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57 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Depth-resolved sagebrush root metabolomics, rhizosphere microbial communities, and geochemistry at the East River Watershed

This data set consists of results from soil nutrient profile, untargeted metabolomics, mass spec imaging, and amplicon sequencing. Data for soil nutrient profile includes common cations (Ca, Mg, Na, and K etc.) extracted from 3 digesting steps – ammonia acetate (for exchangeable cations), nitric acid (for acid dissolved fraction), and hydrofluoric acid/perchloric acid (HF/HClO4) for whole soil digestion. It also includes concentration of organic carbon, inorganic nitrogen (ammonia and nitrate) and phosphorus (Bray-1 P and nitric acid extract), and total nitrogen and phosphorus. Data for untargeted metabolomics includes metabolomic profile for root exudate/tissues and soil extracts from depths at surface soil to saprolite, that were measured using gas chromatography – mass spectrometry (GC-MS), and liquid chromatography – tandem mass spectrometry (LC-MS/MS). Data for mass spec imaging includes spatial distribution of metabolites that were detected and annotated with Fourier transformation ion cyclotron resonance mass spectrometer (FTICR-MS). Data for amplicon sequencing includes the base paired 16S and ITS ribosomal RNA sequences from Miseq Illumina sequencing. All samples were collected from 2 sampling campaign October 2022 and June 2023. Collectively, these datasets enable a mechanistic evaluation of how nutrient acquisition, especially nitrogen and phosphorus, differs between shallow roots operating in soil and deep roots functioning within the fractured bedrock zone. All files are provided as comma-separated values (CSV) fies (.csv) and (GZIP) file (.gz). The compressed .gz FASTQ files can be read directly in R using the dada2 package as part of the amplicon sequence analysis workflow. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research was performed on a project award 60563 (https://dx.doi.org/10.46936/expl.proj.2022.60563/60008727) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830.

EARTH SCIENCE > AGRICULTURE > SOILS > CARBON↗
DOE OSTI2021

Filling gaps in our understanding of belowground plant traits across the world: an introduction to a Virtual Issue

The belowground world is one of the final frontiers in terrestrial ecology. The tangling of plant roots with the surrounding soil below is a lifeline for the humble forbs and towering trees above, and roots play a key role in shaping ecosystem carbon, water and nutrient cycling (Bardgett et al., 2014). Ecologists have long sought to better understand the ecosystem-scale consequences of differing plant strategies, above- and belowground, by relating plant characteristics, or traits, to plant function (Grime, 1977; Pregitzer, 2002). While developing trait–function linkages is arguably more difficult for plant traits that are hidden belowground, root and rhizosphere ecologists continue to fan out across grasslands and forests with their shovels, isotopes, and specialized cameras, seeking a better understanding of the secret lives of roots. Over the years, New Phytologist has served as a virtual town square for scientists to discuss their hard-won observations on the interplay among belowground plant traits, microbial activity, and edaphic and environmental conditions from biomes around the world (Norby & Jackson, 2000; Pregitzer, 2002; Matamala & Stover, 2013; Norby & Iversen, 2017). In this Editorial we highlight the newest papers that update and add to our understanding of the role of root and rhizosphere traits in broader ecosystem processes. We focused on papers published in New Phytologist between 1 January 2019 and 31 December 2020 and extended this window to papers still in ‘early view’ up to the time of writing. Because of the overwhelming number of papers, we did not include those with a decidedly genomic focus or that served primarily as data syntheses, reviews, insights or commentaries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Low soil phosphorus availability triggers maize growth stage specific rhizosphere processes leading to mineralization of organic P

Phosphorus (P) is one of the essential nutrients for all living organisms. High-quality mineral P fertilizer is a finite resource with only an estimated 80-100 years of reserves remaining globally. Both plants and microbes have developed several mechanisms such as secretion of organic acids, acidification of the rhizosphere, and production of extracellular enzymes to enhance the acquisition of P from soils. Increased activity of phosphatase occurs in response to P deficiency as part of P starvation responses which catalyze the hydrolysis of P o from soil organic matter (SOM) and release inorganic P (P i ). However, the specific interactions between plants and microbial communities in the rhizosphere soil triggered by P deficiency are largely unknown. In a greenhouse study we grew maize plants in low and high P containing soils and examined the role of rhizosphere processes on mineralization of organic P (P o ) in soils with low and high P availability and different P speciation 23 (Po dominated versus P i dominated) and determine its effect on plant growth. Plant biomass was determined and rhizosphere soils, and soil samples from pots with and without plants were collected at key vegetative growth stages (VGS). A variety of biogeochemical parameters (e.g. microbial biomass C and P, potential phosphatase activities, plant biomass P, soil P species etc.) were determined using both conventional (sequential chemical extraction) and advanced (e.g. high resolution mass spectrometry (FTICR-MS) and 3129 P solution NMR) techniques. Here, we used phospholipid fatty acid (PLFA) and DNA based microbial community analysis to track changes in microbial community structure and diversity. Low P availability induced changes in biogeochemical processes and microbial community composition in the rhizosphere soils of plants grown in low P containing soil. At early VGS, the plants in low P soil were visually struggling which correlated with greater rhizosphere potential acid phosphatase activity and a reduction in P o fractions. At late VGS, the plants appeared to recover which correlated with a decrease in Meh (III) extractable P, an increase in microbial biomass C and P and greater total P in the plant biomass (roots, shoots and leaves). In high P containing soil, on the other hand, greater P availability masked these rhizosphere processes. Our results confirmed the degradation of SOM and Po mineralization in rhizosphere soils driven by microbe and plant need for P. P deficiency may have favored the abundance of fungi which utilized easily degradable root exudates for the production of extracellular enzymes responsible for the mineralize of SOM P o . This study highlights the intertwined mechanisms involved, and emphasizes the importance of, P o sources for plant nutrition and survival in marginal soils.

59 BASIC BIOLOGICAL SCIENCES↗