Long-Term Tillage and Crop Rotation Regimes Reshape Soil-Borne Oomycete Communities in Soybean, Corn, and Wheat Production Systems.

Soil-borne oomycetes include devastating plant pathogens that cause substantial losses in the agricultural sector. To better manage this important group of pathogens, it is critical to understand how they respond to common agricultural practices, such as tillage and crop rotation. Here, a long-term field experiment was established using a split-plot design with tillage as the main plot factor (conventional tillage (CT) vs. no till (NT), two levels) and rotation as the subplot factor (monocultures of soybean, corn, or wheat, and corn-soybean-wheat rotation, four levels). Post-harvest soil oomycete communities were characterized over three consecutive years (2016-2018) by metabarcoding the Internal Transcribed Spacer 1 (ITS1) region. The community contained 292 amplicon sequence variants (ASVs) and was dominated by Globisporangium spp. (85.1% in abundance, 203 ASV) and Pythium spp. (10.4%, 51 ASV). NT decreased diversity and community compositional structure heterogeneity, while crop rotation only affected the community structure under CT. The interaction effects of tillage and rotation on most oomycetes species accentuated the complexity of managing these pathogens. Soil and crop health represented by soybean seedling vitality was lowest in soils under CT cultivating soybean or corn, while the grain yield of the three crops responded differently to tillage and crop rotation regimes.

Subarctic soil carbon losses after deforestation for agriculture depend on permafrost abundance.

The northern circumpolar permafrost region is experiencing considerable warming due to climate change, which is allowing agricultural production to expand into regions of discontinuous and continuous permafrost. The conversion of forests to arable land might further enhance permafrost thaw and affect soil organic carbon (SOC) that had previously been protected by frozen ground. The interactive effect of permafrost abundance and deforestation on SOC stocks has hardly been studied. In this study, soils were sampled on 18 farms across the Yukon on permafrost and non-permafrost soils to quantify the impact of land-use change from forest to cropland and grassland on SOC stocks. Furthermore, the soils were physically and chemically fractionated to assess the impact of land-use change on different functional pools of SOC. On average, permafrost-affected forest soils lost 15.6 ± 21.3% of SOC when converted to cropland and 23.0 ± 13.0% when converted to grassland. No permafrost was detected in the deforested soils, indicating that land-use change strongly enhanced warming and subsequent thawing. In contrast, the change in SOC at sites without permafrost was not significant but had a slight tendency to be positive. SOC stocks were generally lower at sites without permafrost under forest. Furthermore, land-use change increased mineral-associated SOC, while the fate of particulate organic matter (POM) after land-use change depended on permafrost occurrence. Permafrost soils showed significant POM losses after land-use change, while grassland sites without permafrost gained POM in the topsoil. The results showed that the fate of SOC after land-use change greatly depended on the abundance of permafrost in the pristine forest, which was driven by climatic conditions more than by soil properties. It can be concluded that in regions of discontinuous permafrost in particular, initial conditions in forest soils should be considered before deforestation to minimize its climate impact.

Extraction methods for untargeted metabolomics influence enzymatic activity in diverse soils.

Soil organic matter (SOM) is the largest carbon pool in terrestrial ecosystems and underpins the health and productivity of soil. Accurate characterization of its chemical composition will improve our understanding of biotic and abiotic processes regulating its stabilization. Our purpose in this study was to estimate the loss of SOM by microbial and exoenzymatic activity that might occur when soil is extracted for analysis of representative low molecular weight mass features using untargeted metabolomics. Two mined clays (kaolinite, montmorillonite) and three diverse soils (varying in texture, specific surface area and cation exchange capacity) were used to assess the extraction efficiency and loss of three enzymatic activity indicators (2,6-dichloroindophenol sodium salt hydrate [DCIP], 4-methylumbelliferyl phosphate [MUBph] and 3,4-dihydroxy-L-phenylalanine [LDOPA]) during extraction with two different solvents (water and methanol). Losses of the indicators were attributed to extraction method (ultrasonication, shaking, or shaking following chloroform fumigation), physical properties associated with the soil/clay type, and microbial activity. Soil/clay type strongly influenced indicator recovery and hence, SOM recovery. Choice of extraction method strongly influenced the composition and recovery of representative SOM mass features, while the choice of solvent determined whether the soil type or extraction method had a greater influence of compositional differences in the SOM mass features extracted. Extraction following chloroform fumigation had the greatest loss of the indicators, due to enzymatic activity and/or adsorption onto the soil matrix. Minimal variation in composition and loss of SOM mass features occurred during extraction by shaking for the soils tested; we therefore recommend it as the method of choice for untargeted SOM extraction studies.

Long-term geothermal warming reduced stocks of carbon but not nitrogen in a subarctic forest soil.

Global warming is accelerating the decomposition of soil organic matter (SOM). When predicting the net SOM dynamics in response to warming, there are considerable uncertainties owing to experimental limitations. Long-term in situ whole-profile soil warming studies are particularly rare. This study used a long-term, naturally occurring geothermal gradient in Yukon, Canada, to investigate the warming effects on SOM in a forest ecosystem. Soils were sampled along this thermosequence which exhibited warming of up to 7.7℃; samples were collected to a depth of 80 cm and analysed for soil organic carbon (SOC) and nitrogen (N) content, and estimates made of SOC stock and fractions. Potential litter decomposition rates as a function of soil temperature and depth were observed for a 1-year period using buried teabags and temperature loggers. The SOC in the topsoil (0-20 cm) and subsoil (20-80 cm) responded similar to warming. A negative relationship was found between soil temperature and whole-profile SOC stocks, with a total loss of 27% between the warmest and reference plots, and a relative loss of 3%℃-1 . SOC losses were restricted to the particulate organic matter (POM) and dissolved organic carbon (DOC) fractions with net whole-profile depletions. Losses in POM-C accounted for the largest share of the total SOC losses. In contrast to SOC, N was not lost from the soil as a result of warming, but was redistributed with a relatively large accumulation in the silt and clay fraction (+40%). This suggests an immobilization of N by microbes building up in mineral-associated organic matter. These results confirm that soil warming accelerates SOC turnover throughout the profile and C is lost in both the topsoil and subsoil. Since N stocks remained constant with warming, SOM stoichiometry changed considerably and this in turn could affect C cycling through changes in microbial metabolism.

Effect of bentonite as a soil amendment on field water-holding capacity, and millet photosynthesis and grain quality.

A field experiment was conducted in a semi-arid region in northern China to evaluate the effects of bentonite soil amendment on field water-holding capacity, plant available water, and crop photosynthesis and grain quality parameters for millet [Setaria italic (L.) Beauv.] production over a 5-year period. Treatments included six rates of bentonite amendments (0, 6, 12, 18, 24 and 30 Mg ha-1) applied only once in 2011. The application of bentonite significantly (P < 0.05) increased field water-holding capacity and plant available water in the 0-40 cm layer. Bentonite also significantly (P < 0.05) increased the emergence rate, above-ground dry matter accumulation (AGDM), net photosynthesis rate (Pr), transpiration rate (Tr), soil and plant analysis development (SPAD) and leaf water use efficiency (WUE). It also increased grain quality parameters including grain protein, fat and fiber content. Averaged over all the years, the optimum rate of bentonite was 24 Mg ha-1 for all plant growth and photosynthesis parameters except for grain quality where 18 Mg ha-1 bentonite had the greatest effect. This study suggests that bentonite application in semi-arid regions would have beneficial effects on crop growth and soil water-holding properties.

Litter decay controlled by temperature, not soil properties, affecting future soil carbon.

Widespread global changes, including rising atmospheric CO2 concentrations, climate warming and loss of biodiversity, are predicted for this century; all of these will affect terrestrial ecosystem processes like plant litter decomposition. Conversely, increased plant litter decomposition can have potential carbon-cycle feedbacks on atmospheric CO2 levels, climate warming and biodiversity. But predicting litter decomposition is difficult because of many interacting factors related to the chemical, physical and biological properties of soil, as well as to climate and agricultural management practices. We applied 13 C-labelled plant litter to soil at ten sites spanning a 3500-km transect across the agricultural regions of Canada and measured its decomposition over five years. Despite large differences in soil type and climatic conditions, we found that the kinetics of litter decomposition were similar once the effect of temperature had been removed, indicating no measurable effect of soil properties. A two-pool exponential decay model expressing undecomposed carbon simply as a function of thermal time accurately described kinetics of decomposition. (R2  = 0.94; RMSE = 0.0508). Soil properties such as texture, cation exchange capacity, pH and moisture, although very different among sites, had minimal discernible influence on decomposition kinetics. Using this kinetic model under different climate change scenarios, we projected that the time required to decompose 50% of the litter (i.e. the labile fractions) would be reduced by 1-4 months, whereas time required to decompose 90% of the litter (including recalcitrant fractions) would be reduced by 1 year in cooler sites to as much as 2 years in warmer sites. These findings confirm quantitatively the sensitivity of litter decomposition to temperature increases and demonstrate how climate change may constrain future soil carbon storage, an effect apparently not influenced by soil properties.

Determining the environmental fate of a filamentous fungus, Trichoderma reesei, in laboratory-contained intact soil-core microcosms using competitive PCR and viability plating.

Trichoderma spp. are used extensively in industry and are routinely disposed of in landfill sites as spent biomass from fermentation plants. However, little is known regarding the environmental fate of this biomass. We tracked the survival of T. reesei strain QM6A#4 (a derivative of strain QM6A marked with a recombinant construct) over a 6-month period in laboratory-contained, intact soil-core microcosms incubated in a growth chamber. Survival was tested in 3 different soils and the effect of a plant rhizosphere (bush lima beans, Phaseolus limensis) was investigated. Levels and viability of the fungus were determined, respectively, by quantitative competitive polymerase chain reaction analysis of total soil DNA extracts and dilution-plating of soil on a semiselective growth medium. Whereas chemically killed QM6A#4 became undetectable within 3 d, QM6A#4 added as a live inoculum decreased approximately 4- to approximately 160-fold over the first 1-3 months and then reached a steady state. After 4 months, soil cores were subjected to a 1.5-month simulated winter period, which did not significantly affect QM6A#4 levels. Throughout the experiment, QM6A#4 remained viable. These results indicate that, following release into the environment, live T. reesei will persist in soil for at least 2 seasons.