86 research outputs found
Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass
There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits
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Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability
Aims: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward).
Methods: Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues.
Results: Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants.
Conclusions: Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture
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Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - a genome comparison
The slow-growing genus Bradyrhizobium is biologically important in soils, with different representatives
found to perform a range of biochemical functions including photosynthesis, induction of root nodules
and symbiotic nitrogen fixation and denitrification. Consequently, the role of the genus in soil ecology
and biogeochemical transformations is of agricultural and environmental significance. Some isolates of
Bradyrhizobium have been shown to be non-symbiotic and do not possess the ability to form nodules.
Here we present the genome and gene annotations of two such free-living Bradyrhizobium isolates,
named G22 and BF49, from soils with differing long-term management regimes (grassland and bare
fallow respectively) in addition to carbon metabolism analysis. These Bradyrhizobium isolates are
the first to be isolated and sequenced from European soil and are the first free-living Bradyrhizobium
isolates, lacking both nodulation and nitrogen fixation genes, to have their genomes sequenced and
assembled from cultured samples. The G22 and BF49 genomes are distinctly different with respect
to size and number of genes; the grassland isolate also contains a plasmid. There are also a number
of functional differences between these isolates and other published genomes, suggesting that this
ubiquitous genus is extremely heterogeneous and has roles within the community not including
symbiotic nitrogen fixation
Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota
This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. Acknowledgements We would like to thank Dr Robert Griffith/CEH for providing DNA from soil samples and Dr Anthony Travis for his help with BioLinux. Sequencing was performed in NERC platform in Liverpool. CG-R was funded by a NERC fellowship NE/J019151/1. CQ was funded by a MRC fellowship (MR/M50161X/1) as part of the cloud infrastructure for microbial genomics consortium (MR/L015080/1).Peer reviewedPublisher PD
Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?
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Managing plant microbiomes for sustainable biofuel production
The development of environmentally sustainable, economical, and reliable sources of energy is one of the great challenges of the 21st century. Large-scale cultivation of cellulosic feedstock crops (henceforth, bioenergy crops) is considered one of themost promising renewable sources for liquid transportation fuels. However, the mandate to develop a viable cellulosic bioenergy industry is accompanied by an equally urgent mandate to deliver not only cheap reliable biomass but also ecosystembenefits, including efficient use of water, nitrogen, and phosphorous; restored soil health; and net negative carbon emissions. Thus, sustainable bioenergy crop production may involve new agricultural practices or feedstocks and should be reliable, cost effective, and minimal input,without displacing crops currently grown for food production on fertile land. In this editorial perspective for the Phytobiomes Journal Focus Issue on Phytobiomes of Bioenergy Crops and Agroecosystems, we consider the microbiomes associated with bioenergy crops, the effects beneficial microbes have on their hosts, and potential ecosystem impacts of these interactions.We also address outstanding questions, major advances, and emerging biotechnological strategies to design and manipulate bioenergy crop microbiomes. This approach could simultaneously increase crop yields and provide important ecosystem services for a sustainable energy future
Structure and composition of barley rhizospheric bacterial community and plant development cultivated with a super absorbent polymer
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Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.
Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth, root morphology, exudate composition, and microbial localization under controlled environmental conditions. We anticipate that these detailed protocols will serve as an important starting point for other researchers, ideally helping create standardized experimental systems for investigating plant-microbe interactions
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Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.
Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth, root morphology, exudate composition, and microbial localization under controlled environmental conditions. We anticipate that these detailed protocols will serve as an important starting point for other researchers, ideally helping create standardized experimental systems for investigating plant-microbe interactions
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