Biology subjects

Acharya, S. M.

Publications and source records attributed to Acharya, S. M..

3 recordsLinked to original sources

bioRxiv2024

A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress

Rhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes that mimic the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging. Here, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla and demonstrates strong stability both in vitro and in planta. Genomic analysis of the individual strains revealed that they encode multiple plant growth-promoting traits, some of which were validated by laboratory phenotypic assays. Additionally, most strains encoded genes both for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ transporters. These traits likely enabled the resilience of Brachypodium to drought stress where plants amended with SynCom recovered better than without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria. Our results represent significant progress towards building and testing stable model SynComs for a better understanding of plant-microbe interactions.

microbiology↗

bioRxiv2023

Iodidimonas, a bacterium unable to degrade hydrocarbons, thrives in a bioreactor treating oil and gas produced water

Iodidimonas is a genus recently described in bioreactors treating oil and gas produced water and in iodide rich brines. Besides the ability to oxidize iodine, little is known about the metabolic capabilities that enable Iodidimonas sp. to occupy this unique ecological niche. We isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor treating produced water. We describe the genomic features of these isolates and compare them with the only other four isolate genomes reported from this genus, as well as a metagenome-assembled genome from the source bioreactor. To survive in the produced water, Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal and organic compound stress. While the isolates could utilize a wide variety of carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines. ImportanceOccupying a niche habitat and having few representative isolates, genus Iodidimonas is a relatively understudied Alphaproteobacterial group. This genus has garnered attention due to its ability to corrode pipes in iodine production facilities and generate iodinated organic compounds during treatment of oil and gas produced water. The iodinated organic compounds are likely to be carcinogenic and may pose issues with recycling the treated water. Hence, detailed characterization of the metabolic potential of these isolates is not only of economic importance, but also sheds light on adaptation of this microbe to its environmental niche.

ecology↗

bioRxiv2023

Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plants

For a deeper and comprehensive understanding of the diversity, composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary across distinct parts of the root giving rise to spatially distinct microbial niches. To address this, we analyzed microbial community from two spatially distinct zones of the primary root (the tip vs. the base) in Brachypodium distachyon, grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a stronger rhizosphere effect in the root base vs. bulk soil compared to the root tips vs. bulk soil, resulting in an enrichment of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, few OTUs belonging to less characterized lineages such as Verrucomicrobia and Acidobacteria. While the microbial community distributions are similar across growth containers, the EcoFAB displayed higher replicate reproducibility. Genome-resolved and bulk metagenomics revealed that genes associated with transcriptional regulation, transport of nutrients and catabolic enzymes indicating active metabolism, biofilm formation and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to the root tips, implying the presence of easily available, labile carbon and nutrients in the rhizosphere relative to bulk soil. Such insights into the relationships between root structure, exudation and microbial communities are critical for developing understanding of plant-microbe interactions.

ecology↗