Methodological considerations for redesigning sustainable cropping systems: the value of data-mining large and detailed farm data sets at the cropping system level

Redesigning cropping and farming systems to enhance their sustainability is mainly addressed in scientific studies using experimental and modeling approaches. Large data sets collected from real farms allow for the development of innovative methods to produce generic knowledge. Data mining methods allow for the diversity of systems to be considered holistically and can take into account the diversity of production contexts to produce site-specific results. Based on the very few known studies using such methods to analyze the crop management strategies affecting pesticide use and their effect on farm performance, we advocate further investment in the development of large data sets that can support future research programs on farming system design.     

How does pasture size alter plant–herbivore interactions among grazing cattle?

Grassland management impacts ecosystem functioning and is critical for livestock production and biodiversity conservation. Decreasing the stocking rate usually benefits biodiversity but also decreases production per unit area. Here, we assessed the combined effects of cattle herd and pasture size on sward structure, diet quality and daily grazing time while maintaining a constant stocking rate. The experiment was conducted over four successive years in two blocks of a species-rich upland grassland that was continuously grazed for 5 months between May and October. Each block consisted of one 3-ha pasture that was grazed by a group of three heifers, one 9-ha pasture grazed by nine heifers, and one 27-ha pasture grazed by 27 heifers. The grazed patches were discriminated using a mathematical model that for each point gave a probability of being grazed based on sward height and spatial dependence. Heifers created fewer patches and had less control over sward height in the smallest (3-ha) plots, while no difference was found between the 9- and 27-ha plots. The small heifer groups also had the shortest daily grazing time. These observations point out a risk that animal impacts on sward structure could be partly missed in grazing experiments conducted with very small groups. Estimated diet quality was unaffected by pasture size. Patch stability was frequent between two successive years but we observed a decrease in interannual patch stability as time intervals increase. Such observations are useful for calibrating spatial interaction models combining foraging behaviour and vegetation dynamics rules and enhance their predictive ability.     

Characterizing the Feeding Injury Caused by Phylloscelis rubra (Hemiptera: Dictyopharidae) to Cranberries

Due to changes in pest management practices, farmers’ reports of severe feeding injury to cranberries, Vaccinium macrocarpon Aiton Ericales: Ericaceae, caused by the cranberry toad-bug, Phylloscelis rubra Ball, have increased in recent years in New Jersey (United States). Currently, however, limited information is available on the effects of P. rubra feeding or density of individuals needed to cause injury to cranberry vines and fruit. In 2015‒2017, we conducted studies to characterize injury to cranberry at a range of P. rubra densities by using cages in a screen-house and field, to establish a correlation between P. rubra density and crop injury in an open field experiment, and to measure the effects of P. rubra injury on the nutritional content (i.e., amounts of macro- and microelements) of cranberry vines. Phylloscelis rubra feeding on cranberry vines produced typical injury symptoms at relatively low densities (i.e., 2 individuals per vine in field cages or <10 individuals per sweep net sample in open fields), which included discolored (yellowish or reddish) or dead (brown) vines. This vine injury could lead to reductions in fruit mass and total fruit number. However, P. rubra injury to cranberry vines did not alter their nutritional composition. In general, this study highlights the ability of P. rubra to cause substantial injury to cranberry vines even when population densities were relatively low, which could result in declines in fruit production (quality and quantity). Therefore, infestations by P. rubra in cranberries must be considered when making pest management decisions in regions where this insect is present.     

Ephemeral-habitat colonization and neotropical species richness of <Emphasis Type="Italic">Caenorhabditis</Emphasis> nematodes

Background

The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar external morphology despite deep genomic divergence.

Methods

To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe. This effort provides the first in-depth quantitative analysis of substrate specificity for Caenorhabditis in natural, unperturbed habitats.

Results

We amassed a total of 626 strain isolates from nine species of Caenorhabditis among 2865 substrate samples. With the two new species described here (C. astrocarya and C. dolens), we estimate that our sampling procedures will discover few additional species of these microbivorous animals in this tropical rainforest system. We demonstrate experimentally that the two most prevalent species (C. nouraguensis and C. tropicalis) rapidly colonize fresh resource patches, whereas at least one rarer species shows specialist micro-habitat fidelity.

Conclusion

Despite the potential to colonize rapidly, these ephemeral patchy resources of rotting fruits and flowers are likely to often remain uncolonized by Caenorhabditis prior to their complete decay, implying dispersal-limited resource exploitation. We hypothesize that a combination of rapid colonization, high ephemerality of resource patches, and species heterogeneity in degree of specialization on micro-habitats and life histories enables a dynamic co-existence of so many morphologically cryptic species of Caenorhabditis.

     

Multi-feature machine learning model for automatic segmentation of green fractional vegetation cover for high-throughput field phenotyping

Background

Accurately segmenting vegetation from the background within digital images is both a fundamental and a challenging task in phenotyping. The performance of traditional methods is satisfactory in homogeneous environments, however, performance decreases when applied to images acquired in dynamic field environments.

Results

In this paper, a multi-feature learning method is proposed to quantify vegetation growth in outdoor field conditions. The introduced technique is compared with the state-of the-art and other learning methods on digital images. All methods are compared and evaluated with different environmental conditions and the following criteria: (1) comparison with ground-truth images, (2) variation along a day with changes in ambient illumination, (3) comparison with manual measurements and (4) an estimation of performance along the full life cycle of a wheat canopy.

Conclusion

The method described is capable of coping with the environmental challenges faced in field conditions, with high levels of adaptiveness and without the need for adjusting a threshold for each digital image. The proposed method is also an ideal candidate to process a time series of phenotypic information throughout the crop growth acquired in the field. Moreover, the introduced method has an advantage that it is not limited to growth measurements only but can be applied on other applications such as identifying weeds, diseases, stress, etc.

     

Evaluation of the Dualex for the Assessment of Corn Nitrogen Status

The Dualex is a new leaf-clip instrument that can be used to monitor corn nitrogen (N) status. It is based on the measurement of polyphenolics (Phen), which are secondary metabolites affected by stress factors. The purpose of this study was to compare Dualex to SPAD (chlorophyll meter), the latter having been used for several years in monitoring crop N status. As well, the interest of combining Dualex and SPAD information in Chl/DUAD (ratio of SPAD to Dualex reading on adaxial side), Chl/DUAB (ratio of SPAD to Dualex reading on abaxial side), and Chl/Phen (ratio of SPAD to the sum of DUAD and DUAB) ratios were considered. Significantly positive and negative correlations with corn leaf N concentration were found for SPAD and Dualex, respectively. Successful N status diagnosis could be achieved with either Dualex or SPAD for corn within 21 days after topdressing while the Dualex lost sensitivity at later stages. Dualex measurements could be limited to leaves abaxial side or adaxial side, instead of adaxial + abaxial sides, with no inconvenience. Among all parameters considered, the combined ratios with SPAD (Chl) and Dualex readings, Chl/DUAD, Chl/DUAB, and Chl/Phen were strongly related to applied N dose at all samplings dates, and found the most sensitive and robust through the season.     

Snow cover and soil moisture controls of freeze–thaw-related soil gas fluxes from a typical semi-arid grassland soil: a laboratory experiment

In situ field measurements as well as targeted laboratory studies have shown that freeze–thaw cycles (FTCs) affect soil trace gas fluxes. However, most of past laboratory studies adjusted soil moisture before soil freezing, thereby neglecting that snow cover or water from melting snow may modify effects of FTCs on soil trace gas fluxes. In the present laboratory study with a typical semi-arid grassland soil, three different soil moisture levels (32 %, 41 %, and 50 % WFPS) were established (a) prior to soil freezing or (b) by adding fresh snow to the soil surface after freezing to simulate field conditions and the effect of the melting snow on CO₂, CH₄, and N₂O fluxes during FTCs more realistically. Our results showed that adjusting soil moisture by watering before soil freezing resulted in significantly different cumulative fluxes of CH₄, CO₂, and N₂O throughout three FTCs as compared to the snow cover treatment, especially at a relatively high soil moisture level of 50 % WFPS. An increase of N₂O emissions was observed during thawing for both treatments. However, in the watering treatment, this increase was highest in the first thawing cycle and decreased in successive cycles, while in the snow cover treatment, a repetition of the FTCs resulted in a further increase of N₂O emissions. These differences might be partly due to the different soil water dynamics during FTCs in the two treatments. CO₂ emissions were a function of soil moisture, with emissions being largest at 50 % WFPS and smallest at 32 % WFPS. The largest N₂O emissions were observed at WFPS values around 50 %, whereas there were only small or negligible N₂O emissions from soil with relatively low soil water content, which indicates that a threshold value of soil moisture might exist that triggers N₂O peaks during thawing.     

Effect of Exogenous Lipase on Dough Lipids During Mixing of Wheat Flours

In control dough, endogenous wheat lipase was inactive, because the triacylglycerol (TAG), 1,2-diacylglycerol (DAG_1,2), and 1,3-diacylglycerol (DAG_1,3) fractions of nonpolar lipids were not affected by mixing. Conversely, the free fatty acid (FFA) and monoacylglycerol (MAG) fractions decreased, mainly due to the oxidation of polyunsaturated fatty acids (PUFA) catalyzed by wheat lipoxygenase. Addition of exogenous lipase to flour (15 lipase units [LU] per gram of dry matter) resulted in substantial modification of nonpolar lipids during dough mixing. Due to the 1,3 specificity of the lipase used in this experiment, the TAG and DAG_1,3 fractions decreased, whereas the MAG and FFA fractions increased. The DAG_1,2 fraction increased at the beginning of mixing and decreased after 40 min of mixing. Moreover, part of the PUFA released by lipase activity was oxidized by wheat lipoxygenase, resulting in major losses of PUFA. Conversely, the net content of the saturated and monounsaturated fatty acids (SMUFA) remained constant, because the free SMUFA content increased primarily at the expense of the esterified forms. For a constant mixing time of 20 min, increasing the amount of lipase added to dough (from 2.5 to 25 LU/g of dry matter) resulted in a linear decrease in the TAG fraction and a linear increase in the SMUFA content in the FFA fraction. At the same time, the PUFA content of the FFA fraction increased only for additions of lipase to flour of >5 LU/g of dry matter, due to partial oxidation by wheat lipoxygenase.     

Effects of Mixing Conditions and Wheat Flour Dough Composition on Lipid Hydrolysis and Oxidation Levels in the Presence of Exogenous Lipase

The lipid profiles of wheat flour doughs containing exogenous lipase were studied under different mixing conditions using a microscale mixer. An experimental design comparing the effects of dough water content (52–68%), the speed of mixing (50–100 rpm), and the mixer temperature (18–32°C) showed that the hydrolysis levels were positively influenced by temperature and speed of mixing and negatively influenced by water content. The positive effect of temperature was enhanced both by highspeed mixing and low water content. The lipid oxidation levels were positively influenced by the speed of mixing and negatively influenced by the water content. The positive effect of temperature on the oxidation levels was less important. A series of experiments conducted with different types of industrial and semi-industrial mixers with equal concentrations of lipase added to the dough showed large differences among the rates of lipid hydrolysis and oxidation. However, the mixing conditions proposed by bakers to obtain doughs with similar handling properties led to similar dough lipid profiles. Sodium chloride did not change the lipid profile when added to dough. Conversely, calcium chloride promoted a large increase of lipid hydrolysis and oxidation due to its activation of lipase activity. Addition of yeast increased the lipid hydrolysis and slightly decreased lipid oxidation.     

Assessing connectivity patterns among management units of the Newfoundland and Labrador shrimp population

The Eastern Canadian northern shrimp population, representing one of the most important fisheries in the region, decreased dramatically since the mid‐2000s to a historical low in 2017, but changes were not spatially uniform. Applying a biophysical model within Newfoundland and Labrador (NL) management areas, we investigated connectivity processes during the long pelagic larval phase (2–3 months) of Pandalus borealis and key drivers of larval dispersal in different environmental conditions. We selected 3 years representative of contrasting North Atlantic Oscillation (NAO) phases to assess potential larval dispersal patterns of the northern shrimp population in NL, and hierarchically assessed the impact of the timing of release (yearly and daily), release location, and vertical migration behaviour on shrimp larval dispersal. Overall, we found that populations located on the northern Newfoundland and Labrador shelf supplied potential settlers to southern populations because of the dominant Labrador Current. Ocean circulation and current velocities during the NAO positive year differed from other years, generating contrasting settlement spatial patterns. Larval release location and vertical migration behaviour were the two most important influences on the strength of larval supply and settlement patterns. Inclusion of diel and ontogenic swimming behaviour increased settlement success of larvae released from inshore areas, regardless of study years. Our study improves understanding of northern shrimp stock‐recruitment relationships, their sensitivity to changing environmental conditions, and spatially non‐homogeneous population decline for bentho‐pelagic species with a long larval phase, which could potentially help improve management strategies.