This study examines the relationship between diatom assemblages from lake sediment surface samples and water depth at Kelly Lake, California. A total of 40 surface sediment samples (top 5 cm) were taken at various depths within the small (3.4 ha) five-meter-deep lake. Secchi depths, water temperature, pH, salinity, conductivity, and total dissolved solids were also measured. Some diatom species showed distinct association with depth (e.g., Fragilaria crotonensis, Nitzschia semirobusta). The relationship between the complete diatom assemblages and water depth was analyzed and assessed by depth-constrained cluster analysis, a one-way analysis of similarity, and principal components analysis. Statistically significant differences were found between the assemblages associated with shallow depth (0 m – 1.25 m), mid-depth (1.25 m – 3.75 m), and deep depth (3.75 m – 5.2 m) locations. The relationship between diatom assemblages and lake depth allowed two transfer models to be developed using the Modern Analogue Technique (MAT) and Weighted Averaging Partial Least Squares (WA-PLS). These models were compared and assessed by residual scatter plots. We demonstrate that the diatom assemblages in the sediments of Kelly Lake are differentiated by lake depth. The results indicate that diatom-inferred transfer models based on surface sediment samples from a single lake can be a useful tool for studying past hydroclimatic variability (e.g. lake depth) from cores taken from such lakes in California.
Research Article
A diatom-inferred water depth transfer function from a single lake in the northern California Coast Range
https://doi.org/10.21203/rs.3.rs-1910717/v1
This work is licensed under a CC BY 4.0 License
Journal Publication
published 18 Mar, 2023
You are reading this latest preprint version
diatoms
lake depth
Klamath Mountains
northern California
surface sediment samples
transfer function
MAT
WA-PLS
California (CA) has experienced prolonged hydroclimatic anomalies over the 21st century (e.g. severe droughts) that appear to be, at least in part, related to anthropogenic climate change (Swain et al. 2018; Zamora-Reyes et al. 2021; Glover et al. 2020; Dong et al. 2019; MacDonald et al. 2016). Understanding how recent CA hydroclimate variability relates to longer timescale (e.g., Holocene) natural variability has been an important topic of research over the past decade (Briles et al. 2011; MacDonald et al. 2016; Kirby et al. 2019). However, instrumental climate records only extend back a little more than a century and do not capture the full range of potential natural hydroclimatic variability. Paleoclimatic approaches can provide proxy hydroclimatic climate records that extend back millennia. The proxy-climate archives provided by lake sediments are one useful source of such information, and although not as plentiful as in some regions, such lake archives are available in most of California.
Diatoms (Class: Bacillariophyceae), single-celled algae and phytoplankton, have been shown to be an important proxy indicator useful to investigate hydroclimatic variability as manifest in lake level changes or changes in lake salinity (Battarbee 2000; Ramón Mercau and Laprida 2016; Zhang et al. 2007; Fritz et al. 1991; Smol and Cumming 2000; Gasse et al. 1995; Kingsbury et al. 2012; Gushulak and Cumming 2020; Gushulak et al. 2017). There are several reasons why diatoms are a good proxy indicator – they are common in lake environments, they are sensitive to limnological (e.g., lake water chemistry) and hydrological (e.g., lake depth) changes, and their distinctive silica shells are well-preserved in lake sediments. Many studies have shown that diatoms can be used to reconstruct past variations in lake depths, including providing quantitative estimates using statistical transfer functions based on modern diatom-water depth relationships (Laird et al. 2010; Yang and Duthie 1995; Laird and Cumming 2009; Laird et al. 2011). Changes in water depth and salinity in lakes are closely related to paleohydroclimatic changes (Smol and Cumming 2000; Laird et al. 2010; Fritz 1990; Kingsbury et al. 2012). This research will focus on water depth. Lacustrine hydrologic budgets, which are related to lake water depth, are closely associated with regional hydrologic budgets and the interplay between precipitation and evaporation. This association is especially robust in regions with strong seasonal precipitation/evaporation contrasts, such as California and the American West (Shuman and Donnelly 2006 as cited in Wigdahl-Perry et al. 2016).
There are very few diatom-inferred paleoecological transfer functions from Californian lakes. Bloom et al. (2003) published a paper that established a diatom-inferred salinity and water temperature transfer function from a network of lakes in the Sierra Nevada. While the initial study was about salinity and water temperature, not water depth, this was expanded to include a water depth transfer function in a subsequent publication (MacDonald et al. 2016). Unfortunately, few areas of California outside formerly glaciated Sierra Nevada provide enough lakes to make a traditional multi-lake-based diatom transfer function model.
In recent years studies have shown that diatom-depth transfer functions can be successfully developed using multiple sediment surface samples taken from different depths in a single lake (Laird et al. 2010; Laird and Cumming 2009; Gushulak et al. 2017). The resulting transfer function can then be applied to sediment cores from the same lake (Faith and Lyman 2019; Laird et al. 2010; Laird and Cumming 2009). This approach is ideal for California where in many regions’ lake basins are rare and the development of a multi-lake transfer function, which requires 30 lakes or more, is not possible. In this study we address the question of whether or not there is a statistically significant difference in the diatom flora found in the sediments taken at different depths from a single lake. Moreover, explore whether or not these relationships are statistically strong enough to develop of a diatom-depth transfer function that could be applied to sediment cores from that same lake. The study site is Kelly Lake, a small lake in the mountains of northwestern California.
Study Site
Kelly Lake (41.91°N, 123.52°W; 1346 m asl) is located in the Klamath Mountains (northern California Coast Range), approximately 10 km from the Oregon border (Fig. 1). The lake is landslide formed, small (~4 ha), with a maximum water depth of 5.2 m. The surface drainage basin is small (~47 ha) and sits in sedimentary rocks and meta volcaniclastic sedimentary rocks (Irwin 1994). Although presently a closed basin (as of 2019) with a small inlet, there is a spill point at the east shoreline, approximately 3-4 m above modern lake level, indicating that overflow is possible during wet years. Dead and felled trees congregate at the outlet and suggest a dynamic lake level. Active springs characterize the surrounding drainage basin with modern inflow occurring at the lake’s northwest shoreline. The vegetation surrounding the lake’s fringe is mostly reeds and sedges, with submergent macrophytes and mosses near the shoreline. Above the shoreline, there is forested vegetation with an overstory of Jeffrey pine (Pinus jeffreyi), Douglas fir (Pseudotsuga menziesii), sugar pine (Pinus lambertiana), incense cedar (Calocedrus decurren) and white fir (Abies concolor).
The mean January and July temperatures of the region are 2.92°C and 18.89°C, and the mean annual precipitation is 176.19 mm (Western Regional Climate Center 2016) (Fig. 2). The data was taken at the Elk Valley Station (42.00°N, 123.43°W), which is the nearest station from the study site (~12km for linear distance) at 521 m asl. The average winter precipitation (December, January, February) is approximately 353 mm, while the average summer precipitation (June, July, August) is roughly 17 mm. Kelly Lake experiences some snows during fall and winter, with ~ 35mm of total snowfall. Therefore, Kelly Lake’s annual hydrologic budget is driven by variations in winter precipitation and summer evaporation.
The study site is in the Karuk/Karok Tribe’s territory. Karuk/Karok means “upriver people” (Bell 1991). Their ancestral boundaries extend from near Orleans in Humboldt County (CA) through Seiad Valley in Sisikiyou County (CA) to southern part of Oregon (Bell 1991), and the indigenous people dwell along the Klamath River. Kelly Lake is near the Happy Camp site, which is the heart of the tribe’s territory (Bell 1991).
Fieldwork
In July 2019, 40 surface sediment samples were obtained at various lake water depths from the top 5cm of the sediment-water interface using a mini-Glew gravity corer (Fig. 3). The samples were designated as KLSS2019 #. KLSS2019 1 to 26 and KLSS2019 33 to 40 were taken along the three transects: nine samples from the Transect 1, seventeen samples from the Transect 2, and eight samples from the Transect 3 (Fig. 3). Each sediment sample was collected at approximately 2 m distance from adjacent samples. KLSS2019 27 to 32 were collected at the very margin of the lake and from the lake’s inlet emergent vegetation (Fig. 3). Lake water depths and Secchi depths (to delineate the modern photic zone) were measured at each sampling point.
The lake’s water chemistry was also measured near surface at the center of the lake three times and averaged. Table 1 shows the average values of all the measurements. Five variables - pH, conductivity, water temperature, total dissolved solids, and salinity - were measured with a digital water testing meter (Apera Instruments PC60 Premium Multiparameter Tester Meter).
Table 1
Average (n = 3) water chemistry for Kelly Lake in July 2019.
Laboratory and diatom counting
Approximately 0.1 g of wet surface sediment was treated with 30% H2O2, distilled water, and sodium hexametaphosphate to remove organic materials in the sediments. Diatoms were mounted by Pleurax (mountmedia) on microscope slides. At least diatom 400 valves were counted per sample. Diatoms were identified at 1000x magnitude under a light microscope with oil immersion. For diatom species identifications we followed the taxonomy of Krammer and Lange-Bertalot (1986, 1988, 1991a, 1991b) with supplementary book and online sources (Spaulding et al. 2019; Potapova et al. 2020; Kulikovskiy et al. 2016; Jüttner et al. 2022).
Data selection and analysis
The taxa used for statistical analysis and calibration set development were selected after screening the diatom data. Taxa which appear at more than 5% abundancy were selected for constructing the stratigraphic diatom diagram, and taxa occurring at more than 1% abundancy in at least one sample were chosen for statistical analyses and transfer function development. A diatom stratigraphy diagram was drawn in R version 4.1.3 (RStudio Team 2020). A depth-constrained cluster analysis (CONISS) was also performed in R to determine if lake depth zones could be discerned in the diatom assemblages from Kelly Lake. A one-way analysis of similarity (ANOSIM) was also conducted using the PAST ((PAleontological STatistics) version 4.01) software package to test statistically the differences in the distribution of diatom assemblages among the identified depth zones (Hammer et al. 2001). Principal component analysis (PCA) was conducted in R on the covariance matrix to further explore differences in the diatom assemblages from different lake depths and the important diatom taxa contributing to those differences. Lastly, two diatom-inferred water depth transfer functions were developed with the modern analogue technique (MAT), and with weighted average partial-least squares (WA-PLS) using the PAST software.
Diatom Diagram with CONISS
We identified over 150 different diatom taxa in Kelly Lake. Among them, 21 taxa (more accurately, 17 species and 13 genera) were selected for the diatom graphical and statistical analysis. These all appeared at >5% abundances in at least one sample (Fig. 4). There were 12 benthic taxa (Navicula genus, Achnanthidium genus, Achnathidium exiguum, Gomphonema acuminatum, Meridion circulare var. constrictum, Nitzschia semirobusta, N. tabellaria, Psammothidium rosenstockii, Pseudostaurosira parasitica, P. brevistriata, Staurosira construens, S. venter), 5 planktonic taxa (Aulacoseira genus, A. italica, A. pusilla, Fragilaria crotonensis, Melosira genus), and 2 benthic or planktonic taxa (Achnanthidium minutum, Staurosirella pinnata). The diatom diagram was drawn in R using rioja package (Juggins 2020) (Fig. 4). The Kelly Lake diatom-water depth zones were divided into shallow-benthic (0 – 1.25 m), mid-depth (1.25 – 3.75 m), and deep-water zones (3.75 – 5.2 m) according to the diatom assemblages using a stratigraphically constrained cluster analysis (CONISS) with the vegan package in R (Oksanen et al. 2020). The cluster communities were calculated with the Bray-Curtis distance method to measure the dissimilarity between communities (Grimm 1987).
ANOSIM
According to the CONISS analysis, Kelly Lake was divided descriptively into three depth zones, which are Shallow (0 m – 1.25m), Mid-depth (1.25 m – 3.75m), and Deep (3.75 – 5.2m). ANOSIM was subsequently conducted to determine whether there was statistically significant difference between the three depth zones by examining the similarity of the diatom communities (Elmslie et al. 2020). The diatom taxa, which appeared more than 1% at least one sample, were analyzed.
There were statistically significant differences between the three depth zones based on the result of ANOSIM. The P values in Table 2-(a) indicate significance differences between the groups. The values were close to 0, which allowed us to reject the null hypothesis (“there is no difference”) and indicated that there were statistically significant differences between the diatom assemblages from the three different water depth zones (i.e., shallow, mid-depth, and deep zones).
R values were also calculated in ANOSIM, which showed the strength of the depth factors on the samples. Generally, if an R value is lower than 0.2, it means that the factors had a small effect on the variables. However, the R values in Table 2-(b) were larger than 0.2. Accordingly, it further indicates that the lake depth was influential on the composition of diatom communities observed in the lake sediments and the differences between the depth zones.
Table 2
Results of ANOSIM. (a) indicates P values showing significance levels, (b) indicates R values showing the strength of the factors on the samples.
Therefore, the ANOSIM results indicate that there were differences in the diatom communities by specific depth zones, and lake depth was an influential factor in the diatom assemblage composition in the sediments of Kelly Lake.
Principal component analysis
Principal component analysis (PCA) was performed on the covariance matrix with the taxa that occurred more than 1% in at least one sample with more data for a reliable analysis. The cumulative variation of PC 1 and 2 was 70.5%, the first two axes were considered in this study (Fig. 5). The diatom assemblages clustered on the PCA biplot by depth, reinforcing the conclusion that lake depth was a strong control on the diatom assemblages preserved in the sediments. PC 1 appeared to represent water depths between middle to deep, while PC 2 reflected shallow to middle water depths. The three most important diatom taxa in determining these PCA axes were Staurosirella pinnata, Staurosira venter, and Nizschia semirobusta.
Diatom-lake depth transfer function models
Two diatom-lake depth transfer functions were developed using MAT and WA-PLS. Model construction incorporated diatom taxa that occur >1% in at least one sample.
WA-PLS
The first diatom-inferred water depth inference model was developed using WA-PLS (Fig. 6-(a)). The R2 value was 0.963 and indicates a high degree of correlation between the observed depths and diatom-inferred depths. The RMSEP value is based on the degree of error between the observed and the expected value. Thus, the lower the value, the more significant it is. In this study, the third component for WA-PLS had the lowest RMSEP value, which was 0.661. Therefore, the third component was selected for the WA-PLS transfer function. As seen in the graphs (Fig. 6-(a)), the WA-PLS model performed better in mid-depths between 2 and 3 m than shallow and deep depths.
MAT
The second transfer function was developed using the Modern Analogue Technique method (Fig. 6-(b)). The dissimilarity for MAT was measured using squared chord distance. The R2 values of the MAT transfer function was 0.9765, and the RMSEP value was 0.387. In general, the MAT model displayed good performance; it performed well in shallow and deep zones and showed a bit over-representation in the mid-depths.
Overall, the MAT transfer model showed better performance than the WA-PLS model with higher R2 and lower RMSEP values. However, for both transfer function the R2 values were higher than 0.95, and both models showed good representations of diatom-inferred water depths.
Residual scatter plots
Residual scatter plots were created to further assess the MAT and WA-PLS models (Fig. 7). This was done to determine whether there was a trend in residuals, and thus a bias, in the models. The residuals in the MAT model showed less trend than the residuals in the WA-PLS model according to the R2 values. The residuals in MAT were more scattered in the mid-depths, while the ones in WA-PLS were more scattered in the edges of the depths. Even though MAT showed less trend than WA-PLS, both had small R2 values and small slopes. That is, the residuals in both MAT and WA-PLS did not suggest a strong bias.
Diatom distributions along with water depth
The statistical analysis indicates that the diatom assemblages found in the surface sediments at Kelly Lake can be statistically grouped by three different depth zones. There are at present few studies that have examined the relationship between the composition of the diatom community and water depth from a single small lake (Gushulak et al. 2017; Laird et al. 2010; Laird and Cumming 2009). Our study adds to growing evidence that differences in diatom assemblages related to lake depth are preserved in the sediments of small lakes and have the potential for developing lake-specific diatom-depth transfer functions. Although there are a variety of factors that affect diatom assemblages in the lacustrine environment, this study indicates that the diatom assemblage compositions in Kelly Lake have a clear correlation with lake water depths. There are three depth zones identified in Kelly Lake: shallow (0–1.25m), mid-depth (1.25–3.75m), and deep zones (3.75–5.2m). These three distinct depth zones are similar to those discerned for a previous single lake conducted in Canada; although there are many overlapped diatom species in the Canadian lakes and this study, there were few equivalent major diatom assemblages (Laird et al. 2010; Laird and Cumming 2009).
Although details of the ecology of many diatom species remain uncertain, the statistical results from Kelly Lake regarding depth and diatom assemblages can be assessed in light of the known ecology for some individual diatom taxa. Some of individual diatom taxa show strong depth preferences. For example, Fragilaria crotonensis rarely appears at shallow depths, but it begins to appear at middle depths and becomes dominant in deep zones (Fig. 4). F. crotonensis is known as planktonic and motile (Morales et al. 2013). The species forms ribbon-like floating colonies, so are associated with the pelagic zone. The colonial characteristics of the F. crotonensis’ life form might enhance their taphonomic resilience in the fossil assemblages. Staurosirella pinnata is also one of the most predominant species in the deep zone. The species is not clearly delineated as either planktonic or benthic. Some studies identified it as benthic, while others confirmed it as planktonic (Fluin et al. 2010; Laird et al. 2011; Hofmann et al. 2020; Park et al. 2017). Moreover, it is said S. pinnata adapts well to low light penetration conditions (Laird et al. 2010), explaining why S. pinnata appears throughout all the depth zones in Kelly Lake but is the most dominant species in the deep aphotic zone at Kelly Lake.
There are also many distinguishing species for mid-depth zones in Kelly Lake. Nitzschia semirobusta is the most predominant species for the mid-depth zone. This species is known as a motile benthic species and has a wide tolerance of trophic status even though it favors oligotrophic conditions (Bartozek et al. 2018). According to the water chemistry results from Kelly Lake, the lake can be considered as oligotrophic to mesotrophic, therefore, the abundance of N. semirobusta seems reasonable. As the species is considered as benthic but motile, it makes sense that they appear the most abundant in mid-depth areas.
Pseudostaurosira parasitica is mainly found in shallow depth zones, and this is readily explainable because the species is benthic and must remain in the photic zone to survive (Morales 2010b). The genus of Aulacoseira is a very distinctive species for the shallow zone. It almost only appears in the shallow zone. The genus is well-known for including a variety of planktonic species; however, they appear predominantly in shallow zone in Kelly Lake. This can be explained by the genus’ life strategy. The genus has heavily-silicified shells, which makes floating difficult. Therefore, Aulacoseira species prefer strong convective lake mixing, so that they can remain in upper waters and conduct photosynthesis, making the shallow zone prefereable.
In addition to the relationships between taxa and three depth zones, there are also a few species typically found in environments at the very margin/edge of the lake or near the shore (e.g., Meridion circulare var. constrictum and Odontidium mesodon). These species inhabit very shallow depth zones or live on emergent plants (Leira et al. 2017; Hoidal 2013; Potapova 2009).
Conversely, some species are abundant at a wide range of depths, such as Achnanthidium minutissimum and Pseudostaurosira brevistriata. For example, A. minutissimum is ubiquitous in diatom-based, paleolimnological studies; however, its habitat preferences remain debated. Some studies have found that A. minutissimum occurs at ~ 2 m or shallower depths (T. Moos et al. 2005; Yang and Duthie 1995), while another study found it occurs at range of depths (Laird et al. 2010). One study concluded that the species is largely found on submerged Isoetes (Haberyan 2018). While A. minutissimum may not be a useful species for representing distinct depth zones, but it may signify zones of overall ecotone changes within a lake (T. Moos et al. 2005). Similarly, P. brevistriata has a complex ecology, classified as either planktonic or benthic and non-motile (Morales 2010a). As a result, it is not surprising that P. brevistriata is found at various depths at Kelly Lake.
By interpreting diatom assemblages according to each species habitat preferences and the subsequent statistical results, it is concluded that there are clear divisions based upon water depth zones, and water depth is a crucial factor in the composition of diatom assemblages preserved in the Kelly Lake surface sediments.
Water Depth inference models
A good transfer-function model should meet two conditions: 1) observations and estimates must be strongly positively correlated, 2) there should be no trends in the residuals (Yoon et al. 2017). There are many ways to develop a transfer function, and WA-PLS and MAT are the two of the most common techniques (e.g. Faith and Lyman 2019; Laird et al. 2011; Park 2011; Bloom et al. 2003; Cunningham et al. 2005). In this study, both MAT and WA-PLS perform well in terms of the requisite conditions. However, in general the MAT transfer function performs better than the WA-PLS transfer model for Kelly Lake.
In this study, the dissimilarity measure for MAT was determined using a squared chord, which is a metric to assess the signal-to-noise relationship. This distance metric is considered the best for evaluating modern analogs (Jackson and Williams 2004 as cited in Kemp and Telford 2015). It is said that chord-squared distance is more acceptable for closed compositional assemblage data, such as relative abundances, because it highlights the major patterns, while it down-weights rare species (Kemp and Telford 2015). Both MAT and WA-PLS are vulnerable to an uneven sampling of the elevation gradient (Kemp and Telford 2015), but most of the samples in this study have been collected evenly, so the weakness should not be influential here.
There are over- and under-estimations at deep and shallow depths in the WA-PLS model, and this could reflect the “edge effect” problem common for weighted average-based models, such as WA and WA-PLS (Birks 2010). This problem causes the over- or under-estimations at the edges of the sample depths. However, Kemp and Telford (2015) argued that the influence of “edge effects” is lessened in WA-PLS. The results of our study show that WA-PLS does seem to present some “edge effect” as there are more variable residuals at deep and shallow depths (the edges) (Fig. 7-(b)). The WA-PLS in this study rather performs better for the middle depths. Conversely, there are over-estimations in the MAT model for the mid-depth ranges, especially in the range of 2 and 3 meters. Both models have over- or under-estimations at different depth zones; therefore, inferences of past depths might best be made by using both models.
There are clear, statistically significant, differences between diatom assemblages and lake depth in the surface sediments of Kelly Lake. The correlations are strong enough to develop a single-lake diatom-inferred lake depth transfer models. Our findings indicate that a quantitative reconstruction of past lake depth using diatom assemblages is reasonable for Kelly Lake. As many parts of California have few natural lakes, yet regional information on long-term hydroclimatic variability is very important in providing a context for 21st century climate change, the ability to use surface samples from a single lake, coupled with a core from that lake to reconstruct past lake depths, is an important methodological development. The transfer models developed here will be applied to the diatom assemblages recovered from core of Kelly Lake in a future paper.
Acknowledgments
This project is funded by the NSF (#1702825) to GM, MK, JC, Reza Ramezan, and Kevin Nichols and the Geography of California and the American West Endowment. Additional support came from the UCLA Geography of California and the American West endowment. We want to thank Jen Leidelmeijer, Kyle Campbell, Jazleen Barbosa, Cody Poulson, and Dr. Laura Levy for the cheerful and cooperative fieldwork in 2019. Also, special thanks to Dr. Kota Katsuki and Dr. Scott Starratt for helping us identify a mystery diatom and special thanks to Dr. Sergey Ivanovich Genkal for kindly sending a book of “Identification Book of Diatoms from Russia”. We want to acknowledge that we are conducting research on the ancestral territory of Karuk/Karok people.
Author Contribution
Jiwoo Han contributed to the main manuscript writing and editing, the data collection, and the data analysis. Glen MacDonald, Matthew Kirby, Joe Carlin, and Benjamin Nauman contributed to collecting data. Glen MacDonald, Matthew Kirby, and Joe Carlin contributed to editing the manuscript. Glen MacDonald advised overall in all procedures, and all authors reviewed the manuscript.
Funding
This manuscript was supported by National Science Foundation #1702825.
Competing Interests
The authors declare that they have no competing interests.
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No competing interests reported.