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Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage : Nature : Nature Publishing Group

Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage : Nature : Nature Publishing Group | Rhizosphere matters | Scoop.it
Soil contains more carbon than the atmosphere and vegetation combined. Understanding the mechanisms controlling the accumulation and stability of soil carbon is critical to predicting the Earth/'s future climate.
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Access : Rhizosphere microbiome assemblage is affected by plant development : The ISME Journal

There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P<0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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Rapid nitrogen transfer in the Sorghum bicolor-Glomus mosseae arbuscular mycorrhizal symbiosis

Rapid nitrogen transfer in the Sorghum bicolor-Glomus mosseae arbuscular mycorrhizal symbiosis | Rhizosphere matters | Scoop.it
We have recently identified two genes coding for ammonium transporters (AMT) in Sorghum bicolor that were induced in roots colonized by arbuscular mycorrhizal (AM) fungi.
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A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultiva...

A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultiva... | Rhizosphere matters | Scoop.it

• Premise of the study: Plant roots comprise more than 50% of the plant’s biomass. Part of that biomass includes the root microbiome, the assemblage of bacteria and fungi living in the 1–3 mm region adjacent to the external surface of the root, the rhizosphere. We hypothesized that the microorganisms living in the rhizosphere and in bulk soils of the harsh environment of the Negev Desert of Israel had potential for use as plant-growth-promoting bacteria (PGPB) to improve plant productivity in nutrient-poor, arid soils that are likely to become more common as the climate changes.

• Methods: We used cultivation-dependent methods including trap experiments with legumes to find nitrogen-fixing rhizobia, specialized culture media to determine iron chelation via siderophores and phosphate-solubilizing and cellulase activities; cultivation-independent methods, namely 16S rDNA cloning and sequencing; and also community-level physiological profiling to discover soil microbes associated with the Negev desert perennials Zygophyllum dumosum andAtriplex halimus during the years 2009–2010.

• Key results: We identified a number of PGPB, both epiphytes and endophytes, which fix nitrogen, chelate iron, solubilize phosphate, and secrete cellulase, as well as many other bacteria and some fungi, thereby providing a profile of the microbiomes that support the growth of two desert perennials.

• Conclusion: We generated a snapshot of the microbial communities in the Negev Desert, giving us an insight in its natural state. This desert, like many arid environments, is vulnerable to exploitation for other purposes, including solar energy production and dry land farming.

  
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In situ microbial metabolism of aromatic-hydrocarbon environmental pollutants

In situ microbial metabolism of aromatic-hydrocarbon environmental pollutants | Rhizosphere matters | Scoop.it
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Annals of Botany, SPECIAL ISSUE: Matching Roots to Environment

Annals of Botany, SPECIAL ISSUE: Matching Roots to Environment | Rhizosphere matters | Scoop.it

Via Andres Zurita, Mary Williams
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Andres Zurita's curator insight, July 2, 2013 9:15 AM
Matching roots to their environment 

Plants rely on their roots to acquire the water and mineral elements necessary for their survival in nature, and their yield and nutritional quality in agriculture. White et al. (pp. 207–222) examine how the roots of land plants evolved, describe how the ecology of roots and their rhizospheres affects the utilization of soil resources, and discuss the influence of plant roots on biogeochemical cycles. They then describe the roles of roots in overcoming the constraints to crop production imposed by hostile or infertile soils, illustrate root phenotypes that improve the acquisition of soil resources, and discuss high-throughput methods to screen for these traits in the laboratory, glasshouse and field. Finally, they consider how adaptations to root systems might enable sustainable agriculture in the future.

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Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Genome assembly for rare, uncultured bacteria is improved by mining deep metagenome sequencing data.
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

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Practical innovations for high-throughput amplicon sequencing : Nature Methods : Nature Publishing Group

Practical innovations for high-throughput amplicon sequencing : Nature Methods : Nature Publishing Group | Rhizosphere matters | Scoop.it
A set of practical improvements and software provide more accurate and less biased metagenomic amplicon sequencing at lower sequencing effort.
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Mycorrhizal Networks: Common Goods of Plants Shared under Unequal Terms of Trade

Plants commonly live in a symbiotic association with arbuscular mycorrhizal fungi (AMF). They invest photosynthetic products to feed their fungal partners, which, in return, provide mineral nutrients foraged in the soil by their intricate hyphal networks. Intriguingly, AMF can link neighboring plants, forming common mycorrhizal networks (CMNs). What are the terms of trade in such CMNs between plants and their shared fungal partners? To address this question, we set up microcosms containing a pair of test plants, interlinked by a CMN of Glomus intraradices or Glomus mosseae. The plants were flax (Linum usitatissimum; a C3plant) and sorghum (Sorghum bicolor; a C4 plant), which display distinctly different13C/12C isotope compositions. This allowed us to differentially assess the carbon investment of the two plants into the CMN through stable isotope tracing. In parallel, we determined the plants’ “return of investment” (i.e. the acquisition of nutrients viaCMN) using 15N and 33P as tracers. Depending on the AMF species, we found a strong asymmetry in the terms of trade: flax invested little carbon but gained up to 94% of the nitrogen and phosphorus provided by the CMN, which highly facilitated growth, whereas the neighboring sorghum invested massive amounts of carbon with little return but was barely affected in growth. Overall biomass production in the mixed culture surpassed the mean of the two monocultures. Thus, CMNs may contribute to interplant facilitation and the productivity boosts often found with intercropping compared with conventional monocropping.

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Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

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Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.

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Microbial Diversity | The Scientist Magazine®

Microbial Diversity | The Scientist Magazine® | Rhizosphere matters | Scoop.it
By sequencing bacterial and archaeal genomes from single cells, scientists have filled in many uncharted branches of the tree of life.
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Tiny Genomes May Offer Clues to First Plants and Animals

Symbiotic bacteria that dwell within insect cells are intricately intertwined with their hosts, prompting scientists to question when these bacteria stop being bona fide organisms and become part of the cell

By Emily Singer and Simons Science News

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