Search

The biomedical domain has shown that in silico analyses over vast data pools enhances the speed and scale of scientific innovation. This can hold true in agricultural research and guide similar multi-stakeholder action in service of global food security as well (Streich et al. Curr Opin Biotechnol 61:217–225. Retrieved from https://doi.org/10.1016/j.copbio.2020.01.010, 2020). However, entrenched research culture and data and standards governance issues to enable data interoperability and ease of reuse continue to be roadblocks in the agricultural research for development sector. Effective operationalization of the FAIR Data Principles towards Findable, Accessible, Interoperable, and Reusable data requires that agricultural researchers accept that their responsibilities in a digital age include the stewardship of data assets to assure long-term preservation, access and reuse. The development and adoption of common agricultural data standards are key to assuring good stewardship, but face several challenges, including limited awareness about standards compliance; lagging data science capacity; emphasis on data collection rather than reuse; and limited fund allocation for data and standards management. Community-based hurdles around the development and governance of standards and fostering their adoption also abound. This chapter discusses challenges and possible solutions to making FAIR agricultural data assets the norm rather than the exception to catalyze a much-needed revolution towards “translational agriculture”.

Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labelling to be interoperable. As recommended by the FAIR principles, data, labels and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no agreed full set of ontologies recommended for data annotation across agricultural research disciplines, which may span genetics, environment, agroecology, biology and socioeconomics. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant ontology expertise. This CoP aims to stimulate knowledge sharing and directly support platform development teams by producing ontologies or contributing missing concepts, recommending best practices and identifying mitigation solutions when gold standard datasets are difficult to attain.

Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but these are not typically trained in good data management practices. That said, we have come a long way in the last decade, with funders, publishers, and researchers themselves making the case for open, interoperable data as a key component of an open science philosophy. In response, recognition of the FAIR Principles (that data should be Findable, Accessible, Interoperable and Reusable) has become commonplace. However, both technical and cultural challenges for the implementation of these principles still exist when storing, managing, analysing and disseminating both legacy and new data.COPO is a computational system that attempts to address some of these challenges by enabling scientists to describe their research objects (raw or processed data, publications, samples, images, etc.) using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share it with the wider scientific community. COPO encourages data generators to adhere to appropriate metadata standards when publishing research objects, using semantic terms to add meaning to them and specify relationships between them. This allows data consumers, be they people or machines, to find, aggregate, and analyse data which would otherwise be private or invisible. Building upon existing standards to push the state of the art in scientific data dissemination whilst minimising the burden of data publication and sharing.AvailabilityCOPO is entirely open source and freely available on GitHub at https://github.com/collaborative-open-plant-omics. A public instance of the platform for use by the community, as well as more information, can be found at copo-project.org.

The possibly higher lignin contents or altered carbon (C) allocation patterns in Bt corn hybrids, compared to their non-transgenic parental varieties, may alter the quality and quantity of plant residues incorporated into soils. In this study, we conducted a greenhouse experiment to investigate C allocation and lignin contents in Cry3Bb Bt and NonBt corn as affected by corn rootworm (CRW, Diabrotica virgifera virgifera) infestation. The partitioning of photosynthate C to various plant components was measured as short-term C allocation by a 13CO2 pulse-labeling system, and the lignin content or concentration was measured by the acid detergent method. Results showed that NonBt corn was significantly taller than Bt corn at all measured stages, likely resulting from inherent variability in the parental lines used in this study. However, there was no significant genotype effect on 13C allocation, total C and lignin content or concentration in plant tissues without CRW infestation. With CRW, the percentage of fixed 13C during labeling allocated to roots was significantly lower in NonBt than in Bt corn, likely caused by CRW damage in NonBt roots. The lignin content in NonBt roots was significantly higher with than without the CRW infestation, implying the stimulating effect of CRW possibly due to the triggered reaction of induced systemic resistance. Overall, the transgenic Cry3Bb event in MON863 corn did not affect measured variables, but CRW resistance in Bt corn affected the pattern of short-term C allocation and root lignin content compared to NonBt corn in the CRW presence, and has implications for soil C dynamics.

In this study, Bt transgenic rice (KMD rice) residue decomposition and the associated microbial community in a rapeseed-rice cropping system were assessed in comparison with its parental non-Bt rice variety (XiuShui 11). Decomposition was measured as mass loss by straw and root decay in litterbags over two consecutive years. Bacterial and fungal community compositions associated with residue decomposition were detected by terminal restriction fragment length polymorphism (T-RFLP) and the additive main effects multiplicative interaction (AMMI) analysis model. Decomposition dynamics and bacterial and fungal communities associated with decomposition were strongly affected by surface and incorporated placements, and by temporal factors. However, no significant differences were observed between Bt and non-Bt rice variety in either decomposition dynamics or in the soil microbial communities associated with residue decay. Our field study indicated that the insertion of the cry1Ab gene into Xiushui 11 rice genome had no significant effect on the residual decay and decomposition-associated microbial community compositions in the rapeseed-rice cropping system.

Purpose Genetic modifications (GM) of commercial crops offer many benefits. However, microbial-mediated decomposition might be affected by GM crop residues in agricultural ecosystems. The objective of this study was to assess the possible impacts of cry1Ab gene transformation of rice on soil microbial community composition associated with residue decomposition in the paddy field under intensive rice cultivation.

Background, aim, and scope Genetic modification of commercial crops may affect their decomposition and nutrient cycling processes in agricultural ecosystems. Intensive rice cultivation under partially submerged conditions (paddy rice) is an important and widespread cropping system, particularly in the tropics, yet there is little data on the decomposition of Bt rice residue under field conditions. We investigated straw and root decomposition of rice modified to express the Cry1Ab protein of Bacillus thuringiensis (Bt) to kill lepidopteran pests, compared with a parental non-Bt isoline. The objective of this study was to assess the possible impacts of cry gene transformation of rice on residue decomposition under intensive rice cultivation with long period of submergence.

Photosynthetic assimilation of CO2 is a primary source of carbon in soil and root exudates and can influence the community dynamics of rhizosphere organisms. Thus, if carbon partitioning is affected in transgenic crops, rhizosphere microbial communities may also be affected. In this study, the temporal effects of gene transformation on carbon partitioning in rice and rhizosphere microbial communities were investigated under greenhouse conditions using the 13C pulse-chase labeling method and phospholipid fatty acid (PLFA) analysis. The 13C contents in leaves of transgenic (Bt) and nontransgenic (Ck) rice were significantly different at the seedling, booting and heading stages. There were no detectable differences in 13C distribution in rice roots and rhizosphere microorganisms at any point during rice development. Although a significantly lower amount of Gram-positive bacterial PLFAs and a higher amount of Gram-negative bacterial PLFAs were observed in Bt rice rhizosphere as compared with Ck at all plant development stages, there were no significant differences in the amount of individual 13C-PLFA between Bt and Ck rhizospheres at any growing stage. These findings indicate that the insertion of cry1Ab and marker genes into rice had no persistent or adverse effect on the photosynthate distribution in rice or the microbial community composition in its rhizosphere.

Oxygen availability in landfill cover soil is a major limitation to the growth and activity of methanotrophs as methane oxidation is an aerobic microbial process. Plants tolerant to high concentrations of landfill gas (LFG) may play an important role in improving methane oxidation within landfill cover soil and reducing emission of methane, a greenhouse gas, from it. In this study, the effect of an LFG tolerant plant Chenopodium album L. on methane oxidation activity (MOA) and bacterial community composition in landfill cover soil was investigated. Soil samples from four simulated lysimeters with and without LFG and plant vegetation were taken at 4 stages during the plant's development cycle. Results showed that the total number of culturable bacteria in soil could be significantly increased (P < 0.05) by the growth of C. album. The total number of methanotrophs and MOA in soils with LFG was significantly higher (P < 0.05) than in soils without LFG on sampling days 90, 150 and 210. The total number of methanotrophs and MOA in lysimeters with LFG added increased in the presence of C. album when the plant entered the seed setting stage. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) gel patterns of 16S rDNA gene fragment and band sequencing analyses showed apparent differences in soil bacterial communities in the presence of LFG and plant vegetation. Members of the genus Methylosarcina were found to be the active and dominant methanotrophs in rhizosphere soil of C. album with LFG, while Methylococcus, Methylocystis, and Methylosinus were the primary methanotroph genera in LFG soil without C. album. Thus, C. album appears to select for specific methanotrophic bacteria in the presence of LFG. Soil MOA and microbial diversity can also be significantly affected by the presence of this plant.

Laboratory and greenhouse studies on transgenic Bacillus thuringiensis (Bt) maize have drawn attention to the persistence and activity of the Cry proteins in soil and their potential effects on soil microorganisms, but there have been few field assessments that evaluate the effects of Bt maize with those of insecticides on soil microbial populations. This study was conducted to determine the effects of Cry3Bb Bt maize with those of the insecticide tefluthrin on soil microbial biomass and activity in the field over a 3-year cropping cycle. The recently commercialized maize variety YieldGard ® Rootworm (MON863), which produces the Cry3Bb protein, was grown along with a non-Bt isoline with and without tefluthrin applied at planting. Microbial biomass, nitrogen (N) mineralization potential, short-term nitrification rate, and respiration rate were measured in rhizosphere and bulk soil samples collected from three replicate field plots just before planting, at anthesis, and at harvest in each year. There were clear seasonal effects on microbial biomass and activity in the field soils—as represented by the consistent changes in all measured variables across years and sampling times. Differences in the measured variables were also sometimes observed between bulk and rhizosphere soil. However, there were no adverse effects of either the Bt or non-Bt maize with insecticide applied compared to the non-Bt controls; on the contrary, microbial biomass and soil respiration data suggested a stimulatory effect of the Bt genotype, particularly in comparison to the non-Bt isoline. Although ‘higher’ does not necessarily mean ‘better’, the higher microbial biomass and respiration rates observed in the Bt and insecticide-applied soils compared to non-Bt soils does allay concerns that either the Bt protein or the tefluthrin typically used to control the corn rootworm reduce microbial biomass or its respiratory activity in field soils. Similarly, the higher N mineralization potential and nitrification rates observed in some soil samples from the Bt and tefluthrin-treated plots indicate higher activity of N-mineralizing microorganisms, a potentially positive consequence as both ammonium and nitrate are effective N sources for maize during grain filling. Our data suggest that cropping MON863 Bt maize is unlikely to adversely affect soil ecology in the short term. Longer-term monitoring of transgenic cropping systems should assure that the biotic functioning of the soil is maintained as a part of studies on overall ecosystem integrity.

Since the first commercial release of a transgenic crop in 1994, the land area planted to these crops has expanded to over 90 million ha worldwide, with approximately 8.5 million farmers in 21 countries cultivating transgenic crops. Public apprehension has mounted apace. Concerns include: (i) the potential for gene flow into wild plant populations or soil organisms; (ii) adverse effects on non-target organisms; (iii) gene products or crop residues persisting in the environment with deleterious effects and, for insecticidal crops; (iv) resistance developing in target pest populations. Numerous studies on the environmental risks of transgenic crops are published. Gene flow to a crop's wild relatives has been demonstrated in the field; hence, the use of these crops is restricted to regions where wild relatives are not endemic. Gene flow to soil organisms is yet to be demonstrated under field conditions and is unlikely given the safeguards employed, but not impossible. The weight of the evidence sugg...

Remediation of contaminated soil by inoculated bacteria requires movement of the bacteria to the site of contamination. However, the surface-inoculated pseudomonad mineralized little of the substrate present in the bottom 0.4-cm portion of nonsterile soil or aquifer sand that had been sterilized prior to inoculation, although mineralization occurred at the bottom of nonsterile aquifer sand. Little biodegradation was evident if the bacterium and the substrate were both at the bottom part of columns of soil and aquifer sand receiving intermittent flows of water, although rapid biodegradation occurred at this site in soil if the water flow was constant. We suggest that bacteria added to the soil surface or to aquifer solids for biodegradation may not be transported sufficiently to reach organic pollutants at sites distant from channels or macropores.

Objective: The research provides an understanding of pandemic information needs and informs professional development initiatives for librarians in disaster medicine. Methods: Utilizing a multisite, comparative case series design, the researchers conducted semi-structured interviews and examined supplementary materials in the form of organizational documents, correspondence, and websites to create a complete picture of each case. The rigor of the case series was ensured through data and investigator triangulation. Interview transcripts were coded using NVivo to identify common themes and points of comparison. Results: Comparison of the four cases revealed a distinct difference between “client-initiated” and “librarian-initiated” provision of pandemic information. Librarian-initiated projects utilized social software to “push” information, whereas client-initiated projects operated within patron-determined parameters to deliver information. Health care administrators were identified as a key audience for pandemic information, and news agencies were utilized as essential information sources. Librarians' skills at evaluating available information proved crucial for selecting best-quality evidence to support administrative decision making. Conclusions: Qualitative analysis resulted in increased understanding of pandemic information needs and identified best practices for disseminating information during periods of high organizational stress caused by an influx of new cases of an unknown infectious disease.

Despite the rapid adoption of crops expressing the insecticidal Cry protein(s) from Bacillus thuringiensis (Bt), public concern continues to mount over the potential environmental impacts. Reduced residue decomposition rates and increased tissue lignin concentrations reported for some Bt corn hybrids have been highlighted recently as they may influence soil carbon dynamics. We assessed the effects of MON863 Bt corn, producing the Cry3Bb protein against the corn rootworm complex, on these aspects and associated decomposer communities by terminal restriction fragment length polymorphism (T-RFLP) analysis. Litterbags containing cobs, roots, or stalks plus leaves from Bt and unmodified corn with (non-Bt+I) or without (non-Bt) insecticide applied were placed on the soil surface and at a 10-cm depth in field plots planted with these crop treatments. The litterbags were recovered and analyzed after 3.5, 15.5, and 25 months. No significant effect of treatment (Bt, non-Bt, and non-Bt+I) was observed on initial tissue lignin concentrations, litter decomposition rate, or bacterial decomposer communities. The effect of treatment on fungal decomposer communities was minor, with only 1 of 16 comparisons yielding separation by treatment. Environmental factors (litterbag recovery year, litterbag placement, and plot history) led to significant differences for most measured variables. Combined, these results indicate that the differences detected were driven primarily by environmental factors rather than by any differences between the corn hybrids or the use of tefluthrin. We conclude that the Cry3Bb corn tested in this study is unlikely to affect carbon residence time or turnover in soils receiving these crop residues.

The paper gives examples of the bioinformatics services provided in a variety of different libraries by librarians with a broad range of educational background and training.Two investigators sent an email inquiry to attendees of the "National Center for Biotechnology Information's (NCBI) Introduction to Molecular Biology Information Resources" or "NCBI Advanced Workshop for Bioinformatics Information Specialists (NAWBIS)" courses. The thirty-five-item questionnaire addressed areas such as educational background, library setting, types and numbers of users served, and bioinformatics training and support services provided. Answers were compiled into program vignettes.The bioinformatics support services addressed in the paper are based in libraries with academic and clinical settings. Services have been established through different means: in collaboration with biology faculty as part of formal courses, through teaching workshops in the library, through one-on-one consultations, and by other methods. Librarians with backgrounds from art history to doctoral degrees in genetics have worked to establish these programs.Successful bioinformatics support programs can be established in libraries in a variety of different settings and by staff with a variety of different backgrounds and approaches.