Genetic analysis and phenotypic characterization of three novel genes of Rhizobium tropici CIAT899 involved in symbiotic interactions with Phaseolus vulgaris

Rhizobium tropici CIAT899 is highly tolerant to many environmental stresses and a good competitor for nodule occupancy of Phaseolus vulgaris. Random transposon mutagenesis was performed with the aim to identify novel genes of this strain involved in symbiosis and stress tolerance. The analysis of the locus disrupted by the Tn5 insertion in mutants 899-PV9 and 899-PV4 led the discovery of three novel genes required for and efficient symbiotic interaction with beans plants. The first gene (syc1) bears significant similarity to voltage-gated chloride channels. A non-polar deletion in this gene caused serious deficiencies for nodule establishment, nodulation competitiveness and N2 fixation, probably due to its reduced ability to invade plant cells and to form stable symbiosomes, as judged by electron transmission microscopy. A second gene (olsC) found downstream of the former was shown to be homologous with aspartyl/asparaginyl β-hydroxylases and involved in the modification of two species of ornithine-containing lipids, presumably by a hydroxylation. A mutant carrying a non-polar deletion in olsC was symbiotically defective, whereas over-expressed OlsC in the complemented strain was related with an acid-sensitive phenotype. The third gene (sigE) codes for a putative σE factor. Analysis performed on the mutant carrying a deletion in this gene also revealed serious deficiencies for nodule development, nodulation competitiveness and N2 fixation when inoculated on bean plants. These three different bacterial activities have not been previously reported as required for the symbiotic interaction of rhizobia with its legume host

Genetic analysis and phenotypic characterization of three novel genes of Rhizobium tropici CIAT899 involved in symbiotic interactions with Phaseolus vulgaris

Rhizobium tropici CIAT899 is highly tolerant to many environmental stresses and a good competitor for nodule occupancy of Phaseolus vulgaris. Random transposon mutagenesis was performed with the aim to identify novel genes of this strain involved in symbiosis and stress tolerance. The analysis of the locus disrupted by the Tn5 insertion in mutants 899-PV9 and 899-PV4 led the discovery of three novel genes required for and efficient symbiotic interaction with beans plants. The first gene (syc1) bears significant similarity to voltage-gated chloride channels. A non-polar deletion in this gene caused serious deficiencies for nodule establishment, nodulation competitiveness and N2 fixation, probably due to its reduced ability to invade plant cells and to form stable symbiosomes, as judged by electron transmission microscopy. A second gene (olsC) found downstream of the former was shown to be homologous with aspartyl/asparaginyl β-hydroxylases and involved in the modification of two species of ornithine-containing lipids, presumably by a hydroxylation. A mutant carrying a non-polar deletion in olsC was symbiotically defective, whereas over-expressed OlsC in the complemented strain was related with an acid-sensitive phenotype. The third gene (sigE) codes for a putative σE factor. Analysis performed on the mutant carrying a deletion in this gene also revealed serious deficiencies for nodule development, nodulation competitiveness and N2 fixation when inoculated on bean plants. These three different bacterial activities have not been previously reported as required for the symbiotic interaction of rhizobia with its legume host

A Salinity Threshold Separating Fungal Communities in the Baltic Sea

Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world’s largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm

Phylogenetic and Functional Diversity of Saprolegniales and Fungi Isolated from Temperate Lakes in Northeast Germany

Funding: This research was funded by the Iranian Ministry of Science, Research, and Technology and DAAD (German Academic Exchange Service). The APC was funded by the Leibniz Association. Acknowledgments: The publication of this article was funded by the Open Access Fund of the Leibniz Association.Peer reviewedPublisher PD

Microplastics in feed cause sublethal changes in the intestinal microbiota and a non-specific immune response indicator of the freshwater crayfish Procambarus clarkii (Decapoda: Cambaridae)

Microplastics (MP) are a hazardous pollutant of global concern that threatens aquatic ecosystems and public health. We used the invasive, cosmopolitan, and environmentally versatile red swamp crayfish Procambarus clarkii as a model to study the effects of MP on the intestinal microbiome. Crayfish collected from the environment were compared with specimens exposed to recycled Polyethylene terephthalate (rPET) MP in feed (30%) for 96 h in the laboratory and a control group. We analyzed the 16S rRNA of the intestinal bacteria by PCR-DGGE and high-throughput sequencing. MP exposure caused dysbiosis of the intestinal microbiota, with an increase in Alphaproteobacteria and Actinobacteria. We detected higher abundance of opportunistic genera such as Klebsiella, Acinetobacter, Hydromonas, Pseudomonas, Gemmobacter, and Enterobacter on MP fed organisms. Moreover, MP exposure reduced the abundance of Clostridia and Bateroidetes, which are important for immune system development and pathogen prevention. Furthermore, MP exposure decreased the phenoloxidase (PO) immune response in crayfish. There was a significant difference in the richness of intestinal bacterial communities after consumption of food contaminated with MP, likely increasing the abundance of opportunistic bacteria in the intestinal microbiota. Our results suggest that MP alter the gut microbial composition and impair the health of P. clarkii

Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.</p

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Relaciones hídricas en árboles del bosque tropical seco: el caso de Enterolobium cyclocarpum

The water relations of Enterolobium cyclocarpum trees of the Santa Rosa National Park, Costa Rica, were studied during different moments of the daily courses and along different periods of the year. The most outstanding feature of this species was its capacity to flush the leaves during the dry season and under conditions of high evaporative demand. The results showed decreased water potentials in stems and coarse roots during early flushing, from -0.3 MPa to -0.55MPa, evidencing the contribution of stem and root water stores in supporting shoot expansion. It was determined that newly flushed leaves constitute a major factor to restrict water loss and to maintain the water balance during the dry season, as observed in the measurements of the stomatal conductance and the leaf water potential (gs de 50 mmol m-2 s-1; ψH de -0.75 MPa). Total daily sap flow showed substantial variations during the year, with daily transpirations of 300 liters during the rainiest months. Simultaneous changes in branch, stem and coarse root sap flow in response to sudden changes in solar radiation indicated that different tree organs were tightly coupled and were highly responsive to environmental changes. This study shows the importance of implementing ecophysiological studies for the best understanding of the processes that occur in forestry systems.Las relaciones hídricas en árboles de Enterolobium cyclocarpum del Parque Nacional Santa Rosa, Costa Rica, se estudiaron en diferentes momentos del curso diurno y a lo largo de dos ciclos fenológicos. La característica más sobresaliente de esta especie fue su capacidad de brotar su follaje durante la época de sequía y en condiciones de alta demanda evaporativa. Los resultados mostraron una disminución del potencial hídrico de tallos y raíces gruesas durante la brotación temprana del follaje, de  -0,3 MPa a -0,55MPa, evidenciando la contribución de las reservas internas de agua para sustentar este proceso. Se determinó que las hojas jóvenes son las principales responsables de evitar la pérdida de agua y de mantener el balance hídrico durante la estación seca, a juzgar por las conductividades estomáticas bajas y la estabilidad de su potencial hídrico (gs de 50 mmol m-2 s-1; ΨH de -0,75 MPa). El flujo total diario de savia presentó una amplia variación estacional, con transpiraciones diarias de 300 litros durante los meses más lluviosos. Cambios simultáneos en la velocidad del flujo de savia en raíces, tallo y ramas luego de cambios en la radiación indican el alto grado acople entre órganos y la rápida capacidad de respuesta a estímulos ambientales. Este trabajo plantea la importancia de contar con estudios ecofisiológicosque permitan entender mejor los procesos que ocurren en los sistemas forestales

Fungi for the bioremediation of pharmaceutical-derived pollutants: A bioengineering approach to water treatment

The excessive amount of pharmaceutical compounds (PhCs) released into aquatic environments poses a risk to humans, wildlife, and environmental health. It is a serious problem that requires urgent attention. In this work, we review various PhCs detected in water treatment plants. We propose that fungi, particularly white-rot fungi (WRF), can be used for their bioremediation and describe the main mechanisms used for degrading this type of emerging pollutants; however, we also highlight the need to prospect for new fungal models. A conceptual proposal is made to develop an immobilization device containing a consortium of fungal species that can be placed in wastewater treatment plants (WWTP). We consider that this device would allow more efficient bioremediation of PhCs and address an environmental problem that remains neglected