https://actinobase.org/api.php?action=feedcontributions&feedformat=atom&user=Louisa+perry+jicActinoBase - User contributions [en-gb]2026-10-17T19:21:46ZUser contributionsMediaWiki 1.39.3https://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2033Wheat root exudate harvesting2022-02-15T17:15:23Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
Plant roots are nutrient rich environments for soil microbes which form root-associated microbial communities. These communities make up the root microbiome consisting of the endosphere (the space inside of the root), the rhizosphere (the soil that is directly influenced by the root) and the bulk soil (any soil exterior to the root rhizosphere).<br />
<br />
16S rRNA gene sequencing has shown us that there is lower bacterial species diversity in the endosphere of roots compared to the rhizosphere and bulk soil (Lundberg et al, 2012; Prudence et al, 2012). This demonstrates that some bacteria have developed adaptations that allows them to acquire this niche; it is hypothesised that this is either through outcompeting other bacteria or a mechanism of protrusion. Some initial studies have found that plants grown side by side in the same environment recruit different microbes which suggest that plants can select for specific microbes which benefit them (Smalla, et al. 2001; Reinhold-Hurek et al., 2015). One factor which is being explored is the role of plant exudates on this selection.<br />
<br />
Exudates are metabolites excreted by plants into the rhizosphere which allows plants to support healthy growth, for example to break down nutrients in a more readily accessible form and to signal PGP soil microbes (Vives-Peris, 2019). This protocol outlines how to extract root exudates.<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes (1 tube = 1 plant)<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentrifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ 500 mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (temp 24C, light 18h)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Separate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.<br />
<br />
<h1>References:</h1><br />
Lundberg, D., Lebeis, S., Paredes, S., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T., Edgar, R., Eickhorst, T., Ley, R., Hugenholtz, P., Tringe, S. and Dangl, J., 2012. Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), pp.86-90.<br />
<br />
Prudence, S., Newitt†, J., Worsley, S., Macey, M., Murrell, J., Lehtovirta-Morley, L. and Hutchings, M., 2021. Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome, 16(1).<br />
<br />
Reinhold-Hurek, B., Bünger, W., Burbano, C., Sabale, M. and Hurek, T., 2015. Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity. Annual Review of Phytopathology, 53(1), pp.403-424.<br />
<br />
References<br />
Lundberg, D., Lebeis, S., Paredes, S., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T., Edgar, R., Eickhorst, T., Ley, R., Hugenholtz, P., Tringe, S. and Dangl, J., 2012. Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), pp.86-90.<br />
<br />
Prudence, S., Newitt†, J., Worsley, S., Macey, M., Murrell, J., Lehtovirta-Morley, L. and Hutchings, M., 2021. Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome, 16(1).<br />
<br />
Reinhold-Hurek, B., Bünger, W., Burbano, C., Sabale, M. and Hurek, T., 2015. Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity. Annual Review of Phytopathology, 53(1), pp.403-424.<br />
<br />
Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., Roskot, N., Heuer, H. and Berg, G., 2001. Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed. Applied and Environmental Microbiology, 67(10), pp.4742-4751.<br />
<br />
Vives-Peris, V., de Ollas, C., Gómez-Cadenas, A. and Pérez-Clemente, R., 2019. Root exudates: from plant to rhizosphere and beyond. Plant Cell Reports, 39(1), pp.3-17.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2032Wheat root exudate harvesting2022-02-15T17:06:24Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
Plant roots are nutrient rich environments for soil microbes which form root-associated microbial communities. These communities make up the root microbiome consisting of the endosphere (the space inside of the root), the rhizosphere (the soil that is directly influenced by the root) and the bulk soil (any soil exterior to the root rhizosphere).<br />
<br />
16S rRNA gene sequencing has shown us that there is lower bacterial species diversity in the endosphere of roots compared to the rhizosphere and bulk soil (Lundberg et al, 2012; Prudence et al, 2012). This demonstrates that some bacteria have developed adaptations that allows them to acquire this niche; it is hypothesised that this is either through outcompeting other bacteria or a mechanism of protrusion. Some initial studies have found that plants grown side by side in the same environment recruit different microbes which suggest that plants can select for specific microbes which benefit them (Reinhold-Hurek et al., 2015). One factor which is being explored is the role of plant exudates on this selection.<br />
<br />
Exudates are metabolites excreted by plants into the rhizosphere which allows plants to support healthy growth, for example to break down nutrients in a more readily accessible form and to signal PGP soil microbes (Vives-Peris, 2019). This protocol outlines how to extract root exudates.<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes (1 tube = 1 plant)<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ 500 mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (temp 24C, light 18h)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.<br />
<br />
<h1>References:</h1><br />
Lundberg, D., Lebeis, S., Paredes, S., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T., Edgar, R., Eickhorst, T., Ley, R., Hugenholtz, P., Tringe, S. and Dangl, J., 2012. Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), pp.86-90.<br />
<br />
Prudence, S., Newitt†, J., Worsley, S., Macey, M., Murrell, J., Lehtovirta-Morley, L. and Hutchings, M., 2021. Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome, 16(1).<br />
<br />
Reinhold-Hurek, B., Bünger, W., Burbano, C., Sabale, M. and Hurek, T., 2015. Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity. Annual Review of Phytopathology, 53(1), pp.403-424.<br />
<br />
Vives-Peris, V., de Ollas, C., Gómez-Cadenas, A. and Pérez-Clemente, R., 2019. Root exudates: from plant to rhizosphere and beyond. Plant Cell Reports, 39(1), pp.3-17.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2031Wheat root exudate harvesting2022-02-15T16:55:37Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
Plant roots are nutrient rich environments for soil microbes which form root-associated microbial communities. These communities make up the root microbiome consisting of the endosphere (the space inside of the root), the rhizosphere (the soil that is directly influenced by the root) and the bulk soil (any soil exterior to the root rhizosphere).<br />
<br />
16S rRNA gene sequencing has shown us that there is lower bacterial species diversity in the endosphere of roots compared to the rhizosphere and bulk soil (Lundberg et al, 2012; Prudence et al, 2012). This demonstrates that some bacteria have developed adaptations that allows them to acquire this niche; it is hypothesised that this is either through outcompeting other bacteria or a mechanism of protrusion. Some initial studies have found that plants grown side by side in the same environment recruit different microbes which suggest that plants can select for different microbes (Reinhold-Hurek et al., 2015). One factor which is being explored is the role of plant exudates on this selection.<br />
<br />
Exudates are metabolites excreted by plants into the rhizosphere which allows plants to support healthy growth, for example to break down nutrients in a more readily accessible form and to signal PGP soil microbes (Vives-Peris, 2019).<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes (1 tube = 1 plant)<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.<br />
<br />
<h1>References:</h1><br />
Lundberg, D., Lebeis, S., Paredes, S., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T., Edgar, R., Eickhorst, T., Ley, R., Hugenholtz, P., Tringe, S. and Dangl, J., 2012. Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), pp.86-90.<br />
<br />
Prudence, S., Newitt†, J., Worsley, S., Macey, M., Murrell, J., Lehtovirta-Morley, L. and Hutchings, M., 2021. Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome, 16(1).<br />
<br />
Reinhold-Hurek, B., Bünger, W., Burbano, C., Sabale, M. and Hurek, T., 2015. Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity. Annual Review of Phytopathology, 53(1), pp.403-424.<br />
<br />
Vives-Peris, V., de Ollas, C., Gómez-Cadenas, A. and Pérez-Clemente, R., 2019. Root exudates: from plant to rhizosphere and beyond. Plant Cell Reports, 39(1), pp.3-17.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2030Wheat root exudate harvesting2022-02-15T16:49:24Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
Plant roots are nutrient rich environments for soil microbes which form root-associated microbial communities. These communities make up the root microbiome consisting of the endosphere (the space inside of the root), the rhizosphere (the soil that is directly influenced by the root) and the bulk soil (any soil exterior to the root rhizosphere).<br />
<br />
16S rRNA gene sequencing has shown us that there is lower bacterial species diversity in the endosphere of roots compared to the rhizosphere and bulk soil (Lundberg et al, 2012; Prudence et al, 2012). This demonstrates that some bacteria have developed adaptations that allows them to acquire this niche; it is hypothesised that this is either through outcompeting other bacteria or a mechanism of protrusion. Some initial studies have found that plants grown side by side in the same environment recruit different microbes which suggest that plants can select for different microbes (Reinhold-Hurek et al., 2015). One factor which is being explored is the role of plant exudates on this selection.<br />
<br />
Exudates are metabolites excreted by plants into the rhizosphere which allows plants to support healthy growth, for example to break down nutrients in a more readily accessible form and to signal PGP soil microbes (Vives-Peris, 2019).<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes (1 tube = 1 plant)<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2029Wheat root exudate harvesting2022-02-15T16:48:19Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
Plant roots are nutrient rich environments for soil microbes which form root-associated microbial communities. These communities make up the root microbiome consisting of the endosphere (the space inside of the root), the rhizosphere (the soil that is directly influenced by the root) and the bulk soil (any soil exterior to the root rhizosphere).<br />
<br />
16S rRNA gene sequencing has shown us that there is lower bacterial species diversity in the endosphere of roots compared to the rhizosphere and bulk soil (Lundberg et al, 2012; Prudence et al, 2012). This demonstrates that some bacteria have developed adaptations that allows them to acquire this niche; it is hypothesised that this is either through outcompeting other bacteria or a mechanism of protrusion. Some initial studies have found that plants grown side by side in the same environment recruit different microbes which suggest that plants can select for different microbes (Reinhold-Hurek et al., 2015). One factor which is being explored is the role of plant exudates on this selection.<br />
<br />
Exudates are metabolites excreted by plants into the rhizosphere which allows plants to support healthy growth, for example to break down nutrients in a more readily accessible form and to signal PGP soil microbes (Vives-Peris, 2019).<br />
<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes (1 tube = 1 plant)<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2024Wheat root exudate harvesting2021-11-23T14:33:46Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
...<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes (1 tube = 1 plant)<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2023Wheat root exudate harvesting2021-11-23T14:30:26Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
...<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the growth tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=2022Wheat root exudate harvesting2021-11-23T14:29:23Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
...<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the growth tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the grow tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1968Plant-Microbe interactions2021-10-29T12:53:34Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
<h3><strong>''Marchantia'' protocols</strong></h3><br />
<br />
*[[Growing Marchantia from gemma spores| Growing ''Marchantia'' from gemma spores]]<br />
<br />
<h3><strong>Wheat protocols</h3></strong><br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Wheat seed sterilisation]]<br />
*[[Wheat root exudate harvesting| Harvesting root exudates]]<br />
<br />
<h2><strong>Further Reading</strong></h2><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1967Plant-Microbe interactions2021-10-29T12:37:28Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
<h3><strong>''Marchantia'' protocols</strong></h3><br />
<br />
*[[Growing Marchantia from gemma spores| Growing ''Marchantia'' from gemma spores]]<br />
<br />
<h3><strong>Wheat protocols</h3></strong><br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Wheat seed sterilisation]]<br />
*[[Wheat root exudate harvesting]]<br />
<br />
<h2><strong>Further Reading</strong></h2><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=1966Wheat root exudate harvesting2021-10-29T12:36:34Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
...<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the grow tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the grow tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=1965Wheat root exudate harvesting2021-10-29T12:35:34Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Harvesting root exudates}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
...<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the grow tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the grow tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Media_recipes&diff=1964Media recipes2021-10-29T12:34:37Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE:Media Recipes}}<br />
<br />
[[File:Actinobase-icons-trans_Media-recipes.png|150px|Media Recipes|link=Media_recipes]]<br />
<br />
=Media Recipes=<br />
<br />
[[A1]]<br />
<br />
[[CM]] (Complete medium)<br />
<br />
[[DNA]] (Difco Nutrient Agar) | [[DNB]] (Difco Nutrient Broth) | [[SNA]] (Soft Nutrient Agar)<br />
<br />
[[Emerson medium]]<br />
<br />
[[Gause's No. 1]]<br />
<br />
[[GYM]] (Glucose + Yeast Extract + Malt Extract) <br />
<br />
[[HT]] (Hickey-Tresner)<br />
<br />
[[HV]]<br />
<br />
[[IMA]] (Smash)<br />
<br />
[[LB]] (Lysogeny Broth) | [[Lennox]] (Lennox agar) | [[Luria]] (Luria agar)<br />
<br />
[[MC agar]] (Milk Casein Agar)<br />
<br />
[[MM]] (Minimal medium)<br />
<br />
[[SFM | MS]] (Mannitol Soya agar - a.k.a. Soya Flour Mannitol (SFM))<br />
<br />
[[1/2 MS0 | 1/2 MS-S]]<br />
<br />
[[MS+B5]]<br />
<br />
[[MYM]] (Maltose + Yeast Extract + Malt Extract) <br />
<br />
[[NMMP]] (minimal liquid medium)<br />
<br />
[[OT]] (oligotrophic agar)<br />
<br />
[[PDA]] (Potato Dextrose Agar)<br />
<br />
[[R2]] | [[R2YE]] | [[R5]]<br />
<br />
[[SC]] (Starch Casein agar)<br />
<br />
[[SFM]] (Soya Flour Mannitol - a.k.a. Mannitol Soya agar)<br />
<br />
[[SMM]] (supplemented liquid minimal medium) | [[SMMS]] (supplemented minimal medium, solid)<br />
<br />
[[SPY]] (Salt Peptone Yeast)<br />
<br />
[[TSB]] (Tryptone Soy Broth)<br />
<br />
[[YEME]] (Yeast Extract + Malt Extract)<br />
<br />
[[YMPD]] (Yeast Meat Peptone Dextrose)<br />
<br />
[[YP]] (Yeast Peptone) | [[YPD]] (Yeast Peptone Dextrose) <br />
<br />
[[2X YT]]<br />
<br />
====<u>International ''Streptomyces'' Project Media (ISP's)</u>====<br />
<br />
[[ISP2]] <br />
<br />
[[ISP3]]<br />
<br />
[[ISP4]]<br />
<br />
[[ISP5]]<br />
<br />
[[ISP6]]<br />
<br />
[[ISP7]]<br />
<br />
==Media Supplements==<br />
<br />
[[Antibiotic stocks and working concentrations]]<br />
<br />
[[Indicator compounds]]<br />
<br />
[[Media supplements for activating cryptic biosynthetic gene clusters]]<br />
<br />
[[Media supplements for induction gene expression from inducible promoters]]<br />
<br />
[[Trace element solution]]</div>Louisa perry jichttps://actinobase.org/index.php?title=1/2_MS0&diff=19631/2 MS02021-10-29T12:31:28Z<p>Louisa perry jic: Created page with "==Preparation== Per Litre: *2.205 g g Murashige & Skoog Medium Without Vitamins *1 L tap water *NaOH '''Instructions''' #Dissolve 2.205g Murashige & Skoog in 1L tap water #..."</p>
<hr />
<div>==Preparation==<br />
Per Litre:<br />
*2.205 g g Murashige & Skoog Medium Without Vitamins<br />
*1 L tap water<br />
*NaOH<br />
<br />
<br />
'''Instructions'''<br />
#Dissolve 2.205g Murashige & Skoog in 1L tap water<br />
#pH 5.8 with NaOH <br />
#Autoclave<br />
<br />
==Uses==<br />
*[[Wheat root exudate harvesting]]</div>Louisa perry jichttps://actinobase.org/index.php?title=Wheat_root_exudate_harvesting&diff=1962Wheat root exudate harvesting2021-10-29T12:24:36Z<p>Louisa perry jic: Created page with "{{DISPLAYTITLE: Wheat root exudate harvesting}} <h1>Wheat root exudates and the recruitment of root microbes</h1> ... <h1>You will need:</h1> Preparation of growth tubes * 5..."</p>
<hr />
<div>{{DISPLAYTITLE: Wheat root exudate harvesting}}<br />
<br />
<h1>Wheat root exudates and the recruitment of root microbes</h1><br />
...<br />
<br />
<h1>You will need:</h1><br />
Preparation of growth tubes<br />
* 50ml falcon/centrifuge tubes<br />
* Electric hand drill<br />
* 10mm drill bit<br />
* 2ml microcentifuge tubes<br />
* Dog nail cutters<br />
* Vermiculite (washed and autoclaved)<br />
Growing of wheat plants<br />
* Wheat seeds<br />
* 70% ethanol<br />
* 3% bleach<br />
* dH<sub>2</sub>O<br />
* Sterile universal tube<br />
* Sterile tweezers<br />
* Water agar plates<br />
* [[1/2 MS0]] liquid media<br />
Exudate harvesting<br />
* 2 1L duran bottles<br />
* 0.22 micron sterile Büchner filter/bottletop vaccum filter funnel<br />
* Vacuum pump<br />
* 50ml falcon/centrifuge tubes<br />
* Syringe needle or sharp pointed item<br />
* -80°C freezer<br />
* Freeze drier<br />
* dH<sub>2</sub>O<br />
* 4ml HPLC vile<br />
<br />
<h1>Protocol:</h1><br />
<br />
<h2>Week 1, Day 1</h2><br />
<br />
<h4>Preparation of growth tubes</h4><br />
# Prepare as many tubes as plants required (1 batch of 50 tubes ~ ... mg final exudate).<br />
# Drill a 10mm hole in each tube and rinse with water to remove any plastic debris.<br />
# Using the dog nail cutters, cut the end of a 2ml microcentrifuge tube to create a ~0.5cm opening. Loosely fill the tube with the prepared vermiculite and close the lid.<br />
# Push the microcentrifuge tube into the hole of the 50ml falcon.<br />
# Autoclave.<br />
<br />
<h4>Growing of wheat plants</h4><br />
# [[Wheat seed sterilisation| Sterilise the wheat seeds]].<br />
# Spreadingly put the seeds onto a water agar plate and place into the fridge.<br />
<br />
<h2>Week 1, Day 3</h2><br />
<h4>Growing of wheat plants</h4><br />
# Remove the water agar plates from the fridge and leave on the bench.<br />
<br />
<h2>Week 1, Day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Fill the falcon tubes with ~45ml 1/2 MS0 media.<br />
# When the seeds have sprouted two roots of ~0.5-1cm long, transfer the seed to the vermiculite tube so that the roots are pointing downwards into the vermiculite.<br />
# Keep the grow tubes in a controlled environment room (...)<br />
<br />
<h2>Week 2-4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with 1/2 MS0 media.<br />
<br />
<h2>Week 4, day 4</h2><br />
<h4>Growing of wheat plants</h4><br />
# Pour away the 1/2 MS0 and rinse the roots and tube with water (to remove any remaining salts).<br />
# Fill the growth tubes with ~45ml fresh water (this will be the media which the exudates will be extracted from).<br />
# Keep the grow tubes in a controlled environment room.<br />
<br />
<h2>Week 5</h2><br />
<h4>Growing of wheat plants</h4><br />
# Keep the growth tubes topped up with sterile water.<br />
<br />
<h2>Week 5, day 4</h2><br />
<h4>Exudate harvesting</h4><br />
# Pour the water from the growth tubes into a clean Duran bottle.<br />
# Attach a sterile 0.22 micron Büchner filter to another sterile Duran bottle and fix to a vacuum pump.<br />
# Pour the exudate solution into the Büchner filter and turn on the vacuum pump.<br />
# Seperate the filtered exudate solution into clean 50ml falcon tubes (about 25-30ml each) and freeze at -80°C.<br />
<br />
<h2>Week 5, day 5</h2><br />
<h4>Exudate harvesting</h4><br />
# Pierce a few holes in the lids of the frozen 50ml falcon tubes.<br />
# Place the tubes into a freeze drier and leave over the weekend.<br />
<br />
<h2>Week 6, day 1</h2><br />
<h4>Exudate harvesting</h4><br />
# The water should have evaporated and be left with some fluffy/web-like exudate.<br />
# Resuspend the exudate in minimal sterile water so that it fits into a pre weighed (without lid) 4ml HPLC vile.<br />
# Dry down your sample again (on a freeze drier or alternatively a Genevac) and weigh.<br />
# Your sample can be resuspended at a known concentration. It is now ready for use.</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1961Plant-Microbe interactions2021-10-29T12:22:50Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
<h3><strong>''Marchantia'' protocols</strong></h3><br />
<br />
*[[Growing Marchantia from gemma spores| Growing ''Marchantia'' from gemma spores]]<br />
<br />
<h3><strong>Wheat protocols</h3></strong><br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Wheat seed sterilisation]]<br />
*[[Harvesting root exudates]]<br />
*[[Wheat root exudate harvesting]]<br />
<br />
<h2><strong>Further Reading</strong></h2><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1953Growing Marchantia from gemma spores2021-10-26T14:11:34Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[MS+B5]] agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1952Growing Marchantia from gemma spores2021-10-26T14:10:45Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[MS+B5]] agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1951Growing Marchantia from gemma spores2021-10-26T14:08:45Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[MS+B5]] agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Louisa perry jichttps://actinobase.org/index.php?title=MS%2BB5&diff=1950MS+B52021-10-26T14:06:49Z<p>Louisa perry jic: Created page with "==Preparation== Per Litre: *2.25 g g Murashige & Skoog Medium Without Vitamins *0.056 g Gamborg B5 Vitamin Mixture *12 g Agar *1 L tap water '''Instructions''' #Dissolve 2.25..."</p>
<hr />
<div>==Preparation==<br />
Per Litre:<br />
*2.25 g g Murashige & Skoog Medium Without Vitamins<br />
*0.056 g Gamborg B5 Vitamin Mixture<br />
*12 g Agar<br />
*1 L tap water<br />
<br />
'''Instructions'''<br />
#Dissolve 2.25g Murashige & Skoog and 0.056g Gamborg B5 in 1L tap water<br />
#Add 1.2g agar to each 250mL flask<br />
#Add 100mL solution to each flask<br />
#Autoclave<br />
<br />
==Uses==<br />
*Routine growth of ''Marchantia'' plants<br />
*[[Growing Marchantia from gemma spores]]</div>Louisa perry jichttps://actinobase.org/index.php?title=Media_recipes&diff=1947Media recipes2021-10-26T13:47:27Z<p>Louisa perry jic: /* Media Recipes */</p>
<hr />
<div>{{DISPLAYTITLE:Media Recipes}}<br />
<br />
[[File:Actinobase-icons-trans_Media-recipes.png|150px|Media Recipes|link=Media_recipes]]<br />
<br />
=Media Recipes=<br />
<br />
[[A1]]<br />
<br />
[[CM]] (Complete medium)<br />
<br />
[[DNA]] (Difco Nutrient Agar) | [[DNB]] (Difco Nutrient Broth) | [[SNA]] (Soft Nutrient Agar)<br />
<br />
[[Emerson medium]]<br />
<br />
[[Gause's No. 1]]<br />
<br />
[[GYM]] (Glucose + Yeast Extract + Malt Extract) <br />
<br />
[[HT]] (Hickey-Tresner)<br />
<br />
[[HV]]<br />
<br />
[[IMA]] (Smash)<br />
<br />
[[LB]] (Lysogeny Broth) | [[Lennox]] (Lennox agar) | [[Luria]] (Luria agar)<br />
<br />
[[MC agar]] (Milk Casein Agar)<br />
<br />
[[MM]] (Minimal medium)<br />
<br />
[[SFM | MS]] (Mannitol Soya agar - a.k.a. Soya Flour Mannitol (SFM))<br />
<br />
[[MS+B5]]<br />
<br />
[[MYM]] (Maltose + Yeast Extract + Malt Extract) <br />
<br />
[[NMMP]] (minimal liquid medium)<br />
<br />
[[OT]] (oligotrophic agar)<br />
<br />
[[PDA]] (Potato Dextrose Agar)<br />
<br />
[[R2]] | [[R2YE]] | [[R5]]<br />
<br />
[[SC]] (Starch Casein agar)<br />
<br />
[[SFM]] (Soya Flour Mannitol - a.k.a. Mannitol Soya agar)<br />
<br />
[[SMM]] (supplemented liquid minimal medium) | [[SMMS]] (supplemented minimal medium, solid)<br />
<br />
[[SPY]] (Salt Peptone Yeast)<br />
<br />
[[TSB]] (Tryptone Soy Broth)<br />
<br />
[[YEME]] (Yeast Extract + Malt Extract)<br />
<br />
[[YMPD]] (Yeast Meat Peptone Dextrose)<br />
<br />
[[YP]] (Yeast Peptone) | [[YPD]] (Yeast Peptone Dextrose) <br />
<br />
[[2X YT]]<br />
<br />
====<u>International ''Streptomyces'' Project Media (ISP's)</u>====<br />
<br />
[[ISP2]] <br />
<br />
[[ISP3]]<br />
<br />
[[ISP4]]<br />
<br />
[[ISP5]]<br />
<br />
[[ISP6]]<br />
<br />
[[ISP7]]<br />
<br />
==Media Supplements==<br />
<br />
[[Antibiotic stocks and working concentrations]]<br />
<br />
[[Indicator compounds]]<br />
<br />
[[Media supplements for activating cryptic biosynthetic gene clusters]]<br />
<br />
[[Media supplements for induction gene expression from inducible promoters]]<br />
<br />
[[Trace element solution]]</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1946Growing Marchantia from gemma spores2021-10-26T13:42:35Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*MS+B5 agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1945Growing Marchantia from gemma spores2021-10-26T13:40:37Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*MS+B5 agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1944Growing Marchantia from gemma spores2021-10-26T13:36:48Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*MS+B5 agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1943Growing Marchantia from gemma spores2021-10-26T13:26:32Z<p>Louisa perry jic: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. …<br />
<br /><br />
''Marchantia polymorpha'' (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*MS+B5 agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.</div>Louisa perry jichttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1942Growing Marchantia from gemma spores2021-10-26T13:24:32Z<p>Louisa perry jic: Created page with "{{DISPLAYTITLE: Growing Marchantia from gemma spores}} ==Marchantia and their lifecycle== Marchantia are a genus of plant in the Bryophyte taxonomic division along with mosse..."</p>
<hr />
<div>{{DISPLAYTITLE: Growing Marchantia from gemma spores}}<br />
<br />
==Marchantia and their lifecycle==<br />
Marchantia are a genus of plant in the Bryophyte taxonomic division along with mosses and liverworts which are thought to be the oldest extant plants on earth. …<br />
<br /><br />
Marchantia polymorpha (The ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy Marchantia plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*MS+B5 agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the Marchantia plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1941Plant-Microbe interactions2021-10-26T13:19:15Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
<br />
<h5>Marchantia</h5><br />
<br />
*[[Growing Marchantia from gemma spores]]<br />
<br />
<h3><strong>Further Reading</strong></h3><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1939Plant-Microbe interactions2021-10-26T12:56:33Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans (Prudence et al, 2021). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
<br />
<h3><strong>Further Reading</strong></h3><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1938Plant-Microbe interactions2021-10-26T12:54:09Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans (Prudence et al, 2021). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
<br />
<h5>Marchantia</h5><br />
<br />
<h3><strong>Further Reading</strong></h3><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jichttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1937Plant-Microbe interactions2021-10-26T12:52:26Z<p>Louisa perry jic: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans (Prudence et al, 2021). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
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<h2><strong>Protocols</strong></h2><br />
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[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
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<h5>Marchantia</h5><br />
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<h3><strong>Further Reading</strong></h3><br />
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Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
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Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
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Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
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Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
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Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
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Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
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van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
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Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Louisa perry jic