Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites.

Obesity and metabolic dysfunction have been shown to be associated with overproduction of reactive oxygen species (ROS) in the gastrointestinal (GI) tract, which contributes to dysbiosis or imbalances in the gut microbiota. Recently, the reversal of dysbiosis has been observed as a result of dietary supplementation with antioxidative compounds including polyphenols. Likewise, dietary polyphenols have been associated with scavenging of GI ROS, leading to the hypothesis that radical scavenging in the GI tract is a potential mechanism for the reversal of dysbiosis. The objective of this study was to investigate the relationship between GI ROS, dietary antioxidants and beneficial gut bacterium Akkermansia muciniphila. The results of this study demonstrated A. muciniphila to be a discriminant microorganism between lean (n = 7) and obese (n = 7) mice. The relative abundance of A. muciniphila was also found to have a significant negative correlation with extracellular ROS in the GI tract as measured using fluorescent probe hydroindocyanine green. The ability of the dietary antioxidants ascorbic acid, β-carotene and grape polyphenols to scavenge GI ROS was evaluated in tandem with their ability to support A. muciniphila bloom in lean mice (n = 20). While the relationship between GI ROS and relative abundance of A. muciniphila was conserved in lean mice, only grape polyphenols stimulated the bloom of A. muciniphila. Analysis of fecal antioxidant capacity and differences in the bioavailability of the antioxidants of interest suggested that the poor bioavailability of grape polyphenols contributes to their superior radical scavenging activity and support of A. muciniphila in comparison to the other compounds tested. These findings demonstrate the utility of the GI redox environment as a modifiable therapeutic target in the treatment of chronic inflammatory diseases like metabolic syndrome.

Microbial degradation of organic matter is a fundamental Earth process, yet a mechanistic understanding of microbial metabolisms and successional ecology involved in decomposition remains poorly understood. Here, we announce the recovery of 277 cadaver-associated soil metagenome-assembled genomes to enhance our understanding of vertebrate decomposition microbial processes.

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix. Previous research has shown that plant root exudate profiles vary between species and genotypes which can likely support different microbial associations. Here, utilizing distinct sorghum genotypes as a model system, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolisms. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments, a High Organic acid Treatment (HOT) and a High Sugar Treatment (HST). Root exudate treatments were added to laboratory soil reactors and 16S rRNA gene profiling illustrated distinct microbial membership in response to HST or HOT amendments. Alpha and beta diversity metrics were significantly different between treatments, (Shannon’s, p < 0.0001, mrpp = 0.01, respectively). Exometabolite production was highest in the HST, with increased production of key organic acids, non-proteinogenic amino acids, and three plant growth-promoting phytohormones (benzoic acid, salicylic acid, indole-3-acetic acid), suggesting plant-derived sugars fuel microbial carbon metabolism and contribute to phytohormone production. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified potential plant growth-promoting microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multi-omics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. Importance: Understanding interactions between plant root exudates and the soil microbiome provides an avenue for a more comprehensive appreciation for how plant roots modulate their microbial counterparts to promote an environment favorable to plant fitness. Although these dynamics are appreciated as indispensable, mechanisms controlling specific rhizobiome membership and complexity are not fully understood. In this study, we investigate how variability in root exudation, modeled after differences observed between distinct sorghum genotypes, contributes to altered microbial membership and metabolisms. The results demonstrate how microbial diversity is influenced by root exudates of differing chemical composition and how changes in microbial membership correspond to modifications in carbon utilization and enhance production of plant-relevant metabolites. Our findings suggest carbon substrate preferences among bacteria in semi-arid climate soils and mechanisms for root exudate utilization. These findings provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.

The breakdown and recycling of carrion is a crucial ecological process that largely relies on a community of necrophagous insects and microbes. Recent work has shown that a specialized microbial network, likely dispersed throughout the environment by insects, assembles during cadaver decomposition to break down flesh regardless of climate and geography. Because of their broad distribution and successional nature, decomposer microbes have been used in machine learning models to predict the postmortem interval (PMI) of human remains, an important contribution to the field of forensics. How factors such as an indoor environment, which alters insect activity, impact the composition of microbial communities decomposing human remains is unclear. Here, we investigate the effects of enclosed shelter on microbial community assembly and successional patterns during human decomposition and provide important considerations for PMI modeling. Compared to outdoor cadavers, we show that indoor cadavers experienced delayed colonization of key decomposer microbes over the course of decomposition due to restricted insect access. Consequently, machine learning models trained on outdoor cadavers frequently underestimated the PMI of cadavers decomposing indoors. Delayed colonization by blow fly maggots (Diptera: Calliphoridae) was correlated with higher PMI prediction errors, suggesting that insects are an important source of microbial decomposers that drive PMI model predictions. Incorporating microbial data from indoor cadavers and insect activity into PMI models significantly improved prediction capabilities for both indoor and outdoor decomposition environments. Ultimately, we demonstrate the important role insects play in the maintenance and distribution of microbes that help to recycle vertebrate remains. IMPORTANCE: Microbes are critical for the decomposition and recycling of organic matter. Recently, microbiome-based models have shown promising performance in estimating the postmortem interval (PMI). However, many deaths occur indoors, yet no studies have investigated the impact of enclosed shelter on the cadaver microbiome in a controlled setting. Here, cadavers were decomposed indoors, and we found that blow fly maggots serve as an important source of decomposer taxa that significantly alter the cadaver microbiome following infestation. Notably, PMI estimation models trained on outdoor data sets failed to accurately predict the PMI when insect colonization was delayed. We show that incorporating 16S rRNA amplicon data from cadavers decomposing indoors, along with environmental variables, significantly improves PMI estimates, suggesting a microbiome-based forensic tool may be feasible across decomposition environments. Importantly, this research demonstrates the critical ecological role insects play in the dispersal of specialized microbes that are involved in the breakdown and recycling of vertebrate remains.