Measuring variation in potato roots in both field and glasshouse: the search for useful yield predictors and a simple screen for root traits

Aims Potatoes have an inadequate rooting system for efficient acquisition of water and minerals and use disproportionate amounts of irrigation and fertilizer. This research determines whether significant variation in rooting characteristics of potato exists, which characters correlate with final yield and whether a simple screen for rooting traits could be developed. Methods Twenty-eight genotypes of Solanum tuberosum groups Tuberosum and Phureja were grown in the field; eight replicate blocks to final harvest, while entire root systems were excavated from four blocks. Root classes were categorised and measured. The same measurements were made on these genotypes in the glasshouse, 2 weeks post emergence. Results In the field, total root length varied from 40 m to 112 m per plant. Final yield was correlated negatively with basal root specific root length and weakly but positively with total root weight. Solanum tuberosum group Phureja genotypes had more numerous roots and proportionally more basal than stolon roots compared with Solanum tuberosum, group Tuberosum genotypes. There were significant correlations between glasshouse and field measurements. Conclusions Our data demonstrate that variability in rooting traits amongst commercially available potato genotypes exists and a robust glasshouse screen has been developed. By measuring potato roots as described in this study, it is now possible to assess rooting traits of large populations of potato genotypes.

Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon

The interplay between dietary nutrients, gut microbiota and mammalian host tissues of the gastrointestinal tract is recognised as highly relevant for host health. Combined transcriptome, metabonome and microbial profiling tools were employed to analyse the dynamic responses of germfree mouse colonic mucosa to colonisation by normal mouse microbiota (conventionalisation) at different time-points during 16 days. The colonising microbiota showed a shift from early (days 1 and 2) to later colonisers (days 8 and 16). The dynamic changes in the microbial community were rapidly reflected by the urine metabolic profiles (day 1) and at later stages (day 4 onward) by the colon mucosa transcriptome and metabolic profiles. Correlations of host transcriptomes, metabolite patterns and microbiota composition revealed associations between Bacilli and Proteobacteria, and differential expression of host genes involved in energy and anabolic metabolism. Differential gene expression correlated with scyllo- and myo-inositol, glutamine, glycine and alanine levels in colonic tissues during the time span of conventionalisation. Our combined time-resolved analyses may help to expand the understanding of host-microbe molecular interactions during the microbial establishment.

Dispersal of soil-dwelling clover root weevil (Sitona lepidus Gyllenhal, Coleoptera: Curculionidae) larvae in mixed plant communities

Insect pests that have a root-feeding larval stage often cause the most sustained damage to plants because their attrition remains largely unseen, preventing early diagnosis and treatment. Characterising movement and dispersal patterns of subterranean insects is inherently difficult due to the difficulty in observing their behaviour. Our understanding of dispersal and movement patterns of soil-dwelling insects is therefore limited compared to above ground insect pests and tends to focus on vertical movements within the soil profile or assessments of coarse movement patterns taken from soil core measurements in the field. The objective of this study was to assess how the dispersal behaviour of the clover root weevil (CRW), Sitona lepidus larvae was affected by differing proportions of host (clover) and non-host (grass) plants under different soil water contents (SWC). This was undertaken in experimental mini-swards that allowed us to control plant community structure and soil water content. CRW larval survival was not affected either by white clover content or planting pattern or SWC in either experiment; however, lower clover composition in the sward resulted in CRW larvae dispersing further from where they hatched. Because survival was the same regardless of clover density, the proportion of infested plants was highest in sward boxes with the fewest clover plants (i.e. the low host plant density). Thus, there is potential for clover plants over a larger area to be colonised when the clover content of the sward is low.

Effects of soil conditions and drought on egg hatching and larval survival of the clover root weevil (Sitona lepidus)

Soil-dwelling insect herbivores are significant pests in many managed ecosystems. Because eggs and larvae are difficult to observe, mathematical models have been developed to predict life-cycle events occurring in the soil. To date, these models have incorporated very little empirical information about how soil and drought conditions interact to shape these processes. This study investigated how soil temperature (10, 15, 20 and 25 °C), water content (0.02 (air dried), 0.10 and 0.25 g g−1) and pH (5, 7 and 9) interactively affected egg hatching and early larval lifespan of the clover root weevil (Sitona lepidus Gyllenhal, Coleoptera: Curculionidae). Eggs developed over 3.5 times faster at 25 °C compared with 10 °C (hatching after 40.1 and 11.5 days, respectively). The effect of drought on S. lepidus eggs was investigated by exposing eggs to drought conditions before wetting the soil (2–12 days later) at four temperatures. No eggs hatched in dry soil, suggesting that S. lepidus eggs require water to remain viable. Eggs hatched significantly sooner in slightly acidic soil (pH 5) compared with soils with higher pH values. There was also a significant interaction between soil temperature, pH and soil water content. Egg viability was significantly reduced by exposure to drought. When exposed to 2–6 days of drought, egg viability was 80–100% at all temperatures but fell to 50% after 12 days exposure at 10 °C and did not hatch at all at 20 °C and above. Drought exposure also increased hatching time of viable eggs. The effects of soil conditions on unfed larvae were less influential, except for soil temperature which significantly reduced larval longevity by 57% when reared at 25 °C compared with 10 °C (4.1 and 9.7 days, respectively). The effects of soil conditions on S. lepidus eggs and larvae are discussed in the context of global climate change and how such empirically based information could be useful for refining existing mathematical models of these processes.

Variation in root-associated phosphatase activities in wheat contributes to the utilization of organic P substrates in vitro, but does not explain differences in the P-nutrition of plants when grown in soils

To understand whether genotypic variation in root-associated phosphatase activities in wheat impacts on its ability to acquire phosphorus (P), various phosphatase activities of roots were measured in relation to the utilization of organic P substrates in agar, and the P-nutrition of plants was investigated in a range of soils. Root-associated phosphatase activities of plants grown in hydroponics were measured against different organic P substrates. Representative genotypes were then grown in both agar culture and in soils with differing organic P contents and plant biomass and P uptake were determined. Differences in the activities of both root-associated and exuded phosphodiesterase and phosphomonoesterase were observed, and were related to the P content of plants supplied with either ribonucleic acid or glucose 6-phosphate, respectively, as the sole form of P. When the cereal lines were grown in different soils, however, there was little relationship between any root-associated phosphatase activity and plant P uptake. This indicates that despite differences in phosphatase activities of cereal roots, such variability appears to play no significant role in the P-nutrition of the plant grown in soil, and that any benefit derived from the hydrolysis of soil organic P is common to all genotypes.

Training pharmacists to deliver a complex information technology intervention (PINCER) using the principles of educational outreach and root cause analysis

Objective: To describe the training undertaken by pharmacists employed in a pharmacist-led information technology-based intervention study to reduce medication errors in primary care (PINCER Trial), evaluate pharmacists’ assessment of the training, and the time implications of undertaking the training. Methods: Six pharmacists received training, which included training on root cause analysis and educational outreach, to enable them to deliver the PINCER Trial intervention. This was evaluated using self-report questionnaires at the end of each training session. The time taken to complete each session was recorded. Data from the evaluation forms were entered onto a Microsoft Excel spreadsheet, independently checked and the summary of results further verified. Frequencies were calculated for responses to the three-point Likert scale questions. Free-text comments from the evaluation forms and pharmacists’ diaries were analysed thematically. Key findings: All six pharmacists received 22 hours of training over five sessions. In four out of the five sessions, the pharmacists who completed an evaluation form (27 out of 30 were completed) stated they were satisfied or very satisfied with the various elements of the training package. Analysis of free-text comments and the pharmacists’ diaries showed that the principles of root cause analysis and educational outreach were viewed as useful tools to help pharmacists conduct pharmaceutical interventions in both the study and other pharmacy roles that they undertook. The opportunity to undertake role play was a valuable part of the training received. Conclusions: Findings presented in this paper suggest that providing the PINCER pharmacists with training in root cause analysis and educational outreach contributed to the successful delivery of PINCER interventions and could potentially be utilised by other pharmacists based in general practice to deliver pharmaceutical interventions to improve patient safety.

Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

Background: Early microbial colonization of the gut reduces the incidence of infectious, inflammatory and autoimmune diseases. Recent population studies reveal that childhood hygiene is a significant risk factor for development of inflammatory bowel disease, thereby reinforcing the hygiene hypothesis and the potential importance of microbial colonization during early life. The extent to which early-life environment impacts on microbial diversity of the adult gut and subsequent immune processes has not been comprehensively investigated thus far. We addressed this important question using the pig as a model to evaluate the impact of early-life environment on microbe/host gut interactions during development. Results: Genetically-related piglets were housed in either indoor or outdoor environments or in experimental isolators. Analysis of over 3,000 16S rRNA sequences revealed major differences in mucosa-adherent microbial diversity in the ileum of adult pigs attributable to differences in earlylife environment. Pigs housed in a natural outdoor environment showed a dominance of Firmicutes, in particular Lactobacillus, whereas animals housed in a hygienic indoor environment had reduced Lactobacillus and higher numbers of potentially pathogenic phylotypes. Our analysis revealed a strong negative correlation between the abundance of Firmicutes and pathogenic bacterial populations in the gut. These differences were exaggerated in animals housed in experimental isolators. Affymetrix microarray technology and Real-time Polymerase Chain Reaction revealed significant gut-specific gene responses also related to early-life environment. Significantly, indoorhoused pigs displayed increased expression of Type 1 interferon genes, Major Histocompatibility Complex class I and several chemokines. Gene Ontology and pathway analysis further confirmed these results.

Bacillus subtilis natto: a non-toxic source of poly-γ-glutamic acid that could be used as a cryoprotectant for probiotic bacteria

It is common practice to freeze dry probiotic bacteria to improve their shelf life. However, the freeze drying process itself can be detrimental to their viability. The viability of probiotics could be maintained if they are administered within a microbially produced biodegradable polymer - poly-γ-glutamic acid (γ-PGA) - matrix. Although the antifreeze activity of γ-PGA is well known, it has not been used for maintaining the viability of probiotic bacteria during freeze drying. The aim of this study was to test the effect of γ-PGA (produced by B. subtilis natto ATCC 15245) on the viability of probiotic bacteria during freeze drying and to test the toxigenic potential of B. subtilis natto. 10% γ-PGA was found to protect Lactobacillus paracasei significantly better than 10% sucrose, whereas it showed comparable cryoprotectant activity to sucrose when it was used to protect Bifidobacterium breve and Bifidobacterium longum. Although γ-PGA is known to be non-toxic, it is crucial to ascertain the toxigenic potential of its source, B. subtilis natto. Presence of six genes that are known to encode for toxins were investigated: three component hemolysin (hbl D/A), three component non-haemolytic enterotoxin (nheB), B. cereus enterotoxin T (bceT), enterotoxin FM (entFM), sphingomyelinase (sph) and phosphatidylcholine-specific phospholipase (piplc). From our investigations, none of these six genes were present in B. subtilis natto. Moreover, haemolytic and lecithinase activities were found to be absent. Our work contributes a biodegradable polymer from a non-toxic source for the cryoprotection of probiotic bacteria, thus improving their survival during the manufacturing process.

Analyzing lateral root development: how to move forward

Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.

Shoot yield drives phosphorus use efficiency in Brassica oleracea and correlates with root architecture traits

The environmental and financial costs of using inorganic phosphate fertilizers to maintain crop yield and quality are high. Breeding crops that acquire and use phosphorus (P) more efficiently could reduce these costs. The variation in shoot P concentration (shoot-P) and various measures of P use efficiency (PUE) were quantified among 355 Brassica oleracea L. accessions, 74 current commercial cultivars, and 90 doubled haploid (DH) mapping lines from a reference genetic mapping population. Accessions were grown at two or more external P concentrations in glasshouse experiments; commercial and DH accessions were also grown in replicated field experiments. Within the substantial species-wide diversity observed for shoot-P and various measures of PUE in B. oleracea, current commercial cultivars have greater PUE than would be expected by chance. This may be a consequence of breeding for increased yield, which is a significant component of most measures of PUE, or early establishment. Root development and architecture correlate with PUE; in particular, lateral root number, length, and growth rate. Significant quantitative trait loci associated with shoot-P and PUE occur on chromosomes C3 and C7. These data provide information to initiate breeding programmes to improve PUE in B. oleracea.

Sucrose transport in the phloem: integrating root responses to phosphorus starvation

Sugars in plants, derived from photosynthesis, act as substrates for energy metabolism and the biosynthesis of complex carbohydrates, providing sink tissues with the necessary resources to grow and to develop. In addition, sugars can act as secondary messengers, with the ability to regulate plant growth and development in response to biotic and abiotic stresses. Sugar-signalling networks have the ability to regulate directly the expression of genes and to interact with other signalling pathways. Photosynthate is primarily transported to sink tissues as sucrose via the phloem. Under phosphorus (P) starvation, plants accumulate sugars and starch in their leaves. Increased loading of sucrose to the phloem under P starvation not only functions to relocate carbon resources to the roots, which increases their size relative to the shoot, but also has the potential to initiate sugar-signalling cascades that alter the expression of genes involved in optimizing root biochemistry to acquire soil phosphorus through increased expression and activity of inorganic phosphate transporters, the secretion of acid phosphatases and organic acids to release P from the soil, and the optimization of internal P use. This review looks at the evidence for the involvement of phloem sucrose in co-ordinating plant responses to P starvation at both the transcriptional and physiological levels.

Sugar signaling in root responses to low phosphorus availability

Over the last decade, major advances have been made in our understanding of how plants sense, signal, and respond to soil phosphorus (P) availability (Amtmann et al., 2006; White and Hammond, 2008; Nilsson et al., 2010; Yang and Finnegan, 2010; Vance, 2010; George et al., 2011). Previously, we have reviewed the potential for shoot-derived carbohydrate signals to initiate acclimatory responses in roots to low P availability. In this context, these carbohydrates act as systemic plant growth regulators (Hammond and White, 2008). Photosynthate is transported primarily to sink tissues as Suc via the phloem. Under P starvation, plants accumulate sugars and starch in their leaves. Increased loading of Suc to the phloem under P starvation primarily functions to relocate carbon resources to the roots, which increases their size relative to the shoot (Hermans et al., 2006). The translocation of sugars via the phloem also has the potential to initiate sugar signaling cascades that alter the expression of genes involved plant responses to low P availability. These include optimizing root biochemistry to acquire soil P, through increased expression and activity of inorganic phosphate (Pi) transporters, the secretion of acid phosphatases and organic acids to release P from the soil, and the optimization of internal P use (Hammond and White, 2008). Here, we provide an Update to the field of plant signaling responses to low P availability and the interactions with sugar signaling components. Advances in the P signaling pathways and the roles of hormones in signaling plant responses to low P availability are also reviewed, and where possible their interactions with potential sugar signaling pathways.

Root transcriptional responses of two melon genotypes with contrasting resistance to Monosporascus cannonballus (Pollack et Uecker) infection

Background: Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo 'Piel de sapo' ('PS') and C. melo 'Pat 81', with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. Results: Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. 'PS' responded with a more rapid infection response than 'Pat 81' at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in 'PS' declined from 451 to 359, while the total number of differentially expressed transcripts in 'Pat 81' increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in 'Pat 81' compared to 'PS' suggested that JA response might be partially responsible for their observed differences in resistance. Conclusions: As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.

High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities

Background and Aims: Phosphate (Pi) deficiency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus. Methods: Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus 'Tapidor' x 'Ningyou 7' (TNDH) using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP. Key Results: In general, root and biomass traits were highly correlated under LP and HP conditions. 'Ningyou 7' had greater LRL, LRN and LRD than 'Tapidor', at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06. Conclusions: High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deficiency, and these QTL warrant further dissection.

Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity

Zinc (Zn)-deficient soils constrain rice (Oryza sativa) production and cause Zn malnutrition. The identification of Zn-deficiency-tolerant rice lines indicates that breeding might overcome these constraints. Here, we seek to identify processes underlying Zn-deficiency tolerance in rice at the physiological and transcriptional levels. A Zn-deficiency-tolerant line RIL46 acquires Zn more efficiently and produces more biomass than its nontolerant maternal line (IR74) at low Zn(ext) under field conditions. We tested if this was the result of increased expression of Zn(2+) transporters; increased root exudation of deoxymugineic acid (DMA) or low-molecular-weight organic acids (LMWOAs); and/or increased root production. Experiments were performed in field and controlled environment conditions. There was little genotypic variation in transcript abundance of Zn-responsive root Zn(2+)-transporters between the RIL46 and IR74. However, root exudation of DMA and LMWOA was greater in RIL46, coinciding with increased root expression of putative ligand-efflux genes. Adventitious root production was maintained in RIL46 at low Zn(ext), correlating with altered expression of root-specific auxin-responsive genes. Zinc-deficiency tolerance in RIL46 is most likely the result of maintenance of root growth, increased efflux of Zn ligands, and increased uptake of Zn-ligand complexes at low Zn(ext); these traits are potential breeding targets.