Using transects to disentangle the environmental drivers of plant-microbiome assembly

Environmental heterogeneity is a major driver of plant-microbiome assembly, but the specific climate and soil conditions that are involved remain poorly understood. To better understand plant microbiome formation, we examined the bacteria and fungi that colonize wild strawberry (Fragaria vesca) plants in North American and European populations. Using transects as replicates, we found strong overlap among the environmental conditions that best predict the overall similarity and richness of the plant microbiome, including soil nutrients that replicate across continents. Temperature is also among the main predictors of diversity for both bacteria and fungi in both the leaf and, unexpectedly, the root microbiome. Our results indicate that a small number of environmental factors, and their interactions, consistently contribute to plant microbiome formation, which has implications for predicting the contributions of microbes to plant productivity in ever-changing environments.

The influence of host genetics on the microbiome

It is well understood that genetic differences among hosts contribute to variation in pathogen susceptibility and the ability to associate with symbionts. However, it remains unclear just how influential host genes are in shaping the overall microbiome. Studies of both animal and plant microbial communities indicate that host genes impact species richness and the abundances of individual taxa. Analyses of beta diversity (that is, overall similarity), on the other hand, often conclude that hosts play a minor role in shaping microbial communities. In this review, we discuss recent attempts to identify the factors that shape host microbial communities and whether our understanding of these communities is affected by the traits chosen to represent them.

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.

The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana

The capacity to tolerate freezing temperatures limits the geographical distribution of many plants, including several species of agricultural importance. However, the genes involved in freezing tolerance remain largely unknown. Here, we describe the variation in constitutive freezing tolerance that occurs among worldwide accessions of Arabidopsis thaliana. We found that although plants from high latitudes tend to be more freezing tolerant than plants from low latitudes, the environmental factors that shape cold adaptation differ across the species range. Consistent with this, we found that the genetic architecture of freezing tolerance also differs across its range. Conventional genome-wide association studies helped identify a priori and other promising candidate genes. However, simultaneously modelling climate variables and freezing tolerance together pinpointed other excellent a priori candidate genes. This suggests that if the selective factor underlying phenotypic variation is known, multi-trait mixed models may aid in identifying the genes that underlie adaptation.

Genome-wide association study of Arabidopsis thaliana leaf microbial community

Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

Genomic variability as a driver of plant-pathogen coevolution?

Pathogens apply one of the strongest selective pressures in plant populations. Understanding plant-pathogen coevolution has therefore been a major research focus for at least sixty years [1]. Recent comparative genomic studies have revealed that the genes involved in plant defense and pathogen virulence are among the most polymorphic in the respective genomes. Which fraction of this diversity influences the host-pathogen interaction? Do coevolutionary dynamics maintain variation? Here we review recent literature on the evolutionary and molecular processes that shape this variation, focusing primarily on gene-for-gene interactions. In summarizing theoretical and empirical studies of the processes that shape this variation in natural plant and pathogen populations, we find a disconnect between the complexity of ecological interactions involving hosts and their myriad microbes, and the models that describe them.

Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana

Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root) and habitat (epiphytes vs endophytes) structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024), while the reverse is true for the leaves (P = 0.032). Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001). The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

GWAPP: a web application for genome-wide association mapping in Arabidopsis

Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.

Adaptation to climate across the Arabidopsis thaliana genome

Understanding the genetic bases and modes of adaptation to current climatic conditions is essential to accurately predict responses to future environmental change. We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino acid-changing variants were significantly enriched among the loci strongly correlated with climate, suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown together in a common environment. Our results provide a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.

Contrasting mechanisms of secondary metabolite accumulation during leaf development in two tropical tree species with different leaf expansion strategies

Young leaves of most species experience remarkably higher herbivore attack rates than mature leaves. Considerable theoretical effort has focused on predicting optimal defense and tradeoffs in defense allocation during leaf expansion. Among others, allocation to secondary chemistry may be dependent on growth constraints. We studied flavanoid production during leaf development in two species of Inga (Fabaceae: Mimosoideae) with different expansion strategies: Inga goldmanii, a species with slowly expanding young leaves, and Inga umbellifera, a species with fast-expanding young leaves. In these two species, the most abundant and toxic class of defensive compounds is flavanoids (which include tannins). We measured their concentration by leaf dry weight, their total content per leaf, their HPLC chemical profile and their toxicity to a generalist herbivore at different expansion levels. Although in both species the flavanoid concentration decreased with increasing leaf expansion, that decrease was twice as pronounced for I. umbellifera as it was for I. goldmanii. I. umbellifera leaves produced flavanoids only during the first half of their development while I. goldmanii leaves continued production throughout. The changes in flavanoid HPLC profiles and toxicity were also more dramatic for I. umbellifera, which had different flavanoids in young than in mature leaves. Relative to I. umbellifera, I. goldmanii showed smaller changes in both flavanoid composition and toxicity in the transition from young to mature leaves. These results indicate that, even though young leaves suffer higher rates of attack and are predicted to have better chemical defenses than mature leaves, growth constraints may modulate defense allocation and thus, evolution of defense strategies.

Multiple-dose pharmacokinetics of pentoxifylline and its metabolites during renal insufficiency

OBJECTIVE

To characterize pentoxifylline (PTF) and metabolite disposition after multiple oral doses given two and three times a day to patients with renal dysfunction.

DESIGN

An open-label, randomized, crossover, parallel group design.

SETTING

Community-based clinical research center. PATIENT POPULATIONS: Subjects with renal function stratified based on 24-hour urinary creatine clearance (Clcr): group I = Clcr > 80 mL/min (n = 9); group II = Clcr 30-80 mL/min (n = 6); and group III = Clcr < 30 mL/min (n = 10).

METHODS

PTF 400 mg bid or tid was administered on days 1-7 and 400 mg bid or tid was given on days 14-20 with a 1-week washout. Timed blood samples were taken on days 1, 7, and 20. Blood samples were analyzed for PTF and its metabolites (M-I, M-IV, M-V) by gas-liquid chromatography.

MAIN OUTCOME MEASURES

Maximum plasma concentrations (Cmax), time to maximum concentration (tmax), average steady-state plasma concentration (CavgSS), and area under the plasma concentration-time curve at steady-state (AUCSS) were determined by visual and model independent methods. ANOVA, paired t-test, and linear regression were used with significance level set at p < 0.05.

RESULTS

The ratio of PTF AUCSS (tid):AUCSS (bid) and M-I AUCSS (bid and tid) were not significantly different between the groups. Significant differences were found in M-IV and M-V Cmax, AUCSS, CavgSS, and AUCSS ratios (M-IV:PTF and M-V:PTF) between renal function groups (p < 0.05 for all). A change in dosage regimen from tid to bid resulted in significant changes in M-IV and M-V CavgSS for subjects with normal renal function and in those with moderate dysfunction, although not in subjects with severe renal dysfunction.

CONCLUSIONS

Renal dysfunction did not cause significant accumulations of PTF or M-I after multiple bid and tid dosing, however, M-IV and M-V had significant accumulation in patients with renal impairment. Dosage reduction to 400 mg bid for patients with moderate renal impairment and 200-400 mg/d for severe renal impairment, as well as close clinical monitoring, seem prudent until the complex pharmacologic interactions of PTF and its metabolites can be further delineated.

Purified factor IX using monoclonal immunoaffinity technique: clinical trials in hemophilia B and comparison to prothrombin complex concentrates

Replacement therapy for hemophilia B (factor IX deficiency) using prothrombin complex concentrate (PCC) has been associated with serious complications of thromboembolic events and transmission of viral infections. Monoclonal antibody-purified factor IX (Mononine) provides a highly purified factor IX concentrate, while eliminating other vitamin K-dependent factors (II, VII, and X). Mononine was evaluated for in vivo recovery, half-life, and for its safety and efficacy in 10 patients with hemophilia B. The in vivo recovery of factor IX with Mononine was a 0.67 +/- 0.14 U/dL (mean +/- SD) increase per 1U/kg of infused factor IX, and the biologic half-life (t1/2), determined using the terminal phase of elimination, was 22.6 +/- 8.1 hours. Comparison of in vivo recovery of other vitamin K-dependent factors following a single infusion of either Mononine or PCC showed that, whereas Mononine infusion caused no changes in other vitamin K-dependent factors or in prothrombin activation fragment (F1+2), PCC infusion was associated with significant increases of factors II (2.7 U/dL per 1 U/dL of IX increase) and X (2.2 U/dL for 1 U/dL for 1 U/dL of IX). Patients who used Mononine as their sole therapeutic material during the 12-month period showed an excellent response in hemostasis for their bleeding episodes. Their experience with long-term use of Mononine was at least equivalent to their previous experience with PCC in the frequency and amount of factor usage. No patients developed antibody against mouse IgG or an increase in IX inhibitor during the 12-month period. These results indicate that monoclonal antibody-purified factor IX concentrate provides hemostatically effective factor IX replacement while avoiding extraneous thrombogenic substances.

Estimation of theophylline clearance during continuous arteriovenous hemofiltration

Pharmacologic agents and other non-protein-bound compounds smaller than 5,000 daltons have the potential to be removed by continuous arteriovenous hemofiltration (CAVH). A proposed method for estimating drug clearance by CAVH (ClCAVH) equates ultrafiltrate clearance to the product of the sieving coefficient and the average ultrafiltration rate. This simplified approach for estimating ClCAVH would be a clinically useful method for calculating replacement doses, as it economizes on the sampling and analytical requirements associated with the conventional method. Presented are some theoretical considerations and a brief evaluation of the accuracy of this proposed method. The evaluation was conducted using an animal model whereby CAVH was performed in four male beagles. During the hemofiltration period, an i.v. bolus of theophylline, 6 mg/kg, was administered over 15 s. Samples for analysis of theophylline were collected from the arterial, venous, and ultrafiltrate ports at 0, 5, 15, 30, 45, 60, 90, 120, 180, 240, 360, and 480 min following dosage administration. The volume of ultrafiltrate produced during each collection interval was measured. Theophylline serum concentrations were determined by a high performance liquid chromatography assay. Statistically, the simplified method was found to result in significantly (p less than 0.05) larger estimates of ultrafiltrate clearance when compared to the conventional method. However, the average magnitude of difference was only 9% and does not constitute a clinically significant margin between the two methods.

Effect of predialysis verapamil on intradialytic blood pressure in chronic hemodialysis patients

Decreased left ventricular compliance because of hypertrophy or fibrosis may contribute to hypotension during hemodialysis. While calcium channel blockade may reduce intradialytic hypotension in patients with left ventricular hypertrophy and refractory pulmonary congestion, it is unknown whether such an effect might be seen in unselected hemodialysis patients. Verapamil (40 mg) or a placebo was given 1 hour before hemodialysis to 10 patients in a double-blind crossover study. Two 2 week verapamil periods alternated with two 2 week placebo periods. Patients received bicarbonate for either 3 hours (7 patients, high-flux, Filtral, Gambro-Hospal Inc., Williamsburg, VA) or for 4 hours (3 patients, Travenol 15.11 or CA 110, Baxter Healthcare, Deerfield, IL). Left ventricular hypertrophy was present by ultrasound in 7 of 8 patients tested and by electrocardiogram in 1 of the remaining 2. Intradialytic blood pressures were similar during the drug and placebo trials. The number of episodes of symptomatic hypotension per hemodialysis was 0.99 with verapamil and 0.93 during the placebo periods (p less than 0.05). Thus, a single predialysis dosage of verapamil has no effect on intradialytic blood pressure in an unselected hemodialysis population.

Marked digoxin-like immunoreactive factor interference with an enzyme immunoassay

A case in which digoxin-like immunoreactive factors (DLIF) interfered with an enzyme immunoassay in a patient with renal insufficiency is reported. A 79-year-old woman was found to have a serum digoxin concentration (SDC) determined by enzyme immunoassay of 5.0 ng/ml. Although all subsequent SDC determined by the enzyme immunoassay system were elevated, identical samples run on a fluorescence polarization immunoassay revealed SDC within the therapeutic range. Marked DLIF-related assay interference has been reported to occur with some digoxin assays; however, the enzyme immunoassay methods have never been reported to cross-react to the magnitude seen in this case.

Continuous arteriovenous hemofiltration: an alternative to hemodialysis

An introduction to the procedure of continuous arteriovenous hemofiltration (CAVH) for management of acute renal failure, as well as a review of hemodialysis, is presented. Initially developed for the management of hemodynamically unstable patients with acute renal failure, CAVH now is also used for management of fluid overload and acid-base disturbances resulting from conditions such as acute pulmonary edema, congestive heart failure, septic shock, and oliguric states in which pharmacologic or parenteral nutrition therapy necessitates administration of large volumes of fluids. CAVH, in contrast to hemodialysis, does not typically involve use of blood pumps but uses the patient's own mean arterial pressure to generate a driving force across the hemofilter membrane. CAVH, like hemodialysis, can remove excess fluid and uremic toxins; however, fluid removal by CAVH is characterized by the slow, continuous process of ultrafiltration and thus avoids the risk of hypotension, muscle cramps, or disequilibrium syndrome. Furthermore, CAVH does not require fluid restriction, allowing for increased administration of parenteral nutrition and intravenous medications; neither does it require expensive equipment or highly trained personnel. Although CAVH membrane materials may differ, they all permit the removal of plasma water and non-protein-bound solutes with molecular weights less than 10,000. To prevent blood from clotting in the hemofilter, most patients will require administration of heparin, which in some patients may increase the possibility of hemorrhaging. CAVH also can remove pharmacologic agents from the blood; however, only the non-protein-bound fraction of the drug has the potential to be cleared from the bloodstream by CAVH.(ABSTRACT TRUNCATED AT 250 WORDS)