There is an increasing recognition of the role coastal vegetated ecosystems play in atmospheric carbon sequestration. However, the development of sudden vegetation dieback (SVD), a phenomenon that causes the rapid death of Spartina alterniflora, followed by no or slow recovery, has affected large-scale alterations in Atlantic coastal systems. This study reports the effects of the development of SVD on the sediment microbial communities. In 1999, Hammonasset Beach State Park in Connecticut experienced the initial appearance of SVD. After more than a decade, the plants have not recovered. Yet, sediment chemistry was similar between vegetated and SVD affected sites, with the exception of water loading, which was significantly higher in the SVD affected sites. Soil CO2 flux, a proxy for soil respiration, was reduced by 64% in SVD sites compared with sites that remained vegetated. This suggests that SVD has affected large changes in carbon cycling in the wetland sediments. The microbial communities between vegetated and SVD sites were significantly different, as assessed by 16S rRNA gene sequencing. The vegetated sediments harbored significantly higher populations of Bacteroidetes-related bacteria, whereas the SVD affected sediments contained a significantly enriched relative abundance of sulfate-reducing bacteria, predominantly within the genus Desulfobulbus. Thus, the development of SVD appears to favor anaerobic metabolic pathways at the expense of saprophytes. Greenhouse experiments testing if the alterations in the sediment microbial communities were associated with differences in S. alterniflora germination or growth were also pursued. Although small differences in growth and disease ratings were noted between seedling and transplants grown in soil mix (control), autoclaved SVD sediments, or non-autoclaved (natural) SVD sediments, mortality was not significantly different, indicating that the alterations in the sediment communities are not likely responsible for SVD, or a primary cause for the failure of S. alterniflora to recolonize the SVD sites.

The textural and geochemical characteristics of the bed sediments in South Creek are examined. The bed substratum in the urbanised reaches differs from that of the rural reaches, in terms of the volume and size of the fine matrix sediment and the concentration of heavy metals. The impact of urbanisation on the river‐bed sediment is variable, with less matrix than ‘expected’ within the substratum of the urban reach and more than ‘expected’ in the below urban reach. The urban matrix sediment is also significantly finer in comparison to the rural reach matrix sediment. Heavy metal concentrations within the urbanised matrix sediment are up to 800 times greater than background levels and are considered to be indicative of extreme contamination despite only SO years of urbanisation.