Engineering topics

McClure, Ryan S

Publications and source records attributed to McClure, Ryan S.

4 records

DOE OSTI2022

16s Amplicon Analysis of Soil Data for Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

Genomic DNA was isolated from soil and rhizosphere samples using the Zymo Quick-DNA fecal/soil microbe miniprep kit (catalog no. D6010) according to the manufacturer’s instructions (Zymo Research; Irvine, CA) with the modification of eluting in 100 uL elution buffer. Sample concentrations were quantified using the Qubit dsDNA HS assay kit (Thermo Fisher). For rhizosphere samples only, DNA was subsequently purified using Zymo’s ZR-96 DNA Clean & Concentrator kit (catalog no. D4024) to account for low DNA concentrations of these samples. . In each replicate block, there were five drip irrigation treatments (T1 = 100% normal irrigation, T2 = 56.25%, T3 = 37.5%, T4 = 18.75% and T5=no irrigation. On July 20, the strength of the drought treatments was increased: T1 remained at 100%, whereas T2 changed from 75% to 56.25%, T2 changed from 50% to 37.5%, and T4 changed from 25% to 18.75%. Sequencing was performed as described previously (Naylor, Fansler, et al. 2020). Sequences were amplified on the MiSeq platform (Illumina, San Diego, CA) using 16S primers (515F and 806R) specific to the V4 region. Raw sequence data was processed with the pipeline Hundo for amplicon quality control and annotation. Downstream statistical analyses on 16S datasets were performed using the program R and the packages ‘phyloseq’ and ‘vegan’.

Soil microbiome, metatranscriptomics↗

DOE OSTI2022

Metatransciptomic Analysis Data for Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

RNA was collected from soil at different depths and after three different levels of irrigation T1 100% of normal field irrigation, T4: 18.75% or normal irrigation and T5: unirrigated controls. Total RNA was isolated using the Zymo Quick-RNA fecal/soil microbe miniprep (catalog no. R2040), incorporating the DNase I treatment using Zymo’s DNase I kit (catalog no. E1010). To increase the yield of RNA, we modified the manufacturer’s instructions by first doubling the amount of soil per extraction (from 0.25 g to 0.5 g) and by performing extractions in triplicate before pooling separate extractions together. Certain soil samples (largely those from deeper soil layers) had low yield (< 100 ng per extraction) so additional rounds of extraction were performed to obtain sufficient RNA. RNA concentration was assessed using a Qubit RNA HS assay kit (Thermo Fisher) and RNA quality was determined using an Agilent 2100 BioAnalyzer (Agilent; Santa Clara, CA). The resultant RNA samples were then sequenced by GENEWIZ using Illumina technology (GENEWIZ; South Plainfield, NJ). Sequences were then aligned to a soil metagenome previously obtained from the same site using the Burrows-Wheeler aligner (BWA). SAM files were then converted to raw counts using HTSeq.

Soil microbiome, metatranscriptomics↗

DOE OSTI2022

Removal of primary nutrient degrading members severely reduces growth of soil microbial communities even when additional degraders are present

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here we used a model substrate, chitin, and a Model Soil Consortium, MSC-2, to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. To characterize specific roles within this representative community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed as well as alterations in the metabolic profile, especially when Streptomyces was removed. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

McClure, Ryan S↗

DOE OSTI2021

Model Soil Consortium 2 (MSC-2) Bacterial Isolate Genomes

Model Soil Consortium 2 (MSC-2) bacterial isolate genome collections are derived from the soil consortium MSC-1 multi-species cultured isolate genome collections from a previously reported WA-IsoC_MSC1.1.0 collection of a naturally evolved, model soil consortia (10.25584/WAIsoCMSC1/1635272). This collection contains 8 different isolate species cultivated under variable carbon and nitrogen sources, originating from the IAREC grassland soil field site located in Prosser, WA, USA. Genomic sequencing of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names of a given organism within a natural environment. The version described here is the first version.

Soil microbiome, defined community, chitin↗