Jansson, Janet K | Engineering Papers

DOE OSTI2023

Global Soil Virus (GSV) Atlas

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset from 2,953 soils that comprises 616,935 uncultivated virus genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents the most extensive characterization of soil viral diversity to date and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Graham, Emily B↗

DOE OSTI2023

Summary Data for paper titled: Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Summary Data

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

Naasko, Katherine I↗

DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Sequence Data

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

Naasko, Katherine I↗

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 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↗