DOI: 10.5061/dryad.hqbzkh1tv
title: Data and code from: Decadal recovery of fungal but not termite deadwood decay in tropical rainforest

description: 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.
description: # Decadal recovery of fungal but not termite deadwood decay in tropical
 rainforest ## 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
 collected * `mass_remaining`: mass remaining of wood block as proportion *
 `termite_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 block * `OTU`: name of the OTU
 * `count`: number of reads of the OTU * `kingdom`: 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
 sample * `pro.mass.loss`: proportion of mass loss of the wood block *
 `FMC`: 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.