Additional file 1: of Community assessment of tropical tree biomass: challenges and opportunities for REDD+

Table S1. List of local names commonly used by Dayaks in Batu Majang, Kutai Barat, East Kalimantan, Indonesia

The number of sequences after filtering of raw reads, the number of identified taxa, the percentage of reads successfully assigned to the phylum, family and genus levels (based on relative abundances) as well as the estimated richness and diversity indices for the bacterial communities (at 2% dissimilarity threshold).

<p>The number of sequences after filtering of raw reads, the number of identified taxa, the percentage of reads successfully assigned to the phylum, family and genus levels (based on relative abundances) as well as the estimated richness and diversity indices for the bacterial communities (at 2% dissimilarity threshold).</p

Summary of gut community changes associated with a shift from a leaf-litter to a fungal diet in <i>Pycnoscelus surinamensis</i>.

<p>(a) Venn diagram showing the shared and unique number of genus-level taxa identified in a combined analysis of gut microbial communities in cockroaches feeding on leaf litter (0% fungus), 100% fungus, and five colonies of <i>Odontotermes</i> sp. (b) Taxa contributing most to separating 0% and 100% fungus (full results in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.t002" target="_blank">Table 2</a>) (c) Most abundant taxa gained in cockroaches on 100% fungus (full results in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.t003" target="_blank">Table 3</a>) (d) Most abundant taxa lost in cockroaches on 100% fungus (full results in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.t004" target="_blank">Table 4</a>).</p

The relative abundance of genus-level taxa present in some cockroaches feeding on 100% fungal diet and in <i>Odontotermes</i> sp., but not in cockroaches fed on a 0% fungal diet.

<p>The relative abundance of genus-level taxa present in some cockroaches feeding on 100% fungal diet and in <i>Odontotermes</i> sp., but not in cockroaches fed on a 0% fungal diet.</p

The identity and number of OTUs within genus-level taxa that were present in some cockroaches feeding on leaf litter (0% fungus), but absent in all cockroaches feeding on 100% fungal diet and their abundances across five colonies of <i>Odontotermes</i> sp. and cockroaches feeding on 0% fungus (only the 40 taxa that were most abundant in cockroaches feeding on 0% fungus are given, for the full results see S10 and S11 Tables).

<p>The identity and number of OTUs within genus-level taxa that were present in some cockroaches feeding on leaf litter (0% fungus), but absent in all cockroaches feeding on 100% fungal diet and their abundances across five colonies of <i>Odontotermes</i> sp. and cockroaches feeding on 0% fungus (only the 40 taxa that were most abundant in cockroaches feeding on 0% fungus are given, for the full results see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.s010" target="_blank">S10</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.s011" target="_blank">S11</a> Tables).</p

Rarefaction curves of sequence depth for the 54 gut samples [41].

<p>Each curve represents the number of identified OTUs as a function of the number of sequenced reads after filtering. The samples ID 8 (0% fungus, replicate 3, technical replicate 2), ID 26 (40% fungus, replicate 3, technical replicate 2), ID46 (100% fungus, replicate 1, technical replicate 1) and ID 54 (100% fungus, replicate 3, technical replicate 3) were omitted from downstream analysis due to low sequence read count and subsequent poor coverage of bacterial communities. The remaining 50 samples had sufficient coverage and were used for analysis of community diversity and taxa abundances.</p

The 20 genus-level taxa that contribute the most to the separation of 0% and 100% fungal diets, based on loading values for a PCoA analysis (S8 Table), and a comparison to the abundances of these bacteria in the gut microbiota of five colonies of <i>Odontotermes</i> sp. [36] (S9 Table).

<p>The 20 genus-level taxa that contribute the most to the separation of 0% and 100% fungal diets, based on loading values for a PCoA analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.s008" target="_blank">S8 Table</a>), and a comparison to the abundances of these bacteria in the gut microbiota of five colonies of <i>Odontotermes</i> sp. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.ref036" target="_blank">36</a>] (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185745#pone.0185745.s009" target="_blank">S9 Table</a>).</p

Sceliphrolactam, a Polyene Macrocyclic Lactam from a Wasp-Associated <i>Streptomyces</i> sp.

A previously unreported 26-membered polyene macrocyclic lactam, sceliphrolactam, was isolated from an actinomycete, <i>Streptomyces</i> sp., associated with the mud dauber, Sceliphron caementarium. Sceliphrolactam’s structure was determined by 1D- and 2D-NMR, MS, UV, and IR spectral analysis. Sceliphrolactam displays antifungal activity against amphotericin B-resistant <i>Candida albicans</i> (MIC = 4 μg/mL, 8.3 μM)

Acquisition source.

<p>a) Subcolony set-up. Newly eclosing <i>Acromyrmex</i> workers were fostered in subcolonies containing the following components 1) <i>Atta cephalotes</i> ants, a genus lacking visible symbiont, 2) minor workers (also lacking visible symbiont), 3) major workers without visible symbiont, 4) dissected thorax from major workers (changed every 48 hours) and minor workers (lacking visible symbiont) and 5) major workers with visible symbiont. Only pupae fostered with living major workers carrying <i>Pseudonocardia</i> developed symbiont coverage. b) The results of this experiment showed that <i>Acromyrmex echinatior</i> and <i>Ac</i>. <i>octospinosus</i> successfully acquired exosymbiotic bacteria only when pupae were raised in the presence of major workers carrying exosymbiont. Sample sizes (n) represent the number of focal ants surviving more than five days after eclosion. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103269#pone.0103269.s001" target="_blank">Figure S1</a> for mortality data. Photo of <i>Atta cephalotes</i> used with permission, ©Alex Wild, Schematic ant drawings modified from Poulsen et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103269#pone.0103269-Poulsen3" target="_blank">[18]</a>.</p

16S <i>Pseudonocardia</i> phylogenetic tree.

<p>A phylogeny showing bacterial sequences associated with individual leaf-cutting ant colonies over time and their free-living relatives (<i>italics</i>). The phylogenetic tree was generated by the maximum likelihood method based on the Tamura-Nei model and bootstrapped 1000 times. The scale bar represents the genetic distance between samples, reflecting the number of nucleotide changes per site. The tree was created from 16 S rDNA sequences of <i>Pseudonocardia</i> exosymbionts obtained from leaf-cutting ants at the time of colony collection (regular text) and up to 9 years later (bold text). Year(s) of isolation noted in parenthesis after the colony code. Identical sequences obtained at different times are represented by a single sequence with multiple dates. Clades of <i>Pseudonocardia</i> associated with leaf-cutting ants are labeled with roman numerals <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103269#pone.0103269-Cafaro1" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103269#pone.0103269-Poulsen4" target="_blank">[19]</a> and depicted in grey boxes. Ant-isolates are labeled by colony number, followed by the year isolated and GenBank identification number in parenthesis. The percentage sequence identity with original isolates is given in brackets after all re-isolates. Isolations from the same colony are boxed in the same color to facilitate comparison. Note that bacteria isolated from all colonies remain in the same phylogenetic clade over time, with the exception of a different morphological type (*) isolated once from a colony with two other independent re-isolates identical to the original sequence isolated.</p