Biology subjects

Cumming, J. R.

Publications and source records attributed to Cumming, J. R..

3 recordsLinked to original sources

bioRxiv2020

Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence by different hardwood tree species

The soil microbiome plays an essential role in processing and storage of nitrogen (N) and carbon (C), and is influenced by vegetation above-ground through imparted differences in chemistry, structure, mass of plant litter, root physiology, and dominant mycorrhizal associations. We used shotgun metagenomic sequencing and bioinformatic analysis to quantify the abundance and distribution of gene families involved in soil microbial N and C cycling beneath three deciduous hardwood tree species: ectomycorrhizal (ECM)-associated Quercus rubra (red oak), ECM-associated Castanea dentata (American chestnut), and arbuscular mycorrhizal (AM)-associated Prunus serotina (black cherry). Chestnut exhibited the most distinct soil microbiome of the three species, both functionally and taxonomically, with a general suppression of functional genes in the nitrification, denitrification, and nitrate reduction pathways. These changes were related to low inorganic N availability in chestnut stands as soil was modified by poor, low-N litter quality relative to red oak and black cherry soils. IMPORTANCEPrevious studies have used field biogeochemical process rates, isotopic tracing, and targeted gene abundance measurements to study the influence of tree species on ecosystem N and C dynamics. However, these approaches do not enable a comprehensive systems-level understanding of the relationship between microbial diversity and metabolism of N and C below-ground. We analyzed microbial metagenomes from soils beneath red oak, American chestnut, and black cherry stands and showed that tree species can mediate the abundance of key microbial genes involved in N and (to a lesser extent) C metabolism pathways in soil. Our results highlight the genetic framework underlying tree species control over soil microbial communities, and below-ground C and N metabolism, and may enable land managers to select tree species to maximize C and N storage in soils.

ecology↗

bioRxiv2019

Phenotypic and physiological responses to salt exposure in Sorghum reveal diversity among domesticated landraces

Soil salinity negatively impacts plant function, development, and yield. Sorghum bicolor is a staple crop known to be drought tolerant, to have adapted to a variety of conditions, and to contain significant standing genetic diversity, making it an exemplary species to study phenotypic and physiological variation in salinity tolerance. In our study, a diverse group of sorghum landraces and accessions was first rank-ordered for salinity tolerance and then individuals spanning a wide range of response were analyzed for foliar proline and ion accumulation. We found that, while proline is often a good indicator of osmotic adjustment and is historically associated with increased salt tolerance, proline accumulation in sorghum reflects stress-response injury rather than acclimation. When combining ion profiles with growth responses and stress tolerance indices, the variation observed in tolerance was similarly not a sole result of Na+ accumulation, but rather reflected accession-specific mechanisms that may integrate these and other metabolic responses. When we compared variation in tolerance to phylogenetic relationships, we conclude that the most parsimonious explanation for the variation observed among accessions is that salinity tolerance was acquired early during domestication and was subsequently maintained or lost in diverged lineages during improvement in areas that vary in soil salinity.

plant biology↗

bioRxiv2019

MCHM acts as a hydrotrope, altering the balance of metals in yeast

While drugs and other industrial chemicals are routinely studied to assess risks, many widely-used chemicals have not been thoroughly evaluated. One such chemical, 4-methylcyclohexane methanol (MCHM), is an industrial coal-cleaning chemical that contaminated the drinking-water supply in Charleston, WV, USA in 2014. While a wide range of ailments was reported following the spill, little is known about the molecular effects of MCHM exposure. We used the yeast model to explore the impacts of MCHM on cellular function. Exposure to MCHM dramatically altered the yeast transcriptome and the balance of metals in yeast. Underlying genetic variation in the response to MCHM and transcriptomics and mutant analysis uncovered the role of the metal transporters, Arn2 and Yke4, to MCHM response. Expression of Arn2, involved in iron uptake, was lower in MCHM-tolerant yeast and loss of Arn2 further increased MCHM tolerance. Genetic variation within Yke4, an ER zinc transporter, also mediated response to MCHM and loss of Yke4 decreased MCHM tolerance. The addition of zinc to MCHM-sensitive yeast rescued growth inhibition. In vitro assays demonstrated that MCHM acted as a hydrotrope and prevented protein-interactions, while zinc-induced the aggregation of proteins. We hypothesized that MCHM altered the structures of extracellular domains of proteins, and the addition of zinc stabilized the structure to maintain metal homeostasis in yeast exposed to MCHM.

biochemistry↗