Why Nitrogen cycling is a keystone indicator in sustaining soil health

sustaining soil health
© Nitsuki

Zachary Senwo, Fulbright Scholar & Professor of Soil Microbial Biochemistry, Environmental Science & Toxicology at Alabama A&M University, explores nitrogen cycling in sustaining soil health and agricultural systems

With a renewed emphasis on sustainable agriculture and food security, comes a reawakening of interest in soil health, quality and fertility. Decline in soil health and exorbitant high fertilizers expenses constitute major limiting food production in several limited-resource countries.

In an article titled, “Soil Health – The Theory of Everything (Terrestrial) or just another Buzzword?”, Dick (2018), concludes ‘soil health’ from a purely scientific perspective is to captivate public interest to view soil as a pertinent resource in sustaining agriculture practices.

Soil health, soil quality, and soil fertility are interchangeable terminologies with similar assessments indicators. In the book “Soil Quality for a Sustainable Environment”, authors defined and proposed certain soil health/quality indicators (Doran et al. 1994).

However, the major challenges for practical assessments of soil health are the changes in soil properties changing over geologic time, and soils subject to geographic regions, soil types, and interpretations. Thus, routine soil health assessments using novel sets of diverse tools offer new insights into the functions and spatial attributes of soils. Indicators must relate to ecosystems functions, such as nutrient cycling and transformations linked to models that emulate ecosystems functionalities because anthropogenically – driven soil changes do constrain locations-specific soils used for agriculture.

In 2019, Cornell University designed and hosted an intensive 2-day “Soil Health Train the Trainer Workshop” for an in-depth understanding of soil health, measurements indicators and monitoring over time, and improvement through holistic, adaptive, and data-driven soil management. Activities included a mix of classroom training, hands-on field and laboratory experiences, and opportunities. From experts, participants acquired soil health principles, analysis, reporting, interpretation, and management planning.

Nitrogen cycling and soil health

Globally, nitrogen losses from agricultural systems are amongst the major pressures on managed and natural ecosystems. Cycling and transforming a major crop nutrient such as nitrogen (N) is crucial in sustaining soil health and agricultural systems. Although the importance of N seems clear, it is often considered an infinite resource that will always be available to provide us with needed agricultural services.

Dr Zachary Senwo and colleagues at Alabama A&M University are linking nitrogen cycle and soil health via organic N transformation and microbial species. Managing such plant macronutrient as nitrogen and improving its usage efficiency is paramount in developing better strategies to contribute to global food solutions.

Nitrogen without any doubts is fundamental in building and strengthening agriculture and pivotal in global food security and climate change. Its supply and availability are site, weather, and forms specific. Nitrogen cycling include such biochemical processes as biochemical N fixation, ammonification, nitrification, and denitrification driven by specific bacteria resident in soils and dependent on specific soil conditions (aerobic versus anaerobic). Using leguminous cover cropping, compost and manure additions increase soil organic matter and improves the soil’s ability to sequester and supply N and other nutrients.

Terrestrial ecosystems, soil proteins, and biochemical processes

Soil protein or amino acid is a major soil health bioindicator. It is estimated that between 20 and 40% of the total N in soils is present as amino acids bound to soil organic matter and mainly in the form of proteins and/or peptides associated with clay-organic matter complexes (Schimel and Bennett, 2004; Roberts and Jones, 2012).

Amino acids and amino sugars are subject to plant uptake, microbial immobilization, leaching losses, organic matter humification and degradation to mineral inorganic N forms as ammonium (NH4) and the subsequent nitrification of the NH4 to nitrite (NO2) and nitrate (NO3).

Amino acid compositions of soil organic matter from surface soils has been shown to significantly correlate with organic C and clay content, however; the type of management practices does affect total soil contents. Their presence in soils and organic matter is inherently due to the breakdown of native proteins derived from plants, microbes and animal tissues (Senwo and Tabatabai, 1998). With the growing recognition of the importance of amino acids to ecosystem N cycling, carefully managing organic N sources is an important priority likely to limit unfavourable N losses into the environment while enhancing soil health.

The terrestrial ecosystems are vast and diversified; hence, it is not strange that they still harbour numerous secrets of indigenous microorganisms hidden within its complex structure. In part are the most important biochemical processes on the planet via soil biochemical nitrogen fixation by nitrogenase enzymes. Nitrogen cycle originates with soil organic matter degradation, then depolymerization and supply of proteins/peptides into free amino acids which not assimilated by plant roots or microorganisms, are further mineralized in aerobic systems to ammonium, followed by nitrification by nitrifiers (Nitrosomonas, Nitrobacter) or denitrified by denitrifiers (nitrate reductases) in anaerobic systems.

Amidohydrolases: Key nitrogen enzymes

Novel soil metagenomics research technologies of rRNA gene-based analysis to link key enzymes from microbes have expanded our knowledge of soil health bioindicators.

Amidohydrolases widely distributed in nature are key N enzymes and specific in their biocatalytic reactions in N biogeochemical cycles processes in soils. Among these, amidase, aspartase, urease, L-asparaginase, and L-glutaminase are the most important. They are primarily of microbial origins but may also originate from plant and animal residues.  Their significance is highlighted in Tabatabai et al. (2010) published article: “Significance of enzyme activities in soil nitrogen mineralization”. They hydrolyze native or organic N substrates added to soils and produce NH4 (Senwo and Tabatabai, 1998). Relationships among these enzymes are important given their significant roles in N biogeochemical cycles in nature. They act on C-N bonds other than peptide bonds in linear amides releasing NH4, but they are specific in that each enzyme catalyzes a specific reaction. They will contribute to increased levels of soil NH4 and NO3 in soils, environment, and water. Native soil proteins or amino acids are substrates for these enzymes in microenvironments.


The contributions of N cycling to soil health cannot be undermined and should be considered a major contributing parameter towards a national and global soil health monitoring and assessment programs in supporting and enhancing the long-term use of valuable soil resources for agricultural productivity and food security.

Soil is an essential resource and a significant component of the natural environment that not only produce most of our global food, but provide living habitats for humans, plants and animals, and in addition support such ecosystem services as regulating water and climate, mitigating greenhouse gases, sequestering plant nutrients, conserving biodiversity, and cultural services.


Dick, R. 2018. Soil Health: The Theory of Everything (Terrestrial) or Just Another Buzzword? Crops, Soils, Agronomy (CSA) news. https://doi.org/10.2134/csa2018.63.1114

Doran, JW., DC Coleman, DF Bezdicek, BA Stewart. 1994. Defining Soil Quality for a Sustainable Environment. Book Series. SSSA

Special Publication, vol. 35.

Roberts, P., DL Jones. 2012. Microbial and plant uptake of free amino sugars in grassland soils. Soil Biology & Biochemistry. 49:139-149.

Schimel, JP., J Bennett. 2004. Nitrogen mineralization: Challenges of a changing paradigm. Ecology. 85:591-602.

Senwo, ZN., MA Tabatabai. 1998. Amino acid composition of soil organic matter. Biology Fertility of Soils. 26:235-242.

Tabatabai, MA., M Ekenler, ZN Senwo. 2010. Significance of enzyme activities in soil nitrogen mineralization. Communications in Soil Science and Plant Analysis. 41:595-605.



This paper is a contribution from the Winfred Thomas Agricultural Research Station, Alabama A & M University and supported by USDA – National Institute of Food and Agriculture. Trade or manufacturers’ names mentioned are for information purposes only and do not constitute endorsement, recommendation, or exclusion by either Alabama A&M University or USDA – National Institute of Food and Agriculture.


Please note: This is a commercial profile

Contributor Profile

Fulbright Scholar & Professor of Soil Microbial Biochemistry, Environmental Science & Toxicology
Department of Biological & Environmental Sciences, College of Agricultural, Life & Natural Sciences Alabama A&M University
Phone: +1 256 372 4216
Website: Visit Website


Please enter your comment!
Please enter your name here