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Soil Health, Quality & Microbial Diversity

By Bob Kremer, Ph.D. 

Soil health and soil quality have evolved as important concepts as we continue to expand our understanding of soil as the vital factor for vigorous plant productivity. These concepts have also stressed our awareness that soil is indeed a limited non-renewable resource that requires deliberate stewardship to avoid or minimize its degradation.

According to John W. Doran, soil health is the capacity of a soil to function and sustain plant and animal productivity, maintain or enhance water and air quality and promote plant and animal health.

Optimal soil health requires a balance between soil functions for productivity, environmental quality and plant and animal health, all of which are greatly affected by management and land-use decisions. Soil health focuses on the living, dynamic nature of soil that incorporates the biological attributes of biodiversity, food web structure, ecosystem functioning and the intimate relationships of soil microorganisms with plants and animals.

Soil quality also refers to the functional capacity of soil, but has a greater emphasis on agricultural productivity and economic benefits. Indeed, the development of the modern soil quality concept by Warkentin and Fletcher in 1977 was within the context of intensive agriculture, where the major concerns were food and fiber production and the capacity of soil to recycle nutrients, presumably from residual fertilizers and crop residues.

The term soil health, with its focus on biological function and protection of environmental quality, is most relevant for eco-agriculture production systems promoting good management practices that foster a balanced focus on all functions of soil health rather than an emphasis on single functions, such as crop yields.

Several articles published in Acres U.S.A. within the past decade illustrate how eco-agriculture embodies soil health, which is an inherent benefit of this production system. In a series of articles from 2012 to 2015, Gary Zimmer focused on the importance of mineral nutrition for both plants and soil microorganisms for improved soil health. He also stated that the capacity of a healthy soil to function could be realized without intervention, suggesting that eco-agricultural systems facilitate functional capacity by minimizing disruptive management of synthetic fertilizer, pesticide inputs and intensive tillage.

John Ikerd, writing in the May 2012 issue of Acres U.S.A., eloquently proposed that declining human health and inadequate nutrition in the United States is related to nutrient-deficient foods produced on soils of poor health resulting from industrial agricultural production practices. A summary of research reported by Reeve et al. in Advances in Agronomy validates Ikerd’s hypothesis and further shows that crops grown in biologically rich soils developed under sustainable farming practices lead to nutrient-dense foods.

Roles & Characterization of Soil Microbial Diversity

In this article we will expand on the role of microbial diversity relative to soil health and demonstrate how this relationship is useful in understanding effects of crop and soil management. Farmers and supporters of eco-agriculture recognize the vital importance of soil microbial diversity as a key resource for maintaining the functional capacity of both agricultural and natural ecosystems.

Previous articles in Acres U.S.A. have discussed the many functions driven by soil microorganisms that are critical for vigorous plant growth including nutrient cycling; decomposition of organic substances leading to soil organic matter (SOM) and aggregate formation; protection from plant pathogens; and synthesis of plant growth-regulating compounds for root growth stimulation and vegetative production. Thriving microbial communities are most abundant on plant roots and within the rhizosphere of plants that exude part of their photosynthetically fixed carbon through roots to feed the microorganisms as they mediate various biological processes (Figure 1).

Bacteria and fungi
Figure 1: Bacteria (small rod-like structures) and fungi (larger spherical shapes) associated with the surface of a root (rhizoplane) readily use organic substances released by the plant as sources of food and energy for mediating many biochemical processes and to maintain dense communities in the rhizosphere. Note the non-random distribution of bacteria showing concentration of cells on the rhizoplane where several processes take place including nutrient transformation, synthesis of plant growth-regulating compounds and antibiotic production for protection from attack by pathogenic microorganisms. Micrograph presented as 5,000X magnification. Source: R.J. Kremer

Although abundance of microorganisms in soils and rhizospheres is readily apparent, we often overlook the importance of microbial biodiversity required for effective performance of most functions. For example, degradation of complex organic substances such as lignin and cellulose in plant residues requires select groups of microorganisms, often termed consortia, wherein each member produces specific enzymes to carry out one or more steps in the degradation pathway.

Bruce Tainio: Amending Soil Microbial Life, from the 2005 Eco-Ag Conference & Trade Show. (1 hour, 2 minutes) Listen in as the popular agronomist explains how to feed the microbial life in your soil, and develop optimal microbial biodiversity.

For example, lignin degradation begins with attack by lignin-decomposing fungi that facilitate initial breakage of the polymer that is sequentially cleaved into simpler compounds by different specialist microorganisms at each step until simple carbon compounds become food and energy for microorganisms or small fragments incorporated in soil organic matter are formed. Thus, practices that disrupt the soil microenvironment and suppress any of the dozen or so microorganisms needed for degradation of lignin or other substances may disrupt overall decomposition and formation of SOM.

Understanding the microbial diversity and functional capabilities of soil in agricultural ecosystems can be used to guide and monitor crop and land management. Despite the widely accepted view that microbial structural and functional diversity are critical components for describing soil health, there are few microbiological indicators assessing soil health compared with those for chemical and physical properties.

The lack of microbiological indicators is because the majority of the microbial world cannot be easily cultured to characterize those individuals or groups that mediate the important biological processes in soil and aquatic environments. However, advancements in methods to overcome challenges of measuring the great numbers of microorganisms in soils and the difficulty in culturing provide some alternate approaches based on microbial community structure and function.

Several laboratories in the United States can now characterize microbial communities in soils based on cellular composition of phospholipid fatty acids (PLFA).

The total PLFA content is a measure of the viable microbial biomass present in soil. Identification of individual PLFAs (“biomarkers”) allows classification of specific functional groups of microorganisms (bacteria, actinobacteria, fungi and protists). These biomarker PLFAs yield a pattern of the members of the microbial community for soils of different ecosystems under various land management practices. Depiction of these microbial PLFA groups combined with information from other soil health indicators provides a robust understanding of the functional capacity of soils.

To show how microbial analysis can be applied for soil health assessment, we used PLFA tests to characterize soils under various management practices on a diversified, organic ecologically based farm on a gently sloping landscape predominated by Sharpsburg silt loam in northwest Missouri.

The farm transitioned to organic farming over the past 15 years with restoration of SOM through organic amendments of composts, mulches and biochar and establishment of a reconstructed native prairie ecosystem. An orchard, including a variety of heirloom fruit trees, was established with native prairie plants positioned in the alleys.

Soil microbial biomass represented by total PLFA content is depicted in Figure 2 below as the total height of the bars indicated for each management treatment.

kremer graph
Soil microbial community structure on an organic farm in northwest Missouri. Microbial components are expressed as content of phospholipid fatty acid (PLFA) markers specific for each component. Cnv Orch = conventional orchard and alley (Cnv Alley) with no organic amendments with tall fescue alleys; Org Orch, Org Alley, Org Alley+BC = organically managed orchard, alley and alley supplemented with on-farm produced biochar; Rest Prairie = restored prairie site established in 1995 on sloping landscape with eroded topsoil; Grass = old cool-season grass and forb hayfield with no management; Cultivated = nearby field cropped to corn-soybean rotation with chemical inputs and no cover crop. VAM, vesicular arbuscular mycorrhizae; Actino, actinobacteria; G pos Bac, Gram-positive bacteria; G neg Bac, Gram-negative bacteria.

Microbial biomass is constantly recycled through rapid cell generation to decomposition cycles (“microbial turnover”) and is incorporated into soil organic matter, which contributes to important soil properties. Decomposition of biomass releases available N to both plants and the living microbial community and thereby sustains biological processes in healthy soils.

The high microbial biomass associated with the continuous presence of living roots of prairie plants helps explain the high productivity and soil fertility observed on this farm.

Microbial biomass and all microbial components were highest in the organic orchard that was managed with perennial native vegetation in the alleys plus compost amendments around each tree. Microbial parameters were increased further in portions of the alley where biochar was applied. Mycorrhizae (VAM) were also more abundant in organic treatments indicating better nutrient (P, N, K) mobilization, water availability and protection from root pathogens with these symbiotic fungi. Microbial status of the restored prairie approaches that of the organically managed orchard, but because it was established on the most eroded landscape, reestablishment of the microbial community has been slower.

The results of this long-term study, reported in 2015 eOrganic News, demonstrate how ecologically based management practices enhanced soil biological function, improved overall soil health, promoted the production of horticultural crops without synthetic chemical inputs and improved environmental quality.

Soil Health Assessment

Despite the current interest in the soil health concept and its popular appeal for potential use in developing management decisions, standardized testing for soil health is not yet available. Several public and private laboratories offer soil health analyses based on various physical, chemical, biological and plant nutrient indicators and may include soil health ratings based on different models that incorporate some of the indicator results. This has prompted establishment of interdisciplinary groups such as the Soil Health Institute and the Soil Health Partnership to develop rigorous research protocols, assemble broad soil health databases for representative soils under different management regimes in various agro- and natural ecosystems across geographic regions; and develop a decision support system for farmer use.

Neal Kinsey, Using Soil Analysis to Grow Crops, from the 2005 Eco-Ag Conference & Trade Show. (50 minutes, 12 seconds). Listen in as agronomist Neal Kinsey, the author of Hands-On Agronomy, teaches about how to test your soils, and use that data, to increase crop yield and decrease weed pressures.

Until a standard and accepted system for soil health assessment is in practice, we can consider the principles of assessment, show how a rating can be derived and how this information can be used to assess and adjust your current management system.

Currently, soil health can be directly measured using a suite of selected biological, chemical and physical properties that are highly sensitive to changes in soil function. Soil health indicators should correlate well with ecosystem processes, integrate soil properties and processes, be user-friendly and be sensitive to management and climate. Soil indicators that indirectly measure soil function should represent the diversity of chemical, biological and physical properties and processes of the complex soil system.

Some soil health indicators in wide use include measurements of SOM or soil organic C, microbial biomass C, potentially mineralizable nitrogen (N), aggregate stability, pH, soil nutrient contents including phosphorus (P), potassium (K), and magnesium (Mg); available soil water-holding capacity (AWC), bulk density; topsoil depth; infiltration rate; and soil enzyme activity, specifically beta-glucosidase activity, which is involved in vegetative residue decomposition.

For purposes of this article, the soil management assessment framework (SMAF), developed by USDA-ARS at Ames, Iowa, is used as an example of a model-based program incorporating multiple indicator measurements into an assessment protocol to rate soil health of various ecosystems within landscapes of similar soils in a climatic region. When SMAF was used to evaluate soil health of various sites on claypan soils in northeastern Missouri, pasture and prairie ecosystems comprised of perennial vegetation rated highest relative to agro-ecosystems (Figure 2).

Interestingly, an organically managed pasture of mixed cover crop species (triticale, birdsfoot trefoil, turnip) combined with grazing sheep attained the next to highest rating, showing this management system allowed soil to achieve 97 percent functional capacity; in contrast, a nearby conventional corn-soybean system managed with tillage and chemical inputs functioned at 77 percent.

The survey also showed that crop rotations using no-till or mulch-till that included wheat and a cover crop or manure amendment functioned higher than the simple corn-soybean rotation with tillage. Although we expect prairie ecosystems to rate highest in soil health, we sampled a hardpan prairie with frequently saturated soil and, combined with accumulated decaying organic matter, results in low pH of 4.5-5.0. The rating index is thereby reduced because the model uses an optimum pH indicator value for acceptable plant growth.

This example evaluation validates the ability of well-managed ecosystems such as organic pasture and long crop rotations with cover crops to promote soil health and may serve as examples for farmers looking to develop improved agricultural practices for improving soil function. We can also see that integration of perennial vegetation may improve soil health and environmental quality within agroecosystems by adapting these systems as conservation strips within crop production fields or as field buffers.

Management Implications

More work is needed to improve soil health assessment by expanding measurements for the soil biological diversity and microbial components to be included as critical indicators of soil biological processes. Current models only accommodate values for soil microbial biomass C and one soil enzyme activity despite the view that soil biological processes, along with SOM, are key factors in achieving adequate long-term soil health and environmental quality. Addition of microbiological indicators for the soil health assessment presented in Figure 3 could likely magnify the contrasts among ratings and yield more insight on management system effects.

kremer chart
Soil health index for assessing crop management systems derived using the Soil Management Assessment Framework (SMAF) for soils collected in the Salt River Basin in northeast Missouri. CRP, Conservation Reserve Program acreage; CSG, cool-season grasses; WSG, warm season grasses; NT, no-till; MT, mulch-till (non-inversion tillage such as disk harrowing to partially incorporate residues left on the soil surface); C, corn; Sb, soybean; Wh, wheat; RCl, red clover; Cont., continuous.

Farmers using eco-agriculture practices already know their effectiveness in improving and maintaining soil health; soil health assessment of their systems would validate their management or suggest that it could be adjusted for further improvement. Soil health assessments of eco-agricultural management can be important as models for other management systems that require adjustment to improve the functional capacity of soils.

Soil expert and author William McKibben, The Art of Balancing Soil Nutrients, from the 2009 Eco-Ag Conference & Trade Show. (1 hour, 8 minutes). Listen in as McKibben talks about the steps you can take after you receive your soil test results to help balance your soil.

As soil health working groups assemble datasets for use in developing assessment models and management guidelines, it is imperative that soils from working eco-agricultural farms are tested to assure that the range of indicator values include the potential for optimum performance achieved by these systems.

Farmers wishing to transition from management based on genetically engineered (GE) crops and Roundup (glyphosate) herbicide for weed control will find proven practices from eco-agriculture to rehabilitate their soils for non-GE crop production.

Soils managed under an industrial production mindset have greatly altered microbial diversity as shown by glyphosate released through corn and soybean roots that increase Fusarium and decrease beneficial bacteria (Figure 4), potentially leading to root disease and disruption of nutrient availability to crops. We also know that repeated use of glyphosate reduces mycorrhizal spore germination and root infection or hinders development of the symbiotic association on infected roots; it also suppresses both symbiotic rhizobial and non-symbiotic nitrogen-fixing bacteria; and inhibits some of the microfauna (nematodes and protozoa) involved in nutrient cycling in the soil food web.

Roundup Ready soybean planted into tall fescue killed with Roundup burndown application (upper left) and not treated (upper right); note difference in apparent plant vigor of soybean due to planting into sod two days post-herbicide application. Soybean plants were excavated and roots cultured on a medium selective for the fungi Fusarium spp. (lower photo); left plate shows proliferation of Fusarium spp. (white circular colonies) on soybean roots from plants planted into Roundup-killed sod due to glyphosatemediated stimulation of Fusarium spp. on dead fescue that also colonize soybean roots; right plate shows soybean roots not affected due to no glyphosate treatment. Soybean grown in Jemerson silt loam on author’s family farm in central Missouri.

We are now finding glyphosate residues in soils of up to 1 ppm even one year after last application — the consequences of these residues on soil biology and health are yet to be determined. Practices based on eco-agriculture management can be effective in restoring such degraded soils by establishment of living root systems through cover cropping and/or extended crop rotations; organic amendments and application of effective biological products including inoculants; and integration of livestock (if plausible) can improve soil health necessary during transition to more sustainable agricultural production systems. Therefore, the soil health status achieved in eco-agricultural systems serves as a valuable guide for restoration of soils for farmers seeking balanced sustainability in their management that reflects the vital soil health functions of productivity, environmental quality and plant and animal health rather than focusing on only economic yields.

This article appeared in the December 2016 issue of Acres U.S.A. magazine.

Bob Kremer, Ph.D., retired after 32 years of service as a research microbiologist with the USDA Agricultural Research Service at Columbia, Missouri and currently holds a position as Adjunct Professor of Soil Microbiology in The School of Natural Resources at the University of Missouri. He has published 150 research articles on biological management of weeds; impacts of transgenic crops and glyphosate on soil biology and ecology; plant-microorganism interactions; and soil health.