultural crop core rhizobiomes and their potential microbial drivers.

ABSTRACT: While our understanding of plant-microbe interactions in the rhizosphere microbiome (rhizobiome) has increased, there is still limited information on which taxa and functions drive these rhizobiome interactions. Focusing on the core rhizobiome (members common to two or more microbial assemblages) of crops may reduce the number of targets for determining these interactions, as they are expected to have greater influence on soil nutrient cycling and plant growth than the rest of the rhizobiome. Here, we examined whether the characterization of a core rhizobiome on the basis of only taxonomic or functional traits rather than the combined analysis of taxonomic and functional traits provides a different assessment of the core rhizobiome of agricultural crops. Sequences of the bacterial 16S rRNA gene from six globally important crops were analyzed using two different approaches in order to identify and characterize the taxonomic and functional core rhizobiome. For all crops examined, we found significant differences in the taxonomic and functional composition between the core rhizobiomes, and different phyla, genera, and predicted microbial functions were dominant depending on the core rhizobiome type. Network analysis indicated potentially important taxa were present in both taxonomic and functional core rhizobiomes. A subset of genera and predicted functions were exclusively or predominately present in only one type of core rhizobiome while others were detected in both core rhizobiomes. These results highlight the necessity of including both taxonomy and function when assessing the core rhizobiome, as this will enhance our understanding of the relationships between microbial taxa and soil health, plant growth, and agricultural sustainability.

SUBMITTER: Castellano-Hinojosa A

PROVIDER: S-EPMC8115259 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.

Project description:BackgroundCover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils.ResultsHere, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs.ConclusionsWe highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.

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Insights into the taxonomic and functional characterization of agricultural crop core rhizobiomes and their potential microbial drivers.

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