Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp

Endofungal Mycetohabitans (formerly Burkholderia ) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus, Rhizopus microsporus. The one known secreted effector family from Mycetohabitans consists of homologs of transcription activator-like (TAL) effectors, which are used by plant pathogenic Xanthomonas and Ralstonia spp. to activate host genes that promote disease. These ‘ Burkholderia TAL-like (Btl)’ proteins bind corresponding specific DNA sequences in a predictable manner, but their impact on transcription and their genomic target(s) in the fungus are not yet known. Recent characterization of two Btl proteins (Btl19-13 and MTAL1/Btl21-1), each from a different Mycetohabitans species, revealed different phenotypes in Rhizopus , underscoring the need to assess the sequence and functional diversity of Btl proteins. We sequenced and assembled nine Mycetohabitans spp. genomes using long-read PacBio technology. All assemblies contained fragments of btl genes, and most had intact copies. We then mined fungal-bacterial metagenomes assembled as part of the ZygoLife project. This analysis showed that btl genes are present across diverse Mycetohabitans strains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested that Mycetohabitans might contain more species than previously recognized. Within our data set, Btl proteins were more conserved across Mycetohabitans rhizoxinica strains than across Mycetohabitans endofungorum , but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial-fungal symbioses in myriad ways. Importance Many Mucoromycota fungi harbor endosymbiotic bacteria, including Rhizopus spp. that are food fermenters and pathogens of plants and immunocompromised people. Rhizopus microsporus has endofungal Mycetohabitans (formerly Burkholderia ) spp. that deploy proteins related to DNA-binding ‘transcription activator-like’ effectors of plant pathogens, which enter plant nuclei and activate disease susceptibility genes. One ‘Burkholderia TAL-like (Btl)’ protein, in M. endofungorum , enhances fungal membrane stress tolerance. Another, from M. rhizoxinica , promotes bacterial colonization of the fungus. By sequencing isolated bacteria and mining fungal holobiont sequences, we found Btl proteins in diverse Mycetohabitans strains, varying in DNA binding specificity, thus in potential host targets. Btl proteins were more conserved within M. rhizoxinica suggesting distinctions among the two named species. The results suggest that Btl proteins contribute to symbiosis in diverse ways, providing insight into effector evolution and arguing for functional characterization of additional Btl proteins to understand establishment and maintenance of these important fungal-bacterial interactions

A TAL effector-like protein of an endofungal bacterium increases the stress tolerance and alters the transcriptome of the host.

Symbioses of bacteria with fungi have only recently been described and are poorly understood. In the symbiosis of Mycetohabitans (formerly Burkholderia) rhizoxinica with the fungus Rhizopus microsporus, bacterial type III (T3) secretion is known to be essential. Proteins resembling T3-secreted transcription activator-like (TAL) effectors of plant pathogenic bacteria are encoded in the three sequenced Mycetohabitans spp. genomes. TAL effectors nuclear-localize in plants, where they bind and activate genes important in disease. The Burkholderia TAL-like (Btl) proteins bind DNA but lack the N- and C-terminal regions, in which TAL effectors harbor their T3 and nuclear localization signals, and activation domain. We characterized a Btl protein, Btl19-13, and found that, despite the structural differences, it can be T3-secreted and can nuclear-localize. A btl19 -13 gene knockout did not prevent the bacterium from infecting the fungus, but the fungus became less tolerant to cell membrane stress. Btl19-13 did not alter transcription in a plant-based reporter assay, but 15 R. microsporus genes were differentially expressed in comparisons both of the fungus infected with the wild-type bacterium vs. the mutant and with the mutant vs. a complemented strain. Southern blotting revealed btl genes in 14 diverse Mycetohabitans isolates. However, banding patterns and available sequences suggest variation, and the btl19-13 phenotype could not be rescued by a btl gene from a different strain. Our findings support the conclusion that Btl proteins are effectors that act on host DNA and play important but varied or possibly host genotype-specific roles in the M. rhizoxinica-R. microsporus symbiosis

A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate

<p>The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host “susceptibility” (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harboring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.</p

Evolutionary social and biogeophysical changes in the Amazon, Ganges–Brahmaputra–Meghna and Mekong deltas

Policy-making in social-ecological systems increasingly looks to iterative, evolutionary approaches that can address the inherent complexity of interactions between human wellbeing, provision of goods, and the maintenance of ecosystem services. Here, we show how the analysis of available time-series in tropical delta regions over past decades can provide important insight into the social-ecological system dynamics in deltaic regions. The paper provides an exploratory analysis of the recent changes that have occurred in the major elements of three tropical deltaic social-ecological systems, such as demography, economy, health, climate, food, and water. Time-series data from official statistics, monitoring programmes, and Earth observation data are analysed to explore possible trends, slow and fast variables, and observed drivers of change in the Amazon, Ganges–Brahmaputra–Meghna and Mekong deltas. In the Ganges–Brahmaputra–Meghna delta zone, increasing gross domestic product and per capita income levels since the 1980s mirror rising levels of food and inland fish production. In contrast, non-food ecosystem services, such as water availability, water quality, and land stability appear to be deteriorating. In the Amazon delta, natural and anthropogenic perturbations are continuously degrading key ecosystem services, such as carbon storage in biomass and soils, the regulation of water balance, and the modulation of regional climate patterns. In the Mekong delta, rapid economic development, changing land-use practices, and salinity intrusion are progressively putting more pressure on the delivery of important provisioning services, such as rice and inland aquaculture production, which are key sources of staple food, farm incomes, and export revenue. Observed changes in many key indicators of ecosystem services point to a changing dynamic state and increased probability of systemic threshold transformations in the near future

Seed exchange networks for agrobiodiversity conservation. A review

The circulation of seed among farmers is central to agrobiodiversity conservation and dynamics. Agrobiodiversity, the diversity of agricultural systems from genes to varieties and crop species, from farming methods to landscape composition, is part of humanity's cultural heritage. Whereas agrobiodiversity conservation has received much attention from researchers and policy makers over the last decades, the methods available to study the role of seed exchange networks in preserving crop biodiversity have only recently begun to be considered. In this overview, we present key concepts, methods, and challenges to better understand seed exchange networks so as to improve the chances that traditional crop varieties (landraces) will be preserved and used sustainably around the world. The available literature suggests that there is insufficient knowledge about the social, cultural, and methodological dimensions of environmental change, including how seed exchange networks will cope with changes in climates, socio-economic factors, and family structures that have supported seed exchange systems to date. Methods available to study the role of seed exchange networks in the preservation and adaptation of crop specific and genetic diversity range from meta-analysis to modelling, from participatory approaches to the development of bio-indicators, from genetic to biogeographical studies, from anthropological and ethnographic research to the use of network theory. We advocate a diversity of approaches, so as to foster the creation of robust and policy-relevant knowledge. Open challenges in the study of the role of seed exchange networks in biodiversity conservation include the development of methods to (i) enhance farmers' participation to decision-making in agro-ecosystems, (ii) integrate ex situ and in situ approaches, (iii) achieve interdisciplinary research collaboration between social and natural scientists, and (iv) use network analysis as a conceptual framework to bridge boundaries among researchers, farmers and policy makers, as well as other stakeholders