Stephen Juggins

• Emeritus Professor at Newcastle University

Graphs, primer site sequences and ASV identies referred to in Kelly et al. 2024 Scientce of the Total Environment

The Pikialasorsuaq (North Water polynya) is an area of local and global cultural and ecological significance. However, over the last decades, the region has been subject to rapid warming, and in some recent years, the seasonal ice arch that has historically defined the polynya's northern boundary has failed to form. Both factors are deemed to alter...

Mediterranean lakes present particular challenges when developing ecological assessment techniques, due partly to long histories of human activity in their catchments but also to strong interactions with climate, intensifying in recent decades due to global warming. A survey of diatoms in lakes in Greece revealed both a strong nutrient gradient and...

Evaluating and understanding bio-environmental relationships at different spatial and temporal scales is important for accurately assessing marine productivity in relation to oceanographic conditions in changing Arctic ecosystems. In this paper, we compare four different bio-environmental datasets, in order to shed new light on the complex marine e...

Fundamental differences in the nature of diatom assemblage composition data generated using light microscopy and molecular barcoding create problems when applying current paradigms and metrics developed for ecological assessment. We therefore describe the development of a new metric designed specifically for diatom rbcL barcode data gathered using...

The reference model underlying the UK phytobenthos (diatom) tool for Water Framework Directive assessments is revisited and a new approach is proposed which uses quantile regression to predict the lowest values of the Trophic Diatom Index (equating to the best available condition) at any level of alkalinity . Whilst a reference model based on least...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

How climate and ecology affect key cultural transformations remains debated in the context of long-term socio-cultural development because of spatially and temporally disjunct climate and archaeological records. The introduction of agriculture triggered a major population increase across Europe. However, in Southern Scandinavia it was preceded by ~...

A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series co...

A long-term perspective is essential for understanding environmental change. To be able to access the past, environmental archives such as marine and lake sediments that store information in the form of diverse proxy records are used. Whilst many analytical techniques exist to extract the information stored in these proxy records, the critical asse...

The large‐scale shifts in the salinity of the Baltic Sea over the Holocene are well understood and have been comprehensively documented using sedimentary proxy records. More recent work has focused on understanding how past salinity fluctuations have affected other ecological parameters (e.g. primary productivity, nutrient content) of the Baltic ba...

Prediction of high latitude response to climate change is hampered by poor understanding of the role of nonlinear changes in ecosystem forcing and response. While the effects of nonlinear climate change are often delayed or dampened by internal ecosystem dynamics, recent warming events in the Arctic have driven rapid environmental response, raising...

In contrast to diatom assemblages in lakes in most other parts of Europe, those in lowland lakes in Romania appear to be determined primarily by biochemical oxygen demand (BOD) and conductivity rather than by nutrients. This has confounded the development of a Water Framework Directive-compatible phytobenthos assessment system for Romanian lakes an...

Sound knowledge of present-day diatom species and their environments is crucial when attempting to reconstruct past climate and environmental changes based on fossil assemblages. For the North Atlantic region, the biogeography and ecology of many diatom taxa that are used as indicator-species in paleoceanographic studies are still not well known. U...

Epiphytic diatom community structure associated with selected macroalgae collected from jetties at Galveston, Port Aransas, and Port Isabel, Texas was investigated using multivariate and community statistics. Redundancy analyses revealed community variation attributable to treatment (4% in Galveston, up to 8–12% at Port Isabel and Port Aransas), to...

A DNA based metabarcoding approach to assess diatom communities in rivers Project summary SC140024 This project has established a novel, DNA based method to monitor and assess the make-up of diatom communities in rivers. We report the results of the first large scale development and testing of a metabarcoding method (Figure 1); combining DNA barco...

Long-chain alkenones (LCAs) have been used for decades to reconstruct quantitative sea-surface temperature records, but they also have a great potential for paleotemperature reconstructions in lacustrine settings. Here, we investigated how the presence and abundance of LCAs in surface sediments from 106 lakes varied with environmental conditions in...

The transition from the last ice age to the present-day interglacial was interrupted by the Younger Dryas (YD) cold period. While many studies exist on this climate event, only few include high-resolution marine records that span the YD. In order to better understand the interactions between ocean, atmosphere and ice sheet stability during the YD,...

Glycerol dialkyl glycerol tetraethers (GDGTs) are temperature-sensitive membrane lipids of Archaea and bacteria. Their relative abundance in surface sediments has been used to create modern-day global temperature calibration models and reconstruct past temperature changes from marine and terrestrial sediment records. The performance of global GD...

Changes in penguin populations on the Antarctic Peninsula have been linked to several environmental factors, but the potentially devastating impact of volcanic activity has not been considered. Here we use detailed biogeochemical analyses to track past penguin colony change over the last 8,500 years on Ardley Island, home to one of the Antarctic Pe...

Key datasets for Figure 3

Key datasets for Figure 5

Yanou Lake sediment record geochemical data

Modern-day Ardley Island penguin count data and statistical analysis

Supplementary Notes, Supplementary Discussion, Supplementary Methods, Supplementary Figures, Supplementary Tables and Supplementary References

Key datasets for Figures 4 and 5

New glass shard Electron Microprobe Analysis (EMPA) data for tephra deposits for this study and published comparison data

Ardley Lake sediment record geochemical data

The well-known and widespread replacement of oysters (abundant during the Mesolithic period) by cockles and mussels in many Danish Stone Age shell middens ca. 5900 cal yrs BP coincides with the transition to agriculture in southern Scandinavia. This human resource shift is commonly believed to reflect changing resource availability, driven by envir...

A regional network of quantitative reconstructions of past climate variability is required to test climate models. In recent studies, temperature calibration models based on the relative abundances of sedimentary glycerol dialkyl glycerol tetraethers (GDGTs) have enabled past temperature reconstructions in both marine and terrestrial environments....

Transfer functions are widely used in palaeoecology to provide quantitative environmental reconstructions using biological proxies. Most models use all but the rarest taxa present in the training set, even though many may be unrelated to the environmental variable of interest. We hypothesise that retaining such non-informative taxa will reduce mode...

In many physical geography settings, principal component analysis (PCA) is applied without consideration for important spatial effects, and in doing so, tends to provide an incomplete understanding of a given process. In such circumstances, a spatial adaptation of PCA can be adopted, and to this end, this study focuses on the use of geographically...

Given an initial spatial sampling campaign, it is often of importance to conduct a second, more targeted campaign based on the properties of the first. Here a network re-design modifies the first one by adding and/or removing sites so that maximum information is preserved. Commonly, this optimisation is constrained by limited sampling funds and a r...

The sampling skills of three common European fish species (Barbus barbus, Chondrostoma nasus and Squalius cephalus) were tested to assess their potential as biomonitors of past changes in river water quality through the analysis of diatoms in fish guts. The study was performed on three rivers with different chemical and physical conditions. Compari...

The European Union’s Water Framework Directive (WFD) requires that all water bodies in Europe achieve good ecological status (GES) by 2015. We developed an ecological classification tool for UK lakes based on benthic diatoms, a key component of the biological-quality element macrophytes and phytobenthos. A database of 1079 epilithic and epiphytic d...

* Priority question exercises are becoming an increasingly common tool to frame future agendas in conservation and ecological science. They are an effective way to identify research foci that advance the field and that also have high policy and conservation relevance. * To date, there has been no coherent synthesis of key questions and priority re...

Fourier Transform Near Infra-Red Reflectance Spectroscopy (FT-NIRS) is a cheap, rapid and non-destructive method for analysing organic sediment components. Here we examine the robustness of a within lake FT-NIRS calibration using a dataset of almost 400 core samples from Lake Suigetsu, Japan, as a means to rapidly reconstruct % total organic carbon...

Outlier detection is often a key task in a statistical analysis and helps guard against poor decision-making based on results that have been influenced by anomalous observations. For multivariate data sets, large Mahalanobis distances in raw data space or large Mahalanobis distances in principal components analysis, transformed data space, are rout...

Modern pollen samples provide an invaluable research tool for helping to interpret the Quaternary fossil pollen record, allowing investigation of the relationship between pollen as the proxy and the environmental parameters such as vegetation, land-use, and climate that the pollen proxy represents. The European Modern Pollen Database (EMPD) is a ne...

Palaeolimnological diatom data comprise counts of many species expressed as percentages for each sample. Reconstruction of past lake-water pH from such data involves two steps; (i) regression, where responses of modern diatom abundances to pH are modelled and (ii) calibration where the modelled responses are used to infer pH from diatom assemblages...

Diatoms respond rapidly to eutrophication and diatom-based models for inferring total phosphorus (TP) have found wide application in palaeolimnology, especially in tracking trajectories of past and recent nutrient enrichment and in establishing pre-disturbance targets for restoration. Using new analysis of existing training sets and sediment-cores...

Quantitative reconstructions from biological proxies have revolutionised palaeolimnology but the methodology is not without problems. The most important of these result from attempts to reconstruct non-causal environmental variables and from the effects of secondary variables. Non-causal variables act as surrogates for often unknown or unquantified...

Quantitative reconstructions of past environmental conditions (e.g., lake-water pH) are an important part of palaeolimnology. Such reconstructions involve three steps: (1) the development of a representative modern organism-environment training-set, (2) the development and application of appropriate numerical techniques to model the relationship be...

Exploratory data analysis (EDA) is an essential first step in numerical or statistical analysis of palaeolimnological data. The main functions of EDA are exploration, analysis and model diagnosis, and presentation and communication. The main tools of EDA are graphical tools such as histograms, box-plots, scatter-plots, pie-charts, smoothers, co-plo...

Palaeosalinity records for groundwater-influenced lakes in the southwest Murray Basin were constructed from an ostracod-based, weighted-averaging transfer function, supplemented with evidence from Campylodiscus clypeus (diatom), charophyte oogonia, Coxiella striata (gastropod), Elphidium sp. (foraminifera), Daphniopsis sp. ephippia (Cladocera), and...

Three large training sets were investigated to determine optimal sample sizes for diatom-based inference models. The sample sets represented (1) assemblages from Great Lakes coastlines, (2) phytoplankton from the pelagic Great Lakes and (3) surface sediment assemblages from Minnesota lakes. Diatom-based weighted average models to infer nutrient con...

In this study, two distinct sets of analyses are conducted on a freshwater acidification critical load dataset, with the objective of assessing the quality of various models in estimating critical load exceedance data. Relationships between contextual catchment and critical load data are known to vary across space; as such, we cater for this in our...

Quantitative climate reconstructions are fundamental to understand long-term trends in natural climate variability and to test climate models used to predict future climate change. Recent advances in molecular geochemistry have led to calibrations using glycerol dialkyl glycerol tetraethers (GDGTs), a group of temperature-sensitive membrane lipids...

Lake sediment records have been widely used to quantitatively reconstruct historical water quality conditions for use in developing regional and lake-specific nutrient standards. Diatom-based water quality reconstructions (namely total phosphorus; TP) have been used as one line of evidence. Weighted averaging reconstructions have worked well to inf...

Introduction One of the goals of modern archeology is to understand how past communities interacted spatially, economically, socially, and culturally with their biophysical environment (Butzer, 1982). To this end archeologists have developed strong links with zoologists, botanists, and geologists to provide information on the environment of past so...

Geographically weighted regression (GWR) is used to investigate spatial relationships between freshwater acidification critical load data and contextual catchment data across Great Britain. Although this analysis is important in developing a greater understanding of the critical load process, the study also examines the application of the GWR techn...

A key concern in the assessment of the recovery of acidified lakes from the effect of acid deposition is the reference pH of acidified lakes and how reference values can be used to establish targets for restoration. In this paper we evaluated the accuracy of three different, although overlapping, diatom-pH transfer functions using UK Acid Waters Mo...

1. Mountain lake sediments are valuable archives of environmental change. However, the presence of multiple drivers of change over similar or overlapping timescales may obscure palaeolimnological signals obtained using traditional statistical analyses. 2. As part of the European Union-funded EMERGE programme, sediment cores were obtained from 209 m...

Lake Suigetsu is a small lake in central Japan under strong influence from both summer and winter monsoonal systems. In 2006 a ~73m continuous sediment record was collected from the lake, spanning the last ~150ka, and with annually laminated (varved) sediments back to ~70ka. The site was recently named a parastratotype of the Holocene onset [1] fol...

The EU’s Water Framework Directive requires all surface water bodies to be classified according to their ecological status. As biological communities show both spatial and temporal heterogeneity, expressions of ecological status will, inevitably, have an element of uncertainty associated with them. A consequence of this environmental heterogeneity...

To date, little is known about the relative importance of dispersal related versus local factors in shaping microbial metacommunities. A common criticism regarding existing datasets is that the level of taxonomic resolution might be too coarse to reliably assess microbial community structure and study biogeographical patterns. Moreover, few studies...

Navicula claytonii has been widely recorded from Britain and Northern Ireland, but not from elsewhere in Europe. It is most abundant in late winter and early spring in circumneutral rivers with moderate nutrient enrichment. The implications for diatom biogeography are discussed and a mistake in the original description is corrected.

We assessed the feasibility of using herbarium specimens to validate reference conditions in the UK by comparing diatom community composition of river sites with both recent and historic diatom samples. The question of substrate specificity was addressed by comparing epilithon (stone-derived) and epiphyton (plant-derived) samples from a number of r...

Observation-based reconstructions of sea surface temperature from relatively stable periods in the past, such as the Last Glacial Maximum, represent an important means of constraining climate sensitivity and evaluating model simulations. The first quantitative global reconstruction of sea surface temperatures during the Last Glacial Maximum was dev...

PALICLAS is a collaborative research project on the palaeoenvironmental analysis of Italian crater lake and Adriatic sediments. Central to the aims of the project is the need to make direct comparisons between different biological, chemical and physical proxy indica-tors measured on a range of lacustrine and marine sediments. To ensure compatibilit...

We investigated relationships between sedimentary solvent-extractable long-chain alkenone (LCA) concentration and composition and environmental factors in a suite of endorheic lakes from inland Spain. LCAs were found in 14 of the 54 lakes examined, with concentrations comparable with those from previously published lacustrine settings. The composit...

a b s t r a c t Fourier transform near-infrared spectroscopy (FT-NIRS) together with partial least squares regression was used to produce calibrations between spectra and concentrations of total organic carbon (TOC) in marine sediments collected from widely varying depositional set-tings. Samples from ODP 664 (oxic Quaternary, low TOC, deep sea ooz...

The overall aim of DEFINE is to provide a methodology to define reference conditions for nutrient concentrations in the coastal zone of the Baltic Sea. This will aid the national authorities that surround the Baltic basin in implementing the EU's Water Framework Directive (WFD) by providing decision-makers with a methodology to assess reference con...

1. The European Union's Water Framework Directive requires all water bodies to achieve ‘good ecological status’ by 2015 and this paper describes a rationale for defining ‘good ecological status’ based on diatoms, a significant component of the biological quality element ‘macrophyte and phytobenthos’. 2. A database of benthic diatom samples collecte...

There is a long-standing belief that microbial organisms have unlimited dispersal capabilities, are therefore ubiquitous, and show weak or absent latitudinal diversity gradients. In contrast, using a global freshwater diatom data set, we show that latitudinal gradients in local and regional genus richness are present and highly asymmetric between b...

The lipid geochemistry of lake sediments can provide information on past environmental change. Detailed interpretation is, however, often hampered by a limited understanding of the provenance of many compounds and the multiple factors influencing their distributions in modern lake sediments. We have quantified the solvent extractable lipid composit...

We compile and compare data for the last 150,000 years from four deep-sea cores in the midlatitude zone of the Southern Hemisphere. We recalculate sea surface temperature estimates derived from foraminifera and compare these with estimates derived from alkenones and magnesium/calcium ratios in foraminiferal carbonate and with accompanying sedimento...

Freshwater sensitivity to acidification varies according to geology, soils and land-use, and consequently it remains difficult to quantify the current extent of acidification, or its biological impacts, based on limited spot samples. The problem is particularly acute for river systems, where the transition from acid to circum-neutral conditions can...

This paper presents a study of changes in eutrophication over the past 100 years in a fertile estuary. The Danish estuary Mariager Fjord is a long, narrow sill-fjord with a permanently anoxic basin. In 1997 anoxia spread from the basin to the entire inner estuary, killing almost all eukaryotes and prompting debate on the causes. This paper reports...

1. Canonical correspondence analysis of a diatom and water chemistry dataset from fifty-nine maritime Antarctic lakes situated on Signy and Livingston Islands showed that nutrients and functions of nutrients (NH4+, chlorophyll a) accounted for a significant fraction of the variance in the diatom data. 2. Weighted averaging regression was used to co...

Diatom dissolution in surface sediment samples from two regional lake datasets in the Northern Great Plains (NGP; n 5 64) and West Greenland (n 5 40) is assessed using a morphological approach categorizing valves during routine diatom analysis. Two dissolution indices are derived to parameterize diatom dissolution, and, when compared between two an...

The basic requirements for diatom analysis have changed little over the last few decades in terms of sampling, slide preparation, microscopy and taxonomy but, on the other hand, there have been major improvements in our knowledge of diatom distribution and ecology and a revolution in our ability to analyse diatom data. These changes have been drive...

We used high-resolution paleoecological records of environmental change to study the rate and magnitude of eutrophication over the last century in two contrasting coastal ecosystems. A multiproxy approach using geochemical and biological indicators and diatom-based transfer functions provides a long-term perspective on changes in nutrient concentra...

Eutrophication of the Baltic Sea has become a serious concern in recent decades. To provide a potential means for quality assessments of coastal waters in this area, we collected a data set of 49 embayments in the Gulf of Finland, and explored the relationship between surface sediment diatom assemblages and 15 environmental variables, with special...

We reconstruct the pre-acidification pH of the Round Loch of Glenhead for 1800 AD using three diatom-pH transfer functions and a diatom-cladocera modern analogue technique (MAT), and compare these palaeo-data with hindcast data for the loch using the dynamic catchment acidification model MAGIC. We assess the accuracy of the transfer functions by co...