The arbuscular mycorrhizal fungi colonising roots and root nodules of New Zealand kauri Agathis australis

Padamsee, Mahajabeen; Johansen, Renee; Stuckey, Alexander; Williams, Stephen E.; Hooker, J. E.; Burns, Bruce R.; Bellgard, Stanley E.

doi:10.1016/j.funbio.2016.01.015

Cited by 30 publications

(26 citation statements)

References 40 publications

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“…Trypan blue staining method was used to confirm whether the pleosporalean fungi colonize the inner roots endophytically ( Padamsee et al, 2016 ). Briefly, the roots were cleaned and fixed in 50% ethanol for 24 h. Then the samples were rinsed three times with sterilized deionized water and then soaked into 5% potassium hydroxide (KOH) for 2–3 h in a water bath at 90°C.…”

Section: Methodsmentioning

confidence: 99%

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

et al. 2017

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Similar to mycorrhizal mutualists, the rhizospheric and endophytic fungi are also considered to act as active regulators of host fitness (e.g., nutrition and stress tolerance). Despite considerable work in selected model systems, it is generally poorly understood how plant-associated fungi are structured in habitats with extreme conditions and to what extent they contribute to improved plant performance. Here, we investigate the community composition of root and seed-associated fungi from six halophytes growing in saline areas of China, and found that the pleosporalean taxa (Ascomycota) were most frequently isolated across samples. A total of twenty-seven representative isolates were selected for construction of the phylogeny based on the multi-locus data (partial 18S rDNA, 28S rDNA, and transcription elongation factor 1-α), which classified them into seven families, one clade potentially representing a novel lineage. Fungal isolates were subjected to growth response assays by imposing temperature, pH, ionic and osmotic conditions. The fungi had a wide pH tolerance, while most isolates showed a variable degree of sensitivity to increasing concentration of either salt or sorbitol. Subsequent plant–fungal co-culture assays indicated that most isolates had only neutral or even adverse effects on plant growth in the presence of inorganic nitrogen. Interestingly, when provided with organic nitrogen sources the majority of the isolates enhanced plant growth especially aboveground biomass. Most of the fungi preferred organic nitrogen over its inorganic counterpart, suggesting that these fungi can readily mineralize organic nitrogen into inorganic nitrogen. Microscopy revealed that several isolates can successfully colonize roots and form melanized hyphae and/or microsclerotia-like structures within cortical cells suggesting a phylogenetic assignment as dark septate endophytes. This work provides a better understanding of the symbiotic relationship between plants and pleosporalean fungi, and initial evidence for the use of this fungal group in benefiting plant production.

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Section: Methodsmentioning

confidence: 99%

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

et al. 2017

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“…Recent extractions of arbuscular mycorrhizal fungal (AMF) DNA from plant roots have used the DNeasy PowerSoil ® kit Padamsee et al 2016), or the DNeasy Plant kit for AMF in the roots of Ammophila arenaria (Johansen et al 2015). It is possible that the DNeasy PowerSoil ® kit gives superior results in samples of tree roots that are higher in phenolic compounds in comparison to softer tissue like grass roots.…”

Section: Extraction Of Dna From Plant Tissuementioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…Mature kauri trees have an extensive network of fine roots which extends from the lateral roots into the interface between organic layer and the mineral soil (Bergin and Steward, 2004;Steward and Beveridge, 2010). A recent study also showed that roots and root nodules of kauri harbour arbuscular mycorrhizal fungi (Padamsee et al, 2016). Roots colonized by mycorrhizal fungi have been found to release more CO 2 than non-mycorrhizal roots (Valentine and Kleinert, 2007;Nottingham et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Soil CO<sub>2</sub> efflux in an old-growth southern conifer forest (<i>Agathis australis</i>) – magnitude, components and controls

Schwendenmann

Macinnis-Ng

2016

SOIL

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Abstract. Total soil CO2 efflux and its component fluxes, autotrophic and heterotrophic respiration, were measured in a native forest in northern Aotearoa–New Zealand. The forest is dominated by Agathis australis (kauri) and is on an acidic, clay rich soil. Soil CO2 efflux, volumetric soil water content and soil temperature were measured bi-weekly to monthly at 72 sampling points over 18 months. Trenching and regression analysis was used to partition total soil CO2 efflux into heterotrophic and autotrophic respiration. The effect of tree structure was investigated by calculating an index of local contribution (Ic, based on tree size and distance to the measurement location) followed by correlation analysis between Ic and total soil CO2 efflux, root biomass, litterfall and soil characteristics. The measured mean total soil CO2 efflux was 3.47 µmol m−2 s−1. Autotrophic respiration accounted for 25 % (trenching) or 28 % (regression analysis) of total soil CO2 efflux. Using uni- and bivariate models showed that soil temperature was a poor predictor of the temporal variation in total soil CO2 efflux (<  20 %). In contrast, a stronger temperature sensitivity was found for heterotrophic respiration (around 47 %). We found significant positive relationships between kauri tree size (Ic) and total soil CO2 efflux, root biomass and mineral soil CN ratio within 5–6 m of the sampling points. Using multiple regression analysis revealed that 97 % of the spatial variability in total soil CO2 efflux in this kauri-dominated stand was explained by root biomass and soil temperature. Our findings suggest that biotic factors such as tree structure should be investigated in soil carbon related studies.

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The arbuscular mycorrhizal fungi colonising roots and root nodules of New Zealand kauri Agathis australis

Cited by 30 publications

References 40 publications

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Soil CO<sub>2</sub> efflux in an old-growth southern conifer forest (<i>Agathis australis</i>) – magnitude, components and controls

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The arbuscular mycorrhizal fungi colonising roots and root nodules of New Zealand kauri Agathis australis

Cited by 30 publications

References 40 publications

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Soil CO&lt;sub&gt;2&lt;/sub&gt; efflux in an old-growth southern conifer forest (&lt;i&gt;Agathis australis&lt;/i&gt;) – magnitude, components and controls

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Soil CO<sub>2</sub> efflux in an old-growth southern conifer forest (<i>Agathis australis</i>) – magnitude, components and controls