The Soil Microbiome with Dr. Wei Shi

Learning about the Soil Microbiome with Dr. Wei Shi

We recently had the opportunity to speak with Dr. Wei Shi; in our discussion, she defined the soil microbiome and its importance; explained its relevancy to her research; and discussed her SSC 532 course and online teaching. 

Soil Microbiome

NC State: Briefly, what is the soil microbiome? Why is it important?

Dr. Wei Shi: Microbiome is a hot term and currently has two meanings. On one hand, the focus is on “-ome”; thus, it simply refers to the collective genomes of microorganisms. On the other hand, microbiome is interpreted as the “biome” of microorganisms; thereby, molecular/genomic techniques are used to examine ecological factors in shaping the microbial community.

The soil microbiome, from ecological perspectives, refers to the collection of microorganisms that inhabit the soil. It comprises, on the basis of per gram soil weight, billions of microbes and also thousands of different taxa from three cellular life domains of archaea, bacteria, and eukaryotes. This diverse and abundant soil microbiome represents a reservoir of important biogeochemical elements, such as carbon, nitrogen and phosphorous and plays multifaceted roles in the functioning of terrestrial ecosystems, such as decomposition of organic matter, nutrient cycling and energy flow.

In agricultural land, soil microbiome has paramount impacts on crop productivity, soil quality and agricultural sustainability. For instance, root-colonizing microbes may exert direct effects on plant production through mutualistic symbiosis or pathogenic diseases, whereas free-living microbes mediate nutrient supply and the partitioning of resources.

Beneficial microbes include, but are not limited to:

  • Nitrogen-fixing bacteria that convert atmospheric N2 to NH4+, a plant-available form of nitrogen;
  • Mycorrhizal fungi that facilitate the acquisition of nutrients often inaccessible to plant roots; and
  • Growth-promoting rhizobacteria that produce plant hormones, antagonize phytopathogens, enhance nutrient mineralization and availability, or alleviate stresses in plants.

Certainly, microbes may also be harmful to crop production as pathogens or competitors for nutrients in soil solution. Promoting beneficial microbes and optimizing their functions present a great challenge when it comes to developing agricultural land use and management practices.

Soil Microbiome + Dr. Wei Shi’s Research

NC State: Does your research focus on the soil microbiome? If so, how?  

Dr. Shi: Yes, it does. Generally, my research centers on soil microbial community structure and function in agricultural and urban ecosystems. The goal of my research is to develop fundamental knowledge and apply it to the practice of sustaining agriculture and the environment. I cover many different topics, including carbon and nutrient cycling; microbial community composition and diversity; soil microbiome and climate variability; and microbes and healthy soil or agricultural sustainability.

In terms of soil microbiome and climate variability, I study how microbes respond to weather extremes, like long-term drought or heat wave, and determine the consequences of that microbial community response.  When studying the topics of soil microbes and healthy soil, I evaluate how microbes respond to agricultural management practices and how that affects soil fertility, quality and overall health.

SSC 532 Soil Microbiology Course

NC State: Tell me about your SSC 532 Soil Microbiology course. Do students learn about the soil microbiome?

Dr. Shi: Students definitely learn about the soil microbiome in my course. The course offers graduate students the opportunity to learn basic concepts and principles of microbial distribution, abundance and activity in the soil environment. Students gain comprehensive knowledge of microbial transformations of elements and molecules vital to the ecosystem’s productivity and to natural resource protection. The course discusses techniques and methodologies for understanding the soil microbiome.

Students engage with soil sustainability issues through a course project; the project enables students to apply learned knowledge to seriously consider the challenges of land use and management. The course project varies as it depends on the students’ interests; I create different projects based on each unique class of students—for example, a project could focus on how soil responds to extreme weathers, like more frequent drought and precipitation events. The project’s goal is to encourage students to link the knowledge learned in the course to real-world issues.

Online Teaching

NC State: Does teaching online present any challenges to teaching about the soil?

Dr. Shi: Online teaching can be challenging since you lose the face-to-face contact with your students. Also, online students are frequently not traditional students; they often are professionals who need to do school work over the weekend. Professors need to consider this factor when responding to students. With that said, teaching online can be rewarding and fun because of the diverse student backgrounds. Since most are professionals, students often present unique questions from their workplaces. These real-world questions challenge me and encourage me to question what I should pursue in my research.

Dr. Wei Shi’s SSC 532 Soil Microbiology is offered every Spring. The course is offered as as a traditional and online course. A senior level course in microbiology and soil science or equivalent is required to take the course.