Name: isolation, characterization, and total dna extraction to identify endophytic fungi in mycoheterotrophic plants
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Description: Watch this Scientific Journal Video about Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants at JoVE.com

We thank funding from FAPESP (2015/26479-6) and CNPq (447453/2014-9). JLSM thanks CNPq for productivity grants (303664/2020-7). MPP thanks Capes (master&#39;s degree scholarship, process 88887.600591/2021-00) and CNPq.

1. Plant sample collection
<ol>
	<li>Sample collection for culture-dependent methods
	<ol>
		<li>Carefully dig the subterranean organs; these can be roots, stems, rhizomes, or storage organs of the plant to be collected. Apart from highly compact soils, collect these samples by hand. 
		NOTE: The use of tools such as trowels or scoops in this step is ill-advised, as it can damage the fragile structures of mycoheterotrophic plants and may cause tissue contamination by non-endophytic fungi.</li>
		<...

<ol>
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L., Kasuya, M. C. M., Borges, A. C., Ara&#250;jo, E. F. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+and+molecular+characterization+of+mycorrhizal+fungi+isolated+from+neotropical+orchids+in+Brazil.">Morphological and molecular characterization of mycorrhizal fungi isolated from neotropical orchids in Brazil.</a> Canadian Journal of Botany. 83 (1), 54-65 (2005).</li><li>Riddell, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Permanent+stained+mycological+preparations+obtained+by+slide+culture.">Permanent stained mycological preparations obtained by slide culture.</a> Mycologia. 42 (2), 265-270 (1950).</li><li>Walsh, T. J., Hayden, R. T., Larone, D. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Larone's Medically Important Fungi: A Guide to Identification. , (2018).</li><li>Microscopy: Chemical Reagents. British Mycological Society Available from: <a target="_blank" href="https://www.britmycolsoc.org.uk/field_mycology/microscopy/reagents">https://www.britmycolsoc.org.uk/field_mycology/microscopy/reagents</a> (2022)</li><li>Senanayake, I. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+approaches+in+studying+fungi:+Collection,+examination,+isolation,+sporulation+and+preservation.">Morphological approaches in studying fungi: Collection, examination, isolation, sporulation and preservation.</a> Mycosphere. 11 (1), 2678-2754 (2020).</li><li>Slifkin, M., Cumbie, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Congo+red+as+a+fluorochrome+for+the+rapid+detection+of+fungi.">Congo red as a fluorochrome for the rapid detection of fungi.</a> Journal of Clinical Microbiology. 26 (5), 827-830 (1988).</li><li>Raeder, U., Broda, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+preparation+of+DNA+from+filamentous+fungi.">Rapid preparation of DNA from filamentous fungi.</a> Letters in Applied Microbiology. 1 (1), 17-20 (1985).</li><li>Martins, M. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+characterization+of+endophytic+microorganisms.">Molecular characterization of endophytic microorganisms.</a> Endophytic microorganisms: theoretical and practical aspects of isolation and characterization. 1st edition. , 189-211 (2014).</li><li>Rayner, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Mycological+Colour+Chart.">A Mycological Colour Chart.</a> Commonwealth Mycological Institute. , (1970).</li><li>Kornerup, A., Wanscher, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Methuen Handbook of Colour. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toluidine+blue:+A+review+of+its+chemistry+and+clinical+utility.">Toluidine blue: A review of its chemistry and clinical utility.</a> Journal of Oral and Maxillofacial Pathology. 16 (2), 251-255 (2012).</li><li>Smith, D., Onions, A. H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+some+preservation+techniques+for+fungi.">A comparison of some preservation techniques for fungi.</a> Transactions of the British Mycological Society. 81 (3), 535-540 (1983).</li><li>Ryan, M. J., Smith, D., Jeffries, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+decision-based+key+to+determine+the+most+appropriate+protocol+for+the+preservation+of+fungi.">A decision-based key to determine the most appropriate protocol for the preservation of fungi.</a> World Journal of Microbiology and Biotechnology. 16 (2), 183-186 (2000).</li><li>Lalaymia, I., Cranenbrouck, S., Declerck, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maintenance+and+preservation+of+ectomycorrhizal+and+arbuscular+mycorrhizal+fungi.">Maintenance and preservation of ectomycorrhizal and arbuscular mycorrhizal fungi.</a> Mycorrhiza. 24 (5), 323-337 (2014).</li><li>Zettler, L. W., Corey, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Orchid+mycorrhizal+fungi:+isolation+and+identification+techniques.">Orchid mycorrhizal fungi: isolation and identification techniques.</a> Orchid Propagation: From Laboratories to Greenhouses-Methods and Protocols. , 27-59 (2018).</li><li>Yu, S., Wang, Y., Li, X., Yu, F., Li, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+factors+affecting+the+reproducibility+of+micro-volume+DNA+mass+quantification+in+Nanodrop+2000+spectrophotometer.">The factors affecting the reproducibility of micro-volume DNA mass quantification in Nanodrop 2000 spectrophotometer.</a> Optik. 145, 555-560 (2017).</li><li>Martos, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Independent+recruitment+of+saprotrophic+fungi+as+mycorrhizal+partners+by+tropical+achlorophyllous+orchids.">Independent recruitment of saprotrophic fungi as mycorrhizal partners by tropical achlorophyllous orchids.</a> New Phytologist. 184 (3), 668-681 (2009).</li><li>Schoch, C. 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The superficial disinfestation of plant samples is one of the most critical stages in the presented protocol. No contamination in the PDA dishes with drops from the last wash are highly desirable. Bacteria are frequently observed as contaminants in the isolation dishes, usually more than airborne sporulating fungi, considering endophytic bacteria are also common within plant tissues3,11. Thus, the addition of antibiotics in the culture medium when installing the ...

An erratum was issued for:&#160;<a href="https://www.jove.com/t/65135">Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants</a>. The Authors section was updated from:
Juliana Lishcka Sampaio Mayer
to:
Juliana Lischka Sampaio Mayer

An erratum was issued for:&#160;<a href="https://www.jove.com/t/65135">Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants</a>. The Authors section was updated.

Erratum: Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants

Endophytic fungi are, by definition, those that inhabit the interior of plant organs and tissues in inconspicuous infections (i.e., without causing harm to their host)1,2. These fungi can neutrally or beneficially interact with host plants, may confer resistance to pathogens and unfavorable environmental conditions, and may contribute to the synthesis of beneficial compounds for the plant (e.g., growth factors and other phytohormones)1,3. Mycorrhizal endophytes are fungi that establish mycorrhizal associations with the plant, taking part in nutrient transfer4. In Orchidaceae, the interaction with mycorrhizal endophytes is fundamental for seed germination in the vast majority of species, and seedling establishment in all the plants in the family5. In such contexts, mycoheterotrophic orchids represent a case of total dependence regarding their mycorrhizal partners, as they depend on mineral nutrients and carbon compounds transference by these fungi during their whole life cycle6. Therefore, the isolation and identification of associating fungi is a fundamental base when investigating mycoheterotrophic life strategies. Moreover, little is known about the roles of fungal endophytes in mycoheterotrophic plants or even the real diversity of these fungi7,8.
The investigation of endophytic fungi may be conducted via different techniques, traditionally described as culture-independent or -dependent, for instance: (a) direct observation, (b) fungal isolation and morphological and/or molecular identification, and (c) total DNA extraction of plant tissues and molecular identification9. In direct observation (a), endophytic fungi may be investigated while still in the interior of plant cells and tissues by light or electron microscopy9, as different microscopy protocols are detailed by Pena-Passos et al.10. By isolation methods (b), fungal endophytes can be characterized according to their colonies, hyphae, and reproductive or resistance structure morphology. Also, via isolation techniques, it is possible to conduct the molecular identification of isolates through DNA extraction, amplification of molecular identification sequences (barcodes or fingerprints), and sequencing11. The latter technique (c) enables the molecular identification of endophytic fungi per DNA extraction while in the interior of plant tissues (metabarcoding), followed by library preparation and sequencing12.
Moreover, fungal isolates may be applied in symbiotic germination trials, using seeds from autotrophic or mycoheterotrophic orchids. An example of such an application is the investigation conducted by Sisti et al.13, describing the germination and initial stages of protocorm development in Pogoniopsis schenckii, a mycoheterotrophic orchid, in association with some of its isolates, comprising non-mycorrhizal endophytic fungi. The applied symbiotic germination protocol is detailed and presented in a video by Pena-Passos et al.10. Isolating fungi in association with different plant organs allows diverse investigation focuses regarding the nature of plant-fungal interactions (e.g., to comprehend either ecological or physiological aspects of the association, as well as inquiries into the nutrient transference from fungi to the plant)9.
The methodologies presented in section 1 are based on a collection of subterranean organ samples, as these organs present the most difficulties in collection, and they are of major interest since mycorrhizal endophytes colonize them. However, both included protocols (steps 1.1 and 1.2) may be applied to other mycoheterotrophic plant organs (e.g., rhizomes, floral stems, and fruits). The collection methodology described in step 1.1 is designated for isolating endophytic fungi (section 2) for morphological characterization (sections 4 and 5) and/or total DNA extraction for isolate identification (section 6). On the other hand, the collection methodology described in step 1.2 is exclusively assigned to total DNA extraction of plant tissues for metabarcoding techniques (section 7). In section 3, four methods for filamentous fungi storage and preservation are presented, two for short-term storage (3-6 months) and the other two adequate for long-term storage (&#62;1 year). The morphological characterization (sections 4 and 5) may be associated with molecular identification to reinforce it and provide important information on fungal macro- and micromorphology. Figure 1 summarizes the collective methodologies described thereafter.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/65135/65135fig01.jpg" /> 
Figure 1: Schematic summarization of the presented methods. Plant collection and fungal isolation, preservation, and molecular identification by culture-dependent and -independent methodologies. <a href="https://www.jove.com/files/ftp_upload/65135/65135fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Adhesive tape</td>
			<td></td>
			<td></td>
			<td>(from any company, for adhesive tape mount in micromorphological analyses)</td>
		</tr>
		<tr>
			<td>Ampicillin</td>
			<td>Sigma-Aldrich</td>
			<td>A5354</td>
			<td>(for installation of plant fragments; other antibiotics may be used - check step 2.2.1)</td>
		</tr>
		<tr>
			<td>Autoclave</td>
			<td></td>
			<td></td>
			<td>(from any company, for materials sterilization in many steps)</td>
		</tr>
		<tr>
			<td>Bacteriological agar</td>
			<td>Sigma-Aldrich</td>
			<td>A1296</td>
			<td>(for many steps)</td>
		</tr>
		<tr>
			<td>C1, C2, C3, C4, C5, and C6 solutions</td>
			<td>Qiagen</td>
			<td>12888-50</td>
			<td>(purchased with DNeasy PowerSoil kit)</td>
		</tr>
		<tr>
			<td>Centrifuge&#160;&#160;</td>
			<td>Merck/Eppendorf</td>
			<td>5810 G</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Centrifuge tubes</td>
			<td>Merck</td>
			<td>CLS430828</td>
			<td>(for samples collection)</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Sigma-Aldrich</td>
			<td>C2432</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Congo red</td>
			<td>Supelco</td>
			<td>75768</td>
			<td>(for hyphae staining)</td>
		</tr>
		<tr>
			<td>Cryotubes</td>
			<td>Merck</td>
			<td>BR114831</td>
			<td>(for many steps)</td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Supelco</td>
			<td>100983</td>
			<td>It will be necessary to carry out the appropriate dilutions (for many steps)</td>
		</tr>
		<tr>
			<td>Ethylenediaminetetraacetic acid (EDTA)</td>
			<td>Sigma-Aldrich</td>
			<td>3609</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Merck</td>
			<td>WHA10010155</td>
			<td>(for many steps)</td>
		</tr>
		<tr>
			<td>Glass test tubes</td>
			<td>Merck</td>
			<td>CLS7082516</td>
			<td>(for cryopreservation in unhulled rice grains)</td>
		</tr>
		<tr>
			<td>Glass wool</td>
			<td>Supelco</td>
			<td>20411</td>
			<td>(for cryopreservation in unhulled rice grains)</td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G8270</td>
			<td>Or dextrose (for cryopreservation in vermiculite)</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Sigma-Aldrich</td>
			<td>G5516</td>
			<td>Or glycerin (for cryopreservation in vermiculite, for preparing LPCB)</td>
		</tr>
		<tr>
			<td>Isopropanol</td>
			<td>Sigma-Aldrich</td>
			<td>563935</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Lactic acid</td>
			<td>Sigma-Aldrich</td>
			<td>252476</td>
			<td>(for preparing LPCB - hyphae staining)</td>
		</tr>
		<tr>
			<td>Lactophenol blue solution (LPCB)</td>
			<td>Sigma-Aldrich</td>
			<td>61335</td>
			<td>(for hyphae staining)</td>
		</tr>
		<tr>
			<td>Laminar flow hood</td>
			<td></td>
			<td></td>
			<td>(class I, from any company, for many steps)</td>
		</tr>
		<tr>
			<td>Light microscope</td>
			<td></td>
			<td></td>
			<td>(from any company, for hyphae observation)</td>
		</tr>
		<tr>
			<td>MB Spin Columns</td>
			<td>Qiagen</td>
			<td>12888-50</td>
			<td>(purchased with DNeasy PowerSoil kit)</td>
		</tr>
		<tr>
			<td>Methyl blue (cotton blue)</td>
			<td>Sigma-Aldrich</td>
			<td>M5528</td>
			<td>(for preparing LPCB - hyphae staining)</td>
		</tr>
		<tr>
			<td>Microcentrifuge tube (1.5 mL)</td>
			<td>Merck</td>
			<td>HS4323</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Microcentrifuge tube (2 mL)</td>
			<td>Merck</td>
			<td>BR780546</td>
			<td>(for many steps)</td>
		</tr>
		<tr>
			<td>Mineral oil</td>
			<td></td>
			<td></td>
			<td>(for preservation of fungal isolates)</td>
		</tr>
		<tr>
			<td>Paper bags</td>
			<td></td>
			<td></td>
			<td>Average size 150 mm x 200 mm (for samples collection)</td>
		</tr>
		<tr>
			<td>Petri dish (Glass, 120 mm x 20 mm)</td>
			<td>Merck/Pyrex</td>
			<td>SLW1480/10D</td>
			<td>(autoclavable, for fungi slide culture, prefer higher ones)</td>
		</tr>
		<tr>
			<td>Petri dish (Glass, 50 mm x 17 mm)</td>
			<td>Merck/Aldrich</td>
			<td>Z740618</td>
			<td>(for purification of fungal isolates); alternatively: polystyrene petri dishes (sterile, &#947;-irradiated, non-autoclavable)</td>
		</tr>
		<tr>
			<td>Petri dish (Glass, 80 mm x 15 mm)</td>
			<td>Merck/Brand</td>
			<td>BR455732</td>
			<td>(for installation of plant fragments); alternatively: polystyrene petri dishes (sterile, &#947;-irradiated, non-autoclavable)</td>
		</tr>
		<tr>
			<td>Phenol</td>
			<td>Sigma-Aldrich</td>
			<td>P1037</td>
			<td>(for total DNA extraction from fungal isolates, for preparing LPCB)</td>
		</tr>
		<tr>
			<td>Porcelain mortar</td>
			<td>Sigma-Aldrich</td>
			<td>Z247464</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Porcelain pestle</td>
			<td>Sigma-Aldrich</td>
			<td>Z247502</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Potato dextrose agar (PDA)</td>
			<td>Millipore</td>
			<td>P2182</td>
			<td>(for many steps)</td>
		</tr>
		<tr>
			<td>PowerBead tubes</td>
			<td>Qiagen</td>
			<td>12888-50</td>
			<td>(purchased with DNeasy PowerSoil kit)</td>
		</tr>
		<tr>
			<td>Rapid mounting medium (Entellan)</td>
			<td>Sigma-Aldrich</td>
			<td>1.0796</td>
			<td>(for fungi slide culture)</td>
		</tr>
		<tr>
			<td>Silica gel</td>
			<td>Supelco</td>
			<td>717185</td>
			<td>(for cryopreservation in unhulled rice grains)</td>
		</tr>
		<tr>
			<td>Sodium chloride (NaCl)</td>
			<td>Sigma-Aldrich</td>
			<td>S9888</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate (SDS)</td>
			<td>Sigma-Aldrich</td>
			<td>L3771</td>
			<td>Lauryl sulfate sodium salt (for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Sodium hypochlorite (w/ 2% active chlorine)</td>
			<td></td>
			<td></td>
			<td>(commercial product, for superficial desinfestation)</td>
		</tr>
		<tr>
			<td>Soil DNA extraction kit (DNeasy PowerSoil kit)</td>
			<td>Qiagen</td>
			<td>12888-50</td>
			<td>(for total DNA extraction from plant organs)</td>
		</tr>
		<tr>
			<td>Spectrophotometer - Nanodrop 2000/2000c</td>
			<td>ThermoFisher Scientific</td>
			<td>ND2000CLAPTOP</td>
			<td>(for total DNA extraction from plant organs)</td>
		</tr>
		<tr>
			<td>Stereomicroscope</td>
			<td></td>
			<td></td>
			<td>(=dissecting microscope, from any company, for macromorphological analyses)</td>
		</tr>
		<tr>
			<td>Tetracycline</td>
			<td>Sigma-Aldrich</td>
			<td>T7660</td>
			<td>(for installation of plant fragments)</td>
		</tr>
		<tr>
			<td>Thermoblock</td>
			<td>Merck/Eppendorf</td>
			<td>EP5362000035</td>
			<td>(or from other companies)</td>
		</tr>
		<tr>
			<td>Tissue homogenizer and cell lyzer</td>
			<td>SPEX SamplePrep</td>
			<td></td>
			<td>2010 Geno/Grinder - Automated Tissue Homogenizer and Cell Lyzer (for total DNA extraction from plant organs)</td>
		</tr>
		<tr>
			<td>Toluidine blue O</td>
			<td>Sigma-Aldrich/Harleco</td>
			<td>364-M</td>
			<td>(for hyphae staining)</td>
		</tr>
		<tr>
			<td>Trehalose</td>
			<td>Sigma-Aldrich</td>
			<td>T9531</td>
			<td>(for cryopreservation in vermiculite)</td>
		</tr>
		<tr>
			<td>Tris Base Solution (Tris)</td>
			<td>Sigma-Aldrich</td>
			<td>T1699</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Unhulled rice grains</td>
			<td></td>
			<td></td>
			<td>(for cryopreservation)</td>
		</tr>
		<tr>
			<td>U-shaped glass rod</td>
			<td></td>
			<td></td>
			<td>(or an adaptation - check step 5.4.1, for fungi slide culture)</td>
		</tr>
		<tr>
			<td>Vermiculite</td>
			<td></td>
			<td></td>
			<td>Fine granulometry (for cryopreservation in vermiculite)</td>
		</tr>
		<tr>
			<td>Vortexer</td>
			<td>Sigma-Aldrich/BenchMixer</td>
			<td>BMSBV1000</td>
			<td>(for total DNA extraction from fungal isolates)</td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>Sigma-Aldrich</td>
			<td>Y1625</td>
			<td>(for cryopreservation in vermiculite)</td>
		</tr>
	</tbody>
</table>

isolation, characterization, and total dna extraction to identify endophytic fungi in mycoheterotrophic plants

Mycoheterotrophic plants present one of the most extreme forms of mycorrhizal dependency, having totally lost their autotrophic capacity. As essential as any other vital resource, the fungi with which these plants intimately associate are essential for them. Hence, some of the most relevant techniques in studying mycoheterotrophic species are the ones that enable the investigation of associated fungi, especially those inhabiting roots and subterranean organs. In this context, techniques for identifying culture-dependent and culture-independent endophytic fungi are commonly applied. Isolating fungal endophytes provides a means for morphologically identifying them, analyzing their diversity, and maintaining inocula for applications in the symbiotic germination of orchid seeds. However, it is known that there is a large variety of non-culturable fungi inhabiting plant tissues. Thus, culture-independent molecular identification techniques offer a broader cover of species diversity and abundance. This article aims to provide the methodological support necessary for starting two investigation procedures: a culture-dependent and an independent one. Regarding the culture-dependent protocol, the processes of collecting and maintaining plant samples from collection sites to laboratory facilities are detailed, along with isolating filamentous fungi from subterranean and aerial organs of mycoheterotrophic plants, keeping a collection of isolates, morphologically characterizing hyphae by slide culture methodology, and molecular identification of fungi by total DNA extraction. Encompassing culture-independent methodologies, the detailed procedures include collecting plant samples for metagenomic analyses and total DNA extraction from achlorophyllous plant organs using a commercial kit. Finally, continuity protocols (e.g., polymerase chain reaction [PCR], sequencing) are also suggested for analyses, and techniques are presented here.

In the isolation protocol, considering there is contamination from the water used on the last wash and the contamination is also detected in the Petri dishes with inoculated fragments, different actions may be taken, depending on the type of contaminant (Table 1). This procedure must be repeated from the beginning in case of highly sporulating fungal contaminants, which also present accelerated growth, and intense-multiplying bacteria, resistant to the chosen antibiotics....

Watch this Scientific Journal Video about Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants at JoVE.com

Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants

The current article aims to provide detailed and adequate protocols for the isolation of plant-associated endophytic fungi, long-term preservation of isolates, morphological characterization, and total DNA extraction for subsequent molecular identification and metagenomic analyses.

Mycoheterotrophic plants present one of the most extreme forms of mycorrhizal dependency, having totally lost their autotrophic capacity. As essential as ...

The techniques presented here are useful for investigating the endophytic fungi community associated with different plant organs. Endophytic fungi isolation allows their identification, and is valuable in other techniques such symbiotic germination. To begin, prepare eight to 10 centimeter PDA culture medium Petri dishes supplemented with three milliliters per liter of antibiotic.Check for contamination by incubating the culture medium Petri dishes at 36 degrees Celsius for 24 hours before use. On the next day, superficially disinfest healthy mychoheterotrophic plant fragments using a standard procedure and place them in a sterile Petri dish. To evaluate the efficacy of superficial disinfestation of samples, inoculate a few drops of distilled water used during the last wash of the samples on PDA.Next, using a flamed scalpel and forceps, section the samples into 0.2 centimeter thick pieces. Section the samples to amplify the surface area to be in contact with the medium. Place five fragments of the subterranean organs in the antibiotic supplemented PDA plate as far apart as possible without touching the dish edges.Seal the Petri dishes with cling film, and store them in the dark at 25 to 27 degrees Celsius for five days. A day before subculturing, prepare five centimeter Petri dishes using five to seven grams per liter AA medium, and incubate the plates at 36 degrees Celsius for 24 hours. To purify fungal isolates, differentiate the PDA plate colonies by color, growth pattern, texture, and margin format.Then delimit the colony margins on the bottom side of the dish. Also identify the colonies with a code. Using the tip of an autoclaved wooden toothpick, recover a tiny amount of mycelium from the margins of the identified fungal colony and striate the AA plate, producing three striae at one centimeter from one another and the dish edges.Label the AA plate with the appropriate code using sticker paper and pencil. Seal the plates before incubating them in the dark at 25 to 27 degrees Celsius for three days. After incubation, meticulously observe the plates to identify fine hyphae forming individual colonies.Delimit the area of individual colonies using a permanent marker. Cut a portion of the medium containing the colony using an autoclaved toothpick, and transfer the cut volume to the center of a new PDA Petri plate without antibiotics. After labeling the Petri dishes with the codes of the isolates, seal them with cling film, and maintain them in the dark at 25 to 27 degrees Celsius for seven to 14 days.To begin the preservation of the fungal isolates with Castellani's method, add 0.5 milliliters of distilled water to the autoclaved two milliliter microcentrifuge tube. Using an autoclaved toothpick, cut 0.5 by 0.5 centimeter cuboid medium from the mycelium margins of already grown purified isolates. Place four to six cuboids in the microcentrifuge tubes with distilled water.Store the tubes in the dark at 25 degrees Celsius for as long as needed. When required, recuperate a cuboid and place it in the center of a new PDA dish to grow a stored isolate. Begin the tease mount method by placing a drop of a Toluidine blue-O stain on a clean glass slide.Different stains can be used in such a technique. Using an autoclaved toothpick, carefully remove some hyphae from the grown isolate, and place them in the drop of stain. Place a cover slip and analyze it under a light microscope.For the adhesive tape mount method, place a drop of a lactophenol cotton blue stain on a clean glass slide. Cut a strip of transparent adhesive tape in a size that fits the glass slide and the central stain drop well. Direct the sticky surface of the adhesive strip to the mycelium surface, and try to collect some hyphae without pressing or collecting too many of them.Then stick the tape to the glass slide, ensuring the stain is in contact with the collected hyphae. Place a drop of water above the tape and place a cover slip before analyzing the slide under a light microscope. The growth of small groups of filamentous fungi mycelia emerging from the interior of the fragments was observed after five days of inoculation of the mychoheterotrophic plant organ fragment on the PDA medium.During seven to 14 days of inoculation of the purified isolate, the centrifugal growth of pure fungal isolate colony was observed on PDA, forming a sole circular mycelium. Possible contaminations were easily identified, compromising the colony homogeneity concerning its growth form aspect, color, and pigment production in the medium. A colony isolated from the fusiform roots of the mychoheterotrophic orchid, Wullschlaegelia aphylla, was opaque with no diffusible pigments or exudates in the medium.The colony was whitish to gray on the upper side, and brownish on the lower side. The mycelia were aerial and abundant, and the margins were irregular and aerial. The colony had a velvety texture, and a wrinkled topography without macroscopic structures.The structures which were not easily visible in the nonstained mycelium were exhibited after staining the fungal mycelium with lactophenol cotton blue and Toluidine blue-O, facilitating their identification. The fungal isolation methods presented here may also be applied to green plants for identifying the fungal endophytes. The isolated fungi can be used in symbiotic germination trials.

isolation-characterization-total-dna-extraction-to-identify

Research

JoVE Journal

Biology

RNA Extraction from Neuroprecursor Cells Using the Bio-Rad Total RNA Kit

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the messagefor review see 1. However, it's now widely accepted that synonymous codon usage is the primary cause of non-uniform translational elongation rates1. Synonymous codons are not used with identical frequency. A bias exists in the use of synonymous codons with some codons used more frequently than others2. Codon bias is organism as well as tissue specific2,3. Moreover, frequency of codon usage is directly proportional to the concentrations of cognate tRNAs4. Thus, a frequently used codon will have higher multitude of corresponding tRNAs, which further implies that a frequent codon will be translated faster than an infrequent one. Thus, regions on mRNA enriched in rare codons (potential pause sites) will as a rule slow down ribosome movement on the message and cause accumulation of nascent peptides of the respective sizes5-8. These pause sites can have functional impact on the protein expression, mRNA stability and protein foldingfor review see 9. Indeed, it was shown that alleviation of such pause sites can alter ribosome movement on mRNA and subsequently may affect the efficiency of co-translational (in vivo) protein folding1,7,10,11. To understand the process of protein folding in vivo, in the cell, that is ultimately coupled to the process of protein synthesis it is essential to gain comprehensive insights into the impact of codon usage/tRNA content on the movement of ribosomes along mRNA during translational elongation.
Here we describe a simple technique that can be used to locate major translation pause sites for a given mRNA translated in various cell-free systems6-8. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA. The rationale is that at low-frequency codons, the increase in the residence time of the ribosomes results in increased amounts of nascent peptides of the corresponding sizes. In vitro transcribed mRNA is used for in vitro translational reactions in the presence of radioactively labeled amino acids to allow the detection of the nascent chains. In order to isolate ribosome bound nascent polypeptide complexes the translation reaction is layered on top of 30% glycerol solution followed by centrifugation. Nascent polypeptides in polysomal pellet are further treated with ribonuclease A and resolved by SDS PAGE. This technique can be potentially used for any protein and allows analysis of ribosome movement along mRNA and the detection of the major pause sites. Additionally, this protocol can be adapted to study factors and conditions that can alter ribosome movement and thus potentially can also alter the function/conformation of the protein.

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

A technique to identify translational pause sites on mRNA is described. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA, followed by the size analysis of the nascent chains using a denaturing gel electrophoresis.

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the ...

Filtration Isolation of Nucleic Acids:  A Simple and Rapid DNA Extraction Method

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad to extract cellular DNA from whole blood in less than 2 min. The blood specimen is treated with detergent, mixed briefly and applied by pipet to the separation membrane. The lysate wicks into the blotting pad due to capillary action, capturing the genomic DNA on the surface of the separation membrane. The extracted DNA is retained on the membrane during a simple wash step wherein PCR inhibitors are wicked into the absorbent blotting pad. The membrane containing the entrapped DNA is then added to the PCR reaction without further purification. This simple method does not require laboratory equipment and can be easily implemented with inexpensive laboratory supplies. Here we describe a protocol for highly sensitive detection and quantitation of HIV-1 proviral DNA from 100 &#181;l whole blood as a model for early infant diagnosis of HIV that could readily be adapted to other genetic targets.

We describe here a simple and rapid paper-based DNA extraction method of HIV proviral DNA from whole blood detected by quantitative PCR. This protocol can be extended for use in detecting other genetic markers or using alternative amplification methods.

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad ...

Modified Methods for Loading of High-Throughput DNA Extraction Plates Reduce Potential for Contamination

High-throughput DNA sequencing techniques have contributed substantially to advances in our understanding of relationships among microbial communities, host characteristics, and broader ecosystem functions. With this rapid increase in breadth and depth of sequencing capabilities have come methods to extract, amplify, analyze, and interpret environmental DNA successfully with maximum efficiency. Unfortunately, performing DNA extractions quickly can come at the cost of increasing the risk of contamination among samples. In particular, high-throughput extractions that are based on samples contained in a 96-well plate offer a relatively quick method, compared to single-tube extractions, but also increase opportunities for well-to-well cross-contamination. To minimize the risk of cross-contamination among samples, while retaining the benefits of high-throughput extraction techniques, we developed a new method for loading environmental samples into 96-well plates. We used pierceable PCR sealing films to cover each plate while loading samples and added samples first to PCR tubes before moving them into wells; together, these practices reduce the risk of sample drift and unintended double loading of wells. The method outlined in this paper provides researchers with an approach to maximize available high-throughput extraction techniques while reducing the risk of cross-contamination inherent to 96-well plates. We provide a detailed step by step outline of how to move from sample collection to DNA extraction while minimizing the risk of unwanted cross-contamination.

Current methods for loading 96-well plates for DNA extractions can be prone to contamination. We detail a new method for loading 96-well plates that reduces risk of cross-contamination among wells. Our method will help other researchers capitalize on the efficiency of high-throughput DNA extraction techniques and minimize risk of contamination.

High-throughput DNA sequencing techniques have contributed substantially to advances in our understanding of relationships among microbial communities, ...

Systematic Approach to Identify Novel Antimicrobial and Antibiofilm Molecules from Plants' Extracts and Fractions to Prevent Dental Caries

Natural products provide structurally different substances, with a myriad of biological activities. However, the identification and isolation of active compounds from plants are challenging because of the complex plant matrix and time-consuming isolation and identification procedures. Therefore, a stepwise approach for screening natural compounds from plants, including the isolation and identification of potentially active molecules, is presented. It includes the collection of the plant material; preparation and fractionation of crude extracts; chromatography and spectrometry (UHPLC-DAD-HRMS and NMR) approaches for analysis and compounds identification; bioassays (antimicrobial and antibiofilm activities; bacterial &#34;adhesion strength&#34; to the salivary pellicle and initial glucan matrix treated with selected treatments); and data analysis. The model is simple, reproducible, and allows high-throughput screening of multiple compounds, concentrations, and treatment steps can be consistently controlled. The data obtained provide the foundation for future studies, including formulations with the most active extracts and/or fractions, isolation of molecules, modeling molecules to specific targets in microbial cells and biofilms. For example, one target to control cariogenic biofilm is to inhibit the activity of Streptococcus mutans glucosyltransferases that synthesize the extracellular matrix&#8217; glucans. The inhibition of those enzymes prevents the biofilm build-up, decreasing its virulence.

Systematic Approach to Identify Novel Antimicrobial and Antibiofilm Molecules from Plants&#039; Extracts and Fractions to Prevent Dental Caries

Natural products represent promising starting points for the development of new drugs and therapeutic agents. However, due to the high chemical diversity, finding new therapeutic compounds from plants is a challenging and time-consuming task. We describe a simplified approach to identify antimicrobial and antibiofilm molecules from plant extracts and fractions.

Natural products provide structurally different substances, with a myriad of biological activities. However, the identification and isolation of active ...

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Epigenomic regulation at the chromatic level, including DNA and histone modifications, behaviors of transcription factors, and non-coding RNAs with their recruited proteins, lead to temporal and spatial control of gene expression. Cleavage under targets and tagmentation (CUT&#38;Tag) is an enzyme-tethering method in which the specific chromatin protein is firstly recognized by its specific antibody, and then the antibody tethers a protein A-transposase (pA-Tn5) fusion protein, which cleaves the targeted chromatin in situ by the activation of magnesium ions. Here, we provide our previously published CUT&#38;Tag protocol using intact nuclei isolated from allortetraploid cotton leaves with modification. This step-by-step protocol can be used for epigenomic research in plants. In addition, substantial modifications for plant nuclei isolation are provided with critical comments.

Cleavage under targets and tagmentation (CUT&amp;Tag) is an efficient chromatin epigenomic profiling strategy. This protocol presents a refined CUT&amp;Tag strategy for the profiling of histone modifications in plants.

Epigenomic regulation at the chromatic level, including DNA and histone modifications, behaviors of transcription factors, and non-coding RNAs with their ...

Isolation and Characterization of Intact Phycobilisome in Cyanobacteria

In cyanobacteria, phycobilisome is a vital antenna protein complex that harvests light and transfers energy to photosystem I and II for photochemistry. Studying the structure and composition of phycobilisome is of great interest to scientists because it reveals the evolution and divergence of photosynthesis in cyanobacteria. This protocol provides a detailed and optimized method to break cyanobacterial cells at low cost by a bead-beater efficiently. The intact phycobilisome can then be isolated from the cell extract by sucrose gradient ultracentrifugation. This method has demonstrated being suitable for both model and non-model cyanobacteria with different cell types. A step-by-step procedure is also provided to confirm the integrity and property of phycobiliproteins by 77K fluorescence spectroscopy and SDS-PAGE stained by zinc sulfate and Coomassie Blue. The isolated phycobilisome can also be subjected to further structural and compositional analyses. Overall, this protocol provides a helpful starting guide that allows researchers unfamiliar with cyanobacteria to quickly isolate and characterize intact phycobilisome.

The current protocol details the isolation of phycobilisomes from cyanobacteria by centrifugation through a discontinuous sucrose density gradient. The fractions of intact phycobilisomes are confirmed by 77K fluorescent emission spectrum and SDS-PAGE analysis. The resulting phycobilisome fractions are suitable for negative staining of TEM and mass spectrometry analysis.

In cyanobacteria, phycobilisome is a vital antenna protein complex that harvests light and transfers energy to photosystem I and II for photochemistry. ...

Isolation and Screening from Soil Biodiversity for Fungi Involved in the Degradation of Recalcitrant Materials

Environmental pollution is an increasing problem, and identifying fungi involved in the bioremediation process is an essential task. Soil hosts an incredible diversity of microbial life and can be a good source of these bioremediative fungi. This work aims to search for soil fungi with bioremediation potential by using different screening tests. Mineral culture media supplemented with recalcitrant substances as the sole carbon source were used as growth tests. First, soil dilutions were plated on Petri dishes with mineral medium amended with humic acids or lignocellulose. The growing fungal colonies were isolated and tested on different substrates, such as complex mixtures of hydrocarbons (petrolatum and used motor oil) and powders of different plastic polymers (PET, PP, PS, PUR, PVC). Qualitative enzymatic tests were associated with the growth tests to investigate the production of esterases, laccases, peroxidases, and proteases. These enzymes are involved in the main degradation processes of recalcitrant material, and their constitutive secretion by the examined fungal strains could have the potential to be exploited for bioremediation. More than 100 strains were isolated and tested, and several isolates with good bioremediation potential were found. In conclusion, the described screening tests are an easy and low-cost method to identify fungal strains with bioremediation potential from the soil. In addition, it is possible to tailor the screening tests for different pollutants, according to requirements, by adding other recalcitrant substances to minimal culture media.

Here, we present a protocol for screening soil biodiversity to look for fungal strains involved in the degradation of recalcitrant materials. First, fungal strains able to grow on humic acids or lignocellulose are isolated. Their activity is then tested both in enzymatic assays and on pollutants such as hydrocarbons and plastics.

Environmental pollution is an increasing problem, and identifying fungi involved in the bioremediation process is an essential task. Soil hosts an ...

Microscopy Techniques for Interpreting Fungal Colonization in Mycoheterotrophic Plants Tissues and Symbiotic Germination of Seeds

Structural botany is an indispensable perspective to fully understand the ecology, physiology, development, and evolution of plants. When researching mycoheterotrophic plants (i.e., plants that obtain carbon from fungi), remarkable aspects of their structural adaptations, the patterns of tissue colonization by fungi, and the morphoanatomy of subterranean organs can enlighten their developmental strategies and their relationships with hyphae, the source of nutrients. Another important role of symbiotic fungi is related to the germination of orchid seeds; all Orchidaceae species are mycoheterotrophic during germination and seedling stage (initial mycoheterotrophy), even the ones that photosynthesize in adult stages. Due to the lack of nutritional reserves in orchid seeds, fungal symbionts are essential to provide substrates and enable germination. Analyzing germination stages by structural perspectives can also answer important questions regarding the fungi interaction with the seeds. Different imaging techniques can be applied to unveil fungi endophytes in plant tissues, as are proposed in this article. Freehand and thin sections of plant organs can be stained and then observed using light microscopy. A fluorochrome conjugated to wheat germ agglutinin can be applied to the fungi and co-incubated with Calcofluor White to highlight plant cell walls in confocal microscopy. In addition, the methodologies of scanning and transmission electron microscopy are detailed for mycoheterotrophic orchids, and the possibilities of applying such protocols in related plants is explored. Symbiotic germination of orchid seeds (i.e., in the presence of mycorrhizal fungi) is described in the protocol in detail, along with possibilities of preparing the structures obtained from different stages of germination for analyses with light, confocal, and electron microscopy.

This protocol aims to provide detailed procedures for collecting, fixing, and maintaining mycoheterotrophic plant samples, applying different microscopy techniques such as scanning and transmission electron microscopy, light, confocal, and fluorescence microscopy to study fungal colonization in plants tissues and seeds germinated with mycorrhizal fungi.

Structural botany is an indispensable perspective to fully understand the ecology, physiology, development, and evolution of plants. When researching ...

Quantification of Skeletal Muscle Fatty Infiltration via Decellularization

Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration

Fatty infiltration is the accumulation of adipocytes between myofibers in skeletal muscle and is a prominent feature of many myopathies, metabolic disorders, and dystrophies. Clinically in human populations, fatty infiltration is assessed using noninvasive methods, including computed tomography (CT), magnetic resonance imaging (MRI), and ultrasound (US). Although some studies have used CT or MRI to quantify fatty infiltration in mouse muscle, costs and insufficient spatial resolution remain challenging. Other small animal methods utilize histology to visualize individual adipocytes; however, this methodology suffers from sampling bias in heterogeneous pathology. This protocol describes the methodology to qualitatively view and quantitatively measure fatty infiltration comprehensively throughout intact mouse muscle and at the level of individual adipocytes using decellularization. The protocol is not limited to specific muscles or specific species and can be extended to human biopsy. Additionally, gross qualitative and quantitative assessments can be made with standard laboratory equipment for little cost, making this procedure more accessible across research laboratories.

Author Spotlight: Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration  

The present study describes decellularization-based methodologies for visualizing and quantifying intramuscular adipose tissue (IMAT) deposition through intact muscle volume, as well as quantifying metrics of individual adipocytes that comprise IMAT.