Microbial Signatures in Fertile Soils Under Long-Term N Management

Long-term reliance on inorganic N to maintain and increase crop yields in overly simplified cropping systems in the U.S. Midwest region has led to soil acidification, potentially damaging biological N2 fixation and accelerating potential nitrification activities. Building on this published work, rRNA gene-based analysis via Illumina technology with QIIME 2.0 processing was used to characterize the changes in microbial communities associated with such responses. Amplicon sequence variants (ASVs) for each archaeal, bacterial, and fungal taxa were classified using the Ribosomal Database Project (RDP). Our goal was to identify bioindicators from microbes responsive to crop rotation and N fertilization rates following 34–35 years since the initiation of experiments. Research plots were established in 1981 with treatments of rotation [continuous corn (Zea mays L.) (CCC) and both the corn (Cs) and soybean (Glycine max L. Merr.) (Sc) phases of a corn-soybean rotation], and of N fertilization rates (0, 202, and 269 kg N/ha) arranged as a split-plot in a randomized complete block design with three replications. We identified a set of three archaea, and six fungal genera responding mainly to rotation; a set of three bacteria genera whose abundances were linked to N rates; and a set with the highest number of indicator genera from both bacteria (22) and fungal (12) taxa responded to N fertilizer additions only within the CCC system. Indicators associated with the N cycle were identified from each archaeal, bacterial, and fungal taxon, with a dominance of denitrifier- over nitrifier- groups. These were represented by a nitrifier archaeon Nitrososphaera, and Woesearchaeota AR15, an anaerobic denitrifier. These archaea were identified as part of the signature for CCC environments, decreasing in abundance with rotated management. The opposite response was recorded for the fungus Plectosphaerella, a potential N2O producer, less abundant under continuous corn. N fertilization in CCC or CS systems decreased the abundance of the bacteria genera Variovorax and Steroidobacter, whereas Gp22 and Nitrosospira only showed this response under CCC. In this latter system, N fertilization resulted in increased abundances of the bacterial denitrifiers Gp1, Denitratisoma, Dokdonella, and Thermomonas, along with the fungus Hypocrea, a known N2O producer. The identified signatures could help future monitoring and comparison across cropping systems as we move toward more sustainable management practices. At the same time, this is needed primary information to understand the potential for managing the soil community composition to reduce nutrient losses to the environment.

Biochar Stability in a Highly Weathered Sandy Soil under Four Years of Continuous Corn Production

Biochar is being considered a climate change mitigation tool by increasing soil organic carbon contents (SOC), however, questions remain concerning its longevity in soil. We applied 30,000 kg ha−1 of biochars to plots containing a Goldsboro sandy loam (Fine-loamy, siliceous, sub-active, thermic Aquic Paleudults) and then physically disked all plots. Thereafter, the plots were agronomically managed under 4 years (Y) of continuous corn (Zea Mays, L.) planting. Annually, incremental soil along with corresponding bulk density samples were collected and SOC concentrations were measured in topsoil (down to 23-cm). The biochars were produced from Lodgepole pine (Pinus contorta) chip (PC) and Poultry litter (PL) feedstocks. An untreated Goldsboro soil (0 biochar) served as a control. After four years, SOC contents in the biochar treated plots were highest in the top 0–5 and 5–10 cm depth suggesting minimal deeper movement. Declines in SOC contents varied with depth and biochar type. After correction for SOC declines in controls, PL biochar treated soil had a similar decline in SOC (7.9 to 10.3%) contents. In contrast, the largest % SOC content decline (20.2%) occurred in 0–5 cm deep topsoil treated with PC biochar. Our results suggest that PC biochar had less stability in the Goldsboro soil than PL biochar after 4 years of corn grain production.

Soil Greenhouse Gas Responses to Biomass Removal in the Annual and Perennial Cropping Phases of an Integrated Crop Livestock System

Diversifying agronomic production systems by combining crops and livestock (i.e., Integrated Crop Livestock systems; ICL) may help mitigate the environmental impacts of intensive single-commodity production. In addition, harvesting row-crop residues and/or perennial biomass could increase the multi-functionality of ICL systems as a potential source for second-generation bioenergy feedstock. Here, we evaluated non-CO2 soil greenhouse gas (GHG) emissions from both row-crop and perennial grass phases of a field-scale model ICL system established on marginally productive, poorly drained cropland in the western US Corn Belt. Soil emissions of nitrous oxide (N2O) and methane (CH4) were measured during the 2017–2019 growing seasons under continuous corn (Zea mays L.) and perennial grass treatments consisting of a common pasture species, ‘Newell’ smooth bromegrass (Bromus inermis L.), and two cultivars of switchgrass (Panicum virgatum L.), ‘Liberty’ and ‘Shawnee.’ In the continuous corn system, we evaluated the impact of stover removal by mechanical baling vs. livestock grazing for systems with and without winter cover crop, triticale (x Triticosecale neoblaringhemii A. Camus; hexaploid AABBRR). In perennial grasslands, we evaluated the effect of livestock grazing vs. no grazing. We found that (1) soil N2O emissions are generally higher in continuous corn systems than perennial grasslands due to synthetic N fertilizer use; (2) winter cover crop use had no effect on total soil GHG emissions regardless of stover management treatment; (3) stover baling decreased total soil GHG emissions, though grazing stover significantly increased emissions in one year; (4) grazing perennial grasslands tended to increase GHG emissions in pastures selected for forage quality, but were highly variable from year to year; (5) ICL systems that incorporate perennial grasses will provide the most effective GHG mitigation outcomes.

No Tillage Improved Soil Pore Space Indices under Cover Crop and Crop Rotation

Assessment of the effects of crop management practices on soil physical properties is largely limited to soil moisture content, air content or bulk density, which can take considerable time to change. However, soil pore space indices evolve rapidly and could quickly detect changes in soil properties resulting from crop management practices, but they are not often measured. The objective of this study was to investigate how soil pore space indices—relative gas diffusion coefficient (Ds/Do) and pore tortuosity factor (τ)—are affected by tillage system (TL), cover crop (CC) and crop rotation (CR). A study was conducted on silt loam soil at Freeman farm, Lincoln University of Missouri during the 2011 to 2013 growing seasons. The experiment design was a randomized complete block with two tillage systems (no tillage or no-till vs conventional tillage), two cover crops (no rye vs cereal rye (Secale cereale L.)) and four crop rotations (continuous corn (Zea mays L.), continuous soybean (Glycine max L.), corn–soybean and soybean–corn successions). All the treatments were replicated three times for a total of 48 experimental units. Soils were collected from two sampling depths (SD), 0–10 and 10–20 cm, in each treatment and soil physical properties, including bulk density (BD), air-filled porosity (AFP, fa) and total pore space (TPS, Φ), were calculated. Gas diffusivity models following AFP and/or TPS were used to predict Ds/Do and τ values. Results showed that, overall, Ds/Do was significantly increased in no-tilled plots planted to cereal rye in 2012 (p = 0.001) and in 2013 (p = 0.05). No-tilled continuous corn, followed by continuous soybean and no-tilled soybean–corn rotations had the highest Ds/Do values, respectively. In magnitude, Ds/Do was also increased in no-till plots at the lower depth (10–20 cm). No-tilled plots planted with cereal rye significantly reduced τ in 2012 (p = 0.001) and in 2013 (p = 0.05). Finally, at the upper depth (0–10 cm), the no-tilled corn–soybean rotation and the tilled soybean–corn rotation had the lowest τ. However, at the lower depth (10–20 cm), the four crop rotations were not significantly different in their τ values. These results can be useful to quickly assess the changes in soil physical properties because of crop management practices and make necessary changes to enhance agricultural resilience.

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Soil properties after 36 years of N fertilization under continuous corn and corn-soybean management

Modern agricultural systems rely on inorganic nitrogen (N) fertilization to enhance crop yields, but its overuse may negatively affect soil properties. Our objective was to investigate the effect of long-term N fertilization on key soil properties under continuous corn [Zea mays L.] (CCC) and both the corn (Cs) and soybean [Glycine max L. Merr.] (Sc) phases of a corn-soybean rotation. Research plots were established in 1981 with treatments arranged as a split-plot design in a randomized complete block design with three replications. The main plot was crop rotation (CCC, Cs, and Sc), and the subplots were N fertilizer rates of 0 kg N ha−1 (N0, controls), and 202 kg N ha−1, and 269 kg N ha−1 (N202, and N269, respectively). After 36 years and within the CCC, the yearly addition of N269 compared to unfertilized controls significantly increased cation exchange capacity (CEC, 65 % higher under N269) and acidified the top 15 cm of the soil (pH 4.8 vs. pH 6.5). Soil organic matter (SOM) and total carbon stocks (TCs) were not affected by treatments, yet water aggregate stability (WAS) decreased by 6.7 % within the soybean phase of the CS rotation compared to CCC. Soil bulk density (BD) decreased with increased fertilization by 5 % from N0 to N269. Although ammonium (NH4+) did not differ by treatments, nitrate (NO3−) increased eight-fold with N269 compared to N0, implying increased nitrification. Soils of unfertilized controls under CCC have over twice the available phosphorus level (P) and 40 % more potassium (K) than the soils of fertilized plots (N202 and N269). On average, corn yields increased 60 % with N fertilization compared to N0. Likewise, under N0, rotated corn yielded 45 % more than CCC; the addition of N (N202 and N269) decreased the crop rotation benefit to 17 %. Our results indicated that due to the increased level of corn residues returned to the soil in fertilized systems, long-term N fertilization improved WAS and BD, yet not SOM, at the cost of significant soil acidification and greater risk of N leaching and increased nitrous oxide emissions.

Rotation and Fertilization Effects on Soil Quality and Yields in a Long Term Field Experiment

Understanding the complex relationships among soil quality, crop productivity, and management practices would help to develop more sustainable agricultural production systems. In this study, we investigated the combined effects of crop rotations and fertilization treatments on soil quality and crop yield in a long term (about 50 years) field experiment. Crop rotations included continuous corn (Zea mays L.), a 2 year corn-wheat (Triticum aestivum L.) rotation, and a 9 year corn-wheat-corn-wheat-corn-wheat-alfalfa-alfalfa-alfalfa (Medicago sativa L.) rotation. Fertilization treatments included control, mineral fertilization with urea and triple superphosphate, and amendment with cattle manure. Crop rotations and fertilization treatments were combined in a factorial experimental design with two replications for each rotation and six replications for each fertilization treatment. The continuous corn and the corn-wheat rotations had negative effects on the main soil quality indicators considered (carbon (C) and nitrogen (N) pools, microbial biomass and activity). On the contrary, the 9 year rotation had positive effects on soil organic carbon (+24%) and total nitrogen (+23%) but resulted in impoverished available P (−5%). Positive effects on soil microbial biomass (+37% of microbial biomass C and +23% of microbial biomass N) and activity (+19%) were also observed. Soil amendment with manure built up soil organic carbon (+13%), increased nutrient content (+31% of extractable C and +19% of extractable N), including that of available P (+47%), and stimulated microbial growth (+34%) and activity (+8%). As compared to manure, mineral fertilization increased the soil nutrient content to a lesser extent. This study showed that the combined use of rotations, including legume forage crops, and soil amendment with manure may help preserve soil quality and crop productivity in the long term.