The importance of aboveground and belowground interspecific interactions in determining crop growth and advantages of peanut/maize intercropping

Intercropping of maize (Zea mays L.) and peanut (Arachis hypogaea L.) often results in greater yields than the respective sole crops. However, there is limited knowledge of aboveground and belowground interspecific interactions between maize and peanut in field. A two-year field experiment was conducted to investigate the effects of interspecific interactions on plant growth and grain yield for a peanut/maize intercropping system under different nitrogen (N) and phosphorus (P) levels. The method of root separation was employed to differentiate belowground from aboveground interspecific interactions. We observed that the global interspecific interaction effect on the shoot biomass of the intercropping system decreased with the coexistence period, and belowground interaction contributed more than aboveground interaction to advantages of the intercropping in terms of shoot biomass and grain yield. There was a positive effect from aboveground and belowground interspecific interactions on crop plant growth in the intercropping system, except that aboveground interaction had a negative effect on peanut during the late coexistence period. The advantage of intercropping on grain came mainly from increased maize yield (means 95%) due to aboveground interspecific competition for light and belowground interaction (61%72% vs. 28%-39% in fertilizer treatments). There was a negative effect on grain yield from aboveground interaction for peanut, but belowground interspecific interaction positively affected peanut grain yield. The supply of N, P, or N + P increased grain yield of intercropped maize and the contribution from aboveground interspecific interaction. Our study suggests that the advantages of peanut/maize intercropping for yield mainly comes from aboveground interspecific competition for maize and belowground interspecific facilitation for peanut, and their respective yield can be enhanced by N and P. These findings are important for managing the intercropping system and optimizing the benefits from using this system. (C) 2021 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd

Comparative Genomic Analysis and Characterization of Two Salmonella enterica Serovar Enteritidis Isolates From Poultry With Notably Different Survival Abilities in Egg Whites

Salmonellaenterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies

Revealing missing human protein isoforms based on Ab initio prediction, RNA-seq and proteomics

Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.publishedVersio

Increased soil phosphorus availability induced by faba bean root exudation stimulates root growth and phosphorus uptake in neighbouring maize

Summary Root growth is influenced by soil nutrients and neighbouring plants, but how these two drivers affect root interactions and regulate plant growth dynamics is poorly understood. Here, interactions between the roots of maize (Zea mays) and faba bean (Vicia faba) are characterized. Maize was grown alone (maize) or with maize (maize/maize) or faba bean (maize/faba bean) as competitors under five levels of phosphorus (P) supply, and with homogeneous or heterogeneous P distribution. Maize had longer root length and greater shoot biomass and P content when grown with faba bean than with maize. At each P supply rate, faba bean had a smaller root system than maize but greater exudation of citrate and acid phosphatase, suggesting a greater capacity to mobilize P in the rhizosphere. Heterogeneous P availability enhanced the root-length density of maize but not faba bean. Maize root proliferation in the P-rich patches was associated with increased shoot P uptake. Increased P availability by localized P application or by the presence of faba bean exudation stimulated root morphological plasticity and increased shoot growth in maize in the maize/faba bean mixture, suggesting that root interactions of neighbouring plants can be modified by increased P availability

Valuing the DEPHY network datasets to analyze relationships between crop diversity and pesticide use, to help the design of sustainable cropping systems

communication orale,National audienceOveruse of pesticides is one of the main hanging issues which impede sustainable crop production. Despite a rapid growing body of research assessing the impact of agricultural diversification (practices/crop/ non-crop/ microorganism diversity) on the ecological perspective of the cropping system (e.g. ecosystem services and biodiversity), a synthesis on the agronomical impact is less documented. A few researches conducted on an experimental scale has proved that crop diversity can reduce agronomical input such as pesticides. However, those results are context-dependent, so it is hard to conclude on a broader view. Therefore, a quantitative analysis is missing about the relationship between crop diversity and pesticide use, on a large range of production situations.This study is focusing on depicting the relationship between two major components of sustainable cropping systems, i.e. crop diversity and pesticide use, based on the French DEPHY network dataset, including data from around 3,000 French commercial farms over ten years. Crop diversity is described using a combination of divisional methods, namely plant taxonomy (e.g. legume crop), ecological functional groups (e.g. nitrogen catching), agronomical functional groups (e.g. minor crop, cover crop, sowing season), and sale type (e.g. Farmers tend to use more pesticide on contracted crops: seed maize, etc.). Indicators from the domains of ecology and agronomy will be used to assess the crop diversity level. An analysis of the effect of preceding crop on pesticide use will also be conducted to test the crop diversity impact on a temporal scale, considering the variance caused by pedoclimate and cropping system characteristics.A reader-friendly summary of the Ph.D. target would be, an attempt to understand the complexity of “taking crop diversity as a tool to reduce pesticide”, during this period of time

Analysing the relationship between yields and farmers' incomes to help the design of more sustainable cropping systems

Book of abstract p.380-381International audienceFarmers often grow only the few high-yielding crops in the area, and target maximum yieldsthrough high levels of inputs. These practices are based on the assumption of a positiverelationship between productivity and profitability over a wide range of cropping systems(Woo et al., 2020; Erythrina et al., 2021). Part of the correlation between productivity andprofitability could be related to differences in production situation and therefore yieldpotential, i.e. characteristics that do not depend on farmers’ decisions. For a given productionsituation, the systems with the highest profitability and the best environmental sustainabilitycould be systems with moderate yields.The objective of our research is therefore to assess the relationship between productivity andprofitability of cropping systems in order subsequently to help design of the most profitableand sustainable cropping systems.In this study, we use the French DEPHY network database collected on about 3,000 Frenchcommercial farms over ten years. Regression tree methods are conducted on the dataset toidentify combinations of farm characteristics associated with the production situation to forma regression tree with a range of varied production situation groups. Crop yields areaggregated on the cropping system level rather than on the crop level to represent the overallcropping system productivity in each farm. Productivity is estimated by converting yields intothe amount of energy produced by surface unit (GJ ha−1 yr−1), based on the energy contentof each given crop calculated by the higher heating value. Profitability (€ ha−1 yr−1) iscomputed by the monetary value generated by the output of the cropping system. Lasso (leastabsolute shrinkage and selection operator) regression method (Tibshirani, 1996) is used tocompute the marginal yielding effects on profitability. Treatment Frequency Index (TFI),energy use efficiency, and their interactions with productivity are also tested with theirexplanatory power at profitability in the Lasso regression model. Marginal yielding effects onprofitability computed by the Lasso regression method is used to explore the correspondedchanges in profitability resulting from a one-unit increase in productivity within eachproduction situation group to assess the relationship between productivity and profitabilityof cropping systems in a consistent context.381Under the same production potential situation, we will test the relationship betweenproductivity and profitability notably to reveal if an intended reduction in targeted yields andan increase in the efficiency of inputs would lead to maximised overall profits compared to anincreased use of inputs targeting high yields. The original oversimplified yield-profitrelationship studied here under consistent production conditions from about 3,000 Frenchcommercial farms over ten years will question current advices targeting maximum yieldsinstead of targeting maximum income and higher sustainability.Reference:Erythrina, E., Anshori, A., Bora, C. Y., Dewi, D. O., Lestari, M. S., Mustaha, M. A., ... &Syahbuddin, H. (2021). Assessing opportunities to increase yield and profit in rainfed lowlandrice systems in Indonesia. Agronomy, 11(4), 777.Tibshirani, R. (1996). Regression shrinkage and selection via the lasso. Journal of the RoyalStatistical Society: Series B (Methodological), 58(1), 267-288.Woo, D. K., Riley, W. J., & Wu, Y. (2020). More fertilizer and impoverished roots required forimproving wheat yields and profits under climate change. Field Crops Research, 249, 107756