Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle

Abstract

Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations were tidal locations, while the other location was impounded. Differences in the community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA genes and by MiSeq 16S rRNA gene-sequencing. The abundances of AOA and AOB were established by quantitative PCR of amoA genes. In addition, we analyzed the total microbial community composition based on 16S rRNA genes and explored the influence of soil physicochemical properties underneath Avicennia germinans and Rhizophora mangle on microbial communities. AOA were always more abundant than AOB, but the effect of mangrove species on total numbers of ammonia oxidizers was location-specific. The microbial communities including the ammonia oxidizers in soils associated with A. germinans and R. mangle differed only at the tidal locations. In conclusion, potential site-specific effects of mangrove species on soil microbial communities including those of the AOA and AOB are apparently overruled by the absence or presence of tide.

Keywords: AOA; AOB; Avicennia germinans; Mangroves; Microbial community structure; Rhizophora mangle.

Fig. 1

Abundance of archaeal (AOA) and bacterial (AOB) amoA gene copies in samples of soil covered with Avicennia germinans and Rhizophora mangle. Error bars represent the standard error of the data (n = 4). Abundances of bacterial gene copies below the quantification limit of the assay (1200 gene copies per μg DNA) are represented by gray circles. The ratio of archaeal to bacterial amoA genes (AOA/AOB) is indicated in the boxes on top of the bars. Within each location, significant differences in the abundance of amoA genes in soils covered with different mangrove species are indicated with different letters above the bars (uppercase letters, comparisons between archaeal amoA genes; lowercase letters, comparisons between bacterial amoA genes)

Fig. 2

Relative abundance of bacterial (a) and archaeal (b) phyla in forest soils dominated by Avicennia germinans (PI-A, SHI-A and NHI-A) or Rhizophora mangle (PI-R, SHI-R and NHI-R)

Fig. 3

NMDS (left panel) and cluster (right panel) analyses based on Bray-Curtis similarities of microbial communities from soil samples dominated by Avicennia germinans (PI-A, SHI-A and NHI-A) or Rhizophora mangle (PI-R, SHI-R and NHI-R)