The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification.

Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.

Early-season plant cover supports more effective pest control than insecticide applications.

Growing evidence suggests that conservation agricultural practices, like no-till and cover crops, help protect annual crops from insect pests by supporting populations of resident arthropod predators. While adoption of conservation practices is growing, most field crop producers are also using more insecticides, including neonicotinoid seed coatings, as insurance against early-season insect pests. This tactic may disrupt benefits associated with conservation practices by reducing arthropods that contribute to biological control. We investigated the interaction between preventive pest management (PPM) and the conservation practice of cover cropping. We also investigated an alternative pest management approach, integrated pest management (IPM), which responds to insect pest risk, rather than using insecticides prophylactically. In a 3-year corn (Zea mays mays L.)-soy (Glycine max L.) rotation, we measured the response of invertebrate pests and predators to PPM and IPM with and without a cover crop. Using any insecticide provided some small reduction to plant damage in soy, but no yield benefit. In corn, vegetative cover early in the season was key to reducing pest density and damage, likely by increasing the abundance of arthropod predators. Further, PPM in year 1 decreased predation compared to a no-pest-management control. Contrary to our expectation, the IPM strategy, which required just one insecticide application, was more disruptive to the predator community than PPM, likely because the applied pyrethroid was more acutely toxic to a wider range of arthropods than neonicotinoids. Promoting early-season cover was more effective at reducing pest density and damage than either intervention-based strategy. Our results suggest that the best pest management outcomes may occur when biological control is encouraged by planting cover crops and avoiding broad-spectrum insecticides as much as possible. As part of a conservation-based approach to farming, cover crops can promote natural-enemy populations that can help provide biological effective control of insect pest populations.

Small-Grain Cover Crops Have Limited Effect on Neonicotinoid Contamination from Seed Coatings.

Neonicotinoids from insecticidal seed coatings can contaminate soil in treated fields and adjacent areas, posing a potential risk to nontarget organisms and ecological function. To determine if cover crops can mitigate neonicotinoid contamination in treated and adjacent areas, we measured neonicotinoid concentrations for three years in no-till corn-soybean rotations, planted with or without neonicotinoid seed coatings, and with or without small grain cover crops. Although neonicotinoids were detected in cover crops, high early season dissipation provided little opportunity for winter-planted cover crops to absorb significant neonicotinoid residues; small grain cover crops failed to mitigated neonicotinoid contamination in either treated or untreated plots. As the majority of neonicotinoids from seed coatings dissipated shortly after planting, residues did not accumulate in soil, but persisted at concentrations below 5 ppb. Persistent residues could be attributed to historic neonicotinoid use and recent, nearby neonicotinoid use. Tracking neonicotinoid concentrations over time revealed a large amount of local interplot movement of neonicotinoids; in untreated plots, contamination was higher when plots were less isolated from treated plots.

Insights into How Spinosad Seed Treatment Protects Onion From Onion Maggot (Diptera: Anthomyiidae).

Onion maggot, Delia antiqua (Meigen), is a serious pest of onion Allium cepa L. in northern temperate regions. Over the last decade, D. antiqua has been managed principally using a pesticide seed treatment package containing the reduced-risk insecticide spinosad. While spinosad protects onion seedlings from D. antiqua, very little is known regarding how protection occurs. The main objectives of this study were to assess susceptibility of 1- and 2-wk-old larvae to spinosad through two different modes of exposure: ingestion and contact, and to evaluate larval feeding behavior in choice and no-choice tests with onion seedlings grown from treated and untreated seeds. Results showed that spinosad was more than twice as lethal to 1-wk than 2-wk-old larvae when it was ingested, but was equally toxic to both larval ages via contact exposure. In choice assays, larvae preferred feeding on untreated plants; however, without a choice, larvae fed and survived equally well on untreated and treated plants, suggesting that spinosad may have a deterrent effect. In a field study, levels of spinosad within young onion plants and in the soil around roots were monitored in addition to the cumulative number of onion seedlings killed by D. antiqua. Spinosad was detected in the soil and in both aboveground and belowground plant tissue, indicating that spinosad translocates into foliage, but declines in plant tissue and soil as plant mortality from D. antiqua feeding increases. Together, these results provide valuable insight into how spinosad protects onion seedlings and reveal key areas in need of further investigation.

Conventional Soil Management May Promote Nutrients That Lure an Insect Pest to a Toxic Crop.

Slow and consistent nutrient release by organic fertilizers can improve plant nutrient balance and defenses, leading to herbivore avoidance of organically managed crops in favor of conventional crops with weaker defenses. We propose that this relative attraction to conventional plants, coupled with the use of genetically modified, insecticidal crops (Bt), has created an unintentional attract-and-kill system. We sought to determine whether Bt and non-Bt corn Zea mays L. plants grown in soil collected from five paired organic and conventional fields differed in attractiveness to European corn borer [Ostrinia nubilalis (Hübner)] moths, by conducting ovipositional choice and flight tunnel assays. We then examined the mechanisms driving the observed differences in attraction by comparing soil nutrient profiles, soil microbial activity, plant nutrition, and plant volatile profiles. Finally, we assessed whether European corn borer abundance near corn fields differed based on soil management. European corn borer preferred plants grown in conventional soil but did not discriminate between Bt and non-Bt corn. Organic management and more alkaline soil were associated with an increased soil magnesium:potassium ratio, which increased plant magnesium, and were linked to reduced European corn borer oviposition. There was an inconsistent trend for higher European corn borer moth activity near conventional fields. Our results extend the mineral balance hypothesis describing conventional plant preference by showing that it can also improve attraction to plants with genetically inserted toxins. Unintentional attract (to conventional) and (Bt) kill is a plausible scenario for pest declines in response to Bt corn adoption, but this effect may be obscured by variation in other management practices and landscape characteristics.

Soil Macroinvertebrate Presence Alters Microbial Community Composition and Activity in the Rhizosphere.

Despite decades of research, our understanding of the importance of invertebrates for soil biogeochemical processes remains incomplete. This is especially true when considering soil invertebrate effects mediated through their interactions with soil microbes. The aim of this study was to elucidate how soil macroinvertebrates affect soil microbial community composition and function within the root zone of a managed grass system. We conducted a 2-year field mesocosm study in which soil macroinvertebrate communities were manipulated through size-based exclusion and tracked changes in microbial community composition, diversity, biomass and activity to quantify macroinvertebrate-driven effects on microbial communities and their functions within the rhizosphere. The presence of soil macroinvertebrates created distinct microbial communities and altered both microbial biomass and function. Soil macroinvertebrates increased bacterial diversity and fungal biomass, as well as increased phenol oxidase and glucosidase activities, which are important in the degradation of organic matter. Macroinvertebrates also caused distinct shifts in the relative abundance of different bacterial phyla. Our findings indicate that within the rhizosphere, macroinvertebrates have a stimulatory effect on microbial communities and processes, possibly due to low-intensity microbial grazing or through the dispersal of microbial cells and spores by mobile invertebrates. Our results suggest that macroinvertebrate activity can be an important control on microbially-mediated processes in the rhizosphere such as nitrogen mineralization and soil organic matter formation.

Author Correction: Impacts of alpine wetland degradation on the composition, diversity and trophic structure of soil nematodes on the Qinghai-Tibetan Plateau.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Impacts of alpine wetland degradation on the composition, diversity and trophic structure of soil nematodes on the Qinghai-Tibetan Plateau.

Alpine wetlands on the Qinghai-Tibetan Plateau are undergoing degradation. However, little is known regarding the response of soil nematodes to this degradation. We conducted investigations in a wet meadow (WM), a grassland meadow (GM), a moderately degraded meadow (MDM) and a severely degraded meadow (SDM) from April to October 2011. The nematode community taxonomic composition was similar in the WM, GM and MDM and differed from that in the SDM. The abundance declined significantly from the WM to the SDM. The taxonomic richness and Shannon index were comparable between the WM and MDM but were significantly lower in the SDM, and the Pielou evenness showed the opposite pattern. The composition, abundance and diversity in the WM and SDM were relatively stable over time compared with other habitats. The abundances of all trophic groups, aside from predators, decreased with degradation. The relative abundances of herbivores, bacterivores, predators and fungivores were stable, while those of omnivores and algivores responded negatively to degradation. Changes in the nematode community were mainly driven by plant species richness and soil available N. Our results demonstrate that alpine wetland degradation significantly affects the soil nematode communities, suppressing but not shifting the main energy pathways through the soil nematode communities.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function.

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

A source of terrestrial organic carbon to investigate the browning of aquatic ecosystems.

There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This "browning" phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances ("Super Hume") as an analog for natural sources of terrestrial DOC. Based on chemical characterizations, comparative surveys, and whole-ecosystem manipulations, we found that the physical and chemical properties of Super Hume are similar to those of natural DOC in aquatic and terrestrial ecosystems. For example, Super Hume attenuated solar radiation in ways that will not only influence the physiology of aquatic taxa but also the metabolism of entire ecosystems. Based on its chemical properties (high lignin content, high quinone content, and low C:N and C:P ratios), Super Hume is a fairly recalcitrant, low-quality resource for aquatic consumers. Nevertheless, we demonstrate that Super Hume can subsidize aquatic food webs through 1) the uptake of dissolved organic constituents by microorganisms, and 2) the consumption of particulate fractions by larger organisms (i.e., Daphnia). After discussing some of the caveats of Super Hume, we conclude that commercial sources of humic substances can be used to help address pressing ecological questions concerning the increased export of terrestrial DOC to aquatic ecosystems.

The origin of litter chemical complexity during decomposition.

The chemical complexity of decomposing plant litter is a central feature shaping the terrestrial carbon (C) cycle, but explanations of the origin of this complexity remain contentious. Here, we ask: How does litter chemistry change during decomposition, and what roles do decomposers play in these changes? During a long-term (730 days) litter decomposition experiment, we tracked concurrent changes in decomposer community structure and function and litter chemistry using high-resolution molecular techniques. Contrary to the current paradigm, we found that the chemistry of different litter types diverged, rather than converged, during decomposition due to the activities of decomposers. Furthermore, the same litter type exposed to different decomposer communities exhibited striking differences in chemistry, even after > 90% mass loss. Our results show that during decomposition, decomposer community characteristics regulate changes in litter chemistry, which could influence the functionality of litter-derived soil organic matter (SOM) and the turnover and stabilisation of soil C.

Roots and fungi accelerate carbon and nitrogen cycling in forests exposed to elevated CO2.

A common finding in multiple CO(2) enrichment experiments in forests is the lack of soil carbon (C) accumulation owing to microbial priming of 'old' soil organic matter (SOM). However, soil C losses may also result from the accelerated turnover of 'young' microbial tissues that are rich in nitrogen (N) relative to bulk SOM. We measured root-induced changes in soil C dynamics in a pine forest exposed to elevated CO(2) and N enrichment by combining stable isotope analyses, molecular characterisations of SOM and microbial assays. We find strong evidence that the accelerated turnover of root-derived C under elevated CO(2) is sufficient in magnitude to offset increased belowground inputs. In addition, the C losses were associated with accelerated N cycling, suggesting that trees exposed to elevated CO(2) not only enhance N availability by stimulating microbial decomposition of SOM via priming but also increase the rate at which N cycles through microbial pools.