Deep learning in agriculture: A survey

Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques.info:eu-repo/semantics/acceptedVersio

Transfer of manure from livestock farms to crop fields as fertilizer using an ant inspired approach

Intensive livestock production might have a negative environmental impact, by producing large amounts of animal excrements, which, if not properly managed, can contaminate nearby water bodies with nutrient excess. However, if animal manure is exported to distant crop fields, to be used as organic fertilizer, pollution can be mitigated. It is a single-objective optimization problem, in regards to finding the best solution for the logistics process of satisfying nutrient crops needs by means of livestock manure. This paper proposes a dynamic approach to solve the problem, based on a decentralized nature-inspired cooperative technique, inspired by the foraging behavior of ants (AIA). Results provide important insights for policy-makers over the potential of using animal manure as fertilizer for crop fields, while AIA solves the problem effectively, in a fair way to the farmers and well balanced in terms of average transportation distances that need to be covered by each livestock farmer. Our work constitutes the first application of a decentralized AIA to this interesting real-world problem, in a domain where swarm intelligence methods are still under-exploited.info:eu-repo/semantics/publishedVersio

Prospective application of melanized fungi for the biofiltration of indoor air in closed bioregenerative systems

Cultures of melanized fungi representative of the black yeast orders Capnodiales (Cladosporium cladosporioides and Neohortaea acidophila) and Chaetothyriales (Cladophialophora psammophila) were confined with indoor air from the laboratory during 48 h. Volatile organic compounds (VOCs) from the headspace were analyzed by thermal desorption gas chromatography time-of-fly mass spectrometry (TD-GC-ToFMS, detection threshold 0.1 μg m−3) and compared against an abiotic control. A mixture of 71 VOCs were identified and quantified in the indoor air (total concentration 1.4 mg m−3). Most of these compounds were removed in the presence of fungal biomass, but 40 newly formed putative volatile metabolites were detected, though at comparatively low total concentrations (<50 μg m−3). The VOCs emission profile of C. cladosporioides, a ubiquitous and well-known species often associated to the sick building syndrome, was consistent with previous literature reports. The specialized C. psammophila and N. acidophila, isolated respectively from gasoline polluted soil and from lignite, displayed rather specific VOCs emission profiles. Mass balances on the fungal uptake and generation of VOCs resulted in overall VOCs removal efficiencies higher than 96% with all tested fungi. Applied aspects and biosafety issues concerning the suitability of black yeasts for the biofiltration of indoor air have been discussed.info:eu-repo/semantics/acceptedVersio

Isolation and Identification of Black Yeasts by Enrichment on Atmospheres of Monoaromatic Hydrocarbons

Black yeast members of the Herpotrichiellaceae present a complex ecological behavior: They are often isolated from rather extreme environments polluted with aromatic hydrocarbons, while they are also regularly involved in human opportunistic infections. A selective technique to promote the in vitro growth of herpotrichiellaceous fungi was applied to investigate their ecophysiology. Samples from natural ecological niches and man-made environments that might contain black yeasts were enriched on an inert solid support at low humidity and under a controlled atmosphere rich in volatile aromatic hydrocarbons. Benzene, toluene, and xylene were provided separately as the sole carbon and energy source via the gas phase. The assayed isolation protocol was highly specific toward mesophilic Exophiala species (70 strains of this genus out of 71 isolates). Those were obtained predominantly from creosote-treated railway ties (53 strains), but isolates were also found on wild berries (11 strains) and in guano-rich soil samples (six strains). Most of the isolates were obtained on toluene (43 strains), but enrichments on xylene and benzene also yielded herpotrichiellaceous fungi (17 and 10 isolates, respectively). Based upon morphological characterizations and DNA sequences of the full internal transcriber spacers (ITS) and the 8.5S rRNA genes, the majority of the obtained isolates were affiliated to the recently described species Exophiala xenobiotica (32 strains) and Exophiala bergeri (nine strains). Members of two other phylogenetic groups (24 and two strains, respectively) somewhat related to E. bergeri were also found, and a last group (three strains) corresponded to an undescribed Exophiala species

Volatile Organic Compounds in the Azteca/Cecropia Ant-Plant Symbiosis and the Role of Black Fungi

Black fungi of the order Chaetothyriales are grown by many tropical plant-mutualistic ants as small so-called “patches” in their nests, which are located inside hollow structures provided by the host plant (“domatia”). These fungi are introduced and fostered by the ants, indicating that they are important for the colony. As several species of Chaetothyriales tolerate, adsorb, and metabolize toxic volatiles, we investigated the composition of volatile organic compounds (VOCs) of selected domatia in the Azteca/Cecropia ant-plant mutualism. Concentrations of VOCs in ant-inhabited domatia, empty domatia, and background air were compared. In total, 211 compounds belonging to 19 chemical families were identified. Ant-inhabited domatia were dominated by ketones with 2-heptanone, a well-known ant alarm semiochemical, as the most abundant volatile. Empty domatia were characterized by relatively high concentrations of the monoterpenes d-limonene, p-cymene and β-phellandrene, as well as the heterocyclic sulphur-containing compound, benzothiazole. These compounds have biocidal properties and are primarily biosynthesized by plants as a defense mechanism. Interestingly, most of the latter compounds were present at lower concentrations in ant inhabited domatia than in non-colonized ones. We suggest that Chaetothyriales may play a role in reducing the VOCs, underlining that the mutualistic nature of these fungi as VOCs accumulation might be detrimental for the ants, especially the larvae.info:eu-repo/semantics/publishedVersio

A comparison of isolation methods for black fungi degrading aromatic toxins

The prevalence of black fungi in the order Chaetothyriales has often been underestimated due to the difficulty of their isolation. In this study, three methods which are often used to isolate black fungi are compared. Enrichment on aromatic hydrocarbon appears effective in inhibiting growth of cosmopolitan microbial species and allows appearance of black fungi. We miniaturized the method for high-throughput purposes. The new procedure saves time, consumes less space and can process multiple samples simultaneously.info:eu-repo/semantics/publishedVersio

Genomic Understanding of an Infectious Brain Disease from the Desert

Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East, and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper, we describe the whole-genome resequencing of two R. mackenziei strains from patients in Saudi Arabia and Qatar. We assessed intraspecies variation and genetic signatures to uncover the genomic basis of the pathogenesis, and potential niche adaptations. We found that the duplicated genes (paralogs) are more susceptible to accumulating significant mutations. Comparative genomics with other filamentous ascomycetes revealed a diverse arsenal of genes likely engaged in pathogenicity, such as the degradation of aromatic compounds and iron acquisition. In addition, intracellular accumulation of trehalose and choline suggests possible adaptations to the conditions of an arid climate region. Specifically, protein family contractions were found, including short-chain dehydrogenase/reductase SDR, the cytochrome P450 (CYP) (E-class), and the G-protein b WD-40 repeat. Gene composition and metabolic potential indicate extremotolerance and hydrocarbon assimilation, suggesting a possible environmental habitat of oil-polluted desert soilinfo:eu-repo/semantics/publishedVersio