Data and code from: Decadal recovery of fungal but not termite deadwood decay in tropical rainforest
Data files
Apr 03, 2025 version files 200.08 KB
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final_otu_rfr.csv
162.90 KB
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finalplots_tables_analysis.Rmd
19.60 KB
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functions.R
6.80 KB
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README.md
2.69 KB
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rfr.csv
8.09 KB
Abstract
Deadwood represents ~11% of carbon stocks in tropical rainforest ecosystems, and its decay is driven largely by fungi and termites, which contribute to the cycling of carbon and nutrients. Due to land use change, such as forest clearing, secondary growth tropical rainforests are increasingly prevalent around the globe. In secondary growth rainforests, studies found lower decay rates of leaf litter; however, little is known about how deadwood decays in these forests. Here, we tested whether termite and fungal species richness, composition, and functions in decaying deadwood were similar in secondary and old-growth tropical rainforests. We assessed termites' ability to discover and consume deadwood, as well as fungi community composition and contributions to wood decay. We placed non-native pine blocks, half of which were accessible to termites, in an old-growth rainforest site as a reference and two secondary-growth rainforest sites that were restored four and eight years before the start of the experiment. Blocks were harvested every 6 months for 4 years (8 harvests). Using fungal ITS amplicon sequencing of sawdust samples from the decaying deadwood blocks at the seventh harvest, we determined wood-dwelling fungal community composition. We found that termites discovered similar proportions of deadwood across the secondary growth and old growth rainforest sites, although the decay rates of the discovered deadwood were lower in the secondary growth rainforest. Further, fungal decay was similar to old growth rainforest levels in the older but not younger secondary growth rainforest where it was slower, although differences among sites were small. Wood-dwelling fungal communities were similar between secondary growth and the old growth rainforest. Contrary to common assumptions, fungal communities and their wood decay functions were resilient and recovered relatively quickly within secondary growth rainforests, however, those of termites did not, which could reduce carbon and nutrient cycling in secondary growth rainforests. Active management methods such as the local transplant of termite- and fungi-occupied logs could accelerate the recovery of these ecosystems.
Files in Repository
The repository contains the following data files:
rfr.csv
This file contains mass remaining of wood blocks through time at the three rainforest regeneration sites. The columns are as follows:site
: site where the wood block was found (DRO = Old-Growth, OLD_RESCUE = “2010 Secondary Growth”, YOUNG_RESCUE = “2014 Secondary Growth”)treatment
: mesh treatment (TI = perforated mesh, TE = unperforated mesh)harvest_number
: collection period at which the wood blocks were collected (1 to 8 with each harvest being approximately 6 months after the previous one)date_diff
: number of days between which the wood block was set out in the field and collectedmass_remaining
: mass remaining of wood block as proportiontermite_disc
: termite discovery treatment (0 = undiscovered, 1 = discovered)
final_otu_rfr.csv
This file contains the information of each OTU found within each woodblock. The columns are as follows:SampleID
: identifier number for the wood blockOTU
: name of the OTUcount
: number of reads of the OTUkingdom
: kingdom to which the OTU belongs (NA means that it could not be identified to that level)phylum
: phylum to which the OTU belongs (NA means that it could not be identified to that level)class
: class to which the OTU belongs (NA means that it could not be identified to that level)order
: order to which the OTU belongs (NA means that it could not be identified to that level)family
: family to which the OTU belongs (NA means that it could not be identified to that level)genus
: genus to which the OTU belongs (NA means that it could not be identified to that level)species
: species to which the OTU belongs (NA means that it could not be identified to that level)trophicMode
: trophic mode of the OTU (NA means that it could not be identified to Trophic Mode)guild
: guild of the OTU according to FUNGUILD (NA means that it could not be identified to Guild)site
: site where the wood block was found (DRO = Old-Growth, OLD_RESCUE = “2010 Secondary Growth”, YOUNG_RESCUE = “2014 Secondary Growth”)count_total
: total number of reads in the samplepro.mass.loss
: proportion of mass loss of the wood blockFMC
: fuel moisture content of the wood block
The repository contains the following code files:
finalplots_tables_analysis.Rmd
This script reads the raw data files and runs the analyses, plots graphs and tables for manuscript.functions.R
This script contains the functions used in the analysis.