Temporal trends in community composition
Chlorophytes, dinoflagellates, ochrophytes and bacillariophytes were well-represented in both the sedDNA and microscopy records (Fig. 3A-D). Generally, data derived from sedDNA and microscopy showed broadly similar long-term trends for these phyla, but with some differences in the exact timing of the onset of change. Of these dominant phyla, chlorophytes and dinoflagellates made up the largest proportion of the sedDNA community. Chlorophytes were initially present in the sedDNA record with a relative abundance between 0.03 and 0.10 from 1916 to 1994. Their relative abundance then increased abruptly to between 0.20 and 0.27 in more recent samples from 1997 to 2021. In the microscopy-based monitoring record, chlorophytes had a low occurrence initially, but increased sharply from the 1980s to become the group with the highest occurrence (Fig 3A).
In the sedDNA record, dinoflagellates had a relative abundance less than 0.01 until 1970. Their relative abundance then increased to two distinct peaks in 1980 when they reached a relative abundance of 0.17, and in 2000 when they reached a relative abundance of 0.25. Dinoflagellates in the microscopy record had three main peaks in 1967, 1986 and 2002 when they reached an occurrence of 2.35, 2.67 and 2.92, respectively (Fig. 3B).
The relative abundance of ochrophytes in the sedDNA record was below 0.006 and relatively stable until the 1980s when there was a slight increasing trend to the 2000s. The occurrence of ochrophytes in the microscopy record remained below 1.00 until 1983, but then increased throughout the 1980s and 1990s to their highest occurrence of 4.08 in 2001 (Fig. 3C).
Bacillariophytes had the lowest relative abundance of the four phyla analysed in the sedDNA record which was consistently below 0.003. There was a general increasing trend in the relative abundance of bacillariophytes from the 1970s, although there was some scatter around this trend. In the microscopy record, bacillariophytes displayed a slight decreasing trend to the 1980s, and then increased to a period of higher occurrence from the 1990s. Bacillariophytes had the highest occurrence of any phylum in the microscopy record until 1980, after which the only phylum with a higher occurrence were chlorophytes (Fig. 3D).
There was a significant positive correlation between the sedDNA and microscopy GAM trends for all four phyla (p < 0.001). The correlation between the two records was strongest for ochrophytes, with an r value of 0.93, followed by 0.76 for chlorophytes and bacillariophytes, and 0.75 for dinoflagellates (Fig. 3A-D). All GAM trends for each dataset were significant (p < 0.01), and statistics associated with the GAMs are provided in Supplementary Information, Table S4 and S5.
Charophytes, cryptophytes and haptophytes were also recorded by microscopy. However, charophytes and haptophytes were only detected with a relative abundance greater than 0.001 in three sediment core samples, and cryptophytes were absent from the sedDNA record. The GAM-fitted trends in occurrence as measured by microscopy for charophytes, cryptophytes and haptophytes are presented in Supplementary Information, Fig. S3.