Progress 07/01/20 to 02/21/23
Outputs
Target Audience:Research scientists (soil science, agronomy, biogeochemistry, climate modeling),Agricultural stakeholders Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?PD Lin received training on bioinformatic analyses through collaboration with specialists. Professional development was obtained through synergistic meetings discussing findings with other researchers in academia and federal agencies. How have the results been disseminated to communities of interest?Novel results were presented as a poster at a scientific conference at the Joint Genome Institute 16th Genomics of Energy and Environment Meeting. (Lin JY, Erikson CB, Wang D, Scow KM, Rodrigues JLM. Metagenomics reveals stratification of microbial taxa and functional genes in soil aggregates of varying sizes. Joint Genome Institute 16th Genomics of Energy and Environment Meeting. Online. August 30, 2021.). Detailed research reports were disserminated to scientific audiences in peer reviewed journals. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
What was accomplished under these goals? 1) Determine the effect of compost or mineral fertilizer amendment on CUE. 2) Characterize the microbial groups contributing to C assimilation3) Evaluate the importance of microbial diversity in affecting CUE
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lin JY, Erikson CB, Wang D, Scow KM, Rodrigues JLM. Metagenomics reveals stratification of microbial taxa and
functional genes in soil aggregates of varying sizes. Joint Genome Institute 16th Genomics of Energy and Environment
Meeting. Online. August 30, 2021.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Wang D, Lin JY, Sayre JM, Schmidt R, Fonte SJ, Rodrigues JLM, Scow KM. 2022. Compost amendment maintains soil structure and carbon storage by
increasing available carbon and microbial biomass in agricultural soil A
six-year field study. Geoderma 427: 116117
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Lin JY, Wang D, Law KC, Scow KM, Rodrigues JLM. Differential responses of prokaryotic and fungal communities in soil microenvironments to drying and wetting as affected by soil aggregate isolation method.
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Progress 07/01/21 to 06/30/22
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?Novel resultswere presented as a poster at a scientific conferenceat the Joint Genome Institute 16th Genomics of Energy and Environment Meeting. Lin JY, Erikson CB, Wang D, Scow KM, Rodrigues JLM. Metagenomics reveals stratification of microbial taxa and functional genes in soil aggregates of varying sizes. Joint Genome Institute 16th Genomics of Energy and Environment Meeting. Online. August 30, 2021. What do you plan to do during the next reporting period to accomplish the goals?All scientific objectives have been completed. 2 manuscript drafts representing the 3 objectives have been completed. The manuscripts are currently under review with all co-authors and intellectual stakeholders. Immediate plans in the next reporting period are to revise, prepare, andsubmit the manuscripts to 2 different peer-reviewed journals for publication. All other training objectives of the Project Director (PD) have been met, and the PD (Lin) will complete dissertation and training program at UC Davis. PD lin anticipates completing degree requirements within the next reporting period.
Impacts
What was accomplished under these goals?
1) Determine the effect of compost or mineral fertilizer amendment on CUE. This objective was completed in the past year (2020). Using soils under mineral fertilizer (MF) or manure compost (MC) treatments at UC Davis' Russell Ranch, we performed soil incubations using isotopically-labeled carbon substrates. Soils sampled in March and April 2020 were incubated with 14C-labeled glutamate or glucose. Respiration of the labeled substrate into 14C-CO2 or incorporation of the substrate into microbial biomass was measured using a scintillation counter following entrapment of CO2 into NaOH and extraction of microbial biomass by chloroform fumigation, respectively. We found significant effects of treatment and time on CUE with glucose as the substrate, with higher CUE under MC than MF treatments and higher CUE in April than in March. No differences in CUE were found across treatments or sampling times using glutamate as the substrate, suggesting that long-term amendment with nutrient-rich compost may prime microbial communities in soil to favor cellulose, simple carbohydrates, and their associated breakdown products. Together, our results show that long-term compost amendment increases CUE in agricultural soils, and that CUE measurements vary with substrate nutrient stoichiometry. 2) Characterize the microbial groups contributing to C assimilation. New analyses were completed over the past year (2021). Soils from under the MC or MF treatment were collected and aggregates were obtained by wet-sieving. DNA was extracted from each aggregate size fraction, and shotgun metagenomics was used to characterized the microbial groups contributing to C assimilation in soils. Using the Illumina Novaseq platform, a total of 1.926 Tbp of sequencing was performed to obtained to reach an average depth of 30.09 Gbp per sample. The sequences were trimmed using Trimmomatic, and the Kraken 2 pipeline was used to obtain a community-wide taxonomic profile of all samples using a database of bacteria, archaea, and viruses downloaded from the NCBI GenBank database. To obtain a community-wide functional gene profile, the reads were assembled using Megahit; Prodigal was used to identify open reading frames from the contigs; and the protein-coding sequences were annotated using KOfamscan, which uses Hidden Markov Model(HMM) profiles with predefined score thresholds to identify genes using the KEGG database. To infer taxonomy from the potential functions assigned at the community level, the assembled contigs were binned using Maxbin2 andCheckM was used to assessed bin quality. The resulting metagenome-assembled genomes (MAGs) were classified using GTDB-TK, Prodigal and KOfamscan were used to annotate each genome as above, and metabolic pathways were reconstructured using KEGG mapper. We found that the overal taxonomic and functional gene composition was significantly different by both aggregate size (P = 0.001, R2 = 0.065;P = 0.001, R2 = 0.105, respectively)and fertilizer treatment (P = 0.001, R2 = 0.021; P = 0.002, R2 = 0.031, respectively). In both cases, aggregates size was the strongest factor explaining the highest variation. The large and small macroaggregates had higher abundances of ammonia oxidizing archaea, whereas the microaggregates and silt & clay had higher abundances of Actinobacteria. The silt and clay and microaggregate fractions possessed a higher abundance of annotated genes for denitrification (NarG/Z, NarH/Y) and biomass recycling through genes for the synthesis and degradation of fatty acids (alkM, ACOX1,3) and microbial co-polymers (AS, tarS, tagF). On the other hand, the large and small macroaggregates had a higher abundance of genes for N recycling (ureC, hpxB), biofilm and toxin formation (tccC, exoP, yegE), and the degradation of various plant-derived compounds including xylan (faeB), xyloglucan (CEL74A),heterocyclics (hmfF), and other phenolic acids (gdo, pht3, pht5). These results were corroborated using untargeted metabolomics showing a higher nutrient availability in the large and small macroaggregates to support microbial growth and energy metabolism. Finally, reconstruction of MAGs revealed the presence of many near-complete genomes belonging to 2 lineages of ammonia oxidizing archaea prevalent in agricultural soils (Order Nitrososphaerales). Both lineages were more abundant in the macroaggregates and possessed genomic capabilities for urease activity, ammonia oxidation, CO2 fixation, and assimilation of organic C compounds. The 2 lineages were phylogenetically distinct and their metabolisms were complementary, suggesting an ability to inhabit different niches within the same macroaggregate habitat. In summary, these results show that aggregate fractions of various size support distinct microbial communities with different functions reflecting resource availability; hence, microbial respiration and nutrient utilization strategies in aggregates of different sizes will ultimately determine the availability and fate of C in soil. 3) Evaluate the importance of microbial diversity in affecting CUE. To identify microbial traits important for carbon storage, we have isolated individual soil aggregates from Russell Ranch using soils collected under long-term MF or MC treatments. Soils were sieved using mesh sizes of 4 mm, 2 mm, and 1 mm and individual aggregates were selected from the >4mm, 4-2mm, and 1-2mm size fractions. The volume, surface area, and bulk density of individual aggregates was measured using a high-throughput 3D photogrammetry method. Over the past year (2021), the images from all samples have been processed and all physical properties (volumne, surface area, bulk density) have been calculated. DNA from all samples have been extracted, quantified, and submitted for shotgun metagenomic sequencing, for which the data and processing for 180 samples have been completed. In summary, this sequence data will be used to correlate microbial diversity and functional traits with soil aggregate volume, surface area, and bulk density. These results will help improve the predictability of soil C dynamics to different combinations of agricultural inputs.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lin JY, Erikson CB, Wang D, Scow KM, Rodrigues JLM. Metagenomics reveals stratification of microbial taxa and functional genes in soil aggregates of varying sizes. Joint Genome Institute 16th Genomics of Energy and Environment Meeting. Online. August 30, 2021.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Wang D, Lin JY, Sayre JM, Schmidt R, Fonte SJ, Rodrigues JLM, Scow KM. 2022. Compost amendment and cover cropping maintains soil structure and carbon storage by increasing available carbon and microbial biomass in agricultural soil a six-year field study. Geoderma. Under Review.
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Progress 07/01/20 to 06/30/21
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Plans for the next reporting year include completing data collection and analysis for objective 3. The samples, already prepared this past year, will be submitted for shotgun metagenomic sequencing. The resulting sequencing data will be analyzed using robust methods that I will receive training for in collaboration with a bioinformatics specialist in the lab. As the data collection have already been completed for objectives 1 and 2, the plan for the next year is to finish all outstanding analysis and draft manuscripts. A total of 2 manuscripts (covering objectives 1 and 2) will be prepared. In addition, a literature review synthesizing these findings within the context of other relevant agricultural studies will also be prepared over the next curricular year. Original plans to present research accomplishments from the first year at scientific conferences were put on hold due to complications with COVID-19. However, as restrictions lessen, abstracts will be submitted for presentation at the DOE JGI Genomics Energy and Environment Meeting as well as for the ASA, CSSA, and SSSA international meeting in Fall 2021. Furthermore, research findings will also be disseminated to public audiences, including farmers and agricultural stakeholders at the Russell Ranch Field Day and the CDFA healthy soils workshop. As labs open, mentorship training of an undergraduate researcher is planned for Fall 2021, which will also help to expedite research progress.
Impacts
What was accomplished under these goals?
The project initiation outline three major objectives for this project, progress on each objective is decribed below. Our objectives are to: 1) Determine the effect of compost or mineral fertilizer amendment on CUE. This objective was completed in the past year. Using soils under mineral fertilizer (MF) or manure compost (MC) treatments at UC Davis' Russell Ranch, we performed soil incubations using isotopically-labeled carbon substrates. Soils sampled in March and April 2020 were incubated with 14C-labeled glutamate or glucose. Respiration of the labeled substrate into 14C-CO2 or incorporation of the substrate into microbial biomass was measured using a scintillation counter following entrapment of CO2 into NaOH and extraction of microbial biomass by chloroform fumigation, respectively. We found significant effects of treatment and time on CUE with glucose as the substrate, with higher CUE under MC than MF treatments and higher CUE in April than in March. No differences in CUE were found across treatments or sampling times using glutamate as the substrate, suggesting that long-term amendment with nutrient-rich compost may prime microbial communities in soil to favor cellulose, simple carbohydrates, and their associated breakdown products. Together, our results show that long-term compost amendment increases CUE in agricultural soils, and that CUE measurements vary with substrate nutrient stoichiometry. 2) Characterize the microbial groups contributing to C assimilation. Soils under MC treatment showed a significantly higher proportion of small and large macroaggregates in the soil structure compared to soils under MF treatment. This suggests that increased microbial incorporation of C under long-term compost amendment may aid in improving the soil structure. Thus, to characterize the microbial groups contributing to C assimilation, we collected samples from each treatment at Russell Ranch and performed wet-sieving to isolate the bulk soil into four fractions: silt and clay (<53 um), microaggregates (53um-250um), small macroaggregates (250um-2mm), and large macroaggregates (>2mm). Total DNA was extracted from each aggregate size fraction and submitted for shotgun metagenomic sequencing using Illumina Novaseq (PE 150) technology. The sequences were processed, assembled, and mapped using the JGI metagenome assembly pipeline implemented in KBASE. Taxonomy of the sequences was assigned using the KRAKEN2 pipeline and functional genes were annotated using the COG and KEGG databases following gene prediction with GeneMarks and Prodigal. We found that the overall taxonomic composition varied by aggregate size (P = 0.004, R2 = 0.05274), but not by MF or MC treatment. Functional gene composition and abundance differed by aggregate size and treatment, with aggregate size being the strongest factor (P = 0.001, R2 = 0.0966). The silt and clay and microaggregate fractions possessed a higher abundance of annotated genes for denitrification (NarG, NarK, NarY, and NirS) compared to the small and large macroaggregates, whereas the small and large macroaggregates had a higher abundance of genes for oxygen scavenging and sulfur oxidation. Aggregate size fractions also differed in the abundance of genes involved with C utilization, including a higher number of reads for an aromatic ring opening dioxygenase gene (LigB) in silt and clay and microaggregates, and a higher number of reads for a glycogen debranching enzyme gene (gDB1) in small and large macroaggregates. In summary, these results show that aggregate fractions of various size support distinct microbial communities with different functions; hence, microbial respiration and nutrient utilization strategies in aggregates of different sizes will ultimately determine the availability and fate of C in soil. 3) Evaluate the importance of microbial diversity in affecting CUE. To identify microbial traits important for carbon storage, we have isolated individual soil aggregates from Russell Ranch using soils collected under long-term MF or MC treatments. Soils were sieved using mesh sizes of 4 mm, 2 mm, and 1 mm and individual aggregates were selected from the >4mm, 4-2mm, and 1-2mm size fractions. The volume, surface area, and bulk density of individual aggregates was measured using a high-throughput 3D photogrammetry method. DNA was extracted from individual aggregates and will be submitted for shotgun metagenomic sequencing. In summary, this sequence data (from a total of 290 samples) will be used to correlate microbial diversity and functional traits with soil aggregate volume, surface area, and bulk density. These results will help improve the predictability of soil C dynamics to different combinations of agricultural inputs.
Publications
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