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The innermost secrets of root development

The innermost secrets of root development | MycorWeb Plant-Microbe Interactions | Scoop.it

For a plant embryo to grow from a single fertilized egg cell to a complex multicellular structure, it must undergo a highly ordered sequence of cell divisions, during which the emerging tissues are patterned and ultimately differentiate. In vascular plants, the vascular tissues lie deep within roots and shoots, where they provide the main mechanism for transporting water and nutrients between organs. The specification of root vascular tissues provides an elegant system to investigate tissue patterning. It had previously been shown that two plant hormones cross regulate each other's activity and transport to control vascular patterning (1). However, on page 636 of this issue, De Rybel et al. (2) identify a new interaction between these hormones through the regulation of their local synthesis, such that collectively these hormonal interactions coordinate the processes of both cell division and tissue patterning to specify the stereotypical vascular pattern in Arabidopsis embryos.

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Mario Sergio Nicolodi's curator insight, August 8, 2014 4:34 PM

Compartilhando: "Para um embrião de planta de crescer a partir de uma única célula de ovo fertilizado de uma estrutura multicelular complexo, devem ser submetidos a uma sequência altamente ordenada de divisões celulares, durante o qual os tecidos são emergentes modelado e, finalmente diferenciar."

Mario Sergio Nicolodi's curator insight, August 8, 2014 4:39 PM

Compratilhando: "Para um embrião de planta crescer a partir de uma única célula [...]"

Mario Sergio Nicolodi's curator insight, August 8, 2014 5:08 PM

Compratilhando: "Para um embrião de planta crescer a partir de uma única célula [...]"

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Giving back to the community: microbial mechanisms of plant–soil interactions

Giving back to the community: microbial mechanisms of plant–soil interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
The role of both plants and soil microbes on ecosystem functioning has been long recognized, but the precise feedback mechanisms between them are more elusive. Definition of these interactions is critical if we aim to achieve an integral understanding of ecosystem functioning, and ultimately explain natural, agricultural and synthetic systems.
Advances in genomic technologies and the development of more appropriate statistical, mathematical and computational frameworks enable researchers to almost fully describe and measure the diversity of microbial communities in soil, rhizosphere and plant tissues. Under the scaffold of community ecology, we integrate the observed patterns of microbial diversity with current mechanistic understanding of plant–microbe mutualistic and pathogenic interactions, and propose a model in which plant microbial communities are shaped by different ecological forces differentially through the plant life cycle.
The same genomic technologies, applied on natural and reconstructed systems, establish that plant genotype has a small, but significant, effect on the microbial community composition in, on and around plant organs. Despite these advances, technical limitations are still important and only a handful of studies exist where a precise genetic element definitively participates in these interactions.
Studies at the field or ecosystem level are dominated by agricultural settings, examining microbial species and communities effects on plant productivity; and conversely, that plant genetics and agricultural practices can potentially impose selective pressures on specific microbes and microbial communities.
Revitalized interest in plant–soil microbial feedbacks requires researchers to systematically pose and evaluate more complex hypotheses with increasingly more realistic microbial settings. Despite the advances reviewed here, most studies focus on one aspect of plant, microbe and soil interactions. Experiments that simultaneously and methodically manipulate multiple components are necessary to establish the ecological principles, and molecular mechanisms, which drive microbially mediated plant–soil interactions. This knowledge will be critical to predict how environmental changes affect microbial and plant diversity, and will guide efforts to improve agricultural and conservation practices.
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Root Development and Endosymbioses: DELLAs Lead the Orchestra

Root Development and Endosymbioses: DELLAs Lead the Orchestra | MycorWeb Plant-Microbe Interactions | Scoop.it
The plasticity of the root system development is crucial for plant adaptation to changing soil environments. External cues control root growth and differentiation as well as beneficial plant–microorganism symbiotic associations. Arbuscular mycorrhizal (AM) and rhizobial endosymbioses are mutualistic interactions respectively formed between most Angiosperms and Glomeromycota soil fungi under nutrient (e.g., phosphorus) starvation, and between legume (Fabacae) plants and soil bacteria collectively referred to as Rhizobia when soil nitrogen availability is limiting. In both cases, microorganisms colonize host roots depending on related signaling pathways, and in the rhizobial symbiosis, the plant additionally forms nodule organs allowing nitrogen fixation.

DELLA proteins are GRAS transcriptional regulators whose accumulation highly depends on the GA hormonal pool [1. Indeed, GAs promote a targeted degradation of DELLA proteins mediated by the SCF/26S proteasome. As a result of their capacity to interact with multiple transcription factors from diverse families [1, 2], DELLA proteins are emerging as integrators of transcriptional networks associated with various signaling pathways, and notably controlling root growth and endosymbiotic associations.

Via Christophe Jacquet
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Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
During infection, both phytopathogenic and endophytic fungi form intimate contact with living plant cells, and need to resist or disable host defences and modify host metabolism to adapt to their host. Fungi can achieve these changes by secreting proteins and enzymes. A comprehensive comparison of the secretomes of both endophytic and pathogenic fungi can improve our understanding of the interactions between plants and fungi. Although Magnaporthe oryzae , Gaeumannomyces graminis , and M . poae are economically important fungal pathogens, and the related species Harpophora oryzae is an endophyte, they evolved from a common pathogenic ancestor. We used a pipeline analysis to predict the H . oryzae , M . oryzae , G . graminis , and M . poae secretomes and identified 1142, 1370, 1001, and 974 proteins, respectively. Orthologue gene analyses demonstrated that the M . oryzae secretome evolved more rapidly than those of the other three related species, resulting in many species-specific secreted protein-encoding genes, such as avirulence genes. Functional analyses highlighted the abundance of proteins involved in the breakdown of host plant cell walls and oxidation-reduction processes. We identified three novel motifs in the H . and M . oryzae secretomes, which may play key roles in the interaction between rice and H . oryzae . Furthermore, we found that expression of the H . oryzae secretome involved in plant cell wall degradation was downregulated, but the M . oryzae secretome was upregulated with many more upregulated genes involved in oxidation-reduction processes. The divergent in planta expression patterns of the H . and M . oryzae secretomes reveal differences that are associated with mutualistic and pathogenic interactions, respectively.

Via Yogesh Gupta
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Researchers discover key genes for climate adaptation shared between distantly related trees

Researchers discover key genes for climate adaptation shared between distantly related trees | MycorWeb Plant-Microbe Interactions | Scoop.it
Despite 140 million years of independent evolution, two types of coniferous trees use the same small set of 47 genes to rapidly adapt to varying climates, an international team of forestry researchers have found in a new study, published today in Science.

Using the same genes suggests Mother Nature is limited in the way she can help western Canadian lodgepole pine and interior spruce trees survive in the sometimes-harsh climates of their home range.

“Evolution is constrained in how many different ways it can solve the same problem,” said Sally Aitken, a University of British Columbia forestry professor and the study’s senior author.

When faced with drought or cold, trees decide to turn thousands of genes on or off to deal with changes in temperature and moisture. This suggests there may be multiple different ways trees in a region can adapt to local climate.

But after sequencing the DNA of 23,000 specific genes from hundreds of pine and spruce trees in B.C. and Alberta, the researchers discovered that the two tree species used DNA variation in 47 of the same genes to adapt to low or high temperatures. This, despite the trees evolving as separate species for roughly as long as humans and kangaroos.

The fact that these two distantly-related types of trees use variation within many of the same genes to brave the elements reveals some limits to successful climate adaptation, but also sheds light on ways scientists can help trees adapt quickly.
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Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal–Microbe Interactions

Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal–Microbe Interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host–microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing host–microbe relationships. However, several outstanding questions remain, including understanding how host and microbial (internal) traits, and ecological and evolutionary (external) processes, influence the origin of beneficial host–microbe associations. Experimental evolution has helped address a range of evolutionary and ecological questions across different model systems; however, it has been greatly underutilized as a tool to study beneficial host–microbe associations. In this review, we suggest ways in which experimental evolution can further our understanding of the proximate and ultimate mechanisms shaping mutualistic interactions between eukaryotic hosts and microbes. By tracking beneficial interactions under defined conditions or evolving novel associations among hosts and microbes with little prior evolutionary interaction, we can link specific genotypes to phenotypes that can be directly measured. Moreover, this approach will help address existing puzzles in beneficial symbiosis research: how symbioses evolve, how symbioses are maintained, and how both host and microbe influence their partner’s evolutionary trajectories. By bridging theoretical predictions and empirical tests, experimental evolution provides us with another approach to test hypotheses regarding the evolution of beneficial host–microbe associations
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EMBO practical course: Plant microbiota, 26 March-07 April, Cologne, Germany

EMBO practical course: Plant microbiota, 26 March-07 April, Cologne, Germany | MycorWeb Plant-Microbe Interactions | Scoop.it
Research on the plant microbiota has developed into a highly dynamic, distinctive and interdisciplinary research field during the last five years. This practical course will focus on microbial communities colonizing the model plant Arabidopsis thaliana grown in natural soils and aims to educate the participants to apply the knowledge gained to any other plant species. The course will educate students in (i) advanced quantitative methods to detect and profile both bacterial and fungal communities that live in intimate association with healthy plants in different compartments of leaves and roots (ii) establishing microbial culture collections of the microbiota by application of high-throughput culturing methods (iii) using gnotobiotic plant systems and synthetic microbial communities to test microbiota functions for plant health (iv) applying metagenomic approaches to identify microbial functionalities of plants grown in extreme environments, e.g. under malnutrition conditions (v) using plant mutants and synthetic microbial communities to dissect the role of the plant innate immune system and plant nutrient sensing on microbial community establishment and function(s) (vi) applying computational and a suite of statistical tools to interpret next generation DNA sequencing data that are key for plant microbiota research and for experimental design.

Via Stéphane Hacquard
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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses | MycorWeb Plant-Microbe Interactions | Scoop.it
Ocean microbes drive biogeochemical cycling on a global scale1. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories2, 3. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known4. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions5, 6, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups7, 8). This roughly triples the number of known ocean viral populations4 and doubles the number of candidate bacterial and archaeal virus genera8, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
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Late Pleistocene climate drivers of early human migration : Nature : Nature Research

Late Pleistocene climate drivers of early human migration : Nature : Nature Research | MycorWeb Plant-Microbe Interactions | Scoop.it
On the basis of fossil and archaeological data it has been hypothesized that the exodus of Homo sapiens out of Africa and into Eurasia between ~50–120 thousand years ago occurred in several orbitally paced migration episodes. Crossing vegetated pluvial corridors from northeastern Africa into the Arabian Peninsula and the Levant and expanding further into Eurasia, Australia and the Americas, early H. sapiens experienced massive time-varying climate and sea level conditions on a variety of timescales. Hitherto it has remained difficult to quantify the effect of glacial- and millennial-scale climate variability on early human dispersal and evolution. Here we present results from a numerical human dispersal model, which is forced by spatiotemporal estimates of climate and sea level changes over the past 125 thousand years. The model simulates the overall dispersal of H. sapiens in close agreement with archaeological and fossil data and features prominent glacial migration waves across the Arabian Peninsula and the Levant region around 106–94, 89–73, 59–47 and 45–29 thousand years ago. The findings document that orbital-scale global climate swings played a key role in shaping Late Pleistocene global population distributions, whereas millennial-scale abrupt climate changes, associated with Dansgaard–Oeschger events, had a more limited regional effect.
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A genomic history of Aboriginal Australia

A genomic history of Aboriginal Australia | MycorWeb Plant-Microbe Interactions | Scoop.it
Empty desThe population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.cription
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The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols | MycorWeb Plant-Microbe Interactions | Scoop.it
The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar ‘Chandler’ to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.
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Alternative splicing – an elegant way to diversify the function of repeat-containing effector proteins?

Alternative splicing – an elegant way to diversify the function of repeat-containing effector proteins? | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants are subjected to associations with organisms throughout all kingdoms, and colonization is often accompanied by the secretion of effector proteins which results in alterations to plant physiology and immune responses to facilitate colonization. In recent years evidence has arisen that many plant-associated organisms make use of repeat-containing effectors, which often seem to be organized in larger protein families with characteristic distribution of repeat elements (Mesarich et al., 2015). RXLR effectors from plant pathogenic oomycetes, for instance, comprise a conserved but highly degenerate C-terminal WYL domain that is often organized in tandem repeats (Jiang et al., 2008). Conversely, there are effectors harbouring perfect, or almost perfect, repeats; for example MpC002, which is an effector from the peach-potato aphid Myzus persicae that contains five hydrophilic perfect tandem repeats, consisting of seven amino acids (Bos et al., 2010). Certainly the most common repeat-containing effectors are the so-called TAL effectors derived from plant-pathogenic Xanthomonas species, whose characteristic feature is a central domain of nearly identical tandem repeats (Boch et al., 2009). Each repeat harbours a variable amino acid pair, termed repeat-variable di-residues (RVDs), which determines nucleotide binding specificity of the effector. In this issue of New Phytologist, Noon et al. (pp. 444–460) identify HgGLAND18 as a novel tandem repeat-containing effector from the soybean cyst nematode Heterodera glycines. Interestingly, HgGLAND18 exists in different isoforms and transcript variants. The isoforms contain different polymorphisms and the variants show irregular numbers of repeats. As a basic structure, HgGLAND18 isoforms are composed of a signal peptide, followed by a series of zero to five tandem repeats, a supercharged stretch of 43 amino acids (aa) terminating the N-terminal region, and a C-terminus of 49 aa. The different transcript versions of HgGLAND18 are herein proposed to be generated either by allelic variations and/or by alternative splicing (AS). This raises the question whether, and to what extent, AS might participate in the synthesis of multiple effector proteins with possible different biological functions.
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Towards integration of population and comparative genomics in forest trees

Towards integration of population and comparative genomics in forest trees | MycorWeb Plant-Microbe Interactions | Scoop.it
The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
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Down-regulation of the glucan synthase-like 6 gene (HvGsl6) in barley leads to decreased callose accumulation and increased cell wall penetration by Blumeria graminis f. sp. hordei

Down-regulation of the glucan synthase-like 6 gene (HvGsl6) in barley leads to decreased callose accumulation and increased cell wall penetration by Blumeria graminis f. sp. hordei | MycorWeb Plant-Microbe Interactions | Scoop.it
The recent characterization of the polysaccharide composition of papillae deposited at the barley cell wall during infection by the powdery mildew pathogen, Blumeria graminis f. sp. hordei (Bgh), has provided new targets for the generation of enhanced disease resistance. The role of callose in papilla-based penetration resistance of crop species is largely unknown because the genes involved in the observed callose accumulation have not been identified unequivocally. We have employed both comparative and functional genomics approaches to identify the functional orthologue of AtGsl5 in the barley genome. HvGsl6 (the barley glucan synthase-like 6 gene), which has the highest sequence identity to AtGsl5, is the only Bgh-induced gene among the HvGsls examined in this study. Through double-stranded RNA interference (dsRNAi)-mediated silencing of HvGsl6, we have shown that the down-regulation of HvGsl6 is associated with a lower accumulation of papillary and wound callose and a higher susceptibility to penetration of the papillae by Bgh, compared with control lines. The results indicate that the HvGsl6 gene is a functional orthologue of AtGsl5 and is involved in papillary callose accumulation in barley. The increased susceptibility of HvGsl6 dsRNAi transgenic lines to infection indicates that callose positively contributes to the barley fungal penetration resistance mechanism.
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The Plant Microbiota: Systems-Level Insights and Perspectives

Plants do not grow as axenic organisms in nature, but host a diverse community of microorganisms, termed the plant microbiota. There is an increasing awareness that the plant microbiota plays a role in plant growth and can provide protection from invading pathogens. Apart from intense research on crop plants, Arabidopsis is emerging as a valuable model system to investigate the drivers shaping stable bacterial communities on leaves and roots and as a tool to decipher the intricate relationship among the host and its colonizing microorganisms. Gnotobiotic experimental systems help establish causal relationships between plant and microbiota genotypes and phenotypes and test hypotheses on biotic and abiotic perturbations in a systematic way. We highlight major recent findings in plant microbiota research using comparative community profiling and omics analyses, and discuss these approaches in light of community establishment and beneficial traits like nutrient acquisition and plant health.

Via Jean-Michel Ané
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Radiocarbon constraints imply reduced carbon uptake by soils during the 21st century

Radiocarbon constraints imply reduced carbon uptake by soils during the 21st century | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil is the largest terrestrial carbon reservoir and may influence the sign and magnitude of carbon cycle–climate feedbacks. Many Earth system models (ESMs) estimate a significant soil carbon sink by 2100, yet the underlying carbon dynamics determining this response have not been systematically tested against observations. We used 14C data from 157 globally distributed soil profiles sampled to 1-meter depth to show that ESMs underestimated the mean age of soil carbon by a factor of more than six (430 ± 50 years versus 3100 ± 1800 years). Consequently, ESMs overestimated the carbon sequestration potential of soils by a factor of nearly two (40 ± 27%). These inconsistencies suggest that ESMs must better represent carbon stabilization processes and the turnover time of slow and passive reservoirs when simulating future atmospheric carbon dioxide dynamics.
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Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity

Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil biodiversity has become a major area of research over the last decade, and the literature on the topic has expanded tremendously in recent years, so much so that a huge number of publications now deal with soil biodiversity every year. This article does not attempt the formidable task of drawing a general picture of where the field is at the moment, but it zeroes in instead on two perspectives that seem to have gathered momentum over time and raise concern about future progress. The first perspective involves the implicit assumption that to make sense of either the species-, genetic-, or functional biodiversity of soils, it is not necessary to consider in detail the features of (micro)habitats provided by soils to organisms, and that analysis of the information provided by extracted DNA or RNA suffices. The second perspective is associated with research on the effect of the physical and chemical characteristics of microhabitats on the activity of microorganisms. It basically hypothesizes that all microorganisms behave similarly, and therefore that observations made mostly with bacteria can be extended readily to all organisms, ignoring taxonomic biodiversity. To illustrate both perspectives, we provide a number of illustrative examples from the relevant literature and analyze them briefly. We argue that these two perspectives, if they spread, will hinder progress in our understanding of soil biodiversity at any level, and especially of its impact on soil processes. In order to return to a more fruitful middle ground, where both a variety of organisms and the characteristics of the microhabitats where they reside are carefully considered, several routes can be envisaged, but our experience suggests that an emphasis on genuinely interdisciplinary research is crucial.
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Convergent local adaptation to climate in distantly related conifers

Convergent local adaptation to climate in distantly related conifers | MycorWeb Plant-Microbe Interactions | Scoop.it
When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial variation in temperature or cold hardiness in both species, providing evidence of convergent local adaptation despite 140 million years of separate evolution. These results show that adaptation to climate can be genetically constrained, with certain key genes playing nonredundant roles.
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New Phytologist - Comparative phylogenomics of symbiotic associations

New Phytologist - Comparative phylogenomics of symbiotic associations | MycorWeb Plant-Microbe Interactions | Scoop.it
Understanding the genetic bases of complex traits has been a main challenge in biology for decades. Comparative phylogenomics offers an opportunity to identify candidate genes associated with these complex traits. This approach initially developed in prokaryotes consists in looking at shared coevolution between genes and traits. It thus requires a precise reconstruction of the trait evolution, a large genomic sampling in the clades of interest and an accurate definition of orthogroups. Recently, with the growing body of sequenced plant genomes, comparative genomics has been successfully applied to plants to study the widespread arbuscular mycorrhizal symbiosis. Here I will use these findings to illustrate the main principles of comparative phylogenomic approaches and propose directions to improve our understanding of symbiotic associations.

Via LRSV, Christophe Jacquet, Stéphane Hacquard
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Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures | MycorWeb Plant-Microbe Interactions | Scoop.it
Biological activity is a major factor in Earth’s chemical cycles, including facilitating CO2 sequestration and providing climate feedbacks. Thus a key question in Earth’s evolution is when did life arise and impact hydrosphere–atmosphere–lithosphere chemical cycles? Until now, evidence for the oldest life on Earth focused on debated stable isotopic signatures of 3,800–3,700 million year (Myr)-old metamorphosed sedimentary rocks and minerals1, 2 from the Isua supracrustal belt (ISB), southwest Greenland3. Here we report evidence for ancient life from a newly exposed outcrop of 3,700-Myr-old metacarbonate rocks in the ISB that contain 1–4-cm-high stromatolites—macroscopically layered structures produced by microbial communities. The ISB stromatolites grew in a shallow marine environment, as indicated by seawater-like rare-earth element plus yttrium trace element signatures of the metacarbonates, and by interlayered detrital sedimentary rocks with cross-lamination and storm-wave generated breccias. The ISB stromatolites predate by 220 Myr the previous most convincing and generally accepted multidisciplinary evidence for oldest life remains in the 3,480-Myr-old Dresser Formation of the Pilbara Craton, Australia4, 5. The presence of the ISB stromatolites demonstrates the establishment of shallow marine carbonate production with biotic CO2 sequestration by 3,700 million years ago (Ma), near the start of Earth’s sedimentary record. A sophistication of life by 3,700 Ma is in accord with genetic molecular clock studies placing life’s origin in the Hadean eon (>4,000 Ma)6.
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Genomic analyses inform on migration events during the peopling of Eurasia

Genomic analyses inform on migration events during the peopling of Eurasia | MycorWeb Plant-Microbe Interactions | Scoop.it
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations | MycorWeb Plant-Microbe Interactions | Scoop.it
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
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Population genetics: A map of human wanderlust

Population genetics: A map of human wanderlust | MycorWeb Plant-Microbe Interactions | Scoop.it
A remarkable feature of modern humans is our wanderlust, which the poet Charles Baudelaire famously referred1 to as “l'horreur du domicile”. From our evolutionary birthplace in Africa2, modern humans have migrated to nearly every habitable corner of Earth (Fig. 1), overcoming obstacles such as ice, deserts, oceans and mountains. The number, timing and routes of human dispersals out of Africa have implications for understanding our past and how that past influenced contemporary patterns of human genomic variation. Three studies online in Nature (Malaspinas et al.3, Mallick et al.4 and Pagani et al.5) describe 787 new, high-quality genomes of individuals from geographically diverse populations, providing opportunities to refine and extend current models of historical human migration.
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Cellulose/callose glucan networks: the key to powdery mildew resistance in plants?

Cellulose/callose glucan networks: the key to powdery mildew resistance in plants? | MycorWeb Plant-Microbe Interactions | Scoop.it
The plant cell wall represents the first barrier against intruding pathogens. Especially in response to fungi and oomycetes, localized cell wall modifications, so-called papillae, occur at sites of attempted pathogen penetration; this is one of the earliest plant defense responses that has been analyzed at a cellular level, and was first recorded over 150 years ago (deBary, 1863). Papillae are generally thought to function as a physical barrier to slow down or even stop pathogen invasion (Stone & Clarke, 1992) and appear to be induced in essentially all plants following pathogen challenge. Hence, papillae formation can be regarded as a ubiquitous plant defense response, which is not specific to a phylum or even a species and thus differs from many other defense responses. Papillae are complex structures that contain diverse chemical components with a clear antimicrobial function, such as phenolic compounds and thionins (McLusky et al., 1999), or hydrogen peroxide as a reactive oxygen species (ROS), used by peroxides to promote cross-linking of proteins and phenolics for cell wall reinforcement (Thordal-Christensen et al., 1997). By contrast, the precise function of the carbohydrate polymers present within papillae has not been elucidated in detail yet. This is surprising as the most prominent cell wall polymer of papillae, the (1,3)-β-glucan callose, was first described by Mangin (1895) over 120 years ago. The existence of the (1,4)-β-glucan cellulose in pathogen-induced papillae was indicated in cellular and biochemical analyses over 100 years ago. Sherwood & Vance (1976) provided the first images of a possible layered callose and cellulose deposition in papillae induced in red canarygrass by noninfecting fungi, which was later confirmed, in greater details in potato tuber infected by the oomycete Phytophthora infestans (Hächler & Hohl, 1982). Recently, a detailed histochemical study revealed a similar distribution of the two glucan polymers in papillae of the important crop barley (Hordeum vulgare), induced by the adapted powdery mildew pathogen Blumeria graminis f.sp. hordei (Bgh). The inner core of so-called effective papillae, where Bgh invasion was unsuccessful, was composed of callose (and in the case of barley also considerable amounts of arabinoxylan) surrounded by cellulose (Chowdhury et al., 2014). In this issue of New Phytologist, Douchkov et al. (2016; pp. 421–433) and Chowdhury et al. (2016; pp. 434–443) make the latest contribution to further support the importance and function of glucan polymers in pathogen-induced papillae in barley. They not only show that both callose and cellulose are required to form and establish effective papillae against Bgh, but also provide precise information about the genes that encode the respective cellulose and callose synthases. This opens up new opportunities for studying regulatory mechanisms of papilla formation in an important crop species and supports new molecular breeding approaches for increased penetration resistance.
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The elusive predisposition to mycoheterotrophy in Ericaceae

The elusive predisposition to mycoheterotrophy in Ericaceae | MycorWeb Plant-Microbe Interactions | Scoop.it
The rise and diversification of land plants was accompanied by mycorrhizal symbiosis, from their emergence to their adaptation to various biomes and ecological situations (Selosse et al., 2015). In most mycorrhizal associations, fungi provide soil minerals to the plant, in exchange for sugars derived from photosynthesis (Smith & Read, 2008; van der Heijden et al., 2015). However, several plant species adapted to shaded forest conditions by secondarily reversing this exchange of carbohydrates: they became achlorophyllous thanks to carbon provided by the fungus. This so-called mycoheterotrophic nutrition is described in over 400 species and evolved at least 40 times independently (Merckx, 2013), raising the question of what predispositions underlie these convergences.
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The barley (Hordeum vulgare) cellulose synthase-like D2 gene (HvCslD2) mediates penetration resistance to host-adapted and nonhost isolates of the powdery mildew fungus

Cell walls and cellular turgor pressure shape and suspend the bodies of all vascular plants. In response to attack by fungal and oomycete pathogens, which usually breach their host's cell walls by mechanical force or by secreting lytic enzymes, plants often form local cell wall appositions (papillae) as an important first line of defence. The involvement of cell wall biosynthetic enzymes in the formation of these papillae is still poorly understood, especially in cereal crops. To investigate the role in plant defence of a candidate gene from barley (Hordeum vulgare) encoding cellulose synthase-like D2 (HvCslD2), we generated transgenic barley plants in which HvCslD2 was silenced through RNA interference (RNAi). The transgenic plants showed no growth defects but their papillae were more successfully penetrated by host-adapted, virulent as well as avirulent nonhost isolates of the powdery mildew fungus Blumeria graminis. Papilla penetration was associated with lower contents of cellulose in epidermal cell walls and increased digestion by fungal cell wall degrading enzymes. The results suggest that HvCslD2-mediated cell wall changes in the epidermal layer represent an important defence reaction both for nonhost and for quantitative host resistance against nonadapted wheat and host-adapted barley powdery mildew pathogens, respectively.
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