Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Biology and Microbiology

First Advisor

Volker Brazel


Soil microbial communities are affected by many factors, such as soil nitrogen (N) and the quantity of grass-root exudates, changing seasons, fertilization method, plant diversity, and their origin. This holds for both natural and fertilized soils. This research was intended to expand the current understanding of soil microbial interactions associated with ecological functions. The objectives of the research were (I) to characterize prokaryotic soil communities, estimate functional potential, and quantify nitrogen cycle-associated prokaryotic gene expressions across three phases of the growing season, (II) to explore the diazotrophic community composition in a natural system using nifH sequencing as well as 16S rRNA gene-derived N-fixing genera, confirm in-situ 15N2 incorporation by soil microbes and map N-cycling activity of soil bacteria using meta-transcriptomics, (III) to identify shifts in prokaryotic and fungal communities and prokaryotic nitrogen cycling potential in the soil amended with novel controlled-release fertilizers, and (IV) to verify nifH gene in cultured diazotrophic isolates from natural prairie soil and study their ability to promote the growth of Bromus inermis. Bacterial community composition was characterized using the V3-V4 of the 16S rRNA gene, and QIIME2, and PICRUSt2 were used to tease apart functional inferences. The N-cycle gene and transcripts were quantified using a high-throughput pre-optimized assay and nitrogen cycle evaluation (NiCE) chip. Diazotrophic and fungal communities were studied using the nifH gene and ITS1 sequences, respectively. Moreover, an in-situ nitrogen-fixation study was performed using a stable isotopic 15N2 incorporation assay. Also, meta-transcriptomic research was done to map the bacterial activity towards Ncycling in the areas devoid of legumes. Surprisingly, the nitrogen cycle genes and transcript quantities were largely stable and unresponsive to seasonal changes. Similar trends were seen in the bacterial community and their predicted functional potential. Furthermore, the bacterial community derived from nifH and 16S rRNA gene showed diversity in diazotroph communities in the prairie. In contrast, the qPCR and metatranscriptomics showed that soil microbes did not actively participate in nitrogen fixation. Furthermore, high-yielding biochar controlled-release nitrogen fertilizers (BCRNFs) caused minimal shifts in soil fungal and microbial communities. This suggests that they can be an excellent alternative to nitrogen fertilizer without affecting the soil microbiota. Unfortunately, the diazotrophs could not support the growth of smooth bromegrass despite multiple attempts to help them sustain in a sterile sand matrix. Thus, this research work provides insights into the potential application of characterized soil communities and functional capabilities to be used for the development of agricultural practices or environmental restoration.

Library of Congress Subject Headings

Soil microbial ecology.
Soil microbiology.
Nitrogen cycle.
Prairie ecology.
Crops -- Ecology.

Number of Pages



South Dakota State University



Rights Statement

In Copyright