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Disputed islands

Disputed islands | MycorWeb Plant-Microbe Interactions | Scoop.it

Genomic islands seemed here to stay. The concept, says Luke Harmon, an evolutionary biologist at the University of Idaho in Moscow, “was viewed by many people as perfect for understanding ecological speciation.” Part of the appeal was the beautiful metaphor: Water represented gene flow, and islands emerged, like volcanoes poking up from the ocean, where gene flow fails and divergent selection occurs. The islands would expand just as volcanic islands grow, until reproductive isolation locked in and a species had split into two. At first, the islands extend beyond the beneficial mutation because DNA right next to the advantageous DNA tends to be transmitted as a unit, due to reduced recombination in this region. Over time, other beneficial mutations in the vicinity would add to this recombination coldspot, expanding the island further. And over subsequent generations, more islands would pop up, as the effects of even small survival advantages accumulated.

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The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation : Nature Genetics

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation : Nature Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it
The grass carp is an important farmed fish, accounting for ~16% of global freshwater aquaculture, and has a vegetarian diet. Here we report a 0.9-Gb draft genome of a gynogenetic female adult and a 1.07-Gb genome of a wild male adult. Genome annotation identified 27,263 protein-coding gene models in the female genome. A total of 114 scaffolds consisting of 573 Mb are anchored on 24 linkage groups. Divergence between grass carp and zebrafish is estimated to have occurred 49–54 million years ago. We identify a chromosome fusion in grass carp relative to zebrafish and report frequent crossovers between the grass carp X and Y chromosomes. We find that transcriptional activation of the mevalonate pathway and steroid biosynthesis in liver is associated with the grass carp's adaptation from a carnivorous to an herbivorous diet. We believe that the grass carp genome could serve as an initial platform for breeding better-quality fish using a genomic approach.
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Genetic isolation between two recently diverged populations of a symbiotic fungus

Genetic isolation between two recently diverged populations of a symbiotic fungus | MycorWeb Plant-Microbe Interactions | Scoop.it

Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na+/H+ exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal Su. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.

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A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus | MycorWeb Plant-Microbe Interactions | Scoop.it
Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.
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Microbiology: Exclusive networks in the sea : Nature

Microbiology: Exclusive networks in the sea : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
The identification of an exchange of nutrients and signalling molecules between a planktonic alga and a bacterium demonstrates that targeted mutualistic interactions occur across domains of life in the oceans.
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Genes and networks regulating root anatomy and architecture

Genes and networks regulating root anatomy and architecture | MycorWeb Plant-Microbe Interactions | Scoop.it

The root is an excellent model for studying developmental processes that underlie plant anatomy and architecture. Its modular structure, the lack of cell movement and relative accessibility to microscopic visualization facilitate research in a number of areas of plant biology. In this review, we describe several examples that demonstrate how cell type-specific developmental mechanisms determine cell fate and the formation of defined tissues with unique characteristics. In the last 10 yr, advances in genome-wide technologies have led to the sequencing of thousands of plant genomes, transcriptomes and proteomes. In parallel with the development of these high-throughput technologies, biologists have had to establish computational, statistical and bioinformatic tools that can deal with the wealth of data generated by them. These resources provide a foundation for posing more complex questions about molecular interactions, and have led to the discovery of new mechanisms that control phenotypic differences. Here we review several recent studies that shed new light on developmental processes, which are involved in establishing root anatomy and architecture. We highlight the power of combining large-scale experiments with classical techniques to uncover new pathways in root development.

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A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera | MycorWeb Plant-Microbe Interactions | Scoop.it
The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system– and sperm motility–related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.
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bioRxiv: Rust fungal effectors mimic host transit peptides to translocate into chloroplasts (2015)

bioRxiv: Rust fungal effectors mimic host transit peptides to translocate into chloroplasts (2015) | MycorWeb Plant-Microbe Interactions | Scoop.it

Parasite effector proteins target various host cell compartments to alter host processes and promote infection. How effectors cross membrane-rich interfaces to reach these compartments is a major question in effector biology. Growing evidence suggests that effectors use molecular mimicry to subvert host cell machinery for protein sorting. We recently identified CTP1 (chloroplast-targeted protein 1), a candidate effector from the poplar leaf rust fungus Melampsora larici-populina that carries a predicted transit peptide and accumulates in chloroplasts. Here, we show that the CTP1 transit peptide is necessary and sufficient for accumulation in the stroma of chloroplasts, and is cleaved after translocation. CTP1 is part of a Melampsora-specific family of polymorphic secreted proteins whose members translocate and are processed in chloroplasts in a N-terminal signal-dependent manner. Our findings reveal that fungi have evolved effector proteins that mimic plant-specific sorting signals to traffic within plant cells.


Via Kamoun Lab @ TSL
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Uncovering hidden worlds of ocean biodiversity

Uncovering hidden worlds of ocean biodiversity | MycorWeb Plant-Microbe Interactions | Scoop.it
A bewildering swirl of tiny creatures dominates life in the oceans. More numerous than the stars in the universe, these organisms serve as the foundation of all marine food webs, recycling major elements and producing and consuming about half the organic matter generated on Earth each year (1). In this issue, five research articles from the Tara Oceans expedition (2–6) provide a vivid, potentially transformative view of the genetic diversity and interconnectivity of these unseen marine communities of viruses, bacteria, archaea, single-celled eukaryotes, and small planktonic animals (see the figure). Together, these studies deliver compelling evidence for extensive networks of previously hidden biological interactions in the sea.

The Tara Oceans expedition harkens back to 18th-century sailing voyages that explored uncharted worlds, including Darwin's voyage aboard the HMS Beagle and the Challenger expedition that heralded the beginning of modern oceanography. The 36-m schooner Tara departed Lorient, France, in 2008 and sailed through the Mediterranean Sea and into the Indian, South Atlantic, and Southern oceans (see the map). Tara visited coral reefs in the South Pacific Ocean and then sailed through the Panama Canal and back across the North Atlantic Ocean, arriving at her homeport nearly 3 years later. At hundreds of locations along the way, scientists and crew collected thousands of samples from surface waters, from the deep chlorophyll maximum layers where microscopic photosynthetic organisms accumulate, and from deeper waters.
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Eukaryotic plankton diversity in the sunlit ocean

Eukaryotic plankton diversity in the sunlit ocean | MycorWeb Plant-Microbe Interactions | Scoop.it
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.
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Environmental characteristics of Agulhas rings affect interocean plankton transport

Environmental characteristics of Agulhas rings affect interocean plankton transport | MycorWeb Plant-Microbe Interactions | Scoop.it
Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.
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Structure and function of the global ocean microbiome

Structure and function of the global ocean microbiome | MycorWeb Plant-Microbe Interactions | Scoop.it
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
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Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
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Seven common mistakes in population genetics and how to avoid them

Since the data resulting from modern genotyping tools are astoundingly complex, genotyping studies require great care in the sampling design, genotyping, data analysis and interpretation. Such care is necessary because, with datasets containing thousands of loci, small biases can easily become strongly significant patterns. Such biases may already be present in routine tasks that are present in almost every genotyping study. Here, I discuss seven common mistakes that can be frequently encountered in the genotyping literature: (i) giving more attention to genotyping than to sampling; (ii) failing to perform or report experimental randomisation in the lab; (iii) equating geopolitical borders with biological borders; (iv) testing significance of clustering output; (v) misinterpreting Mantel's r statistic; (vi) only interpreting a single value of k; (vii) forgetting that only a small portion of the genome will be associated with climate. For every of those issues, I give some suggestions how to avoid these mistakes. Overall, I argue that genotyping studies would benefit from establishing a more rigorous experimental design, involving proper sampling design, randomisation and better distinction of a priori hypotheses and exploratory analyses.
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Demystifying computer science for molecular ecologists

Demystifying computer science for molecular ecologists | MycorWeb Plant-Microbe Interactions | Scoop.it

In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373–389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated.

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Population genomic analyses reveal possible drivers of population divergence

Population genomic analyses reveal possible drivers of population divergence | MycorWeb Plant-Microbe Interactions | Scoop.it

Recent advances in sequencing technology and efficiency enable new and improved methods to investigate how populations diverge and species evolve. Fungi have relatively small and simple genomes and can often be cultured in the laboratory. Fungal populations can thus be sequenced for a relatively low cost, which makes them ideal for population genomic analyses. In several recent population genomic studies, wild populations of fungal model organisms and human pathogens have been analysed, for example Neurospora crassa (Ellison et al. 2011), Saccharomyces uvarum (Almeida et al. 2014), Coccidioides spp. (Neafsey et al. 2010) and Cryptococcus gatti (Engelthaler et al. 2014). In this issue of Molecular Ecology, Branco et al. (2015) apply population genomic tools to understand population divergence and adaptation in a symbiotic (mycorrhizal) fungus. This study exemplifies the possibilities of diving deeper into the genomic features involved in population divergence and speciation, also for nonmodel organisms, and how molecular and analytical tools will improve our understanding of the patterns and mechanisms that underlie adaptation to habitats, population divergence and dispersal limitation of fungi.

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Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria : Nature : Nature Publishing Group

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria : Nature : Nature Publishing Group | MycorWeb Plant-Microbe Interactions | Scoop.it
Interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape ecosystem diversity. In marine ecosystems, these interactions are difficult to study partly because the major photosynthetic organisms are microscopic, unicellular phytoplankton. Coastal phytoplankton communities are dominated by diatoms, which generate approximately 40% of marine primary production and form the base of many marine food webs. Diatoms co-occur with specific bacterial taxa, but the mechanisms of potential interactions are mostly unknown. Here we tease apart a bacterial consortium associated with a globally distributed diatom and find that a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan. Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia. The potential prevalence of this mode of signalling in the oceans is corroborated by metabolite and metatranscriptome analyses that show widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments. Our study expands on the emerging recognition that marine microbial communities are part of tightly connected networks by providing evidence that these interactions are mediated through production and exchange of infochemicals.
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Microbiome: The puzzle in a bee's gut

Microbiome: The puzzle in a bee's gut | MycorWeb Plant-Microbe Interactions | Scoop.it
Sometimes, serendipity arrives on the wings of disease. It was colony collapse disorder (CCD), a mysterious condition that hit honeybee hives in autumn 2006, that brought bees to the laboratory of evolutionary biologist Nancy Moran. Moran, working at the time at Yale University in New Haven, Connecticut, had been studying microbes that live inside aphids and leafhoppers since the early 1990s. Owing to her knowledge of insect-associated bacteria, she was brought in by a team of genome sleuths to analyse RNA samples from sick honeybees. The quest1 yielded no culprit for CCD, but Moran was surprised to find that whether the bees were healthy or ill, their hindgut (equivalent to the mammalian intestine and rectum) carried a characteristic handful of species that make up 99% of the gut microbial population. “Every single bee had the same bacteria,” says Moran, who is now at the University of Texas at Austin.
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Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry

Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry | MycorWeb Plant-Microbe Interactions | Scoop.it
Linking community composition to ecosystem function is a challenge in complex microbial communities. We tested the hypothesis that key biological features of fungi - evolutionary history, functional guild, and abundance of functional genes – can predict the biogeochemical activity of fungal species during decay. We measured the activity of 10 different enzymes produced by 48 model fungal species on leaf litter in laboratory microcosms. Taxa included closely related species with different ecologies (i.e. species in different “functional guilds”) and species with publicly available genomes. Decomposition capabilities differed less among phylogenetic lineages of fungi than among different functional guilds. Activity of carbohydrases and acid phosphatase was significantly higher in litter colonized by saprotrophs compared to ectomycorrhizal species. By contrast, oxidoreductase activities per unit fungal biomass were statistically similar across functional guilds, with white rot fungi having highest polyphenol oxidase activity and ectomycorrhizal fungi having highest peroxidase activity. On the ecosystem level, polyphenol oxidase activity in soil correlated with the abundance of white rot fungi, while soil peroxidase activity correlated with the abundance of ectomycorrhizal fungi in soil. Copy numbers of genes coding for different enzymes explained the activity of some carbohydrases and polyphenol oxidase produced by fungi in culture, but were not significantly better predictors of activity than specific functional guild. Collectively, our data suggest that quantifying the specific functional guilds of fungi in soil, potentially through environmental sequencing approaches, allows us to predict activity of enzymes that drive soil biogeochemical cycles.
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Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Molecular mechanisms underlying the close association between soil Burkholderia and fungi | MycorWeb Plant-Microbe Interactions | Scoop.it

Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glatheiproteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.

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Leaf bacteria fertilize trees, researchers claim

Leaf bacteria fertilize trees, researchers claim | MycorWeb Plant-Microbe Interactions | Scoop.it

The fastest growing trees outside the tropics are poplars. Tall and slender, they can reach 30 meters in less than a decade despite the seemingly inhospitable ground they favor—burned areas and sandy riverbanks, for example. Sharon Doty says the credit goes to microbes in their leaves and other tissues. While the poplar's leaf cells are busy converting sunlight to energy, she says, bacteria between those cells are transforming nitrogen from the air into a form the tree needs to sustain this rapid growth.

That's a radical notion, because nitrogen fixation is generally thought to happen primarily in bacteria-rich nodules on the roots of legumes and a few other plants, and not in the treetops. “We are completely fighting dogma,” says Doty, a plant microbiologist at the University of Washington, Seattle.

 
Francis Martin's insight:

“There's a change in attitude, not from skepticism to believing but from skepticism to cautious questioning,” says Gerald Tuskan, a plant geneticist at Oak Ridge National Laboratory in Tennessee.

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Determinants of community structure in the global plankton interactome

Determinants of community structure in the global plankton interactome | MycorWeb Plant-Microbe Interactions | Scoop.it
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.
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Patterns and ecological drivers of ocean viral communities

Patterns and ecological drivers of ocean viral communities | MycorWeb Plant-Microbe Interactions | Scoop.it

Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity

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Tara Oceans studies plankton at PLANETARY SCALE

Tara Oceans studies plankton at PLANETARY SCALE | MycorWeb Plant-Microbe Interactions | Scoop.it

The ocean is the largest ecosystem on Earth, and yet we know very little about it. This is particularly true for the plankton that inhabit the ocean. Although these organisms are at least as important for the Earth system as the rainforests and form the base of marine food webs, most plankton are invisible to the naked eye and thus are largely uncharacterized. To study this invisible world, the multinational Tara Oceans consortium, with use of the 110-foot research schooner Tara, sampled microscopic plankton at 210 sites and depths up to 2000 m in all the major oceanic regions during expeditions from 2009 through 2013 (1).
Success depended on collaboration between scientists and the Tara Expeditions logistics team. The journey involved not only science but also outreach and education as well as negotiation through the shoals of legal and political regulations, funding uncertainties, threats from pirates, and unpredictable weather (2). At various times, journalists, artists, and teachers were also on board. Visitors included Ban Ki-moon (Secretary-General of the United Nations) and numerous youngsters, including schoolchildren from the favelas in Rio de Janeiro.

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Le voilier « Tara » remonte la vie des océans dans ses filets

Le voilier « Tara » remonte la vie des océans dans ses filets | MycorWeb Plant-Microbe Interactions | Scoop.it

Un océan de données génétiques, moléculaires, physico-chimiques, microphotographiques… La pêche au plancton effectuée par le voilier Tara, entre 2009 et 2013, sur toutes les mers du globe, vient de connaître sa première traduction scientifique, avec la publication conjointe d’articles dans plusieurs revues prestigieuses, dont le journal Science, vendredi 22 mai. Un aboutissement, pour le consortium international Tara Océans, associant des équipes de chercheurs aux marins de la fondation Tara, qui a choisi de faire de sa célèbre goélette un navire de recherche océanographique à part entière, en même temps qu’un étendard de la défense des mers.
En savoir plus sur http://www.lemonde.fr/planete/article/2015/05/21/le-voilier-tara-remonte-la-vie-des-oceans-dans-ses-filets_4638225_3244.html#X4oqvd5g1vEwiVDR.99

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Microbiology: Taking the bad with the good

Microbiology: Taking the bad with the good | MycorWeb Plant-Microbe Interactions | Scoop.it
Modelling of the interactions between antibiotic production and antibiotic degradation reveals that these opposing activities are key to maintaining diversity in microbial communities.

We commonly expect competitive ecological interactions to be transitive: if ravens displace crows and crows displace jays, then ravens should displace jays as well. But the world does not always work this way. Increasingly, researchers are finding intransitive relationships, in which ravens displace crows, which displace jays, which in turn displace ravens. Intransitive relationships occur in animals1, 2, plants3, 4 and microbes5, 6. Theoretical models show that species abundances can cycle in intransitive communities, in principle preserving species diversity7, 8. However, in finite populations, extinction can readily occur when one type cycles to low abundance. In a paper published on Nature's website today, Kelsic et al.9 model an intransitive system in which microbial species produce antimicrobial compounds and exhibit differing sensitivities to the products of their competitors. By demonstrating that antimicrobial degradation can stabilize a multi-species community, the authors suggest a new solution to the puzzle of how bacterial diversity is maintained10.
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