The Saltpan Microbiome is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

Abstract

Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles.

Keywords: 16S rRNA; halophiles; soil microbial communities; tidal wetlands.

Figure 1

Saltpan wetland within the Grand Bay National Estuarine Research Reserve (GBNERR) on the Mississippi Gulf coast in June 2018 (A) under the desiccated state and in October 2018 (B) following a storm tide. The storm tide was generated by Tropical Storm Gordon, which made landfall east of Pascagoula, Mississippi on September 5, 2018.

Figure 2

Representation of bacterial phyla (A) and genera (B) in saltpan wetland sediments collected from the Mississippi Gulf Coast and characterized by 16S rRNA gene sequencing. Major phyla (A) are shown as proportions of the total dataset of 96,391 bacterial sequences. Minor phyla are grouped as “other.” The ten most abundant overall genera (B) are shown as proportions of the total dataset. These ten represent 19.6% of the total sequences and ~82% of the sequences identified at the genus level.

Figure 3

Non-metric multidimensional scaling (NMDS) ordination of bacterial (A) and archaeal (B) communities in saltpan wetland sediments collected from the Mississippi Gulf Coast. Sediment was collected from the surface and the 30 cm subsurface. Duplicate cores were taken from the same site in a desiccated state and flooded state. Ordinations are based on Bray–Curtis dissimilarity matrices derived from 16S rRNA gene sequence data. Red circles indicate genera that were most influential in separating samples and the position in the NMDS ordination that they pulled samples toward. Only one operational taxonomic unit (OTU) (Halarchaeum) was influential in separating archaeal communities.

Figure 4

NMDS ordination of bacterial (A) and archaeal (B) communities in wetland sediment, collected from Grand Bay National Estuarine Research Reserve in southeast Mississippi, USA. Wetland salinity class is represented by color and soil level represented by shape. Ordinations are based on Bray–Curtis dissimilarity matrices derived from 16S rRNA gene sequence data.

Figure 5

Differential abundance of MetaCyc subsystems in microbial communities in saltpan wetland sediment when hydrated compared to desiccated. Log₂FC, fold change, represents the shift from the desiccated to the hydrated state and those functional groups which were represented by more amplicons following the flood event show positive change and those which had fewer amplicons show negative change. MetaCyc enrichment analysis determined which functional groups showed a significant change (*), based on the raw number of daughter pathways which changed in amplicon number.

Figure 6

Differential abundance of MetaCyc subsystems in microbial communities in brackish and tidal fresh wetlands as compared to a saltpan wetland in the same area of Grand Bay National Estuarine Research Reserve in southeast Mississippi, USA. Log₂FC was used as a measure, of which functional groups had more or fewer pathways expressed when comparing each tidal wetland to the saltpan based on differences in the taxa present. Fold change represents the difference between the saltpan amplicon counts and the amplicons counts of the brackish (red) and fresh (blue) tidal wetlands. Those functional groups which were represented by more amplicons in either the brackish or fresh wetland show positive change and those which had more amplicons in the saltpan sediment show negative change. MetaCyc enrichment analysis determined which functional groups showed a significant difference (*), based on the raw number of daughter pathways which differed in amplicon number.