Engineering Papers⌕ Search

Engineering topics

Howe, Adina

Publications and source records attributed to Howe, Adina.

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data for Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils

Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteu s ( M × g ) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M × g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M × g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in M × g soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M × g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Carbon↗
DOE OSTI2023

Contrasting geochemical and fungal controls on decomposition of lignin and soil carbon at continental scale

Lignin is an abundant and complex plant polymer that may limit litter decomposition, yet lignin is sometimes a minor constituent of soil organic carbon (SOC). Accounting for diversity in soil characteristics might reconcile this apparent contradiction. Tracking decomposition of a lignin/litter mixture and SOC across different North American mineral soils using lab and field incubations, here we show that cumulative lignin decomposition varies 18-fold among soils and is strongly correlated with bulk litter decomposition, but not SOC decomposition. Climate legacy predicts decomposition in the lab, and impacts of nitrogen availability are minor compared with geochemical and microbial properties. Lignin decomposition increases with some metals and fungal taxa, whereas SOC decomposition decreases with metals and is weakly related with fungi. Decoupling of lignin and SOC decomposition and their contrasting biogeochemical drivers indicate that lignin is not necessarily a bottleneck for SOC decomposition and can explain variable contributions of lignin to SOC among ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production

Abstract Oilcane is a metabolically engineered sugarcane ( Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI 1 transgene. The WRI 1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.

09 BIOMASS FUELS↗
DOE OSTI2023

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗