The next 9 blog posts will summarize my reading assignments for the EBIO 3rd semester exam. The exam is scheduled for 3 hours and involves my four committee members asking me questions about anything at all! I was required to put together a reading list covering 4 main topics: biological soil crusts & drylands, microbial ecology, ecosystem services, and community, restoration, and disturbance-succession ecology. Obviously, I actually have 7 topics, which I managed to squeeze into "4". The reading list is a guide for the exam. To help me through this exam preparation process, I will use these blogs to summarize what I am learning over the next 9 weeks.
What are we building toward? With threats to soil (described in previous blog posts) we can expect human populations to become more vulnerable to food insecurity, water insecurity, and health risks due to erosion and climate change. A goal of applied soil microbiology might be to monitor soil quality in vulnerable regions and have early warning systems in place that would alert local authorities to soil needs for continued delivery of services. Some functions may decline slowly over time depending on the soil type, climate, and land use, but some may occur quickly as thresholds are reached. The goal would be to correct human use or apply rehabilitation strategies in ethical, consistent, and appropriate ways around the world in response to the multitude of pressures that continue to be placed on Earth's Critical Zone. In this way, we may be able to prolong different regions' self sufficiency to produce food for people and clean water. In order to reach such a lofty goal, there is quite a bit of basic science that needs to be done to understand the ecology of soil environments (though much has been done already!). My reading this week delved into dominant soil taxa, how water and drought influence the soil as microbial habitat, and ways to measure soil health. The rest of this blog details these topics. This week, I will move on to two textbooks. One is on soil ecology and ecosystem services and the other is focused on the field of community ecology. There are five main microbial phyla in soils (Actinobacteria, Acidobacteria, Pseudomonads, Bacteroidetes, and Verrumicrobia). One reading this week indicated that there must have been an ancient selective pressure in soil environments where these 5 phyla were selected for globally. When you compare soils to other environments, the diversity (at lower taxonomic levels) is "unparalleled" with thousands to millions of taxa in 10 g of soil. One of the challenges is determining what drives the distribution and diversity of these organisms and how the communities are maintained. At a continental scale, soil pH is a major driver of microbial community composition. This is different from plant and animal communities that are often shaped by precipitation and temperature. At smaller spatial scales (regional to local), important drivers of microbial community composition include precipitation, temperature, location, vegetation types, soil characteristics, elevation, land use, and land management. It is also important to know that there can be large temporal patterns to community composition (wet-dry events or seasonal shifts) as well as significant changes with depth. Resources like water, oxygen, nutrients, pH, and temperature can shift dramatically with soil depth and microbes respond to that. Soil is a complex environment and multiple factors come together to provide a huge number of niches and thus a lot of diversity. The key to this is soil structure ... the fundamental unit is the soil agglomerate. Agglomerates depend on soil type, organic matter, and activity of biota. Agglomerates can be anaerobic on the inside and aerobic on the outside such that many different types of organisms live in a small space, relying on different resources. You can imagine agglomerates of various sizes together with pore spaces between. With wetting events, pore spaces fill with water. As soils dry, the pore spaces empty of water. Water is important to microbes in three different ways. It is a resource, a solvent, and a transport medium. As a resource, water dictates the physiological states of cells and metabolism. As a solvent, water presence means that solutes are available for use. And as a transport medium, water presence means that new resources can come your way. If you are a cell, stuck to a well watered agglomerate, it is still important that you are connected (via water) to other agglomerates with resources. An important measure in soils is water potential. There are 4 components of total water potential (osmotic, matric, gravity, and pressure). Cells have to adjust themselves and their surroundings to be able to survive with these stresses. At -14 Mpa water potential, biologic activities cease. Initially, researchers thought this was due to direct stress on a cell, but the more important limitation is often the lack of nutrient availability (connectivity between cells and resources). As water leaves pore spaces, thin films remain on soil agglomerates through adhesion and capillary forces. These films become too thin for microbes to move or for nutrients to diffuse to cells. Thus biological activity stops. Some organisms have developed adaptations and do better under dry conditions than wet. For instance, fungi grow large hyphae across dry soil pores, connecting to water patches and surviving better than soil fauna or bacteria under dry conditions. Following this idea, one might expect that dry ecosystems would have more fungi, but you actually see lower fungi:bacterial ratios and this is likely driven by plant limitations (which are more tightly responsive to moisture conditions). There is some variation in how each organism responds to drying, but overall, Manzoni et al. (2012) found that there is a consistent decrease in microbial community activity as soil moisture declines across biomes and climatic conditions. Drought was the focus of one reading this week. They discussed four organismal responses to drought: osmotic acclimation, allocating resources to survival instead of growth, enhancing the environment via EPS, and using an altered physiological state (dormancy). At the community level, you might expect that microbial biomass would decrease with drought, but that is not always the case. Seasonally, sometimes biomass is higher during drought periods or with a dry-wet cycle, there can be an immediate biomass decline that later rebounds. Shifts in composition may occur for many reasons (directly or indirectly) related to drought for example through plant phenology, which microbes then respond to. I am learning that microbial community analyses cannot be separated from the plant communities around them, since both influence one another. Again, microbial composition shifts may actually be shifts in activity (you'd have to measure RNA to see it). At the ecosystem level, there were four examples of how moisture can affect biogeochemical cycles. Carbon cycling can be affected by moisture through enzymatic activity and through CO2 pulses with rewetting. The rate limiting step of metabolic pathways is often the depolymerization of large macromolecules in the soil (outside of cells). To get at these resources, microbes excrete degradative enzymes. Both the production of enzymes and the enzyme activity can change with changes in moisture...affecting carbon cycling. Second, as soils are rewet, there is a well-known pulse of CO2 released (called the Birch Effect). People are not sure why this occurs or the sources of the carbon. One guess is that the CO2 is released from microbes (without cell lysis) and is due to the soil agglomerates slaking (breaking open and exposing internal spaces to water). This CO2 pulse is sensitive to the soils' history of drought. Nitrogen cycling can also be affected at the nitrogen mineralization and nitrification steps. Overall, studying dry-rewetting cycles can be challenging because many chemicals are water soluble and you have to extract them. How can you extract water-soluble compounds under drought conditions? The Makhalanyane et al (2015) paper focuses on the soil microbial ecology in hot deserts characterized by minimal and erratic precipitation, extreme temperature fluctuations, low nutrient status, high UV levels, and strong winds. These systems can be different: there are fewer genes for N, K, S metabolism in deserts, nutrient cycling rates are lower, higher # of genes for dormancy and stress response, fewer antibiotic-resistance genes in deserts, competitive interactions might be less important. Factors explaining community assembly in deserts is similar to the list above for soils generally: water availability, nitrogen, salts, pH, temperature. This paper also describes two community types: biological soil crusts (dominated by filamentous cyanobacteria) and hypoliths (dominated by coccoid cyanobacteria). In both cases, the bulk soil is considered a seed bank for the more specialized community. The last two papers were on soil microbe measurements. Prosser et al (2015) describes the use of 'omics' in microbial ecology including the biases, limitations, and future directions. The main idea from this paper is that when possible, you should use metagenomics in a specific way (not a descriptive study). Do not assume spatial/temporal homogeneity. Most importantly, the metagenomic data should be paired with metadata...studies should always be linked to soil functions! Schloter et al. (2018) was on microbial indicators of soil quality. They list five life-support functions of soils: fertile ground for food, biodiversity maintenance, clean water, protection from erosion, and sink for greenhouse gases. Soils are multifunctional and we want to be able to maintain multiple functions simultaneously. Some threats to soil's ability to perform these functions include climate change, land use, mining, pollution, and urbanization. The authors provide examples for three of the five functions listed ... how one could develop a quantitative bioindicator based on the microbial community that would tell you when a function is failing. Their main framework consists of modeling the "normal operating range" for various microbial indicators with thresholds in place. You could then map your soil to these models and determine if the soil was within a normal range or if some intervention needed to be arranged. References Makhalanyane, T. et al. 2015. Microbial ecology of hot desert edaphic systems. FEMS Microbiology Reviews, 39, 203-221. https://doi.org/10.1093/femsre/fuu011 Manzoni, S. et al. 2012. Responses of soil microbial communities to water stress: results from a meta-analysis. Ecology, 93(4), 930-938. https://doi.org/10.1890/11-0026.1 Prosser, J. 2015. Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology. Nature Reviews Microbiology 13, 439-446. https://doi.org/10.1038/nrmicro3468 Schimel, J.P. 2018. Life in dry soils: Effects of drought on soil microbial communities and processes. Annu. Rev. Ecol. Evol. Syst., 49, 409-432. https://doi.org/10.1146/annurev-ecolsys-110617-062614 Schloter, M. et al. 2018. Microbial indicators for soil quality. Biol Fertil Soils, 54, 1-10. https://doi.org/10.1007/s00374-017-1248-3 Tecon, R. & D. Or. 2017. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiology Reviews, 41, 599-623. DOI: 10.1093/femsre/fux039
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AuthorSierra is a graduate student in the Barger Lab at CU Boulder studying microbial ecology for dryland restoration. Archives
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