In this study, we used a 10-year long reciprocal garden system, and reports that different ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii can maintain or recruit distinct bacterial but not fungal rhizobiomes after 10 years in an arid environment. We used both 16S rRNA and ITS2 amplicons to analyze the bacterial and fungal communities in the rhizospheres of the respective ecotypes.

Microbial interactions in natural environments are intricately complex. High numbers and rich diversity of microorganisms, along with compositional heterogeneities complicate the cause. It is essential to simplify these complex communities to understand the microbial interactions. We proposed a concept of “simple state community,” which represents a subset of microbes and/or microbial functions of the original population that is necessary to build a stable community. By combining microbial culturing and high-throughput sequencing, we can better understand microbe-microbe and microbe-host interactions. To support our proposed model, we used carbon-based and nitrogen-based media to capture the simple state communities. We used 16S rRNA amplicon sequencing and assigned taxonomic identity to the bacterial populations before and after simple state communities. We showed that simple state communities were a subset of the original microbial communities at both phyla and genera level. We further used shotgun metagenomics to gain insights into the functional potential of the assembled simple state communities. Our proposed model supported the goal of simplifying the complex communities across diverse systems to provide opportunity to facilitate comprehension of both the structure and function of the subset communities. Further applications of the concept include the high-throughput screening of simple state communities using the BIOLOG® system and continuous culturing (Chemostat). This concept has the potential to test diverse experimental hypotheses in simplified microbial communities, and further extend that knowledge to answer the overarching questions at a more holistic level.

Background: Climate change will result in more frequent droughts that impact soil inhabiting microbiomes in the agriculturally vital North American perennial grasslands. In this study, we used the combination of culturomics and high-resolution genomic sequencing of microbial consortia isolated from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host associated microbes under artificial drought induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Results: Phylogenetic analysis of the non redundant metagenome-assembled genomes (MAGs) identified the bacterial population of interest MAG-Pseudomonas. Further metabolic pathway and pangenome analyses detected genes and pathways related to nitrogen transformation and stress responses in MAG-Pseudomonas. Conclusions: Our data indicate that the metagenome assembled MAG Pseudomonas has the functional potential to contribute to the plant host growth during stressful conditions. This study provided insights into optimizing plant productivity under drought conditions.

The microbiota has profound influence on the host through interactions with the immune system early in host development. These interactions are crucial in understanding complex autoimmune diseases, such as Inflammatory Bowel Disease (IBD). Here, we examined how specific groups of microbes in dysbiotic mice impacted outcomes of colitis, host immune response, gene expression, and microbial functional changes. Vertically transmitted dysbiotic pups received fecal microbiota transplantation (FMT) from control mice, at 2, 3, and 8 weeks after birth. After 23 weeks, remaining mice were supplemented with 2.5% dextran sulfate sodium to induce colitis. Colon histology revealed mice receiving FMT displayed less colon inflammation than mice with no gavage. We assembled 190 non-redundant Metagenome-Assembled Genomes (MAGs) from pup fecal content and highlighted microbial community differences in FMT mice compared to dysbiotic groups. Enterococcus sp. and Enterobacteriaceae members were highly detected in dysbiotic mice only. These MAGs shared a large number of antimicrobial resistance genes as well as several virulence factors including a T6SS along with multiple inflammation inducing metabolic pathways. The Enterobacteriaceae sp. displayed the ability to uptake and utilize cysteine and taurine for sulfur metabolism, in addition to utilizing the host immune response production of nitrate and nitrite as energy sources. Here, we find that potentially pathogenic microbes in the dysbiotic gut have the metabolic capability to compete with the host for sulfur-containing amino acids as well as host derived nitrate and nitrite to further inflame the gut, and worsening IBD symptoms.

Background Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. Results In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest – MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. Conclusions Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host’s growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.