Biology subjects

Herman, D.

Publications and source records attributed to Herman, D..

5 recordsLinked to original sources

bioRxiv2022

Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics

Plants exude large quantities of rhizosphere metabolites that can modulate composition and activity of microbial communities in response to environmental stress. While rhizodeposition dynamics have been associated with rhizosphere microbiome succession, and may be particularly impactful in stressful conditions, specific evidence of these connections has rarely been documented. Here, we grew the bioenergy crop switchgrass (Panicum virgatum) in a marginal soil, under nutrient limited, moisture limited, +nitrogen (N), and +phosphorus (P) conditions, to identify links between rhizosphere chemistry, microbiome dynamics, and abiotic stressors. To characterize links between rhizosphere microbial communities and metabolites, we used 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics. We measured significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of diverse bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions enhanced the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin, ectoine, and acetylcholine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were found in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions. SignificancePlants and microorganisms release metabolites that mediate rhizosphere host-microbe interactions and modulate plant adaptation to environmental stresses. However, the molecular mechanisms that underpin rhizosphere metabolite-microbiome dynamics, their functional relationships, and the biological role of plant- or microbial-produced soil metabolites remain largely unknown. Here, we found the abundances of specific classes of rhizosphere soil metabolites were responsive to abiotic stressors, and also connected to specific shifts in the rhizosphere microbial community and plant phenotypes. We propose a suite of understudied rhizosphere compounds as keystone metabolites that may structure the rhizosphere microbiome and influence plant metabolism in response to nutrient availability. These links between rhizosphere metabolites and microbial communities point to research avenues where we might leverage plant-microbe interactions to engineer enhanced rhizosphere microbiome function, plant and ecosystem health.

microbiology↗

bioRxiv2021

Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil

Plant roots and the organisms that surround them are a primary source for stabilized organic C, particularly in grassland soils, which have a large capacity to store organic carbon belowground. To quantify the flow and fate of plant fixed carbon (C) in a Northern California annual grassland, we tracked plant carbon from a five-day 13CO2 pulse field labeling for the following two years. Soil and plant samples were collected immediately after the pulse labeling, and again at three days, four weeks, six months, one year, and two years. Soil organic matter was fractionated using a sodium polytungstate density gradient to separate the free-light fraction (FLF), occluded-light fraction (OLF), and heavy fraction (HF). Using isotope ratio mass spectrometry, we measured 13C enrichment and total C content for plant shoots, roots, soil, soil dissolved organic carbon (DOC), and the FLF, OLF, and HF. The HF was further analyzed by solid state 13C NMR spectroscopy. At the end of the labeling period, the largest amount of 13C was recovered in plant shoots (60%), but a substantial amount (40%) was already found belowground in roots, soil, and soil DOC. Density fractionation of 4-week soil samples (from which living roots were removed) indicated that the highest isotope enrichment was in the mineral-rich heavy fraction, with similar enrichment of the FLF and OLF. At the 6-month sampling, after the dry summer period during which plants senesced and died, the amount of label in the FLF increased such that it was equal to that in the HF. By the 1-year sampling, 13C in the FLF had declined substantially and continued to decline by the 2-year sampling. 13C recovery in the OLF and HF, however, was qualitatively stable between sampling times. By the end of the 2-year experiment, 69% of remaining label was in the HF, 18% in the FLF and 13% in the OLF. While the total 13C content of the HF did not change significantly from the 4-week to the 2-year sample time, 13C NMR spectroscopic analysis of spring HF samples from 2018, 2019, and 2020 suggests that the relative proportion of aliphatic/alkyl functional groups declined in the newly formed SOC over the 2-year period. Simultaneously, aromatic and carbonyl functional groups increased, and the proportion of carbohydrate groups remained relatively constant. In summary, our results indicate that initial associations between minerals and root-derived organic matter are significant and form rapidly; by 4 weeks, a substantial amount (17%) of the total plant-derived 13C had become associated with the heavy fraction (HF) of soil. While the majority of annual C input cycles rapidly (<2-year timescale), a sizeable proportion ([~]12% of the original inputs) persisted for 2 years.

biochemistry↗

bioRxiv2020

Mismatch Negativity Predicts Pattern Separation

We are so tuned to sensory changes that we can detect novelty within hundreds of milliseconds. To what extent does our capacity to automatically discriminate auditory inputs influence encoding of long-term memories? We recorded mismatch negativity (MMN), an event-related potential (ERP) indexing perceptual discrimination, as participants were presented with sound patterns while watching a muted movie. MMN strength predicted how well naive listeners separated the previously heard from new micropatterns on a subsequent recognition test, providing evidence that the MMN translates into mnemonic pattern separation. Our investigation is the first to show that our capacity to discriminate auditory inputs, as measured by MMN, gives rise to unique memories.

neuroscience↗

bioRxiv2020

Using single-plant -omics in the field to link maize genes to functions and phenotypes

Most of our current knowledge on plant molecular biology is based on experiments in controlled lab environments. Over the years, lab experiments have generated substantial insights in the molecular wiring of plant developmental processes, stress responses and phenotypes. However, translating these insights from the lab to the field is often not straightforward, in part because field growth conditions are very different from lab conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field, and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional lab-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict at least some individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.

systems biology↗

bioRxiv2020

Conversion of marginal land into switchgrass conditionally accrues soil carbon and reduces methane consumption

Switchgrass (Panicum virgatum L.) is a perennial C4 grass native to tallgrass prairies of the Central US, and a promising bioenergy feedstock. Switchgrass can be cultivated on soils with low nutrient contents and its rooting depth, of up to 2 m, has brought attention to the crop as a potential mechanism to sequester and build soil carbon (C). Switchgrass, therefore, offers multifaceted benefits on degraded soils by enhancing soil organic matter content. However, to evaluate the sustainability of switchgrass-based biofuel production, it is crucial to understand the impacts of land conversion and switchgrass establishment on biotic/abiotic characteristics of various soils. In this study, we characterized the ecosystem-scale consequences of switchgrass growing at two highly-eroded, Dust Bowl remnant field sites from Oklahoma US, with silt-loam (SL) or clay-loam (CL) soil textures having low nitrogen (N), phosphorus (P), and C contents. Paired plots at each site, including fallow control and switchgrass-cultivated, were assessed. Our results indicated that switchgrass significantly increased soil C at the SL site and reduced microbial diversity at the CL site. The CL site exhibited significantly higher CO2 flux and higher respiration from switchgrass plots. Strikingly, switchgrass significantly reduced the CH4 consumption by an estimated 39% for the SL site and 47% for the CL site. Structural equation modeling identified soil temperature, P content, and soil moisture levels as the most influential factors regulating both CO2 and CH4 fluxes. CO2 flux was also influenced by microbial biomass while CH4 flux was influenced by microbial diversity. Together, our results suggest that site selection by soil type is a crucial factor in improving soil C stocks and mitigating greenhouse gas (GHG) fluxes, especially considering our finding that switchgrass reduced methane consumption, implying that carbon balance considerations should be accounted for to fully evaluate the sustainability of switchgrass cultivation.

molecular biology↗