Soil Environment

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I. Introduction

The soil environment consists of a variety of physical, biological and chemical factors that affect the abundance and diversity of microbes found in the soil. [4] At its basic level, the soil environment consists of a solid and porous fraction. Within these fractions, a variety of chemical and physical factors are affected by and and affect microbes. These include, but are not limited to texture, temperature, pH, oxygen, cation exchange capacity and redox reactions.

The soil environment directly affects the types of microbes, as well as the rates of processes they perform. For example, microbial activity increases with temperature, which in turn affects rates of decomposition. On the other hand, microbial processes directly affect their environments as well, contributing to the carbon and nitrogen cycles, which are important for microbial and plant health. [5] At the micro scale, bacteria and other microbes participate in a variety of reactions that affect nutrient cycling, pH, as well as oxygen and CO2 content. At the macro scale, these processes can change the landscape in drastic ways, assisting in weathering of the soil and development of soil layers.

II. Soil Environment Overview

Solid Fraction

The solid fraction of the soil consists of mineral and organic matter, which is typically about 50% of the soil by volume (see figure 1), and it has a dominant influence on heat, water, and chemical transport and retention process. [4] Most of the solid particles are derived from mineral sources such as decomposed rocks or sediments. [13] Soil organic matter (SOM) consists of all of the organic components of a soil, including living biomass, decomposing tissue, and fully decomposed tissue called humus. [5] The rate and pathway of carbon decomposition and SOM formation directly affects the carbon cycle . Texture can also influence chemical properties such as cation exchange capacity (CEC). Finer textured soils with high clay content will have great CEC than soils with low clay content.

Figure 1. Volume composition of the solid and porous fractions of a typical loam surface soil. [5]

Soil Pores

Soil pores consist of the air and water filled fractions of the soil, and together they make up about 50% of the soil by volume. Pore space is largely determined by size and arrangement of aggregates and affects the movement of water, air, and organisms in soil. Soil pores are typically classified based on size: Macropores ( >75um) Mesopores ( 30-70um) Micropores ( 5-30um) Ultramicropores (0.1-5um) Cryptoporus ( <0.1um). [5]

The air filled pores of the soil typically have a similar distribution of gases as the atmosphere above the soil, with slightly lower oxygen and slightly more CO2. The soil atmosphere consists of about 18-20% oxygen near the surface, which decreases with depth. CO2 is around 1%, and N2 is about 78% of the soil air filled pore space. [5] Oxygen (O2) content will be lower when available carbon is high (high O2 demand). Soil that is high in clay content and/or compacted may have trouble exchanging gases to the atmosphere. Soil air generally has a very high moisture content when compared to the atmosphere (~100% unless the soil is very dry). The amount and composition of air in a soil is largely determined by the water content in the soil. [4]

The main source of soil water is rainfall and overland flow. The amount of water that enters the soil is a function of soil structure and texture. Water moves in soil through mass flow and capillary action. The water in soil is often called the soil solution, which can move nutrients from the surface through the soil column. The water fraction of the pores is typically between 20 to 30% but can vary depending on precipitation, soil texture, and soil structure. The water content of a soil influences gas exchange, controls movement and concentrations of nutrients, and buffers the temperature of the soil. [5]

Soil Aggregates & Structure

Soil aggregates are groups of soil particles that bind to each other more strongly than to adjacent particles. The space between the aggregates provide pore space for retention and exchange of air and water. Aggregation affects erosion, movement of water, and plant root growth. [7] Polysaccharides produced by soil bacteria, and humic substances and hyphae produced by fungi improve aggregation.

Figure 2. A soil aggregate at the micro and macro scale. [11]

Soil structure is the arrangement of primary soil particles into aggregates which describes the arrangement of the solid parts of the soil and the pore spaces between them. Soil structure has a major influence on water movement, SOM leaching, and gas exchanges of the soils. The water movement, affected by structure can bring SOM in the surface to deep inside the soil. Soil with high clay content and/or poor structure, may have reduced infiltration and will cause runoff, erosion and surface crusting. [11] This can cause nutrient loss and increase the potential of desertification.

III. Physical & Chemical Factors that Control Biological Activity in the Soil

Soil Texture

Soil texture is defined as the distribution of sand (0.05-2.0 mm), silt (0.002-0.05mm), and clay ( < 0.002mm) in soil. Soil texture indirectly influences properties such as: water holding capacity, porosity, aeration and nutrient availability. Clay particles have a very high surface to volume ratio, which makes them very chemically active and have high nutrient availability. Due to the adhesion of water, soils high in clay will also have a high water holding capacity. Soils with a high clay content will often have a very active microbial community, especially in areas the rhizosphere. [5]

One study by Hamarshid 2010 found that CO2 production rates were greatest in fine textured soil compared to coarse textured soil. [6] This was due to finer textured soils’ greater ability to hold nutrients and water, allowing microbial populations to thrive. However, this is not always the case, as other chemical or physical properties may affect the ability of microbes to perform processes such as carbon decomposition. (e.g. temperature, pH and quality of substrate).

Temperature

Soil temperature changes with depth: the surface soil (~0-20cm) is highly affected by the solar radiation. Moving deeper (~below 27cm) temperatures are very stable over time (see figure 5). This is because heat moves in soil mainly by conduction, which does not allow much heat to reach deep in the soil profile. Soil temperature is also affected by the soil color, soil cover, and the water content of the soil. A darker soil can absorb more heat compared to lighter color soil. A dry soil is more easily heated than a wet one due to the higher heat capacity of water. Heat moving in soil is analogous to the movement of water. [5] Generally, the higher the temperature, the more active microbes are, with microbial activity typically doubling with a 10° rise in temperature. However, some bacteria thrive at very low temperatures (psychrophiles) and very high temperatures (extremophiles), which can be seen in figure 6. [4]

Figure 4. Soil temperature fluctuation as a function of depth. [5]

Figure 5. Microbial growth rate as a function of temperature for different types of bacteria. [7]

pH

pH changes in soils is due to both biotic and abiotic processes. Microbes consume and release H+ through redox reactions and fermentation. Abiotic processes such as rainfall can also affect the pH of the soil. In areas of high rainfall, acidic soils can be created through leaching of bases from the soil, while more basic soils are typically located in arid environments. One study by Fierer et al. found that pH was the single most important factor influencing microbial diversity at the continental scale. [10] The study used 98 samples from across North and South America, and found that the greatest microbial diversity coincided with a neutral pH, even between two soil from the same forest.

pH affects microbial diversity because many microbial species cannot tolerate extreme levels of pH (high or low). Alterations in pH can render essential microbe enzymes inactive and/or denature proteins within the cells and prevent microbial activity from occurring. [4] However, there are microbes that can withstand extreme pH environments. At pH below 5, fungi and acidophilic bacteria have a competitive advantage over other bacteria that thrive at a more neutral pH.

pH can also affect the availability of nutrients in this soil. Below a pH of 5, essential plant nutrients such as phosphorous, calcium and magnesium are not available. Low pH can also cause aluminum (Al3+) to be released from soil minerals. Al3+ in soil solution is not only toxic to plants and microbes, it can combine with OH- ions causing the free H+ ions to lower the pH further. [5] The effect of pH on nutrient availability and microbe survivability can be seen in figure 7.

Figure 6. Nutrient availability and microbial diversity as a function of pH. [2]

Oxygen

Oxygen (O2) is a very important component of the productivity of both microbes and plant roots. Oxygen has a very high electrical potential (Eh), meaning that it has a lot of potential to produce energy when used as an electron acceptor in an oxidation-reduction reaction. [5] An example oxidation-reduction reaction can be seen in equation 1, where glucose is being oxidized, and oxygen is being reduced.

                                              6O2+C6H12O6→6CO2+6H2O		[eq.1]

The amount of oxygen available in a soil depends on a number of factors, including soil porosity, water content, and consumption by respiring organisms. If soil pores are large and interconnected, oxygen can flow easily. However, even in a well aerated soil, micro-aggregates may contain anaerobic zones in which oxygen flow is very limited. In a flooded soil environment oxygen content will be very limited because oxygen diffuses about 10,000 times more slowly through water than through air. [4]

In areas where oxygen is not present, soil microbes may use alternative electron acceptors such as nitrate, manganese, iron, sulfate, and carbon dioxide. An example of the result of the use of an alternative electron acceptor can be seen in figure 8.

Figure 7. Without oxygen, bacteria can potentially use iron as an electron acceptor, reducing it, and creating the blue/gray soil in the photo. The mottled red areas are the result of oxygen getting in (perhaps through root canals) and oxidizing the iron. [3]

Cation Exchange Capacity

Cation exchange capacity (CEC) is the ability of a soil to hold and exchange cations. The amount of CEC in soil is highly dependent on the texture and organic matter of the soil. The high surface area and negative charge of clay allows it to bind and exchange with soil solution, which contains cations that are important for plant and microbial health. [4]

For many soils, especially those with low clay and organic carbon content , CEC is dependant upon soil pH (see figure 9). As pH decreases , an increasing amount of H+ ions are attracted to negatively charged clay particles and functional groups in SOM. This causes other cations, that were attached to these surfaces to fall off into the soil solution. CEC will increase as pH increases as less cations are being pushed out by H+ ions. [5]

At typical soil pH values (5-8), microbes and clay particles are both negatively charged, but microbes still to bind to clay. This binding could be due van der waals, hydrogen bonding, sharing electrons and ion exchange.

Figure 8. Figure 9 : Cation exchange capacity and anion exchange capacity of a soil as function of soil pH. [9]

Biological Factors

Soil Fauna

Soil animals are divided into macrofauna (>2 mm, earthworms), mesofauna (0.1-0.2 mm, mites and nematodes), and microfauna (<0.1 mm, protozoa). These eukaryotes have a range of effects on microbial communities:

• Grazing: Grazing increases decomposition rates, freeing nutrients. Grazing also includes direct consumption of other organisms.
• Nutrient cycling: Soil fauna is responsible for up to 30% of the total soil mineralizable nitrogen. Additionally, soil fauna can remobilize nutrients as waste products. This allows for increases in microbial growth.
• Microbial community composition: Other organisms in the community are directly effected through consumption. Some soil fauna feed selectively, consuming certain organisms instead of others. This changes the makeup of the microbial community.

In addition to these direct effects, soil fauna has several indirect effects on microbes. One of these effects is habitat alteration. Earthworms especially alter the soil habitat through the formation of burroughs, which changes gas exchange, water movement, and resource locations. Microorganisms are sensitive to the presence of oxygen in their enviroment, and water is essential for microbial existence. Changes in resource locations may allow for microorganisms to colonize another area. [1]

Organism Interactions

There are several types of interactions between organisms. The table below outlines the positive, negative, and neutral aspects that each organism receives as a result of the interaction. These interactions can create environments that promote or discourage specific microbial growth.

- Interaction Type	- Population 1	- Population 2	- Example
Mutualism (symbiosis)	+	+	Rhizobia/legumes, mycorrhizal fungi/most plants (Bradyrhizobium), fungi/green algae, fungi/cyanobacteria (Anabaena)
Commensalism	+	0	Aerobic oxygen consumption creates an anaerobic environment to support anaerobes
Synergism	+	+ or 0	Flooded soils: fermenters provide carbon and hydrogen gas for [methanogens]] and sulfate reducers (Desulfosarcina), which in turn reduce toxic effects of acetate and hydrogen gas to fermenters
Amensalism	-	+ or 0	Production of acidic or toxic chemicals
Predation	-	+	Protozoa, nematodes, and slime molds are all major soil predators that consume bacteria
Competition (antagonism)	-	+	Growth rates that allow for utilization of a resource before a competitor
Parasitism	-	+	Viruses

[1, 2]

Bioavailability

Bioavailability is a term that refers to the availability of a soil substrate (both nutrients and toxins) to an organism. The EPA lists this definition of bioavailability:

“The term bioavailability designates the state of that fraction of a chemical that is available for uptake and/or transformation by living organisms. Although associated primarily with ecotoxicology, and usually in reference to organic and metallic pollutants, the term bioavailability is also relevant to native organic material. Thus, the “problem” of bioavailability, has existed for microorganisms far longer than has the presence of xenobiotic chemicals in the environment. Sorption, insolubility, and related processes are largely responsible for controlling bioavailability of many pollutants to microorganisms in soils and sediments” [3].

Bioavailability is of special interest to environmental groups because of it's correlation with bioremediation. A common assumption made when discussing bioavailability is that only what is in solution can be metabolized. There are three major factors that effect bioavailability:

• Sorption: how a substrate bonds to surfaces, especially charged surfaces such as clay and organic matter.
• Solubility: the capacity for a substance to dissolve in solution. (Insolubility refers to a substance that is unable to dissolve.)
• Chemical speciation: some substrates may be less available at certain pH or are less available because of charge [2]

Plant Growth-Promoting Rhizobacteria (PGPR)

Rhizobacteria colonize roots. PGPR bacteria colonization promotes plant growth and seed germination and helps plants resist environmental stresses and diseases. Harmful root colonization is caused by deleterious rhizosphere microorganisms (DRMO). DRMO bacteria remove water and nutrients from the plant supply. PGPR bacteria are able to promote plant growth by colonizing before and thus preventing the colonization of DRMO. Pseudomonas is a genus containing many PGPR bacteria. Azotobacter and Azospirillum are also PGPR bacteria because of their production of gibberellic and indoleacetic acid, which are plant growth-stimulating hormones. [1]

Relevant Organisms

Acidobacterium capsulatum - it was found in acid mine drainage (AMD)

Acidobacterium capsulatum picture [13]

Sinorhizobium meliloti is isolated from soil, which synthesizes an extracellular polymer that facilitates the transport of such hydrophobic pollutants as polynuclear aromatic hydrocarbons, as well as the toxic metals lead and cadmium in soil.[9]

Some microbial environments are extreme for life. Organisms inhabiting extreme environments are called extremophiles. Extremophilic microorganisms could be found in the harsh environment, such as hot springs, ice-covered lakes, salty water, and in soils or waters with pH lower than 0 or as high as 12. Those microorganisms cannot live without the extreme environment.[10] One of recent discovery is Spirochaeta Americana.

Extreme condition	Descriptive term	Genus/ species	Domain
High temperature	Hyperthermophile	Pyrolobus fumarii	Archaea
Low temperature	Psychophile	olaromonas vacuolata	Bacteria
Low pH	Acidophile	Picrophilus oshimae	Archaea
High pH	Alkaliphile	Natronobacterium	Archaea
Pressure	Barophile	Moritella yayanosii	Bacteria
Salt	Halophile	Halobacterium	Archaea

Current Research

To find out what is new in the according to the American Academy of Microbiology (AAM) click: http://www.asm.org/Academy/index.asp

An Overview of Extremophiles:

" Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology." [11]

Molecular Genetics from Michigan State University:

" Bacteria in the phylum Acidobacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23°C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named Acidobacteria, to warrant creation of a new genus, Terriglobus, with Terriglobus roseus defined as the type species. The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil." [12]

Andrew D. Cartmill, Luis A. Valdez-Aguilar, Donita L. Bryan and Alejandro Alarcon, Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water, Scientia HorticulturaeVolume 115, Issue 3, , 1 February 2008, Pages 275-284. (http://www.sciencedirect.com/science/article/B6TC3-4PYRKM2-1/2/64bcf8c9a8286c08606ec95ada501b97)

Apendix

Figure 3. Diagram that is used to determine soil texture class if percent sand, silt and clay are known. [11]

References

1. "Soil_Microaggregate_and_bacteria." UC Berkeley, n.d. Web. 25 Feb. 2016. <http://em-lab.berkeley.edu/EML/images/TEM-Gallery1/pages/Soil_Microaggregate_and_bacteria.htm>.

2. " Soil Reaction (pH)." University of New South Wales, n.d. Web. 25 Feb. 2016. <http://www.terragis.bees.unsw.edu.au/terraGIS_soil/sp_soil_reaction_ph.html>.

3. "Soil Images - Redoximorphic Features." New England Soil, n.d. Web. 25 Feb. 2016. <http://nesoil.com/images/redox.htm>.

4. Sylvia, D. M. Principles and Applications of Soil Microbiology. Upper Saddle River, NJ: Pearson Prentice Hall, 2005. Print.

5. Brady, Nyle C., and Ray R. Weil. Elements of the Nature and Properties of Soils. Upper Saddle River, NJ: Pearson Prentice Hall, 2010. Print.

6. Hamarshid N.H., Othman M.A., and Hussain M.-A.H., 2010. Effects of soil texture on chemical compositions, microbial populations and carbon mineralization in soil. Egypt. J. Exp. Biol. (Bot.), 6(1), 59-64. Kabala C. and Zapart J., 2012.

7. Todar, Kenneth. "Nutrition and Growth of Bacteria." N.p., n.d. Web. 13 Mar. 2016. <http://textbookofbacteriology.net/nutgro_5.html>.

8. Munkholm, L. J., Heck, R. J., Deen, B., & Zidar, T. (2016). Relationship between soil aggregate strength, shape and porosity for soils under different long-term management. Geoderma, 26852-59. doi:10.1016/j.geoderma.2016.01.005

9. "PH and Organic Substrate Nutrients." N.p., n.d. Web. 13 Mar. 2016. <http://organicsoiltechnology.com/ph-and-organic-substrate-nutrients.html>.

10. Fierer, N., and R. B. Jackson. "The Diversity and Biogeography of Soil Bacterial Communities." Proceedings of the National Academy of Sciences 103.3 (2006): 626-31. Web.

11. "Soil Structure and Macropores." Soil Quality: Indicators:. NRCS, n.d. Web. 13 Mar. 2016. <http://soilquality.org/indicators/soil_structure.html>.

12. "Electron Tower Theory." Bioremediation Specialists, n.d. Web. 14 Mar. 2016. <http://bioremediation-specialists.com/Electron-Tower-Theory.php>.

13. Moravec, C., Whiting, D., and Reeder, J. “Introduction to Soils.” CMG GardenNotes. Colorado State University Extension. Oct. 2015. <http://www.cmg.colostate.edu/>

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Edited by students of Kate Scow