The Ashfield Flats is the largest saltmarsh in the Perth Metropolitan area and contains a subtropical and temperate coastal saltmarsh threatened ecological community. Hydrological modelling suggests that the Swan River water levels will rise over the next 70 years due to climate change resulting in large parts of the seasonally wet salt flat becoming permanently flooded, consequently changing the ecological communities present (DBCA, 2021). While the floral communities under threat have been characterised and mapped (DBCA, 2019), and sediment, soil, and water quality are being monitored (Rate & McGrath, 2022), subsurface microbial communities have not yet been explored.
In March 2022, the top 10 cm of eight saltmarsh and three drain sediments were sampled in a transect across the Ashfield Flats. Physico-chemical parameters were measured, and microbial diversity was assessed by 16S rRNA gene sequencing. Enrichment cultures targeted ferric iron and sulfate reducers, and selected enrichments were subjected to long-read metagenomics.
Saltmarsh sediment microbiomes showed great variability with distinct phyla dominating at various sites. For example, Actinobacteria contributed between 1.2% and 63.9% in relative abundance. Interestingly, four samples contained sequences affiliated with Truepera radiovictrix (Deinococcota, between 12% and 61% relative abundance). This species is a thermophilic, chemoorganotrophic aerobe capable of using carbohydrates, organic and amino acids as carbon and energy sources. The microbial communities of the three drain sediments were very similar to each other and dominated by Proteobacteria, Actinobacteria, and Chloroflexi. Here, the most prominent taxa were affiliated with Acidobacteria Gp16 and Caldilineaceae (Chloroflexi). Obtained sulfate-reducing isolates belonged to the genera Desulfomicrobium, Desulfovibrio, Desulfosporosinus, and Desulfotomaculum. One ferric iron-reducer was isolated and identified as Geomonas ferrireducens. A near complete genome (4.74 megabases, 99.7% complete) of this strain was recovered from metagenome data of the enrichment.
This first study of sediment microbial diversity at the Ashfield Flats lays the foundation for future surveys assessing the impact of climate change on the connectivity between below and above-ground biodiversity changes.