Niche-Partitioning of Edaphic Microbial Communities in the Namib Desert Gravel Plain Fairy Circles

<div><p>Endemic to the Namib Desert, Fairy Circles (FCs) are vegetation-free circular patterns surrounded and delineated by grass species. Since first reported the 1970's, many theories have been proposed to explain their appearance, but none provide a fully satisfactory explanation of their origin(s) and/or causative agent(s). In this study, we have evaluated an early hypothesis stating that edaphic microorganisms could be involved in their formation and/or maintenance. Surface soils (0–5cm) from three different zones (FC center, FC margin and external, grass-covered soils) of five independent FCs were collected in April 2013 in the Namib Desert gravel plains. T-RFLP fingerprinting of the bacterial (16S rRNA gene) and fungal (ITS region) communities, in parallel with two-way crossed ANOSIM, showed that FC communities were significantly different to those of external control vegetated soil and that each FC was also characterized by significantly different communities. Intra-FC communities (margin and centre) presented higher variability than the controls. Together, these results provide clear evidence that edaphic microorganisms are involved in the Namib Desert FC phenomenon. However, we are, as yet, unable to confirm whether bacteria and/or fungi communities are responsible for the appearance and development of FCs or are a general consequence of the presence of the grass-free circles.</p></div

One-way ANOSIM statistics comparing the bacterial and fungal community structures the predefined zones of each FC studied.

<p>R: ANOSIM statistic; p: probability level. *: Significantly different (p <0.05).</p><p>One-way ANOSIM statistics comparing the bacterial and fungal community structures the predefined zones of each FC studied.</p

Results of two-way crossed ANOSIM tests based on Bray-Curtis similarity matrices from square-root transformed bacterial and fungal T-RFLP profiles.

<p>R: ANOSIM statistic; p: probability level. *: Significantly different (p <0.05).</p><p>Results of two-way crossed ANOSIM tests based on Bray-Curtis similarity matrices from square-root transformed bacterial and fungal T-RFLP profiles.</p

Fairy Circle sampling.

<p>Photograph of a Fairy Circle in the gravel plains of the Namib Desert (A) with the schematic of the sampling strategy employed (B).</p

Models hypothesizing microbial community assembly in Namib Desert Fairy Circles.

<p>Arrow indicate the assembly processes (purple: stochastic/black: niche-partitioning/blue: neutral). Colors are represent virtually the FC zones (Green: vegetated covered control soils/Yellow: FC margins/Red: FC Centers) where these processes occur. Red arrows indicate the origin in time and length of the environmental disturbance responsible for FC appearance. The x-axis does not reflect proportionally the time scale.</p

Phylogenetic classification of the most abundant bacterial genera in the gut samples of <i>P</i>. <i>endroedyi</i> and <i>P</i>. <i>striatum</i>: i.e., representing >2% reads.

<p>Phylogenetic classification of the most abundant bacterial genera in the gut samples of <i>P</i>. <i>endroedyi</i> and <i>P</i>. <i>striatum</i>: i.e., representing >2% reads.</p

Cytochrome oxidase I gene Parsimony tree phylogeny of 13 <i>Pachysoma</i> spp.

<p>Branch colours indicate the diet of the <i>Pachysoma</i> spp.: dung (brown), plant detritus (green), polyphagous (blue) and unknown (no colour). This phylogentic tree was adapted, with permission, from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161118#pone.0161118.ref042" target="_blank">42</a>] and the dietary information taken from both [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161118#pone.0161118.ref043" target="_blank">43</a>] and personal observations by Prof C. Scholtz. Two species of <i>Scarabaeus</i>, (<i>S</i>. <i>proboscideus</i> and <i>S</i>. <i>rugosus</i>) which is the sister-genus to <i>Pachysoma</i> and a typical wet-dung-feeder, were used as outgroups. Numbers to the right of the tree indicate the three <i>Pachysoma</i> lineages. The two species considered in this study, <i>P</i>. <i>endroedyi</i> and <i>P</i>. <i>striatum</i>, are indicated with stars (Adapted from C. Sole [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161118#pone.0161118.ref042" target="_blank">42</a>]).</p

Values for sequence reads, Operational Taxonomic Units (OTUs), phyla and diversity indices for bacterial and fungal gut communities of <i>P</i>. <i>endroedyi</i> and <i>P</i>. <i>striatum</i> individuals.

<p>Values for sequence reads, Operational Taxonomic Units (OTUs), phyla and diversity indices for bacterial and fungal gut communities of <i>P</i>. <i>endroedyi</i> and <i>P</i>. <i>striatum</i> individuals.</p

nMDS ordination plot based on Bray-Curtis distance matrices of bacterial 16S rRNA gene pyrosequencing data for <i>P</i>. <i>endroedyi</i> and <i>P</i>. <i>striatum</i> individuals.

<p>A stress value of less than 0.1 represents a high quality ordination. <i>Pachysoma endroedyi</i> and <i>P</i>. <i>striatum</i> are represented by green and inverted brown triangles, respectively.</p

Additional file 1: Table S1. of Assembling metagenomes, one community at a time

Attributes of de novo assemblers used in this study. Included in this table are the versions of each assembler used in this study, along with the release date of each version. We provide a link to each assemblers’ website accompanied by its reference and number of citations. We gauge ease of use by providing the programming language and MPI compatibility of each tool as well as assessing the completeness of each tools’ available documentation. Table S2. Characteristics of the metagenomic datasets used in this study. Three metagenomes from three distinct environments (Soil, Aquatic and Human gut) were selected, and we provide accession numbers, sequencing platforms used and basic sequence characteristics (pre- and post-filtering) of each metagenome. Table S3. Assembly statistics for the assembled aquatic metagenomes. Table S4. Assembly statistics for the assembled soil metagenomes. Table S5. Assembly statistics for the assembled human gut metagenomes. Table S6. Assembly statistics for the synthetic metagenomes. Figure S1. Nonpareil estimates of sequence coverage (redundancy) for the 3 synthetic metagenomes studied. Figure S2. Computational requirements for the Tara Ocean metagenome. A) Total assembly span proportional to wall time required. B) Total assembly span in relation to peak memory usage. Figure S3. Correlation between assembly span and mapping rate. The exponential trendline indicates a very strong positive correlation between the amount of data utilized and the size of the generated assembly (R2 = 0.83). (DOCX 357 kb