Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites

Kirker, Grant T.; Bishell, Amy B.; Jusino, Michelle A.; Palmer, Jonathan M.; Hickey, William J.; Lindner, Daniel L.

doi:10.3389/fmicb.2017.01997

Cited by 10 publications

(7 citation statements)

References 78 publications

(77 reference statements)

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“…In detail, the genus Trechispora, which belongs to the phylum Basidiomycota, was found only in grassland soils. This saprophytic fungus is involved in wood decomposition processes, and its occurrence in grasslands rather than under shrub canopies is consistent with the results of Kirker et al, (2017), who found higher abundance of wood decomposition fungi for the exposed areas compared to the unexposed areas, and many of these species are well-studied wood decay fungi or at least the genera, with the exception of Trechispora spp, which is more abundant on decaying wood debris on the forest oor than on solid wood. Finally, we recored a high abundance of the genus Claviceps in the grassland soil, whereas it was almost absent under all shrub canopies.…”

Section: Grassland Matrixsupporting

confidence: 88%

Specific Microbiome Signatures under the Canopy of Mediterranean Shrubs

Idbella¹,

Filippis²,

Zotti³

et al. 2021

Preprint

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Background: Shrub encroachment (SE) is a phenomenon in which grasses and herbaceous vegetation are replaced by woody shrubs. The progressive spread of shrubs represents a form of land cover change that is widespread in arid and semi-arid grassland ecosystems. Many previous studies have highlighted the effects of SE on soil respiration rates and nutrient storage, but little is known about its belowground effects. While previous work considered shrubs to be non-species specific or as a single intervening species, we selected an Ampelodemsos mauritanicus grassland and six coexisting shrubs (i.e. Pistacia lentiscus L., Juniperus phoenicea L., Myrtus communis L., Rosmarinus officinalis L., Olea europaea L., and Euphorbia dendroides L.) to investigate the effects of their encroachment on soil microbiota. We used high-throughput sequencing, coupled with soil chemical analyses and litter using 13C CPMAS NMR spectroscopy.Results: Results showed a strong influence of shrub canopy on bacterial and fungal community diversity, species richness and overall community composition in the soil. Litter chemistry was dominated by O-alkyl-C, with the highest content in Ampelodesmsos and Euphorbia, but richer of aromatic C in Pistacia and Rosmarinus. Bacterial diversity was highest under Juniperus and Euphorbia, while lowest under Rosmarinus and grassland. Conversely, fungal diversity was highest under Olea and Euphorbia, while lowest under Myrtus and grassland. Moreover, soil C and N contents were highest under Olea, Pistacia and Myrtus compared to the other canopies. In addition, grassland and Rosmarinus had the highest Fe content. Furthermore, increased co-occurrence network size and connectivity were recorded under shrubs compared to the grassland matrix.Conclusions: Our results suggest that the individual effect of each shrub on the grassland matrix depends mainly on the chemical properties of the shrub litter, which alters the chemical profile of the soil and, in cascade, shapes the associated microbiota.

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Section: Grassland Matrixsupporting

confidence: 88%

Specific Microbiome Signatures under the Canopy of Mediterranean Shrubs

Idbella¹,

Filippis²,

Zotti³

et al. 2021

Preprint

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“…This might be due to primer bias, inability of DNA extraction methods to break thickly melanized cell walls, removing larger sclerotia through sample sieving before DNA extraction, and/or ephemeral or sporadic hyphal growth in soil from a stable population of ectomycorrhizas. To examine whether some of these issues could have contributed to the non-detectability of C. geophilum in our soil dataset, we i) manually verified the identity of the binding region of the fITS7 primer in all C. geophilum OTUs found in roots and the respective UNITE reference sequences; ii) verified that no hits of C. geophilum were observed using Blast on all centroid sequences from the soil dataset against the UNITE+INSD v8.0 database, and iii) verified the detection of C. geophilum in other studies using the same DNA extraction kit and similar analyses in soil (Kirker et al, 2017), roots (Evans et al, 2015), mesh bags (Ning et al, 2019) and cultures (Peter et al, 2016). Thus, our findings may reflect limited extraradical growth by a dominant EcM fungus.…”

Section: Fungal Community Richness and Compositionmentioning

confidence: 67%

Plant-fungal interactions in hybrid zones: Ectomycorrhizal communities of willows (Salix) in an alpine glacier forefield

et al. 2020

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Ectomycorrhizal (EcM) fungi are essential in the establishment of woody perennial plants in the European Alps. From continental to local scales, environmental conditions and plant host characteristics can predict EcM community structure and composition. However, it is unclear whether EcM communities of congeneric host species and their hybrids are differentially structured at local scales. We aimed to i) characterize EcM communities of Salix helvetica, S. purpurea and their hybrids and ii) elucidate the abiotic and biotic factors affecting EcM communities in hybrid zones. We analyzed willows in a glacier valley by combining molecular identification of fungi from individual ectomycorrhizas and from soil. We detected diverse EcM fungi forming non-modular and unnested networks, but we did not find significant differences in the overall EcM fungal community richness and composition among parental species and hybrids. Nevertheless, preference of individual fungal OTU per host varied. Our results demonstrate that in a sub-alpine hybrid zone with heterogeneous geomorphology, host genotype was not a strong predictor of overall EcM fungal community, but it influenced the occurrence of particular fungal OTUs.

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“…It is worth noting the abundance of ectomycorrhizal (ECM) fungi found within each of the above comparisons which indicates ECM fungi may contribute to the overall litter and wood decay fungi processes although they are not always considered as such. ECM fungi were also abundant in previous samplings by Kirker et al [83] looking at soil fungal communities in soils subjected to long term preservative exposure. Prior studies have also noted the importance of ECM fungi in the overall decay process [78,[84][85][86] as well as potential soil bioremediation tools [87][88][89][90].…”

Section: Community and Richness Analysismentioning

confidence: 70%

Role of Leaf Litter in Above-Ground Wood Decay

et al. 2020

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The effects of leaf litter on moisture content and fungal decay development in above-ground wood specimens were assessed. Untreated southern pine specimens were exposed with or without leaf litter contact. Two types of leaf litter were evaluated; aged (decomposed) and young (early stages of decomposition). The moisture content of specimens was monitored, and specimens were periodically removed for visual evaluation of decay development. In addition, amplicon-based sequencing analysis of specimens and associated leaf litter was conducted at two time points. Contact with either type of leaf litter resulted in consistently higher moisture contents than those not in contact with leaf litter. Visually, evident decay developed most rapidly in specimens in contact with the aged leaf litter. Analysis of amplicon-based sequencing revealed that leaf litter contributes a significant amount of the available wood decay fungal community with similar communities found in the litter exposed wood and litter itself, but dissimilar community profiles from unexposed wood. Dominant species and guild composition shifted over time, beginning initially with more leaf saprophytes (ascomycetes) and over time shifting to more wood rotting fungi (basidiomycetes). These results highlight the importance of the contributions of leaf litter to fungal colonization and subsequent decay hazard for above-ground wood.

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Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites

Cited by 10 publications

References 78 publications

Specific Microbiome Signatures under the Canopy of Mediterranean Shrubs

Specific Microbiome Signatures under the Canopy of Mediterranean Shrubs

Plant-fungal interactions in hybrid zones: Ectomycorrhizal communities of willows (Salix) in an alpine glacier forefield

Role of Leaf Litter in Above-Ground Wood Decay

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