Recurrence of IgA nephropathy after kidney transplantation: experience from the Swiss transplant cohort study.

BACKGROUND: Recurrence of IgA nephropathy (IgAN) after kidney transplantation occurs in about 30% of patients. The relevance of recurrence for the long-term graft survival is expected to increase, since graft survival continues to improve. METHODS: In a nested study within the Swiss Transplant Cohort Study the incidence of IgAN recurrence, predictive factors, graft function and graft and patient survival were evaluated. Serum concentration of total IgA, total IgG, Gd-IgA1 and IgA-IgG immune complex were measured using ELISA-based immunologic assays. RESULTS: Between May 2008 and December 2016, 28 women and 133 men received their kidney allograft for end-stage kidney disease due to IgAN in Switzerland. Over a median follow-up time of 7 years after transplantation, 43 out of 161 patients (26.7%) developed an IgAN recurrence, of which six (13.9%) had an allograft failure afterwards and further four patients (9.3%) died. During the same follow-up period, 6 out of 118 patients (5%) each experienced allograft failure or died without prior IgAN recurrence. After 11 years the risk for IgAN recurrence was 27.7% (95%-CI: 20.6-35.3%). Renal function was similar in patients with and without recurrence up to 7 years after transplantation, but worsened thereafter in patients with recurrence (eGFR median (interquartile range) at 8 years: 49 ml/min/1.73m2 (29-68) vs. 60 ml/min/1.73m2 (38-78)). Serum concentration of total IgA, total IgG, Gd-IgA1 and IgA-IgG immune complex within the first year posttransplant showed no significant effect on the recurrence of IgAN. Younger recipients and women had a higher risk of recurrence, but the latter only in the short term. CONCLUSIONS: Our study showed a recurrence risk of 28% at 11 years after transplantation, which is consistent with previous literature. However, the predictive value of known biomarkers, such as serum Gd-IgA1 and IgA-IgG IC, for IgAN recurrence could not be confirmed.

Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression.

Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.

Insights into the molecular mechanisms of pesticide tolerance in the Aporrectodea caliginosa earthworm.

Diffuse pollution of the environment by pesticides has become a major soil threat to non-target organisms, such as earthworms for which declines have been reported. However some endogeic species are still abundant and persist in intensively cultivated fields, suggesting they become tolerant to long-term anthropogenic pressure. We thus considered the working hypothesis that populations of Aporrectodea caliginosa earthworms from conventionally managed fields developed a tolerance to pesticides compared with those from organically managed fields. To investigate this hypothesis, we studied earthworm populations of the same genetic lineage from soils that were either lowly or highly contaminated by pesticides to detect any constitutive expression of differentially expressed molecular pathways between these populations. Earthworm populations were then experimentally exposed to a fungicide-epoxiconazole-in the laboratory to identify different molecular responses when newly exposed to a pesticide. State-of-the-art omics technology (RNA sequencing) and bioinformatics were used to characterize molecular mechanisms of tolerance in a non-targeted way. Additional physiological traits (respirometry, growth, bioaccumulation) were monitored to assess tolerance at higher levels of biological organization. In the present study, we generated the de novo assembly transcriptome of A. caliginosa consisting of 64,556 contigs with N50 = 2862 pb. In total, 43,569 Gene Ontology terms were identified for 21,593 annotated sequences under the three main ontologies (biological processes, cellular components and molecular functions). Overall, we revealed that two same lineage populations of A. caliginosa earthworms, inhabiting similar pedo-climatic environment, have distinct gene expression pathways after they long-lived in differently managed agricultural soils with a contrasted pesticide exposure history for more than 22 years. The main difference was observed regarding metabolism, with upregulated pathways linked to proteolytic activities and the mitochondrial respiratory chain in the highly exposed population. This study improves our understanding of the long-term impact of chronic exposure of soil engineers to pesticide residues.

Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics.

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.

Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects.

Agriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested.

Response of phytoplankton community to low-dose atrazine exposure combined with phosphorus fluctuations.

The effects of atrazine on a controlled phytoplankton community derived from a natural freshwater wetland exposed to low doses of this photosynthesis-inhibiting herbicide were examined. The community was exposed for 7 weeks to doses of 0.1, 1, and 10 microg L(-1) atrazine, combined with changes in nutrient concentration, and the photosynthetic activity, biomass, and community structure were noted during the experiment. Responses of the phytoplankton community were examined in terms of photosynthetic activity, biomass, and community structure. Significant effects of atrazine on the phytoplankton assemblage, in terms of primary production and community structure, were highlighted, even at doses as low as 1 and 0.1 microg L(-1), when associated with phosphorus fluctuations. The most abundant Chlorophyceae decreased in concentration with increasing atrazine dose, whereas cyanobacteria were more tolerant to atrazine, particularly with increased nutrient supply. The subinhibitory doses of atrazine used in the present study confirmed the higher sensitivity of long-term exposure of multispecies assemblages under resource competition. Our study supports the emerging hypothesis that the increasing prevalence of cyanobacterial blooms in European aquatic systems may result from a combination of unbalanced nutrient enrichment and selective pressures from multiple toxicants.

Higher serum galactose-deficient immunoglobulin A1 concentration is associated with stronger mesangial cellular inflammatory response and more severe histologic findings in immunoglobulin A nephropathy.

BACKGROUND: Galactose-deficient immunoglobulin A1 (Gd-IgA1) is known to play a key role in the pathogenesis of IgA nephropathy (IgAN). We aimed to evaluate whether serum Gd-IgA1 is associated with in vitro activation of mesangial cells in individual patients and how this affects the clinical and histologic parameters. METHODS: Serum samples and clinical and histologic data were collected in the University Hospital Basel and Hammersmith Hospital, London. Serum levels of IgA1 and Gd-IgA1 were measured by enzyme-linked immunosorbent assay (ELISA) and lectin-binding assay using lectin Helix aspersa (HA). Primary human mesangial cells were stimulated with IgA1 isolated from serum from individual patients and the concentrations of monocyte chemoattractant protein-1 and interleukin-6 were measured in cell culture supernatant by ELISA. RESULTS: Thirty-three patients were enrolled. A significant correlation was observed between serum Gd-IgA1 levels and the concentration of MCP-1 in the culture supernatant in individual patients (Spearman r = 0.5969, P = 0.0002). There was no significant correlation between serum Gd-IgA1 levels and proteinuria or estimated glomerular filtration rate at diagnosis. However, the serum Gd-IgA1 level was significantly higher in patients with segmental glomerulosclerosis (S0 versus S1, P = 0.0245) and tubular atrophy/interstitial fibrosis (T0 versus T1 and T2, P = 0.0336; T0 versus T2, P = 0.0225). CONCLUSIONS: Higher serum Gd-IgA1 concentration is associated with stronger mesangial cell inflammatory response with production of a greater amount of MCP-1 in vitro. This in turn is associated with severe histologic changes. The disease progression with worse renal outcome in patients with higher serum Gd-IgA1 may be therefore mediated by more pronounced mesangial cell inflammatory response leading to more severe histologic changes.

Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization.

Agriculture is undergoing important changes in order to meet sustainable soil management with respect to biodiversity (namely agroecology). Within this context, alternative solutions to mineral fertilizers such as agricultural biostimulants are thus promoted and being developed. The mechanisms by which some soil biostimulants sustain soil biological functioning and indirectly increase crop yields are still unknown. Our goal in the present study was to demonstrate if and to what extent the application of a soil biostimulant affects the soil heterotrophic microbial communities that are involved in organic matter decomposition and carbon mineralization. We hypothesized that the addition of a biostimulant results in changes in the composition and in the biomass of soil microbial communities. This in turn increases the mineralization of the organic matter derived from crop residues. We performed soil microcosm experiments with the addition of crop residues and a biostimulant, and we monitored the organic carbon (orgC) mineralization and the microbial biomass, along with the microbial community composition by sequencing 16S rRNA gene and ITS amplicons. The addition of a soil biostimulant caused a pH neutralizing effect and simultaneous enhancement of the orgC mineralization of crop residues (+ 400 µg orgC g-1 dry soil) and microbial biomass (+ 60 µg orgC g-1 dry soil) that were linked to changes in the soil microbial communities. Our findings suggest that the soil carbon mineralization enhancement in the presence of the biostimulant was supported by the specific recruitment of soil bacteria and fungi. Whereas archaea remained stable, several operational taxonomic units (OTUs) of indigenous soil bacteria and fungi were enriched and affiliated with known microbial decomposers such as Cytophagaceae, Phaselicystis sp., Verrucomicrobia, Pseudomonas sp., Ramicandelaber sp., and Mortierella sp., resulting in lower soil microbial richness and diversity.

Sucrose amendment enhances phytoaccumulation of the herbicide atrazine in Arabidopsis thaliana.

Growth in the presence of sucrose was shown to confer to Arabidopsis thaliana (thale cress or mustard weed) seedlings, under conditions of in vitro culture, a high level of tolerance to the herbicide atrazine and to other photosynthesis inhibitors. This tolerance was associated with root-to-shoot transfer and accumulation of atrazine in shoots, which resulted in significant decrease of herbicide levels in the growth medium. In soil microcosms, application of exogenous sucrose was found to confer tolerance and capacity to accumulate atrazine in Arabidopsis thaliana plants grown on atrazine-contaminated soil, and resulted in enhanced decontamination of the soil. Application of sucrose to plants grown on herbicide-polluted soil, which increases plant tolerance and xenobiotic absorption, thus appears to be potentially useful for phytoremediation.

Interactions of earthworms with Atrazine-degrading bacteria in an agricultural soil.

In the last 10 years, accelerated mineralization of Atrazine (2-chloro-ethylamino-6-isopropylamino-s-triazine) has been evidenced in agricultural soils repeatedly treated with this herbicide. Here, we report on the interaction between earthworms, considered as soil engineers, and the Atrazine-degrading community. The impact of earthworm macrofauna on Atrazine mineralization was assessed in representative soil microsites of earthworm activities (gut contents, casts, burrow linings). Soil with or without earthworms, namely the anecic species Lumbricus terrestris and the endogenic species Aporrectodea caliginosa, was either inoculated or not inoculated with Pseudomonas sp. ADP, an Atrazine-degrading strain, and was either treated or not treated with Atrazine. The structure of the bacterial community, the Atrazine-degrading activity and the abundance of atzA, B and C sequences in soil microsites were investigated. Atrazine mineralization was found to be reduced in representative soil microsites of earthworm activities. Earthworms significantly affected the structure of soil bacterial communities. They also reduced the size of the inoculated population of Pseudomonas sp. ADP, thereby contributing to the diminution of the Atrazine-degrading genetic potential in representative soil microsites of earthworm activities. This study illustrates the regulation produced by the earthworms on functional bacterial communities involved in the fate of organic pollutants in soils.

Earthworm tolerance to residual agricultural pesticide contamination: field and experimental assessment of detoxification capabilities.

This study investigates if acclimatization to residual pesticide contamination in agricultural soils is reflected in detoxification, antioxidant enzyme activities and energy budget of earthworms. Five fields within a joint agricultural area exhibited different chemical and farming histories from conventional cultivation to organic pasture. Soil multiresidual pesticide analysis revealed up to 9 molecules including atrazine up to 2.4 ng g(-1) dry soil. Exposure history of endogeic Aporrectodea caliginosa and Allolobophora chlorotica modified their responses to pesticides. In the field, activities of soluble glutathione-S-transferases (sGST) and catalase increased with soil pesticide contamination in A. caliginosa. Pesticide stress was reflected in depletion of energy reserves in A. chlorotica. Acute exposure of pre-adapted and naïve A. caliginosa to pesticides (fungicide Opus(®), 0.1 µg active ingredient epoxiconazole g(-1) dry soil, RoundUp Flash(®), 2.5 µg active ingredient glyphosate g(-1) dry soil, and their mixture), revealed that environmental pre-exposure accelerated activation of the detoxification enzyme sGST towards epoxiconazole.

Relationship between bacterial diversity and function under biotic control: the soil pesticide degraders as a case study.

In soil, the way biotic parameters impact the relationship between bacterial diversity and function is still unknown. To understand these interactions better, we used RNA-based stable-isotope probing to study the diversity of active atrazine-degrading bacteria in relation to atrazine degradation and to explore the impact of earthworm-soil engineering with respect to this relationship. Bulk soil, burrow linings and earthworm casts were incubated with (13)C-atrazine. The pollutant degradation was quantified by liquid chromatography-mass spectrometry for 8 days, whereas active atrazine degraders were identified at 2 and 8 days by sequencing the 16S ribosomal RNA in the (13)C-RNA fractions from the three soil microsites. An original diversity of atrazine degraders was found. Earthworm soil engineering greatly modified the taxonomic composition of atrazine degraders with dominance of α-, ß- and γ-proteobacteria in burrow linings and of Actinobacteria in casts. Earthworm soil bioturbation increased the γ-diversity of atrazine degraders over the soil microsites generated. Atrazine degradation was enhanced in burrow linings in which primary atrazine degraders, closely related to Pelomonas aquatica, were detected only 2 days after atrazine addition. Atrazine degradation efficiency was not linearly related to the species richness of degraders but likely relied on keystone species. By enhancing soil heterogeneity, earthworms sustained high phylogenetic bacterial diversity and exerted a biotic control on the bacterial diversity-function relationships. Our findings call for future investigations to assess the ecological significance of biotic controls on the relationships between diversity and function on ecosystem properties and services (for example, soil detoxification) at larger scales.

Development of a new tool to improve gene transfer frequency calculations.

Gene transfer frequency can be determined experimentally on plates, but the methods currently in use do not discriminate between independent transfers and clonal multiplication of initial transformants. In order to overcome this bias, we engineered an Acinetobacter baylyi population in which cells differed by a specific molecular signature and used it as recipient in transformation experiments. Our results suggest that a corrective factor of 0.52 should be applied in order to accurately report natural transformation when using the plate counting method.