THE LIVING INTERFACE:

Soil and Water Conservation vis-à-vis Soilborne Microbes

Abstract
A primary literature review on the implications maintaining soilborne microbial biodiversity
within agricultural production systems has on soil and water conservation, and vice versa.

Key words: agriculture, pedofauna, soil and water conservation, natural resources management.

Noah R. McVay
SCSCI 4350
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Introduction

Globally, there are now slightly more than seven billion people living on this planet, and

that number is expected to increase dramatically over the coming decade, surpassing eight billion

by the year 2025 (Nan et al., 2015). This growing, swelling sea of humanity requires additional

natural resources to meet the needs of its complicated biosocial and economic structures. A

likely consequence will be increased food production to satisfy a burgeoning population, at a

detriment to natural ecosystems sensitive to human exploitation. However, with food insecurity

and extreme poverty still ripe throughout the undeveloped world, the question remains: How can

we deliver enough food so as to sustain our species, whilst not further converting more and more

land towards agricultural production? The root of the problem – and the solution – lies in the

realization that responsible agricultural production derives from successful soil and water

conservation measures focused on maintaining the biodiversity of soilborne microbes in

agroecosystems, so as to benefit the biology and ecologic function of responsible field crop

production. Increased biodiversity of soilborne microbes facilitates conservation of soil and

water resources within agricultural production systems, and vice versa. This is largely driven by

the biology, ecosystemic function and anthropogenic management of soilborne fungi, bacteria,

archaea and similar microorganisms within the wider agroecosystem.

However, what even is an agroecosystem? Agroecosystems are the in situ organismal

communities and incidental abiotic components, such as the soil itself, together imparting

ecological services to agricultural production systems. More simply put, the persistence of an

agroecosystem “depends upon the maintenance of biological integrity and diversity” (Altieri,

1999). Altieri (1999) further performs a satisfactory summarization of the topic, stating:

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“Increasingly research suggests that the level of internal regulation of function in

agroecosystems is largely dependent on the level of plant and animal biodiversity present.

In agroecosystems, biodiversity performs a variety of ecological services beyond the

production of food, including recycling of nutrients, regulation of microclimate and local

hydrological processes, suppression of undesirable organisms and detoxification of

noxious chemicals.”

Methods

In this literature review, pieces of primary literature were employed to convey incumbent

information and suggest new conclusions in the area of soilborne microbial biodiversity and its

impacts on both soil and water conservation. Published, peer-reviewed journal articles drawn

upon for this literature review covered topics as varied as quantifying pedofaunal biodiversity,

agroecosystemic function of soilborne microbes, the diversity on the forms and function of

soilborne microorganisms, implications of agricultural practices on the agroecosystem, etcetera.

Specific literature referenced herein was obtained via the Elton S. Karrmann Library at The

University of Wisconsin – Platteville, and via Google Scholar. All figures presented herein are

reproduced with permission from the authors of the cited primary literature.

Results and Discussion

Microbial Diversity, Biology and Ecology on Agricultural Soils

Worldwide, soil is alive with biologic activity. Soil microorganisms only account for

0.5%, dry weight, of soil biomass, but they play a key role in the composition and function of

soils (Lehman et al., 2015). Within the soil microbiome, pedofauna – or soilborne microbes –

consist of various groups of archaea, bacteria, and fungi – arbuscular mycorrhizae,

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ectomycorrhizae, yeasts, oomycetes, etcetera (Zak et al., 1994). Many of these organisms inhabit

the rhizosphere of plants, metabolizing root exudates and other secondary metabolites from

photosynthesis. While a detailed understanding of these symbioses is still as yet unknown,

research over the last two decades indicates that osmolysis – that is, the rupture of the cell

membrane due to excessive accumulation of solvent under saline conditions – is mitigated for

both plant hosts and rhizosphere-inhabiting symbionts as a result of their symbioses. This may

possibly be due to an exchange of K+ during periods of drought stress, which is most often

observed in symbiotic bacterial cells – although most soil microorganisms appear to employ this

behavior (Wagg et al., 2013).

Nevertheless, pedofauna are not just limited to the rhizosphere. In fact, they extend well

beyond into the deeper strata of soil profiles. Proteobacteria and archaea are capable of

surprising ecosystemic dynamism, often taking up niches not filled by other soil microbiota due

to intraspecific competition for soil carbon. Much of soilborne microbial biodiversity is

contingent upon population dynamics, whereby specific groups of soil microbes ebb and flow in

direct response to carbon resources, environmental conditions and soil quality. Certain clades,

such as fungi, are better able to seek out and locate soil carbon under perennial crops or untilled

fields on account of limited disturbance to their sensitive mycelia (Griffiths et al., 2013). Under

such circumstances, anaerobic conditions control, leading to different soilborne carbonic

metabolizations (Alguacil et al., 2012).

On the other hand, archaea and bacteria respond to their own ideal soil microbiome

conditions – including an aerobic soil medium and herbaceous plant material – by multiplying

rapidly. By and through quorum sensing, these microorganisms can quickly locate and

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metabolize soil carbon (Brussaard et al., 2007). On account of these disparate carbonic

metabolizations and subsequent soil microbiome preferences, the pedofauna incident to any

particular soil within a given locale varies over time (Nan et al., 2015). Soil microbiota is never

static. Ultimately, this constant intraspecific, multi-clade competition is what fuels the carbon

cycle in the world’s arable soils (FIG. 1.)

Putting that information aside, it is important to identify the actual players in the soil

microbiome performance. What kind of microorganisms are being dealt with here? Soil culturing

assays indicate much is ado in agricultural soils. Production systems reliant upon tillage tend to

be well-aerated as a result of frequent soil disturbance. However, reduced tillage – and thereby

decreased soil disturbance – promotes greater microbial biodiversity among bacterial clades

(Lupwayi et al., 1998). A typified soil microbiome in such soils is predominated by bacterial

genera within the Phylum Proteobacteria, followed by smaller but nonetheless still significant

populations of Acidobacteria, Actinobacteria, and various other bacterial clades, altogether

accounting for approximately 38%, 20.4%, 12% and 29.6% of total, living soil biomass

attributed to bacteria (FIG. 2.) (Chuntao et al., 2010). Likewise, archaea and cyanobacteria also

thrive in agroecosystems, with populations accounting for roughly 10% of total, living soil

biomass. This diverse ensemble of microbes facilitates adaptation and resiliency of the carbon

sequestration process in arable soils, and thusly are important biologic actors on the conservation

of soil and water resources in agricultural systems.

While likely the most abundant in agricultural soils, bacteria and similar prokaryotes are

not alone. The agroecosystem in general and the soil microbiome in particular hosts a diverse

menagerie of other soil inhabitants, including ectomycorrhizal saprophytes which decompose

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and incorporate organic matter into the soil profile, and arbuscular mycorrhizae responsible for

colonizing and promoting host health via metabolites synthesized in return for root exudates and

photosynthetic compounds. Altogether, these fungi – which in unaltered non-anthropogenic

ecosystems usually outnumber soil bacteria 2:1 – perform part of a host-mycobiont symbiosis

carried out over the course of geologic time: mitigation of abiotic and biotic stresses caused by

such variables as adverse environmental conditions or plant pathogens (Emmerling, 2006). This

symbiosis of shared nutrients and other metabolized information is responsible for much of a

host plant’s health in situ, whether as a rare orchid in a naturally-occurring ecosystem or as a

field crop within the agroecosystem.

However, disruption of the plant-microbe symbiosis – as what happens during routine

soil disturbance from crop tillage – means that conventional agricultural production systems are

largely devoid of these beneficial fungi. Those mycobionts which are present in any significant

quantity are species of arbuscular mycorrhizae of the Phylum Glomeromycota. Consisting of

approximately 375 or so species, the Glomeromycota are an ancient clade of fungi with an

immensely broad host range and a corresponding fossil record dating back 675 million years:

these fungi are responsible for the formation of vesicles arising from the infection of host root

cortex, and aide in the acquisition and transport of soilborne nutrients to the host. Likewise, the

colonization of the rhizosphere of host plants by arbuscular mycorrhizae directly competes with

soilborne fungal and oomycete pathogens; this competition has been attributed to the promotion

of systematic host health through the symbiosis of the host and mycobiont.

Nevertheless, Glomeromycotans do not tolerate soil disturbance well. For that reason, the

genera Glomus and Gigaspora account for nearly all known arbuscular mycorrhizal activity

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within agricultural soils. The factors contributing to this limited diversity are as yet unknown.

Even so, the sum function of the soil microbiome within the agroecosystem is driven by these

microorganisms, bacteria and those species as yet unknown to science. This speciation

demonstrates the complexity of soilborne ecosystems and their biodiversity, and the

agroecosystem is no exception to this reality (FIG. 3.)

Ecosystemic Function of Microbes within Soil Agroecosystems

Functional soil is only capable of performing its ecosystemic role in concert with a

biodiverse composition of soilborne microorganisms. Resilient soil – that is, soil capable of

recovering from or adapting to stress – has long been perceived to harbor the greatest microbial

diversity among all ecosystems, and the viability of agriculture and human civilization is

dependent upon the health and wellbeing of the living component therein. Advances in analytical

and computational tools have suggested that approximately one billion bacterial cells, grouped

into 1,000 to 1,000,000 species, reside in a single gram of soil. The rate of discovering and

characterizing bacterial diversity since 1987 is astounding, growing from a modest 12 phyla to

more than 70 by 2009. However, many of these phyla contain few, if any, organisms that can be

grown and studied in the laboratory. Within these new phyla are bacteria that can fix carbon

dioxide via multiple pathways not found in plants, alongside bacteria that generate energy from

sunlight using alternative light receptors not previously known to science. Given the recency of

these discoveries, it is not surprising that the contribution of autotrophic soil bacterial organisms

like these to terrestrial carbon cycling and sequestration has not yet been determined (Lehman et

al., 2015). Amazingly enough, all these microorganisms together conduct the ecosystemic

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functions incidental to and performed by resilient soil – arable soils in agricultural production

systems included.

Soil seems to be characterized by a redundancy of functions. As an example, no

relationship has been shown to exist between microbial diversity and decomposition of organic

matter. Generally, a reduction in any group of species has little effect on overall processes in soil

because other microorganisms can take on its function (Nannipieri et al., 2003). Nevertheless,

ecosystemic functions performed by resilient agricultural soils continue. A key function is soil

water homeostasis. Namely, an increased presence and diversity of soil microbes contributes to

an equitable increase in the number of water-stable aggregates, the quantity of soil organic

matter per square foot of field, and the ability of precipitation to permeate and/or infiltrate soils

within the agroecosystem (Six et al., 1999). This strong correlation is likely due to the efficiency

in large, redundantly diverse populations of soil microorganisms in the acquisition,

decomposition, metabolization and sequestration of organic matter into soil environs (Coleman,

1994).

Furthermore, Skopp et al. (1990) iterates that continuity in both aerobic and anaerobic

microbial activity within the agroecosystem moderates and facilitates soil water diffusion

throughout the substrate by and through the creation of microburrows, fractures, and like

structures within sediment. This continuity in metabolization of soil carbon so as to conserve soil

water is only possible through stable pedofaunal communities not stressed by disturbance,

however, which simultaneously are not nutrient limited by carbon and certain natural sources of

nitrates (Wagg, 2013).

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A separate ecosystemic function incidental to the agroecosystem, as with any other

agroecosystem, is the mediating role soil microorganisms undertake vis-à-vis host plants and soil

particulates in the acquisition of macro- and micronutrients available to the crop. Arbuscular

mycorrhizae and ectomycorrhizae in particular infect host roots and extend their mycelia into the

soil profile, mining for nutrients far out of reach of plant roots (Reeves, 1997). This mass

colonization of the rhizosphere by mutualistic symbionts, moreover, stimulates direct

competition of plant parasites and the exudation of secondary metabolites that elicit systematic

defenses from host plants and consequential aggregations of other microorganisms in the

immediate vicinity. And of course, these mass concordats of pedofauna inadvertently executes

their basic duty of aggregating soil particulates together, stabilizing entire soil profiles and

thereby mitigating or preventing soil erosion (Pimentel et al., 1995).

Management of Agricultural Soilborne Microbes to Conserve Water and Soil Resources

Having discussed the important ecological functions performed by pedofauna in regards to

the soil microbiome, it is not difficult to see the significant role microbial diversity plays in the

management decisions necessary for comprehensive soil and water conservation. To promote

microbial biodiversity and thereby promote augmented soil and water conservation strategies,

managers should consider the following actions: tillage, cover cropping, irrigation and

fertilization. They will be considered accordingly. It is important to bear in mind, however, that

the type and abundance of microbial biodiversity in arable soils will differ across

agroecosystems which differ in age, diversity, structure, and management. In fact, there is great

variability in basic ecological and agronomic patterns among the various dominant

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agroecosystems. In general, the degree of biodiversity in agroecosystems depends on four main

characteristics of the agroecosystem, as described by Altieri (1999):

1. The diversity of vegetation within and around the agroecosystem;

2. The permanence of the various crops within the agroecosystem;

3. The intensity of management; and,

4. The extent of the isolation of the agroecosystem from natural vegetation.

Taking the four main characteristics of the agroecosystem into consideration, it’s an

imperative to commence with the action having the greatest influence on soilborne microbial

biodiversity: tillage. And it is true: tillage in agricultural fields is the single greatest factor

governing the biodynamics of soilborne microbial biodiversity (Swanepoel, 2015). Certain

soilborne microbes, including mycobionts such as arbuscular mycorrhizae, elicit soil-binding and

pathogen-fighting compounds in return for root cortex exudates and other secondary metabolites

resulting from photosynthesis. However, considerable amounts of carbon from complex

carbohydrates and humic acids within soil organic matter are necessary for this symbiosis to

occur.

To promote improve ecosystemic function, managers of agricultural production systems

should consider modifying current production regimes so that soil is minimally disturbed and

crop residue is permitted to decompose into mulch: in short, no-till, multispecies cropping

systems with a cover crop – preferably perennial – which accumulates organic matter at an

adequate rate so as to sustain a diverse community of soilborne microorganisms with the

augmented ability to create microburrows, fractures and like structures within agricultural soils

for improved infiltration and water retention. This recommendation derives from research

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suggesting increases in the amount of available carbon by and through crop residue in such no-

till systems simultaneously increases both the respiratory activity and respiratory quotient of

pedofaunal metabolisms (Entry et al., 2003). While the microbial communities in agricultural

soils are less efficient in utilization of carbon relative to forest soils, they are nonetheless still

impacted by metabolization of available soil carbon (Dilly, 2003). Appropriate management

regimes concerned with carbon cycling are therefore in order (FIG. 4.).

Living cover crops have immediate impacts on soil microbial community structure and

function. Permanent cover crops in particular contribute to significantly larger and more

biodiverse populations of soil microbes (Virto et al., 2012). Likewise, cover cropping is a widely

promoted strategy to enhance soil health in agricultural soils. However, an understanding of how

specific cover crop species influenced pedofaunal communities in the agroecosystem was up

until recently limited. Finney et al. (2017) examined the effects of eight fall-sown cover crop

species grown singly and in multispecies mixtures on microbial community structure and soil

biological activity using phospholipid fatty acid (PLFA) profiles and daily respiration rates,

respectively. Fourteen cover crop treatments and a no cover crop control were established in

August of 2011 and 2012 on adjacent fields in central Pennsylvania following spring oats (Avena

sativa L.). Soil communities were sampled from bulk soil collected to a depth of 20 cm (7.9 in)

in fall and spring, approximately two and nine months after cover crop planting and prior to

cover crop termination. In both fall and spring, cover crops led to an increase in total PLFA

concentration relative to the arable weed community present in control plots (increases of 5.37

nmol g–1 and 10.20 nmol g–1, respectively).

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While there was a positive correlation between aboveground plant biomass (whether from

arable weeds or cover crops) and total PLFA concentration, it was found individual cover crop

species favored particular microbial functional groups. Arbuscular mycorrhizae were more

abundant beneath oat and cereal rye (Secale cereale L.) cover crops, whereas ectomycorrhizae

were positively associated with hairy vetch (Vicia villosa L.). In the same breath, these cover

crop-microbial group associations were present not only in monocultures, but also in

multispecies cover crop mixtures. Moreover, arable weed communities were associated with

higher proportions of actinomycetes and Gram-positive bacteria. Soil biological activity varied

by treatment and was positively correlated with both the size and composition of the microbial

community, establishing a clear link between cover crops and the microbial communities they

undergo mutualisms with (FIG. 5.). This cover cropping study thereby demonstrates that – while

cover crops generally promote microbial biomass and activity – there are species-specific cover

crop effects on soil microbial community composition that ultimately influence soil biological

activity. This novel information therefore paves the way for intentional management of the soil

microbiome to enhance the performance of the agroecosystem within agricultural production

systems through appropriate cover crop selection (Finney et al., 2017).

Given the sensitivity of pedofauna to many irrigative and fertilizing inputs, and on account of

the previously mentioned roles pedofauna play in soil and water conservation, irrigation and

fertilization practices should be directed towards maintaining and growing soilborne microbial

biodiversity. In general, wastewater should never be used to irrigation fields, as it contributes to

reductions in speciation of arbuscular mycorrhizae on tree fruit including citrus (Alguacil et al.,

2012. In the same breath, long-term applications of nitrogen fertilizers decrease diversity of

arbuscular mycorrhizae in arable soils in North China (Xiangui et al., 2012). Similar impacts

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have been found on archaea and cyanobacteria in Canadian wheat fields (Sharma et al., 2011).

Moreover, Lupwayi et al. (1999) demonstrate carbon sequestration decreases under wheat as

populations of certain mycobionts decline due to modifications of the fertilizer regime in concert

with tillage and crop rotation. Further research on the role fertilizer applications play in carbon

metabolization in crop plants is warranted.

Conclusion

Available literature indicates that high-input agriculture, particularly tilled

agroecosystems with narrow crop rotation or short fallow management, leads to a decrease in

species richness and the predominance of select pedofauna. This imbalance negatively reduces

the sum ability of the agroecosystem to perform essential ecological functions, such as carbon

cycling, water retention, aggregation of soil particulates, etcetera. In contrast, management

characterized by rotations, no-tillage, organic amendments and maintenance of non-productive

components leads to an increase in species richness and overall density. Still, further research is

needed to understand the evolutionary history, molecular biology and host preferences of

pedofauna within agricultural soils, and how the sum of their host-symbiont interactions

promotes agroecosystemic function, comprehensive crop health, and the conservation of precious

soil and water resources for future generations.

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Literature Cited
Alguacil MdM, et al. 2012. Long-term effects of irrigation with waste water on soil AM fungi
diversity and microbial activities: The implications for agro-ecosystem resilience. PLoS
One 7(10): 1-7.
Altieri, MA. 1999. The ecological role of biodiversity in agroecosystems. Agriculture,
Ecosystems and Environment 74: 19-31.
Brussaard, L, et al. 2007. Soil biodiversity for agricultural sustainability. Agriculture,
Ecosystems and Environment 121: 233-244.
Chuntao, Y, et al. 2010. Members of soil bacterial communities sensitive to tillage and crop
rotation. Soil Biology and Biochemistry 42: 2111-2118.
Coleman, DC. 1994. Water-stable aggregates and organic matter fractions in conventional and
no-tillage soils. Soil Science Society of America Journal 58: 777-786.
Dilly, O, 2003. Regulation of the respiratory quotient of soil microbiota by availability of
nutrients. FEMS Microbiology Ecology 43: 375-381.
Emmerling, RG. 2006. Methods for evaluating human impact on soil microorganisms based on
their activity, biomass, and diversity in agricultural soils. Journal of Plant Nutrition and
Soil Science 169: 295-309.
Entry, JA, et al. 2003. Influence of irrigated agriculture on soil carbon and microbial community
structure. Environmental Management 33: 363-373.
Finney, DM, et al. 2017. Living cover crops have immediate impacts on soil microbial
community structure and function. Journal of Soil and Water Conservation 72(4): 361-
373.
Griffiths, BS, et al. 2013. Insights into the resistance and resilience of the soil microbial
community. FEMS Microbiology Review 37: 112-129.
Lehman, RM, et al. 2015. Soil biology for resilient, healthy soil. Journal of Soil and Water
Conservation 70(1): 12-18.
Lupwayi, NZ, et al. 1999. Soil microbial biomass and carbon dioxide flux under wheat as
influenced by tillage and crop rotation. Canadian Journal of Soil Science 79: 273-280.
Nan, Y, et al. 2015. Influence of salinity and water content on soil microorganisms. International
Soil and Water Conservation Research 3: 316-323.
Nannipieri, P, et al. 2003. Microbial diversity and soil functions. European Journal of Soil
Science 54: 655-670.
Pimentel, D, et al. 1995. Environmental and economic costs of soil erosion and conservation
benefits. Science, 267(5201): 1117-1123.

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Reeves, D. 1997. The role of soil organic matter in maintaining soil quality in continuous
cropping systems. Soil and Tillage Research 43: 131-167.
Sharma, P, et al. 2011. Conservation tillage, optimal water and organic nutrient supply enhance
soil microbial activities during wheat (Triticum aestivum L.) cultivation. Brazilian
Journal of Microbiology 42: 531-542.
Six, J, et al. 1999. Aggregate and soil organic matter dynamics under conventional and no-tillage
systems. Soil Science Society of America Journal 63: 1350-1358.
Skopp, J, et al. 1990. Steady-state aerobic microbial activity as a function of soil water content.
Soil Science Society of America Journal 54: 1619-1625.
Swanepoel, JH. 2015. Effects of conservation agriculture and fertilization on soil microbial
diversity and activity. Environments 2: 358-384.
Virto, I, et al. 2012. Soil quality evaluation following the implementation of permanent cover
crops in semi-arid vineyards. Organic matter, physical and biological soil properties.
Spanish Journal of Agricultural Research 10(4): 1121-1132.
Wagg, MG. 2013. Soil microbial diversity and agro-ecosystem functioning. Plant and Soil
Science 363: 1-5.
Xiangui, L, et al. 2012. Long-term balanced fertilization decreases arbuscular mycorrhizal fungal
diversity in an arable soil in North China revealed by 454 pyrosequencing.
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Appendix of Figures
Listed and annotated in order of their citation herein.

FIG. 1. Conceptualized model of carbon cycle emphasizing transfers amidst biotic and abiotic
components of carbon metabolism (Nan et al., 2015).

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FIG. 2. A depiction of the diversity of bacterial phyla from samples taken in a test plot over a
period of two years (Chuntao et al., 2010). The graph on the left illustrates frequency of bacterial
phyla from clusters of both years. Numbers after taxa represent median percent similarity values
calculated using Naive Bayesian rDNA Classifier Version 1.0, November 2003 (Ribosomal
Database Project). The nomenclatural taxonomy of Garrity and Lilburn, release 6.0 was used. N
¼ 299 clusters in pie chart. Phyla are ordered counterclockwise on pie chart, starting with black
at the 12:00 position. The graph on the right, meanwhile, considers frequency of classes within
the Phylum Proteobacteria from clusters of both years. Numbers after taxa represent percent
similarity values calculated using Naive Bayesian rDNA Classifier Version 1.0, November 2003
(Ribosomal Database Project). The nomenclatural taxonomy of Garrity and Lilburn, release 6.0
was used. N ¼ 115 clusters in pie chart. Classes are ordered counterclockwise on pie chart,
starting with Gammaproteobacteria (black) at the 12:00 position.

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FIG. 3. A conceptual model relating genetic, taxonomic and functional diversity to total
biodiversity. Biodiversity has a genetic foundation because diversity arises as a consequence of
evolutionary differentiation, e.g., speciation. Functional diversity results as a consequence of
genetic variability within a taxon, environmental effects on gene expression, and ecological
interactions among taxa. A comprehensive understanding of biodiversity, especially as it applies
to ecosystem properties, requires consideration of genetic, taxonomic and functional components
(Zak et al., 1994).

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FIG. 4. A conceptualized model for the design and management of cropping systems that
promote pedofaunal biodiversity. The potential entry points for biological management of
beneficial and pest soil organisms, cropping systems, OM inputs and soil fertility, affecting plant
production (Brussaard et al., 2007).

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FIG. 5. Distance-based redundancy analysis of soil microbial community composition as

influenced by cover crop treatment in (a) fall and (b) spring, approximately two and nine months,
respectively, after cover crop planting in 2011 and 2012 in central Pennsylvania (Finney et al.,
2017). Vectors indicate the degree of correlation between each PLFA biomarker group (labeled
in italics) and the axes. Axes labeled with an asterisk are significant. Labeled points represent the
mean community composition of the corresponding treatment. CA = canola. CR = cereal rye. FR
= forage radish. HV = hairy vetch. NO = no cover crop. OA = oat. RC = red clover. SB =
soybean. SH = sun hemp.

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