Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity

Abstract

There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests) due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM) fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

Keywords: Southeast Asia; biodiversity; microbial communities; soil pH; tropical rainforest.

FIGURE 1

(A) Soil sample locations of different forest types in Brunei. (B) Sampling scheme, three clusters of samples (designated as A–C) were taken in each forest type within a 3 km transect. Within each cluster, three quadrats (10 m × 10 m in size) were collected at least 30 m apart along a smaller scale linear transect. Soil collected from the four corners and center of the each quadrat was pooled to make one samples for DNA extraction and soil property analysis.

FIGURE 2

Non-metric multidimensional scaling plot of (A) bacterial, and (B) fungal communities based on pairwise Bray–Curtis distances. A vector overlay of the significantly correlated variables is shown on the plot. GWC, gravimetric water content and OM, organic matter content.

FIGURE 3

Relative abundance of dominant (A) bacterial phyla observed in 16S rRNA gene sequences and (B) fungal phyla in ITS1 sequences in different forest types.

FIGURE 4

The relationships between (A) bacterial, and (B) fungal Shannon index and soil properties with symbols coded by forest types. Linear regressions were used to test the correlation between Shannon index and soil properties.

FIGURE 5

The Whittaker beta-diversity of (A) bacterial community and (B) fungal community in five different forest types in Brunei, Borneo. Significant differences (P < 0.05) between forest types, when present, are indicated by different letters.