The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management

The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.

Plant-derived biostimulant as priming agents enhanced antioxidant and nutritive properties in brassicaceous microgreens

BACKGROUND

Microgreens constitute dietary sources of bioactive compounds imparting numerous health benefits and enhancing sensory experience. They can be successfully cultivated in soilless systems where biostimulants can be easily integrated as seed-priming and post-germination agents improving the sustainability of a crop's final production. Compared to an untreated control, three priming agents (a commercial legume-derived protein hydrolysate (A250), a novel protein hydrolysate derived from peanut biomass (H250) and hydropriming (H2O)) were applied to Komatsuna and Mibuna seeds grown as microgreens and compared for their effects on yield parameters, mineral composition, ABTS and FRAP antioxidant capacity, carotenoid concentration and phenolic compounds.

RESULTS

Significant effects of the main experimental factors and their interactions were identified on antioxidant capacity. Compared to the control and hydropriming, the highest ABTS and FRAP values were observed in Mibuna with the A250 and H250 treatments, respectively. Additionally, the H250 treatment increased the total concentrations of phenolic acid derivatives and flavonoid derivatives in Mibuna and Komatsuna, in tune with the levels of total flavonoids. Concerning mineral composition, the highest concentrations in both species were those of phosphorus and nitrate.

CONCLUSION

These results highlight the potential of select plant-based biostimulants as priming agents to enhance the antioxidant capacity, nutrient content and bioactive compound content, thus further increasing their functional and nutritive quality. In the light of this, the possibility of reducing the application of fertilizers by promoting a green transition for the intensive production of microgreens could subsequently be evaluated. © 2024 Society of Chemical Industry.

Low-Cost Optical Sensors for Soil Composition Monitoring

Studying soil composition is vital for agricultural and edaphology disciplines. Presently, colorimetry serves as a prevalent method for the on-site visual examination of soil characteristics. However, this technique necessitates the laboratory-based analysis of extracted soil fragments by skilled personnel, leading to substantial time and resource consumption. Contrastingly, sensor techniques effectively gather environmental data, though they mostly lack in situ studies. Despite this, sensors offer substantial on-site data generation potential in a non-invasive manner and can be included in wireless sensor networks. Therefore, the aim of the paper is to develop a low-cost red, green, and blue (RGB)-based sensor system capable of detecting changes in the composition of the soil. The proposed sensor system was found to be effective when the sample materials, including salt, sand, and nitro phosphate, were determined under eight different RGB lights. Statistical analyses showed that each material could be classified with significant differences based on specific light variations. The results from a discriminant analysis documented the 100% prediction accuracy of the system. In order to use the minimum number of colors, all the possible color combinations were evaluated. Consequently, a combination of six colors for salt and nitro phosphate successfully classified the materials, whereas all the eight colors were found to be effective for classifying sand samples. The proposed low-cost RGB sensor system provides an economically viable and easily accessible solution for soil classification.

Soil Carbon Stocks and Greenhouse Gas Mitigation of Agriculture in the Brazilian Cerrado-A Review

New agricultural practices and land-use intensification in the Cerrado biome have affected the soil carbon stocks. A major part of the native vegetation of the Brazilian Cerrado, a tropical savanna-like ecoregion, has been replaced by crops, which has caused changes in the soil carbon (C) stocks. To ensure the sustainability of this intensified agricultural production, actions have been taken to increase soil C stocks and mitigate greenhouse gas emissions. In the last two decades, new agricultural practices have been adopted in the Cerrado region, and their impact on C stocks needs to be better understood. This subject has been addressed in a systematic review of the existing data in the literature, consisting of 63 articles from the Scopus database. Our review showed that the replacement of Cerrado vegetation by crop species decreased the original soil C stocks (depth 0-30 cm) by 73%, with a peak loss of 61.14 Mg ha^-1. However, when analyzing the 0-100 cm layer, 52.4% of the C stock data were higher under cultivated areas than in native Cerrado soils, with a peak gain of 93.6 Mg ha^-1. The agricultural practices implemented in the Brazilian Cerrado make low-carbon agriculture in this biome possible.

Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.

Persistent soil carbon enhanced in Mollisols by well-managed grasslands but not annual grain or dairy forage cropping systems

Soil organic carbon (C) responses to agricultural management are highly uncertain, hindering our ability to assess the C sequestration potential of croplands and develop sound policies to mitigate climate change while enhancing other ecosystem services. Combining experimental evidence from a long-term field experiment and a meta-analysis of published literature, we show that the accrual of mineral-associated soil C in intensively managed Mollisols was only achieved by managing ruminant grazing on perennial grasslands. Although modifying dominant grain-based systems with reduced tillage, diversified rotations, and legumes and manure additions improve soil health metrics—which is critical to soil, nutrient, and water conservation—they are unlikely to enhance persistent forms of soil C in Mollisols to help drawdown atmospheric C and stabilize climate.

Intensive crop production on grassland-derived Mollisols has liberated massive amounts of carbon (C) to the atmosphere. Whether minimizing soil disturbance, diversifying crop rotations, or re-establishing perennial grasslands and integrating livestock can slow or reverse this trend remains highly uncertain. We investigated how these management practices affected soil organic carbon (SOC) accrual and distribution between particulate (POM) and mineral-associated (MAOM) organic matter in a 29-y-old field experiment in the North Central United States and assessed how soil microbial traits were related to these changes. Compared to conventional continuous maize monocropping with annual tillage, systems with reduced tillage, diversified crop rotations with cover crops and legumes, or manure addition did not increase total SOC storage or MAOM-C, whereas perennial pastures managed with rotational grazing accumulated more SOC and MAOM-C (18 to 29% higher) than all annual cropping systems after 29 y of management. These results align with a meta-analysis of data from published studies comparing the efficacy of soil health management practices in annual cropping systems on Mollisols worldwide. Incorporating legumes and manure into annual cropping systems enhanced POM-C, microbial biomass, and microbial C-use efficiency but did not significantly increase microbial necromass accumulation, MAOM-C, or total SOC storage. Diverse, rotationally grazed pasture management has the potential to increase persistent soil C on Mollisols, highlighting the key role of well-managed grasslands in climate-smart agriculture.

Agronomic Factors Influencing the Scale of Fusarium Mycotoxin Contamination of Oats

Seven agronomic factors (crop season, farming system, harvest date, moisture, county, oat variety, and previous crop) were recorded for 202 oat crops grown across Ireland, and samples were analysed by LC-MS/MS for four major Fusarium mycotoxins: deoxynivalenol (DON), zearalenone (ZEN), T-2 toxin and HT-2 toxin. Type A trichothecenes were present in 62% of crops, with 7.4% exceeding European regulatory limits. DON (6.4%) and ZEN (9.9%) occurrences were relatively infrequent, though one and three samples were measured over their set limits, respectively. Overall, the type of farming system and the previous crop were the main factors identified as significantly influencing mycotoxin prevalence or concentration. Particularly, the adherence to an organic farming system and growing oats after a previous crop of grass were found to decrease contamination by type A trichothecenes. These are important findings and may provide valuable insights for many other types of cereal crops as Europe moves towards a much greater organic-based food system.

A parsimonious mechanistic model of reproductive and vegetative growth in fruit trees predicts consequences of fruit thinning and branch pruning

Productivity of fruit tree crops depends on the interaction between plant physiology, environmental conditions and agricultural practices. We develop a mechanistic model of fruit tree crops that reliable simulates the dynamics of variables of interest for growers and consequences of agricultural practices while relying on a minimal number of inputs and parameters. The temporal dynamics of carbon content in the different organs (i.e., shoots-S, roots-R and fruits-F) are the result of photosynthesis by S, nutrient supply by R, respiration by S, R and F, competition among different organs, photoperiod and initial system conditions partially controlled by cultural practices. We calibrate model parameters and evaluate model predictions using unpublished data from a peach (Prunus persica) experimental orchard with trees subjected to different levels of branch pruning and fruit thinning. Fiinally, we evaluate the consequences of different combinations of pruning and thinning intensities within a multi-criteria analysis. The predictions are in good agreement with the experimental measurements and for the different conditions (pruning and thinning). Our simulations indicate that thinning and pruning practices actually used by growers provide the best compromise between total shoot production, which impacts next year's abundance of shoots and fruits, and current year's fruit production in terms of quantity (yield) and quality (average fruit size). This suggests that growers are not only interested in maximizing current year's yield but also in its quality and its durability. The present work provides for modelers a system of equations based on acknowledged principles of plant science easily modifiable for different purposes. For horticulturists, it gives insights on the potentialities of pruning and thinning. For ecologists, it provides a transparent quantitative framework that can be coupled with biotic and abiotic stressors.

Impact of Anthropic Activities on Soil Quality under Different Land Uses

Anthropization often leads to land use transformation, causing deep changes to soil properties and its quality. Land use change could be an environmental and socioeconomic problem, as it impacts soil quality and ecosystem services. There is an urgent need to understand the pressures affecting soil quality. The aim of the work is to quantify the impact of different land uses on soil abiotic and biotic properties and on its quality. To achieve the aims, soils from different land uses (forest, urban and agricultural) were collected in the surroundings of Naples and analyzed for pH, water content, contents of C and N, C/N ratio and total and available concentrations of Cu, Ni and Pb, microbial and fungal biomasses, basal respiration and metabolic quotient. Then, a soil quality index (SQI) was calculated for each land use. The results showed that soil abiotic and biotic properties of the agricultural sites differed from those of forest and urban sites. At agricultural sites, microbial abundances decreased due to low amount of C and N and to high amount of Cu and Pb. This caused low use efficiency of energetic substrates and a reduced soil quality of agricultural sites as compared to forest and urban sites.

Using Matching Traits to Study the Impacts of Land-Use Intensification on Plant-Pollinator Interactions in European Grasslands: A Review

Simple Summary

Permanent grasslands are main habitats for many plant species and pollinators. Their destruction as well as their intensification has a major impact on plant and pollinator biodiversity, which has a cascading effect on pollination. However, we lack an understanding of these effects, thereby limiting our ability to predict them. In this review, we synthesised the literature on the mechanisms behind this cascade to provide new insights into the relationship between land-use intensification and pollination. By matching functional traits that mediate the relationship between the two trophic levels, we identified major knowledge gaps about how land-use intensification affects plant–pollinator interactions and how it favours plants with generalised floral traits, which are likely harmful to pollination.

Abstract

Permanent grasslands are suitable habitats for many plant and animal species, among which are pollinating insects that provide a wide range of ecosystem services. A global crisis in pollination ecosystem service has been highlighted in recent decades, partly the result of land-use intensification. At the grassland scale, however, the underlying mechanisms of land-use intensification that affect plant–pollinator interactions and pollination remain understudied. In this review, we first synthesise the literature to provide new insights into the relationships between land-use intensification and pollination by using matching community and interaction traits. We then identify knowledge gaps and summarise how land-use intensification of grassland influences floral traits that may in turn be associated with modifications to pollinator matching traits. Last, we summarise how these modifications may affect pollination function on permanent grasslands. Overall, land-use intensification may lead to a shift in flower colour, a decrease in mean nectar tube depth and a decrease in reward production and pollen quality at the community level. This, in turn, may generate a decrease in pollinator mouthparts length and body size, that may favour pollinators that require a low amount of floral reward. We found no study citing the effect of land-use intensification on volatile organic compounds emitted by flowers despite the importance of these molecules in pollinator community composition. Overall, our review highlighted major knowledge gaps about the effects of land-use intensification on plant–pollinator interactions, and suggests that land-use intensification could favour plants with generalised floral traits that adversely affect pollination.

Phenological growth stages of Korean ginseng (Panax ginseng) according to the extended BBCH scale

BACKGROUND

Phenological studies are a prerequisite for accomplishing higher productivity and better crop quality in cultivated plants. However, there are no phenological studies on Panax ginseng that improve its production yield. This study aims to redefine the phenological growth stages of P. ginseng based on the existing Biologische Bundesanstalt, Bundessortenamt und Chemische Industrie (BBCH) scale and proposes a disease control reference.

METHODS

This study was conducted at the Korea Ginseng Corporation Experiment Station in Gyeonggi province, South Korea. Phenological observations were performed once weekly or twice monthly, based on the developmental stages. The existing BBCH scale with a three-digit code was used to redefine and update P. ginseng's phenological growth codes.

RESULTS

The phenological description is divided into eight principal growth stages: three for vegetative growth (perennating bud, aerial shoot, and root development), four for reproductive growth (reproductive organ development, flowering, fruit development, and fruit maturation), and one for senescence according to the extended BBCH scale. A total of 58 secondary growth stages were described within the eight principal growth stages. Under each secondary growth stage, four mesostages are also taken into account, which contains the distinct patterns of the phenological characteristics in ginseng varieties and the process of transplanting seedlings. A practical management program for disease control was also proposed by using the BBCH code and the phenological data proposed in this work.

CONCLUSION

The study introduces an extended BBCH scale for the phenological research of P. ginseng.

The Sources, Synthesis and Biological Actions of Omega-3 and Omega-6 Fatty Acids in Red Meat: An Overview

The maximisation of available resources for animal production, food security and maintenance of human-animal wellbeing is important for an economically viable, resilient and sustainable future. Pasture and forage diets are common sources of short chain omega-3 (n-3) polyunsaturated fatty acids (PUFA), while grain-based and feedlot diets are common sources of short chain omega-6 (n-6) PUFA. Animals deposit n-3 and n-6 PUFA as a result of their direct consumption, as feeds or by synthesis of longer chain PUFA from short chain FA precursors in the body via desaturation and elongation processes. Research conducted over the last three decades has determined that the consumption of n-3 PUFA can improve the health and wellbeing of humans through its biological, biochemical, pathological and pharmacological effects. n-6 PUFA also play an important role in human health, but when consumed at high levels, are potentially harmful. Research shows that current consumption of n-6 PUFA by the human population is high due to their meal choices and the supplied food types. If consumption of n-3 PUFA from land- and marine-based foods improves human health, it is likely that these same food types can improve the health and wellbeing of livestock (farm animals) by likewise enhancing the levels of the n-3 PUFA in their circulatory and tissue systems. Modern agricultural systems and advanced technologies have fostered large scale animal and crop production systems. These allow for the utilisation of plant concentrate-based diets to increase the rate of animal growth, often based on economics, and these diets are believed to contribute to unfavourable FA intakes. Knowledge of the risks associated with consuming foods that have greater concentration of n-6 PUFA may lead to health-conscious consumers avoiding or minimising their intake of animal- and plant-based foods. For this reason, there is scope to produce food from plant and animal origins that contain lesser amounts of n-6 PUFA and greater amounts of n-3 PUFA, the outcome of which could improve both animal and human health, wellbeing and resilience to disease.

A real-world implementation of a nationwide, long-term monitoring program to assess the impact of agrochemicals and agricultural practices on biodiversity

Biodiversity has undergone a major decline throughout recent decades, particularly in farmland. Agricultural practices are recognized to be an important pressure on farmland biodiversity, and pesticides are suspected to be one of the main causes of this decline in biodiversity. As part of the national plan for reduction of pesticides use (Ecophyto), the French ministry of agriculture launched the 500 ENI (nonintended effects) monitoring program in 2012 in order to assess the unintended effects of agricultural practices, including pesticide use, on biodiversity represented by several taxonomic groups of interest for farmers. This long-term program monitors the biodiversity of nontargeted species (earthworms, plants, coleoptera, and birds), together with a wide range of annual data on agricultural practices (crop rotation, soil tillage, weed control, fertilizers, chemical treatments, etc.). Other parameters (e.g., landscape and climatic characteristics) are also integrated as covariates during the analyses. This monitoring program is expected to improve our understanding of the relative contribution of the different drivers of population and community trends. Here, we present the experience of setting up the 500 ENI network for this ambitious and highly complex monitoring program, as well as the type of data it collects. The issue of data quality control and some first results are discussed. With the aim of being useful to readers who would like to set up similar monitoring schemes, we also address some questions that have arisen following the first five years of the implementation phase of the program.

A Fumonisin Prevention Tool for Targeting and Ranking Agroclimatic Conditions Favoring Exposure in French Maize-Growing Areas

The levels of fumonisins (FUMO)-mycotoxins produced by Fusarium verticillioides-in maize for food and feed are subject to European Union regulations. Compliance with the regulations requires the targeting of, among others, the agroclimatic factors influencing fungal contamination and FUMO production. Arvalis-Institut du végétal has created a national, multiyear database for maize, based on field survey data collected since 2003. This database contains information about agricultural practices, climatic conditions and FUMO concentrations at harvest for 738 maize fields distributed throughout French maize-growing regions. A linear mixed model approach highlights the presence of borers and the use of a late variety, high temperatures in July and October, and a water deficit during the maize cycle as creating conditions favoring maize contamination with Fusarium verticillioides. It is thus possible to target a combination of risk factors, consisting of this climatic sequence associated with agricultural practices of interest. The effects of the various possible agroclimatic combinations can be compared, grouped and classified as promoting very low to high FUMO concentrations, possibly exceeding the regulatory threshold. These findings should facilitate the creation of a national, informative and easy-to-use prevention tool for producers and agricultural cooperatives to manage the sanitary quality of their harvest.

Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches

Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant–microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.

Medico-administrative data combined with agricultural practices data to retrospectively estimate pesticide use by agricultural workers

This work is part of a global project aiming to use medico-administrative big data from the whole French agricultural population (~3 millions), collected through their mandatory health insurance system (Mutualité Sociale Agricole), to highlight associations between chronic diseases and agricultural activities. At the request of the French Agency for Food, Environmental and Occupational Health & Safety (ANSES), our objective was to estimate which pesticides were probably used by each agricultural worker, in order to include this information in our analyses and search for association with diseases. We selected five databases to achieve this objective: the Graphical Land Parcel Registration (RPG), the French Agricultural Census, "Cultivation Practice" surveys from the Agriculture ministry, the MATPHYTO crop-exposure matrix and the Compilation of Phytosanitary Indexes from the French Public Health Agency. A geographical grid was designed to use geographical location while maintaining worker anonymity, dividing France into square tracts of variable surface each containing a minimum of 1500 agricultural workers. We developed an automated algorithm to predict each individual potential exposure by crossing her/his occupational activity, the geographical grid and the RPG to deduce cultivation practices and use it as a gateway to estimate pesticides use. This approach allowed drawing, from administrative data, a list of substances potentially used by each agricultural worker throughout France. Results of the algorithm are illustrated at collective level (descriptive statistics for the whole population), as well as at individual level (some workers taken as examples). The generalization of this method in other national contexts is discussed. By linking this information with the health insurance databases, this approach could contribute to the agricultural workers health surveillance.

Dormancy, a critical trait for weed success in crop production systems

Agricultural practices exert selective forces on weed populations. As these practices change over time, weed adaptive traits also evolve, allowing weeds to persist in the new environment. However, only weeds having individuals showing the trait with adaptive significance will be able to cope with these changes, thus allowing a sub-population to be selected for persistence. In addition, changes in agricultural practices can select new weed species showing functional traits with characteristics adaptive to the modified system. Seed dormancy has long been recognized as a trait with enormous adaptive value to adjust weed biology to cropping systems. In this paper, we illustrate with examples of success and failure, the value of seed dormancy as a functional trait to cope with long-term changes in crop production systems. We show that successful outcomes are mostly related to the existence of sufficient variability for the functioning of physiological mechanisms that control dormancy characteristics as influenced by the agricultural environment. Presented examples illustrate how knowledge about the relationship that exists between agricultural practices and their selective pressure on seed dormancy can be instrumental in predicting changes in weed biotype dormancy characteristics or foreseeing the appearance of new weed species in future agricultural scenarios. © 2019 Society of Chemical Industry.

Urban forest fragments as unexpected sanctuaries for the rare endemic ghost butterfly from the Atlantic forest

Anthropogenic land expansion, particularly urbanization, is pervasive, dramatically modifies the environment and is a major threat to wildlife with its associated environmental stressors. Urban remnant vegetation can help mitigate these impacts and could be vital for species unable to survive in harsh urban environments. Although resembling nonurban habitats, urban vegetation remnants are subject to additional environmental stresses. Here, we evaluate the occurrence and density of the endemic ghost butterfly (Morpho epistrophus nikolajewna) that was once common, in the highly fragmented Atlantic forest of NE Brazil. We tested whether this butterfly would be found at lower densities in urban forest fragments of contrasting sizes as opposed to rural ones, given the number of environmental stressors found in urban areas. We surveyed 14 forest fragments (range 2.8 to over 3,000 ha) of semideciduous Atlantic forest in rural and urban locations using transect based distance sampling. The ghost butterflies showed strong seasonality; flying only from April to June. They were only identified in an urban fragment (515 ha), with an estimate of 720 individuals and a density 1.4 ind/ha. All forest fragments had experienced some level of logging in the past, which might have had an effect in the butterfly population. Nevertheless, rural forest fragments were subject to increased particulate matter concentrations, associated to biomass burning that we suggest might have had a more influential role driving the collapse of rural populations. Our findings show the importance of urban forest remnants to sustain population of this endangered species.

Mow the Grass at the Mouse's Peril: Diversity of Small Mammals in Commercial Fruit Farms

Simple Summary

For the first time in the Baltic countries, small mammal communities were evaluated in commercial orchards and berry plantations to test for the influence of crop type and intensity of agricultural practices. Out of ten species registered in the fruit farms, the most dominant were common vole and striped field mouse, confirming the spread of the latter species in the country. Small mammal diversity and abundance were not dependent on crop type but decreased in line with the intensity of agricultural practices, not being found in the most intensively cultivated farms. Unexpectedly, small mammal diversity in apple orchards exceeded the diversities found in most types of forests and was significantly higher than in crop fields.

Abstract

Small mammals are not only pests but also an important part of agricultural ecosystems. The common vole is a reference species for risk assessment of plant protection products in the European Union, but no data about the suitability of the species in the Baltic countries are present so far. Using the snap-trap line method, we evaluated species composition, abundance, and diversity of small mammal communities in commercial orchards and berry plantations in Lithuania, testing the predictions that (i) compared with other habitats, small mammal diversity in fruit farms is low, and (ii) the common vole is the dominant species. The diversity of small mammals was compared with control habitats and the results of investigations in other habitats. Out of ten small mammal species registered, the most dominant were common vole and striped field mouse. Small mammal diversity and abundance increased in autumn and decreased in line with the intensity of agricultural practices but were not dependent on crop type. In the most intensively cultivated fruit farms, small mammals were not found. The diversity of small mammal communities in fruit farms was significantly higher than in crop fields and exceeded the diversities found in most types of forests except those in rapid succession.

Biological clocks, some clock-related diseases, and medicinal plants

Progress in chronobiology thus far has been built on botanical field investigation records, experiments on the development of biological clocks, open questions, established rules, and molecular mechanisms. In this review, three clock-related diseases, namely cancer, Alzheimer's disease (AD), and depression, are discussed. Evidence-based mechanisms of action of active compounds, namely epigallocatechin-3-gallate (EGCG), curcumin, and melatonin, from three medicinal plants, Camellia sinensis K., Curcuma longa L., and Hypericum perforatum L., respectively, as potential therapies against cancer, AD, and depression, respectively, have been explained. Feedback loops of basic inputs and application outputs of various studies will lead to the development of chronobiology for applications in time-keeping, disease prevention, and control, and future agricultural practices.

Global trends in infectious diseases of swine

Pork accounts for more than one-third of meat produced worldwide and is an important component of global food security, agricultural economies, and trade. Infectious diseases are among the primary constraints to swine production, and the globalization of the swine industry has contributed to the emergence and spread of pathogens. Despite the importance of infectious diseases to animal health and the stability and productivity of the global swine industry, pathogens of swine have never been reviewed at a global scale. Here, we build a holistic global picture of research on swine pathogens to enhance preparedness and understand patterns of emergence and spread. By conducting a scoping review of more than 57,000 publications across 50 years, we identify priority pathogens globally and regionally, and characterize geographic and temporal trends in research priorities. Of the 40 identified pathogens, publication rates for eight pathogens increased faster than overall trends, suggesting that these pathogens may be emerging or constitute an increasing threat. We also compared regional patterns of pathogen prioritization in the context of policy differences, history of outbreaks, and differing swine health challenges faced in regions where swine production has become more industrialized. We documented a general increasing trend in importance of zoonotic pathogens and show that structural changes in the industry related to intensive swine production shift pathogen prioritization. Multinational collaboration networks were strongly shaped by region, colonial ties, and pig trade networks. This review represents the most comprehensive overview of research on swine infectious diseases to date.

Agricultural Practices Influence Salmonella Contamination and Survival in Pre-harvest Tomato Production

Between 2000 and 2010 the Eastern Shore of Virginia was implicated in four Salmonella outbreaks associated with tomato. Therefore, a multi-year study (2012-2015) was performed to investigate presumptive factors associated with the contamination of Salmonella within tomato fields at Virginia Tech's Eastern Shore Agricultural Research and Extension Center. Factors including irrigation water sources (pond and well), type of soil amendment: fresh poultry litter (PL), PL ash, and a conventional fertilizer (triple superphosphate - TSP), and production practices: staked with plastic mulch (SP), staked without plastic mulch (SW), and non-staked without plastic mulch (NW), were evaluated by split-plot or complete-block design. All field experiments relied on naturally occurring Salmonella contamination, except one follow up experiment (worst-case scenario) which examined the potential for contamination in tomato fruits when Salmonella was applied through drip irrigation. Samples were collected from pond and well water; PL, PL ash, and TSP; and the rhizosphere, leaves, and fruits of tomato plants. Salmonella was quantified using a most probable number method and contamination ratios were calculated for each treatment. Salmonella serovar was determined by molecular serotyping. Salmonella populations varied significantly by year; however, similar trends were evident each year. Findings showed use of untreated pond water and raw PL amendment increased the likelihood of Salmonella detection in tomato plots. Salmonella Newport and Typhimurium were the most frequently detected serovars in pond water and PL amendment samples, respectively. Interestingly, while these factors increased the likelihood of Salmonella detection in tomato plots (rhizosphere and leaves), all tomato fruits sampled (n = 4800) from these plots were Salmonella negative. Contamination of tomato fruits was extremely low (< 1%) even when tomato plots were artificially inoculated with an attenuated Salmonella Newport strain (10⁴ CFU/mL). Furthermore, Salmonella was not detected in tomato plots irrigated using well water and amended with PL ash or TSP. Production practices also influenced the likelihood of Salmonella detection in tomato plots. Salmonella detection was higher in tomato leaf samples for NW plots, compared to SP and SW plots. This study provides evidence that attention to agricultural inputs and production practices may help reduce the likelihood of Salmonella contamination in tomato fields.

Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale

Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long‐term research study catchment (12 km²) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape‐scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.

Rust and Thinning Management Effect on Cup Quality and Plant Performance for Two Cultivars of Coffea arabica L

Beverage quality is a complex attribute of coffee ( Coffea arabica L.). Genotype (G), environment (E), management (M), postharvest processing, and roasting are all involved. However, little is known about how G × M interactions influence beverage quality. We investigated how yield and coffee leaf rust (CLR) disease (caused by Hemileia vastatrix Berk. et Br.) management affect cup quality and plant performance, in two coffee cultivars. Sensory and chemical analyses revealed that 10 of 70 attributes and 18 of 154 chemical volatile compounds were significantly affected by G and M. Remarkably, acetaminophen was found for the first time in roasted coffee and in higher concentrations under more stressful conditions. A principal component analysis described 87% of the variation in quality and plant overall performance. This study is a first step in understanding the complexity of the physiological, metabolic, and molecular changes in coffee production, which will be useful for the improvement of coffee cultivars.

Networking our science to characterize the state, vulnerabilities, and management opportunities of soil organic matter

Soil organic matter (SOM) supports the Earth's ability to sustain terrestrial ecosystems, provide food and fiber, and retains the largest pool of actively cycling carbon. Over 75% of the soil organic carbon (SOC) in the top meter of soil is directly affected by human land use. Large land areas have lost SOC as a result of land use practices, yet there are compensatory opportunities to enhance productivity and SOC storage in degraded lands through improved management practices. Large areas with and without intentional management are also being subjected to rapid changes in climate, making many SOC stocks vulnerable to losses by decomposition or disturbance. In order to quantify potential SOC losses or sequestration at field, regional, and global scales, measurements for detecting changes in SOC are needed. Such measurements and soil-management best practices should be based on well established and emerging scientific understanding of processes of C stabilization and destabilization over various timescales, soil types, and spatial scales. As newly engaged members of the International Soil Carbon Network, we have identified gaps in data, modeling, and communication that underscore the need for an open, shared network to frame and guide the study of SOM and SOC and their management for sustained production and climate regulation.

Ethiopian agriculture has greater potential for carbon sequestration than previously estimated

More than half of the cultivation-induced carbon loss from agricultural soils could be restored through improved management. To incentivise carbon sequestration, the potential of improved practices needs to be verified. To date, there is sparse empirical evidence of carbon sequestration through improved practices in East-Africa. Here, we show that agroforestry and restrained grazing had a greater stock of soil carbon than their bordering pair-matched controls, but the difference was less obvious with terracing. The controls were treeless cultivated fields for agroforestry, on slopes not terraced for terracing, and permanent pasture for restrained grazing, representing traditionally managed agricultural practices dominant in the case regions. The gain by the improved management depended on the carbon stocks in the control plots. Agroforestry for 6-20 years led to 11.4 Mg ha^-1 and restrained grazing for 6-17 years to 9.6 Mg ha^-1 greater median soil carbon stock compared with the traditional management. The empirical estimates are higher than previous process-model-based estimates and indicate that Ethiopian agriculture has greater potential to sequester carbon in soil than previously estimated.

Understanding the Impacts of Soil, Climate, and Farming Practices on Soil Organic Carbon Sequestration: A Simulation Study in Australia

Carbon sequestration in agricultural soils has the capacity to mitigate greenhouse gas emissions, as well as to improve soil biological, physical, and chemical properties. The review of literature pertaining to soil organic carbon (SOC) dynamics within Australian grain farming systems does not enable us to conclude on the best farming practices to increase or maintain SOC for a specific combination of soil and climate. This study aimed to further explore the complex interactions of soil, climate, and farming practices on SOC. We undertook a modeling study with the Agricultural Production Systems sIMulator modeling framework, by combining contrasting Australian soils, climates, and farming practices (crop rotations, and management within rotations, such as fertilization, tillage, and residue management) in a factorial design. This design resulted in the transposition of contrasting soils and climates in our simulations, giving soil-climate combinations that do not occur in the study area to help provide insights into the importance of the climate constraints on SOC. We statistically analyzed the model's outputs to determinate the relative contributions of soil parameters, climate, and farming practices on SOC. The initial SOC content had the largest impact on the value of SOC, followed by the climate and the fertilization practices. These factors explained 66, 18, and 15% of SOC variations, respectively, after 80 years of constant farming practices in the simulation. Tillage and stubble management had the lowest impacts on SOC. This study highlighted the possible negative impact on SOC of a chickpea phase in a wheat-chickpea rotation and the potential positive impact of a cover crop in a sub-tropical climate (QLD, Australia) on SOC. It also showed the complexities in managing to achieve increased SOC, while simultaneously aiming to minimize nitrous oxide (N2O) emissions and nitrate leaching in farming systems. The transposition of contrasting soils and climates in our simulations revealed the importance of the climate constraints on SOC.

The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system

Agriculture is the main source of terrestrial emissions of N2O, a potent greenhouse gas and the main cause of ozone layer depletion. The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only biological process known to eliminate this greenhouse gas. Recent studies showed that a previously unknown clade of N2O-reducers was related to the capacity of the soil to act as an N2O sink, opening the way for new strategies to mitigate emissions. Here, we investigated whether the agricultural practices could differently influence the two N2O reducer clades with consequences for denitrification end-products. The abundance of N2O-reducers and producers was quantified by real-time PCR, and the diversity of both nosZ clades was determined by 454 pyrosequencing. Potential N2O production and potential denitrification activity were used to calculate the denitrification gaseous end-product ratio. Overall, the results showed limited differences between management practices but there were significant differences between cropping systems in both the abundance and structure of the nosZII community, as well as in the [rN2O/r(N2O+N2)] ratio. More limited differences were observed in the nosZI community, suggesting that the newly identified nosZII clade is more sensitive than nosZI to environmental changes. Potential denitrification activity and potential N2O production were explained mainly by the soil properties while the diversity of the nosZII clade on its own explained 26% of the denitrification end-product ratio, which highlights the importance of understanding the ecology of this newly identified clade of N2O reducers for mitigation strategies.

Isotopic characterization as a screening tool in authentication of organic produce commercially available in western North America

The use of nitrogen stable isotopes to discriminate between conventionally and organically grown crops has been further developed in this study. Soil and irrigation water from different regions, as well as nitrogen fertilizers used, have been examined in detail to determine their effects on nitrogen isotope composition of spinach, lettuce, broccoli and tomatoes. Over 1000 samples of various types of organically and conventionally grown produce of known origin, along with the samples of nitrogen fertilizers used for their growth, have been analysed in order to assemble the datasets of crop/fertilizer correlations. The results demonstrate that the developed approach can be used as a valuable component in the verification of agricultural practices for more than 25 different types of commercially grown green produce, either organic or conventional. Over a period of two years, various organic and non-organic greens, from different stores in Seattle (WA, USA) and Victoria (BC, Canada), were collected and analysed using this methodology with the objective of determining any pattern of misrepresentation.

Population genetic structure of Anopheles arabiensis (Diptera: Culicidae) in a rice growing area of central Kenya

Studies were conducted to examine the population genetic structure of Anopheles arabiensis (Patton) in Mwea Rice Irrigation Scheme and surrounding areas in Central Kenya, under different agricultural systems. This study was motivated by observed differences in malaria transmission indices of An. arabiensis within the scheme compared with adjacent nonirrigated areas. Agricultural practices can modify local microclimate and influence the number and diversity of larval habitats and in so doing may occasion subpopulation differentiation. Thirty samples from each of the three study sites were genotyped at eight microsatellite loci. Seven microsatellite loci showed high polymorphism but revealed no genetic differentiation (FST = 0.006, P = 0.312) and high gene flow (Nm = 29-101) among the three populations. Genetic bottleneck analysis showed no indication of excess heterozygosity in any of the populations. There was high frequency of rare alleles, suggesting that An. arabiensis in the study area has a high potential of responding to selective pressures from environmental changes and vector control efforts. These findings imply that An. arabiensis in the study area occurs as a single, continuous panmictic population with great ability to adapt to human-imposed selective pressures.