Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Metabolic niches in the rhizosphere microbiome: dependence on soil horizons, root traits and climate variables in forest ecosystems

Understanding belowground plant-microbial interactions is important for biodiversity maintenance, community assembly and ecosystem functioning of forest ecosystems. Consequently, a large number of studies were conducted on root and microbial interactions, especially in the context of precipitation and temperature gradients under global climate change scenarios. Forests ecosystems have high biodiversity of plants and associated microbes, and contribute to major primary productivity of terrestrial ecosystems. However, the impact of root metabolites/exudates and root traits on soil microbial functional groups along these climate gradients is poorly described in these forest ecosystems. The plant root system exhibits differentiated exudation profiles and considerable trait plasticity in terms of root morphological/phenotypic traits, which can cause shifts in microbial abundance and diversity. The root metabolites composed of primary and secondary metabolites and volatile organic compounds that have diverse roles in appealing to and preventing distinct microbial strains, thus benefit plant fitness and growth, and tolerance to abiotic stresses such as drought. Climatic factors significantly alter the quantity and quality of metabolites that forest trees secrete into the soil. Thus, the heterogeneities in the rhizosphere due to different climate drivers generate ecological niches for various microbial assemblages to foster beneficial rhizospheric interactions in the forest ecosystems. However, the root exudations and microbial diversity in forest trees vary across different soil layers due to alterations in root system architecture, soil moisture, temperature, and nutrient stoichiometry. Changes in root system architecture or traits, e.g. root tissue density (RTD), specific root length (SRL), and specific root area (SRA), impact the root exudation profile and amount released into the soil and thus influence the abundance and diversity of different functional guilds of microbes. Here, we review the current knowledge about root morphological and functional (root exudation) trait changes that affect microbial interactions along drought and temperature gradients. This review aims to clarify how forest trees adapt to challenging environments by leveraging their root traits to interact beneficially with microbes. Understanding these strategies is vital for comprehending plant adaptation under global climate change, with significant implications for future research in plant biodiversity conservation, particularly within forest ecosystems.

Effect of aridity on the β-diversity of alpine soil potential diazotrophs: insights into community assembly and co-occurrence patterns

Microbial diversity plays a vital role in the maintenance of ecosystem functions. However, the current understanding of mechanisms that shape microbial diversity along environmental gradients at broad spatial scales is relatively limited, especially for specific functional groups, such as potential diazotrophs. Here, we conducted an aridity-gradient transect survey from 60 sites across the Tibetan Plateau, the largest alpine ecosystem of the planet, to investigate the ecological processes (e.g., local species pools, community assembly processes, and co-occurrence patterns) that underlie the β-diversity of alpine soil potential diazotrophic communities. We found that aridity strongly and negatively affected the abundance, richness, and β-diversity of soil diazotrophs. Diazotrophs displayed a distance-decay pattern along the aridity gradient, with organisms living in lower aridity habitats having a stronger distance-decay pattern. Arid habitats had lower co-occurrence complexity, including the number of edges and vertices, the average degree, and the number of keystone taxa, as compared with humid habitats. Local species pools explained limited variations in potential diazotrophic β-diversity. In contrast, co-occurrence patterns and stochastic processes (e.g., dispersal limitation and ecological drift) played a significant role in regulating potential diazotrophic β-diversity. The relative importance of stochastic processes and co-occurrence patterns changed with increasing aridity, with stochastic processes weakening whereas that of co-occurrence patterns enhancing. The genera Geobacter and Paenibacillus were identified as keystone taxa of co-occurrence patterns that are associated with β-diversity. In summary, aridity affects the co-occurrence patterns and community assembly by regulating soil and vegetation characteristics and ultimately shapes the β-diversity of potential diazotrophs. These findings highlight the importance of co-occurrence patterns in structuring microbial diversity and advance the current understanding of mechanisms that drive belowground communities.IMPORTANCERecent studies have shown that community assembly processes and species pools are the main drivers of β-diversity in grassland microbial communities. However, co-occurrence patterns can also drive β-diversity formation by influencing the dispersal and migration of species, the importance of which has not been reported in previous studies. Assessing the impact of co-occurrence patterns on β-diversity is important for understanding the mechanisms of diversity formation. Our study highlights the influence of microbial co-occurrence patterns on β-diversity and combines the drivers of community β-diversity with drought variation, revealing that drought indirectly affects β-diversity by influencing diazotrophic co-occurrence patterns and community assembly.

Automating methods for estimating metabolite volatility

The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called volcalc that uses chemoinformatic tools to automate these volatility estimates for all metabolites in an extensive and continuously updated pathway database: the Kyoto Encyclopedia of Genes and Genomes (KEGG) that connects metabolites, organisms, and reactions. We first benchmark the automated pipeline against a manually curated data set and show that the same category of volatility (e.g., nonvolatile, low, moderate, high) is predicted for 93% of compounds. We then demonstrate how volcalc might be used to generate and test hypotheses about the role of volatility in biological systems and organisms. Specifically, we estimate that 3.4 and 26.6% of compounds in KEGG have high volatility depending on the environment (soil vs. clean atmosphere, respectively) and that a core set of volatiles is shared among all domains of life (30%) with the largest proportion of kingdom-specific volatiles identified in bacteria. With volcalc, we lay a foundation for uncovering the role of the volatilome using an approach that is easily integrated with other bioinformatic pipelines and can be continually refined to consider additional dimensions to volatility. The volcalc package is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems.