scholarly journals Fire impacts tropical communities of soil fungi through changes to plant community composition, litter and soil chemistry

2021 ◽  
Author(s):  
Jed Calvert ◽  
Alistair McTaggart ◽  
Lília Costa Carvalhais ◽  
André Drenth ◽  
Roger Shivas

Fire has been predicted to be more severe and frequent in forests of the Australian Monsoon Tropics over the coming decades. The way in which groups of ecologically important soil fungi respond to disturbance caused by fire has not been studied in tropical forest ecosystems. Ectomycorrhizal (EM) fungi are important tree symbionts and saprotrophic fungi drive soil nutrient cycles. We analysed both publicly-available environmental DNA sequence data as well as soil chemistry data to test a hypothesis that fire events (1970 - 2017) in a contiguous tropical forest have altered the composition and diversity of EM and saprotrophic soil fungi. We tested this hypothesis by measuring community-level taxonomic composition, fungal diversity, species richness and evenness. We determined whether changes in fungal communities were associated with fire-altered soil chemical/physical properties, vegetation types, or the direct effect of fire. Soil fungi differed in abundance and community phylogenetic structure between forest sites that had experienced fire, and those sites dominated by unburned forest. Communities of EM fungi were structurally altered by fire at shallow soil horizons, as well as by vegetational changes between burned and unburned sites at deeper soil horizons. In contrast, fires influenced community composition of saprotrophic fungi by changing soil nutrient levels and altering litter composition. Pyrophilic, truffle-like EM fungi that rely on mycophagous mammals for dispersal were abundant at recently burned sites. We conclude that fire impacts EM fungi primarily by changing plant communities, whereas fire impacts saprotrophic fungi by reducing soil nutrient levels and altering litter composition.

Crop Science ◽  
1991 ◽  
Vol 31 (6) ◽  
pp. 1629-1633 ◽  
Author(s):  
J. E. Funderburk ◽  
I. D. Teare ◽  
F. M. Rhoads

1993 ◽  
Vol 41 (3) ◽  
pp. 275 ◽  
Author(s):  
RJ Fensham

Radiocarbon dates confirm a chronological sequence for late Holocene beach ridges at Wangiti Beach on Bathurst Island. The vegetation on these beach ridges can be clearly related to topography and distance from the sea. Monsoon rainforest occurs on the fore-dunes where the nutrient levels of the young sediments are relatively high. The mid-dunes support woodland dominated by Melalueca viridiflora and have nutrient-poor acid soils. Vegetation with a high component of monsoon rainforest species occupies the rear dunes, which have a high concentration of seawater macronutrient cations despite their older age than more seaward dunes. The relatively low elevation of the rear dunes supports the suggestion that soil nutrient levels are enriched by sea water or marine sediments during infrequent inundation events such as those during cyclones.


2019 ◽  
Author(s):  
Katharine S. Walter ◽  
Caroline Colijn ◽  
Ted Cohen ◽  
Barun Mathema ◽  
Qingyun Liu ◽  
...  

AbstractPathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet there is no current consensus on how to measure genomic variation. We investigated the effects of variant identification approaches on transmission inferences for M. tuberculosis by comparing variants identified by five different groups in the same sequence data from a clonal outbreak. We then measured the performance of commonly used variant calling approaches in recovering variation in a simulated tuberculosis outbreak and tested the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant calling approaches used by different groups do not recover consistent sets of variants, often leading to conflicting transmission inferences. Further, performance in recovering true outbreak variation varied widely across approaches. Finally, stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. We conclude that measurements of genetic distance and phylogenetic structure are dependent on variant calling approach. Variant calling algorithms trained upon true sequence data outperform other approaches and enable inclusion of repetitive regions typically excluded from genomic epidemiology studies, maximizing the information gleaned from outbreak genomes.


2021 ◽  
Author(s):  
Yiheng Hu ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Tavish Eenjes ◽  
Abigail Graetz ◽  
...  

Background: The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in culture. They can have complex genomes of over 1 Gb in size and are still underrepresented in whole genome sequence databases. Overall their description and analysis lags far behind other microbes such as bacteria. At the same time, classification of species via high throughput sequencing without prior purification is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. However, standardized procedures for characterizing unknown fungi from complex sequencing data have not yet been established. Results: We compared different metagenomics sequencing and analysis strategies for the identification of fungal species. Using two fungal mock communities of 44 phylogenetically diverse species, we compared species classification and community composition analysis pipelines using shotgun metagenomics and amplicon sequencing data generated from both short and long read sequencing technologies. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungi-specific database. During the assessment of classification algorithms, we found that applying cut-offs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without significant data loss. Conclusion: Overall, our study expands the toolkit for identifying fungi by improving sequence-based fungal classification, and provides a practical guide for the design of metagenomics analyses.


2018 ◽  
Vol 10 (3) ◽  
pp. 945-953 ◽  
Author(s):  
Akash . ◽  
Navneet . ◽  
B.S. Bhandari

In present study, we present data on tree diversity, stand structures and community composition in six sites of tropical forest in Rajaji tiger reserve, Northern India. The enumeration of 72 plots results a total of 19,050 individuals, 47 species, 42 genera, 25 families in which Holoptelia integrifolea, Dalbergia sissoo, Shorea robusta, Cassia fistula and Trewia nudiflora were the species which showed higher importance value index (IVI) in the study area. The stand density of the six sites ranges from 149.99 - 397.91 hac-1 where as the total basal area of trees ranges from 3.612 - 46.813 m2/hac-1. The Shannon diversity index ranged from 1.35 to 2.51, Simpson index ranged from 0.097 - 0.446, Margalef index ranged 2.584 - 4.9, The Evenness index ranged from  0.551 - 0.852 in the study area. Further the studied area has showed ample evidences from indices in supporting the higher floristic diversity and stand structure after providing the present area as a status of tiger reserve.


2019 ◽  
Author(s):  
◽  
Sarah Unruh

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Phylogenetic trees show us how organisms are related and provide frameworks for studying and testing evolutionary hypotheses. To better understand the evolution of orchids and their mycorrhizal fungi, I used high-throughput sequencing data and bioinformatic analyses, to build phylogenetic hypotheses. In Chapter 2, I used transcriptome sequences to both build a phylogeny of the slipper orchid genera and to confirm the placement of a polyploidy event at the base of the orchid family. Polyploidy is hypothesized to be a strong driver of evolution and a source of unique traits so confirming this event leads us closer to explaining extant orchid diversity. The list of orthologous genes generated from this study will provide a less expensive and more powerful method for researchers examining the evolutionary relationships in Orchidaceae. In Chapter 3, I generated genomic sequence data for 32 fungal isolates that were collected from orchids across North America. I inferred the first multi-locus nuclear phylogenetic tree for these fungal clades. The phylogenetic structure of these fungi will improve the taxonomy of these clades by providing evidence for new species and for revising problematic species designations. A robust taxonomy is necessary for studying the role of fungi in the orchid mycorrhizal symbiosis. In chapter 4 I summarize my work and outline the future directions of my lab at Illinois College including addressing the remaining aims of my Community Sequencing Proposal with the Joint Genome Institute by analyzing the 15 fungal reference genomes I generated during my PhD. Together these chapters are the start of a life-long research project into the evolution and function of the orchid/fungal symbiosis.


Mycorrhiza ◽  
2020 ◽  
Vol 30 (5) ◽  
pp. 541-553
Author(s):  
Tanja Mrak ◽  
Emira Hukić ◽  
Ines Štraus ◽  
Tina Unuk Nahberger ◽  
Hojka Kraigher

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