Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes

Phenazines are natural bacterial antibiotics that can protect crops from disease. However, for most crops it is unknown which producers and specific phenazines are ecologically relevant, and whether phenazine biodegradation can counter their effects. To better understand their ecology, we developed and environmentally-validated a quantitative metagenomic approach to mine for phenazine biosynthesis and biodegradation genes, applying it to >800 soil and plant-associated shotgun-metagenomes. We discover novel producer-crop associations and demonstrate that phenazine biosynthesis is prevalent across habitats and preferentially enriched in rhizospheres, whereas biodegrading bacteria are rare. We validate an association between maize and Dyella japonica, a putative producer abundant in crop microbiomes. D. japonica upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This work provides a global picture of phenazines in natural environments and highlights plant-microbe associations of agricultural potential. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems

Benchmarking organic electrochemical transistors for plant electrophysiology

Plants are able to sense and respond to a myriad of external stimuli, using different signal transduction pathways, including electrical signaling. The ability to monitor plant responses is essential not only for fundamental plant science, but also to gain knowledge on how to interface plants with technology. Still, the field of plant electrophysiology remains rather unexplored when compared to its animal counterpart. Indeed, most studies continue to rely on invasive techniques or on bulky inorganic electrodes that oftentimes are not ideal for stable integration with plant tissues. On the other hand, few studies have proposed novel approaches to monitor plant signals, based on non-invasive conformable electrodes or even organic transistors. Organic electrochemical transistors (OECTs) are particularly promising for electrophysiology as they are inherently amplification devices, they operate at low voltages, can be miniaturized, and be fabricated in flexible and conformable substrates. Thus, in this study, we characterize OECTs as viable tools to measure plant electrical signals, comparing them to the performance of the current standard, Ag/AgCl electrodes. For that, we focused on two widely studied plant signals: the Venus flytrap (VFT) action potentials elicited by mechanical stimulation of its sensitive trigger hairs, and the wound response of Arabidopsis thaliana. We found that OECTs are able to record these signals without distortion and with the same resolution as Ag/AgCl electrodes and that they offer a major advantage in terms of signal noise, which allow them to be used in field conditions. This work establishes these organic bioelectronic devices as non-invasive tools to monitor plant signaling that can provide insight into plant processes in their natural environment

Karstification in the Cuddapah Sedimentary Basin, Southern India: Implications for Groundwater Resources

The Cuddapah sedimentary basin extends over a significant part of the southern part of Andhra Pradesh State, Southern India. Proterozoic carbonate rocks in the basin are constituted by as three main units- the Vempalle dolomite, the Narji and Koilkuntla limestones. These carbonate rocks are of strategic importance for local communities as they provide the main water source for irrigation and domestic use and they are also intensively quarried for cement production and building stones. It is therefore, of primary importance to assess to which extent these carbonate units are karstified so as to provide recommendations for appropriate land and water resource management. The field investigations carried out indicate that these carbonate units are significantly karstified and karstification has been an ongoing process with several phases under variable climatic conditions. As a result, a significant part of aquifer recharge occurs as point-recharge through swallow-holes and groundwater flow is channelized by conduit networks which emerge at karst springs. Karst development was possibly more active during past humid conditions; however karstification is still an ongoing process under the present semi-arid climate especially in the favorable case where karst drains the runoff issued from upstream quartzitic hills. The karstic nature of these carbonate units need to be integrated in future research and development programmes to avoid practices that may lead to unexpected collapses, reservoir leaks, inaccurate groundwater budgeting, etc

A rhlI 5′ UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in Pseudomonas aeruginosa

N-Acyl homoserine lactone (AHL) quorum sensing (QS) controls expression of over 200 genes in Pseudomonas aeruginosa. There are two AHL regulatory systems: the LasR-LasI circuit and the RhlR-RhlI system. We mapped transcription termination sites affected by AHL QS in P. aeruginosa, and in doing so we identified AHL-regulated small RNAs (sRNAs). Of interest, we noted that one particular sRNA was located within the rhlI locus. We found that rhlI, which encodes the enzyme that produces the AHL N-butanoyl-homoserine lactone (C4-HSL), is controlled by a 5′ untranslated region (UTR)-derived sRNA we name RhlS. We also identified an antisense RNA encoded opposite the beginning of the rhlI open reading frame, which we name asRhlS. RhlS accumulates as wild-type cells enter stationary phase and is required for the production of normal levels of C4-HSL through activation of rhlI translation. RhlS also directly posttranscriptionally regulates at least one other unlinked gene, fpvA. The asRhlS appears to be expressed at maximal levels during logarithmic growth, and we suggest RhlS may act antagonistically to the asRhlS to regulate rhlI translation. The rhlI-encoded sRNAs represent a novel aspect of RNA-mediated tuning of P. aeruginosa QS

Assessment and visualization of phenome-wide causal relationships using genetic data:an application to dental caries and periodontitis

Hypothesis-free Mendelian randomization studies provide a way to assess the causal relevance of a trait across the human phenome but can be limited by statistical power, sample overlap or complicated by horizontal pleiotropy. The recently described latent causal variable (LCV) approach provides an alternative method for causal inference which might be useful in hypothesis-free experiments across human phenome. We developed an automated pipeline for phenome-wide tests using the LCV approach including steps to estimate partial genetic causality, filter to a meaningful set of estimates, apply correction for multiple testing and then present the findings in a graphical summary termed causal architecture plot. We apply this pipeline to body mass index (BMI) and lipid traits as exemplars of traits where there is strong prior expectation for causal effects, and to dental caries and periodontitis as exemplars of traits where there is a need for causal inference. The results for lipids and BMI suggest that these traits are best viewed as contributing factors on a multitude of traits and conditions, thus providing additional evidence that supports viewing these traits as targets for interventions to improve health. On the other hand, caries and periodontitis are best viewed as a downstream consequence of other traits and diseases rather than a cause of ill health. The automated pipeline is implemented in the Complex-Traits Genetics Virtual Lab ( https://vl.genoma.io ) and results are available in https://view.genoma.io . We propose causal architecture plots based on phenome-wide partial genetic causality estimates as a new way visualizing the overall causal map of the human phenome

Investigating a Potential Causal Relationship Between Maternal Blood Pressure During Pregnancy and Future Offspring Cardiometabolic Health

Observational epidemiological studies have reported that higher maternal blood pressure (BP) during pregnancy is associated with increased future risk of offspring cardiometabolic disease. However, it is unclear whether this association represents a causal relationship through intrauterine mechanisms. We used a Mendelian randomization (MR) framework to examine the relationship between unweighted maternal genetic scores for systolic BP and diastolic BP and a range of cardiometabolic risk factors in the offspring of up to 29 708 genotyped mother-offspring pairs from the UKB study (UK Biobank) and the HUNT study (Trøndelag Health). We conducted similar analyses in up to 21 423 father-offspring pairs from the same cohorts. We confirmed that the BP-associated genetic variants from the general population sample also had similar effects on maternal BP during pregnancy in independent cohorts. We did not detect any association between maternal (or paternal) unweighted genetic scores and cardiometabolic offspring outcomes in the meta-analysis of UKB and HUNT after adjusting for offspring genotypes at the same loci. We find little evidence to support the notion that maternal BP is a major causal risk factor for adverse offspring cardiometabolic outcomes in later life