Basics of Microbial Ecology and Function in Urban Agriculture

Abstract

In this chapter, we will explore the following topics: Soil as a complex multiphasic habitat for growing crops The form and function of soils microbes The connection between soil microbes , soil fertility, and plant health

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Chapter Objectives

In this chapter, we will explore the following topics:

• Soil as a complex multiphasic habitat for growing crops

• The form and function of soils microbes

• The connection between soil microbes , soil fertility, and plant health

Introduction to Urban Soils – The Physical Setting

Imagine a type of environment on Earth characterized by immense empty spans, rivers and oceans that drain and fill daily, and massive boulder-sized solids perched precariously against one another. Now imagine a suite of organisms, interacting in complete darkness, going about their lives in the environment described above. Does the image of an eight-legged animal quietly stalking its prey come to mind or a population density of organisms that reaches over a million in one single spoonful?

Are you intrigued? You might be wondering where this strange place is and how you might be able to visit. Good news! This world exists right below your feet. Soil is a highly complex habitat , filled with all the biological drama of your favorite soap opera, but it largely goes ignored due to the small size of the organisms and soil particles. Learning about the organisms in the soil is crucial to a gardener’s success and in this chapter we will explore the role of soil microbes in the urban garden .

Physical Properties of Soil

Soil is unique in the fact that it exists as three different material states, all at once. The term we use to describe this property is multiphasic (Brady and Weil 1999). Soils are roughly characterized as 50 % soil material (e.g., rock minerals and organic matter ), 25 % gaseous voids or pores, and 25 % water . Of course, these percentages change from soil to soil, as some are much drier or wetter than others. The almost infinite combination of these percentages allows for a surprising number of unique habitats for belowground microbes and animals . Furthermore, these habitats are home to two very important resources for the soil microbes in your garden : organic matter and soil moisture.

Organic Matter

Organic matter initially enters the soil system as detritus. Detritus refers to any former biologically active organic material that is now non-living (Moore et al. 2004). Examples of detritus include fallen leaves, carcasses, and compounds that leak from plant roots. Roughly 90 % of the biological materials produced by a plant become detritus at some point in time (Lavelle 2012). Soil organic matter is the energy source and nutrient source, or food, for soil microbes . In short, the leaves that fall on to your lawn in autumn “fuel” microbial activity. Too little food and your microbes will starve (Fig. 1).

Fig. 1

The relationship between soil organic matter and microbial health. The arrows represent directions that soil organic matter content can be “pushed” for optimized soil microbial activity

Complex biological materials are decomposed by soil microbes and animals , broken down into simpler structures, and remain in the soil as a complex mixture of carbon-rich compounds referred to generally as organic matter . Organic matter can range from <1 % in desert soils to >25 % in tundra and bog soils. Organic matter has properties that warrant the attention of any serious urban gardener. For example, organic matter can greatly increase the water holding capacity of a soil, via charge interactions between water molecules and the surfaces of organic matter particles.

Soil organic matter is also a critical factor for soil nutrients , or elements that are crucial to plant growth, production, and survival (Table 1). Soil organic matter is explicitly connected with the supply of the mineral nutrients, which come from the soil and are absorbed by the plant roots. The most important of these types are referred to as macronutrients and include nitrogen (N), phosphorus (P), and potassium (K). Macronutrients are contained in detritus and are released when dead plant and animal materials are decomposed in the soil environment. Soil organic matter, thus, can serve as a source (when decomposed) of nutrients and a sink (nutrient storage) where N, P, or K remain bound to carbon chains and unavailable for plant uptake. The non-mineral nutrients: carbon, oxygen, and water , are derived from the atmosphere or soil and are critical for plant photosynthesis.

Table 1 Essential mineral and non-mineral nutrients and their use in plants

Soil Moisture

As we reviewed earlier, soils is roughly 25 % water , give or take a bit depending on climate and landscape position of your soil sample. Water is critical to all life on earth, including the microbes that inhabit your vegetable patch. Water provides a habitat to live in, a “lab bench” on which to perform chemical reactions, and a solution that can move nutrients towards plant roots. While many gardeners intuitively understand that their vegetation need water; they have often not thought of how their watering practices affect the microbes associated with their favorite plants. Water, shown here as soil moisture, has a convex relationship with microbial activity (Fig. 2).

Fig. 2

The relationship between soil moisture and microbial health. The arrows represent directions that soil moisture content can be “pushed” for optimized soil microbial activity

Too little water and your microbes cannot function properly because they are dried out. Too much water and you are essentially drowning them. These same effects can be observed with plant roots. Many gardeners are guilty of overwatering or, in some case, of ignoring their plots for too long between watering intervals. Many troublesome plant problems are associated with the dry soil /wet soil interval flip-flop, including blossom end rot. Blossom end rot is familiar to gardeners who have grown tomatoes (Fig. 3) in soils with low calcium supply and irrigation issues. Symptoms include dark spots on the end of the fruit before they are fully ripe.

Fig. 3

Blossom end rot symptoms on a tomato plant (Photo courtesy of T.A. Zitter, Cornell University, Ithaca, NY)

The key to a successful microbial community and garden is to water at regular intervals suitable to your climate and to the right depth. You can check soil moisture levels by feeling the soil by hand. Furthermore, you can check for moisture at depth by using a long, flat head screwdriver. Dry soils will resist penetration by the screwdriver and this will help you determine if your watering efforts are acutally travelling below the soil surface and into the rooting zone. Proper oversight of both organic matter and moisture will promote a healthy microbe population. With that being said, we now turn our attention to the “middle men” that link detritus and the supply of nutrients that your plants need to grow.

Soil Microbes – The Unseen Heroes of Your Garden !

When one hears them term soil microbes , you should know that we are talking about three separate and very different groups of organisms (Fig. 4). The commonalty between all three is the habitat they share (soil) and their important role in your garden (decomposition and plant nutrient supply).

Fig. 4

Soil microbes are a diverse group. Here bacteria dot the surface of strands of fungal hyphae (Photo Courtesy: R. Campbell. In R. Campbell. 1985. Plant Microbiology. Edward Arnold; London. P. 149. Reprinted with the permission of Cambridge University Press)

Bacteria

The Bacteria , are organisms that do not have a nucleus (membrane-bound “library” for genetic material), nor do they have large organelles (specialized cellular machinery), (Fig. 5). Despite this seemingly simple structure, bacteria are incredibly diverse in terms of their roles they play in an ecosystem.

Fig. 5

Actinomycetes give soil its pleasant “earthy” smell (Photo Courtesy: No. 14 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds. SSSA, Madison, WI)

They are also incredible abundant in soil . To illustrate how many bacteria you can find in an area, consider a teaspoon used for baking. If you were to fill this teaspoon with soil, it would hold between 100 million and 1 billion soil bacteria (Tugel et al. 2000). If you were to weigh all the soil bacteria beneath your feet, there would be enough mass to equal about two cows per acre. However, despite their abundance, you will not be able to see the soil bacteria, as they are very small (1 μm).

I mentioned the numerical abundance of soil bacteria and, as you might have guessed, this group plays many different roles in the soil environment. For simplicity, we will only discuss the three major roles relative to urban gardening. The decomposer group are critical for turning previously living stuff (e.g., old seed husks, corn tassels, watermelon rinds, etc.) back into their simpler forms. Decomposer bacteria use the energy stored in complex substances by breaking the chemical bonds that hold the molecule together. Essential nutrients, such as nitrogen and phosphorus, are also “liberated” this way and reincorporated into the living biological structures inhabiting the soil matrix, including plant roots.

The mutualism group are perhaps the most famous bacteria in the gardening world. The members of this group are why we plant beans, cowpeas, soybeans, etc. in our garden , especially after growing things like squashes and zucchini. We are essentially repaying a “debt” by following this strategy. The squash, like many plants, use nutrients found in soil , particularly nitrogen, to create biomass and, hopefully, a nice delicious fruit for your table. However, we are now facing a state of localized N depletion. By exploiting the relationship between bacteria, particularly the genera Rhizobia¸ and plants, we can repay our N debt. Rhizobia have the unique ability to turn N gas (N₂) into a more biologically useful form called ammonia (NH₃), thus adding N back to the soil (Fig. 6).

Fig. 6

Nodules formed where Rhizobium bacteria infected soybean roots. The bacteria can now turn gaseous nitrogen into something biologically useful (Photo Courtesy: Stephen Temple, New Mexico State University)

However, this process must occur and can only occur in the roots of a plant capable of supporting this relationship (e.g., plants in the bean family) and thus most garden stalwarts cannot support populations of Rhizobia, such as tomatoes and squash, are not able to replenish your soil of lost N.

The last group of important soil bacteria are the pathogens . These are the more nefarious members of the bacteria group that a gardener can come across. Bacteria pathogens can cause diseases in your favorite vegetables such as bacteria blight, soft rot, ring rot, spot, and wilt (Fig. 7).

Fig. 7

Bacterial leaf spot on cauliflower is caused by a pathogen that can be transmitted to crops by the splashing of water on the soil surface (Photo Courtesy: T.A. Zitter, Cornell University, Ithaca, NY)

One wishes that controlling the spread of pathogens were as simple as weeding, but you can try to prevent conditions that promote bacterial growth. If one avoids overly damp soil conditions, uses clean equipment, and stays away from dense plantings, the transfer of harmful bacteria, between plants, can be reduced substantially. Another approach to controlling soil borne pathogens is to promote a healthy microbial population. Scientists have recently discovered that a diverse community of soil microbes can actively suppress plant pathogens and improve plant yields. For example, researchers found that sugar beet fields exhibiting active suppression of a deadly root pathogen also had the largest abundance of 17 unique types of pathogen fighting bacteria when compared to control plots (Mendes et al. 2011).

Archaea

The Archaea resemble the bacteria in terms of appearance and size but also share some commonalties with the more familiar Eukaryotic relatives (e.g., plants, animals , fungi , and protists) at the molecular level. However, this group is poorly known as a whole, relative to the bacteria and fungi, and their role in urban agriculture is not well understood. Recent evidence suggests that the Archaea play a large role in biogeochemical cycles, especially in dry, arid regions, and can decompose a variety of different chemicals, including oils, acidic mine tailings, and sulfur containing compounds (Offre et al. 2013). Work has also shown that Archaea play a role in the nitrogen cycle- converting ammonia into nitrate, the preferred version of this nutrient for plants. Stayed tuned for future news about how this group might connect to your gardening efforts.

Fungi

The Fungi are the last of the soil microbes that we will consider and are of interest to many gardeners (Fig. 8). Fungi belong to the group of organisms that have a nucleus and membrane bound organelles called the Eukaryotes.

Fig. 8

Many plants depend on fungi to help extract nutrients from the soil . Roots are connected to the fungal hyphae (thin white strands) extending outward into the soil (Photo Courtesy: Randy Molina, Oregon State University, Corvallis)

Plant, animals , and protists are also in this large group. Relative to Bacteria and Archaea , the Eukaryotes are much larger and a single cell can be seen easily by the naked eye. Most gardeners have experienced the fungi in one of two ways: the aboveground reproductive structure that we refer to colloquially as the mushroom and the white, web-like netting found in moist garden soil and often under potted flowers. The two structures previously mentioned are not separate entities but rather a continuous extension of a unique network of tissues called the hyphae. Hyphae is characterized as a multicellular, thread-like filament that is strong, yet flexible. The cells that make up the hyphae are interlinked with pores and these openings allow for a variety of cellular materials to move unhindered between cells and even across long distances. A network of multiple hyphae is called the mycelium. The mycelium usually escapes our eye because much of it lies underground, intermingling and networking extensively throughout the soil profile , binding particles together and limiting soil erosion. Amazingly, scientists have found a single fungal mycelium network that covers roughly ~3.5 miles in diameter and weighs into the hundreds of tons!

If one were to measure the distance of a mycelium network in a bucketful of soil , you would tally roughly a kilometer of individual threads (hyphae) at the end of your arduous experiment. Interestingly, when it comes time for reproduction, some fungi push their mycelium upward through the soil and forms the familiar sight of a mushroom (Fig. 9).

Fig. 9

Various types of mushrooms that you might encounter. Most garden soil mushrooms resemble those pictures in image three and are an indicator of chronic overwatering (Photo Courtesy: Sally J. Brown, University of Washington, Seattle, WA)

The mushroom’s sole job is to release fungal spores on air currents and spread the fungi elsewhere. That’s right, when you eat mushrooms, you are eating reproductive parts. Think about that next time you have them on your pizza.

Fungi , similarly to the bacteria involved in decomposition, degrade a variety of non-living biological compounds and gain both energy and nutrients from this process. An interesting and intriguing aside about fungi is the way they go about decomposing these biological compounds. Fungi acquire their energy and nutrients via adsorption. In this process, fungi release digestive chemicals into the surrounding soil matrix and the fungi then absorbs the simpler organic materials into the hyphal tissue.

Not all fungi are a friend to the gardener and they can take considerable toll on your crop yields. For example, another scourge of the garden superstars – the tomatoes, include early blight and Septoria leaf spot (Fig. 10).

Fig. 10

Septoria Leaf Spot symptoms on a tomato plant (Photo Courtesy: T.A. Zitter, Cornell University, Ithaca, NY)

These diseases can appear any time during the growing season but often show up after the flowers appear (Kennelly 2009). For Septoria leaf spot, symptoms include dark lesions and reproductive structures on the lower leaves, working their way upward as the plant grows. Early blight can be recognized by light brown, irregularly shaped lesions that can be up to 1/2 in. wide and are marked by concentric rings. If you are constantly plagued by sick plants, you might have a fungus problem (Table 2).

Table 2 A list of plant diseases caused by soil -borne fungi

Instead of reaching for a fungicide, double-check your watering habits. Most pathogenic fungi can be controlled by following the old gardening axiom, “ Water the soil , not the foliage”. Keeping the leaves dry will keep most fungal spores from growing on the plant where they can cause extensive damage. Furthermore, staking sprawling plants, such as indeterminate growing tomatoes, will increase airflow around the plant and will help keep fungal pests at bay (Fig. 11).

Fig. 11

An intrepid urban gardener poses near his tomatoes. Staking the plants allows for increased airflow, which helps reduce microbial pathogens and increases plant health (Photo Courtesy: Vicky Zeph)

Soil Microbes , Nutrients, and Plant Health

The Connection Between Organic Matter and Soil Microbes

We have now established the physical habitat and the main agents of decomposition and nutrient cycling (soil microbes ). In this section, we will discuss the connection between soil and the microbes that inhabit it and also broader issues of nutrient availability and how plant health is affected. Decomposition and nutrient liberation is an ecosystem service that microbes perform free of charge. However, you must keep the microbes happy, via organic matter and moisture inputs, so they decompose materials at a proper rate. This ecosystem service is critical for vegetable growth.

Interestingly, plants can only take up nutrients that are dissolved in the soil water that surrounds plants roots. However, most nutrients are not available in this form and are instead locked up tight in soil organic matter and detritus. Microbes (bacteria and fungi ), via decomposition of organic materials, release bound nutrients from more complex molecules, and thus largely control the supply of nutrients available for plants. As such, microbes are critical for gardening success and annual yields and should be treated as a “silent partner” in your growing operation.

How Microbes Control Nutrient Supply

As we have discussed previously, soil microbes (bacteria and fungi ) decompose organic materials in soils and release important nutrients for plant uptake. However, it important to note that microbes are not simply providing a free service for the gardener at their own expense. Bacteria and fungi only release nutrients to plants once they meet their own personal Nitrogen (N) and Phosphorus (P) demands. Soil microbes decompose materials in order to gain energy, by breaking the carbon-carbon bonds, to fuel biological activities such as reproduction, tissue maintenance, etc. Along with energy demands, nutrients, such as N and P, are assimilated into biomass and form the base components of most proteins, DNA, and other cellular structures.

After soil microbes use the nutrients for their own purposes, the excess is excreted back into the soil environment or released when they die. These leftover nutrients are how plants meet their biological demand for nutrients. Microbes serve as the “middle man” between the nutrients locked in organic materials and the nutrients, held in soil water , being absorbed by the plant root. Thus, microbes and plants are interlinked in a nutrient cycle. Plant materials are created from the nutrients absorbed in the soil and carbon dioxide from the air and, when these materials die, are returned to the soil to fuel the microbial activity that releases nutrients for plants (Fig. 12).

Fig. 12

The mineral nutrient cycle in gardens. (a) Microbes decompose the detritus in the soil ; (b) Soil microbes excrete excess nutrients into soil solution and return to the organic matter pool upon death; (c) Microbes can also assimilate nutrients from the soil pool that plants use; (d) Plant roots can only take up nutrients in soil solution; (e) Plant materials are returned to the soil organic matter pool upon death. This might be the most successful recycling program on Earth!

Managing Microbes in Your Garden

I hope you are now convinced of the role soil microbes can play in your gardening success. A practical gardener might wonder how to best manage soil microbial populations and thus maintain a healthy nutrient cycle. An important part of managing microbes is to consider their needs from a biological perspective. You can promote healthy microbial populations by adding extra organic matter to your soil. Common types of organic matter available to the gardener are manure inputs from cows and chickens , composts from food (no meats or fats!) and yard plant clippings, and soil products from municipal biosolids . If you live in an area with an annual leaf fall, you can add your leaf piles to your garden and later incorporate it into your garden soil. Organic matter will serve as a food source (carbon) for soil microbes, thus promoting a healthy population in your garden.

Organic matter has a myriad of other benefits besides serving as a food source for microbes . Organic materials will help moderate the effects of low pH in acidic soils and will help hold onto soil moisture during dry periods. Furthermore, the electrical charges on decaying organic matter will provide sites for excess soil nutrients to “hang out”. This will serve as a future source of soil fertility akin to a bank savings account. Other benefits of adding organic matter included reduced compaction and better water and oxygen infiltration around plant roots.

Disturbances to Soil Microbes

Disturbance to the soil in your garden can severely disrupt the life cycle of microbes . Common disturbances include tilling the soil in excess, compaction due to foot traffic, and watering practices that promote erosion. Gardeners often till their plots in order to break up tough soil, incorporate organic matter throughout the soil profile , and reduce the infiltration of weeds. However, tilling can upset the activities of soil microbes , particularly the fungi . If you recall from the previous section, fungi are made up of an extensive belowground network called the mycelium. When you till, you sever this network and compromise the function of fungi in your garden. Thus, by supposedly helping your garden, you can actually limit nutrient availability in your soils for future growing seasons. In order to reduce the effects of tilling, try to only till as minimally as possible and on the extreme bookends of your growing season.

Compaction

Soil compaction in the garden is primarily caused by foot or tire traffic. These forces compress the large pores in your soil . If you recall from our description of the physical nature of soil, pore spaces are crucial for moving both gasses and water throughout the soil profile . This can result in hypoxic conditions, which can essentially starve important microbes of oxygen. In order to reduce compaction, one should take great care to not step on the soils in which you will be growing plants. Establish paths for foot traffic in your garden that allow you ease of access to all sides of your plot. If you must walk in your plots, try to keep your weight spread out on a wooden board to reduce soil compaction.

Watering, although obviously helpful in the garden , can be detrimental to your success. Many gardeners, the author included, are guilty of overwatering. Overwatering, similar to soil compaction, displaces the oxygen gas in the soil and will prevent beneficial microbes from carrying out biological functions. Also, if you apply your water in a rough matter (e.g., with a jet nozzle or straight from the hose), you can physically tear apart soil and promote needless erosion, in a manner similar to tilling. Watering in this manner, not surprisingly, will disrupt the life cycle of soil fungi in a manner disproportionate to soil bacteria . In order to avoid problems associated with water application; make sure you apply water gently and only when the plants need it according to your local climate .

Chapter Summary

In this chapter, we established the following:

• Soil is a complex, multiphasic habitat that is crucial for gardening success.

• Microbes serve as the middle-man between soil organic matter and plant available nutrients.

• The connection between soil microbes , soil health , and gardening success cannot be ignored and soils should be managed to maximize microbial populations.

• Adding organic matter to soils is the best way to support a healthy soil microbial population.

• Be aware of compacting soil and overwatering, both will be detrimental to soil microbes .

Suggested Readings and Online Resources for the Urban Gardener

• 1. Tugel AJ, Lewandowski AM, Happe-vonArb D (eds) (2000) Soil biology primer. Soil and Water Conservation Society, Ankeny

• 2. Pavao-Zuckerman MA (2012) Urbanization, soils, and ecosystem services. In: Wall DH (eds) Soil ecology and ecosystem services . pp 270–278

• 3. Directory of Cooperative Extension Services – http://www.csrees.usda.gov/Extension/

• 4. Hoorman JJ, Islam R (2010) Understanding soil microbes and nutrient recycling. Fact Sheet SAG-16-10. The Ohio State University Cooperative Extension Service

• 5. Hoorman JJ (2011) The role of soil bacteria . Fact Sheet SAG-13-11. The Ohio State University Cooperative Extension Service

• 6. Hoorman JJ (2011) The role of soil fungi . Fact Sheet SAG-14-11. The Ohio State University Cooperative Extension Service

• 7. Mazza CP, Cunningham SK, Harrison EZ (2001) Using organic matter in the garden . Soils and Composting Fact Sheets. Cornell University. Department Of Horticulture

Glossary

Adsorption

 the adhesion of atoms, ions, or molecules from a gas, liquid, or dissolved solid to a surface

Archaea

 a domain of single-celled Prokaryote microorganisms

Assimilation

 the conversion of nutrients into biological mass

Bacteria

 a domain of single-celled Prokaryote microorganisms

Biogeochemical Cycles

 the pathway of a chemical substance as it moves through living and non-living components in an ecosystem

Compaction

 an increase in the solid density of a volume of soil and displacement of water and gas from soil pores

Decomposer

 organisms that break down dead or decaying organisms

Decomposition

 the biotic and abiotic process of decay

Detritus

 non-living biological materials

Ecosystem Service

 a benefit provided to humankind from the normal functioning of an ecosystem

Erosion

 the process by which soil and rock are removed from the Earth’s surface

Excretion

 the act of eliminating biological waste from an organism

Fungi

 single or multicellular Euklaryotic organisms

Hyphae

 multicellular, thread-like filaments made of chitin

Mineral Nutrients

 chemical elements that are known to be important to a plant’s growth, which come from the soil , are dissolved in water , and absorbed through a plant’s roots

Multiphasic

 consisting of three states (solid, gas, liquid)

Mutualists

 a biological relationship in which both entities derive benefit

Mycelium

 vegetative part of a fungus, consisting of a mass of branching hyphae

Nitrogen (N)

 essential macronutrient needed by all plants for structural, genetic and metabolic compounds in plant cells. It is also one of the basic components of chlorophyll.

Non-Mineral Nutrients

 known to be important to a plant’s growth and derived from air and water

Overwatering

 the application of water in a manner that promotes anoxia and waterlogging

Pathogens

 an infectious agent that can produce disease

Phosphorus (P)

 macronutrient important for the construction of genetic materials, energy storage, and protein synthesis

Potassium (K)

 macronutrient important for protein synthesis and photosynthesis

Soil Microbes

 community of Bacteria , Archaea , and Fungi that lives belowground

Soil Nutrients

 mineral elements that are critical for successful plant production

Soil Water

 water held in soil pores

Tilling

 the breaking up and cultivating of soil for agricultural use