Eric CapoUmeå University | UMU · Department of Ecology and Environmental Science
Eric Capo
PhD
Aquatic microbial ecologist
About
62
Publications
24,556
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1,119
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Introduction
I am using molecular ecology tools to study past and modern microbial communities and their responses to environmental changes. My current research lines are centered on microbial metabolisms in marine (coastal ecosystems, oxygen minimum zones) and lake ecosystems.
Skills and Expertise
Additional affiliations
November 2021 - April 2023
July 2019 - August 2021
Position
- PostDoc Position
Description
- The goal of this project was to investigate mercury methylation of the microbial communitiy in the Baltic Sea waters
June 2017 - May 2019
Position
- PostDoc Position
Description
- The research works aims were - to quantify fish abundance in northern lakes via eDNA analysis - to study climate change-induced regime shifts in northern lake ecosystems
Education
October 2013 - September 2016
Field of study
- Environmental microbiology, limnology, molecular paleoecology
September 2011 - June 2013
Publications
Publications (62)
In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes i...
Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal‐ash amended sediments, chlor‐alkali plants discharges and geothermal springs. Here we present the first attempt at a s...
This book, entitled Tracking Environmental Change Using Lake Sediments: Volume 6 – Sedimentary DNA, provides an overview of the applications of sedimentary DNA-based approaches to paleolimnological studies. These approaches have shown considerable potential in providing information about the long-term changes of overall biodiversity in lakes and th...
Antibiotic Resistance Genes (ARGs) are widespread in freshwater environments and represent a concealed threat to public health and aquatic eco-system safety. To date, only a limited number of studies have investigated the historical distribution of ARGs and their hosts through the analysis of freshwater sedimentary archives. This research gap const...
The impacts of environmental change on Lake Biwa have been explored for decades, with water monitoring and palaeolimnological studies revealing how environmental forcing, including climate warming, eutrophication, water level manipulation and human manipulation of fish populations, has influenced the food web of Lake Biwa. However, these studies ha...
The ocean’s mercury (Hg) content has tripled due to anthropogenic activities, and although the dark ocean (>200 m) has become an important Hg reservoir, concentrations of the toxic and bioaccumulative methylmercury (MeHg) are low and therefore very difficult to measure. As a consequence, the current understanding of the Hg cycle in the deep ocean i...
Understanding the transient dynamics of interlinked social–ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended histor...
Anthropogenic‐driven environmental change, including current climate warming, has influenced lake ecosystems globally during the Anthropocene. Phytoplankton are important indicators of environmental changes in lakes and play a fundamental role in maintaining the functioning and stability of these ecosystems. However, the extent to which lake phytop...
Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of...
Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We seq...
Human impacts on Earth’s atmosphere, hydrosphere, litosphere and biosphere are so significant as to naming a new geological epoch, the Anthropocene. Lakes and their biota are highly sensitive to environmental changes. Among aquatic organisms, microbial eukaryotes play fundamental roles associated with lake ecosystem functioning, food webs, nutrient...
Aquatic sediments harbour a diverse array of microorganisms that drive organic matter recycling, carbon sequestration and greenhouse gases (e.g., CO 2 , CH 4 , N 2 O) emissions. Although largely studied in water columns, vertical profiles of the diversity and composition of prokaryotic communities (i.e., Bacteria and Archaea) in aquatic sediments a...
Ecosystems are continuously responding to both natural and anthropogenic environmental change. Lake sediments preserve local and global evidence of these ecological transitions through time. This archived information can yield crucial insights through the reconstruction of past changes over hundreds to many thousands of years. This chapter provides...
Protists are unicellular eukaryotes found in almost all biomes on Earth. Despite their critical importance in aquatic ecosystems, there is still a lack of information about how and if anthropogenic disturbances impact protists diversity and abundance. Improvements in molecular ecology techniques, and more specifically the study of protist communiti...
For over two decades, ancient DNA (aDNA) from various organisms has been successfully recovered from lake sediments from all over the world, ranging from decades to hundreds of thousands of years old. Analysis of lake sedimentary DNA (sedDNA) has provided new information about past aquatic and terrestrial biodiversity in various biomes, even in abs...
Lake sediments consist of organic and inorganic matter originating from autochthonous (in-lake) and allochthonous (from the catchment and beyond) sources. Thus far, paleolimnological studies of biological communities have focussed primarily on morphological subfossils preserved in sediments, and as such most analyses are based on a relatively limit...
Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used cul...
Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short- and long-term data on a wide range of biological groups (e.g., photosynthetic organisms...
In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black...
Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age in...
Harmful algal blooms (HABs) producing toxic metabolites are increasingly threatening environmental and human health worldwide. Unfortunately, long-term process and mechanism triggering HABs remain largely unclear due to the scarcity of temporal monitoring. Retrospective analysis of sedimentary biomarkers using up-to-date chromatography and mass spe...
Increased concentration of mercury, particularly methylmercury, in the environment is a worldwide concern because of its toxicity in severely exposed humans. Although the formation of methylmercury in oxic water columns has been previously suggested, there is no evidence of the presence of microorganisms able to perform this process, using the hgcA...
Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the div...
Analyses of sedimentary DNA ( sed DNA) have increased exponentially over the last decade and hold great potential to study the effects of anthropogenic stressors on lake biota over time.
Herein, we synthesise the literature that has applied a sed DNA approach to track historical changes in lake biodiversity in response to anthropogenic impacts, wit...
Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature...
Locations of sampling sites from sedimentary ancient environmental DNA (aeDNA) studies. aeDNA is DNA that has degraded into short fragments, exhibits post-mortem damage signatures, and is recovered from a non-living tissue, organism, or environmental sample. Here we focus on sedimentary archives with contiguous records such as lake and marine sedim...
Since the industrial revolution, Lake Biwa (Japan) has been subjected to multiple stressors of human origins causing alterations in the composition and function of its resident biota and thus its ecosystem services. Lake eutrophication in the 1960s, the manipulation of lake water level since 1990s and concomitantly rising of water temperatures have...
Mercury methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standa...
Microbes carrying the hgcAB gene pair are primarily responsible for methylmercury (MeHg) production, transforming inorganic mercury (HgII) into MeHg. Recent work based on the detection of hgcAB genes in publicly available genomic data and metagenome-assembled genomes expanded our understanding of the phylogenetic diversity of potential Hg-methylato...
Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature...
Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (HgII) under oxygen-deficient conditions. A negative consequence of the expansion of oxyge...
PaleoEcoGen is a new working group that was launched with the aim of bringing together scientists from around the world who use ancient environmental DNA (ancient eDNA) as a novel proxy to examine the response of past biological communities to environmental changes (pastglobalchanges.org/paleoecogen). We are particularly interested in exploiting th...
During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change i...
Historical deposits of sedimentary DNA are a promising target for molecular tools with potential to inform about long-term changes in aquatic microbiome (i.e., bacteria, archaea protists, fungi, viruses) and how microorganisms are controlled by viral infection, pathogens, and larger predators (e.g. zooplankton and fish). As sedimentary DNA archives...
Anthropogenic and climatic stressors on freshwater ecosystems are of global concern. However, the interactions and effects of multiple stressors (e.g., nutrient enrichment, climate warming, altered wind and precipitation) acting over different spatial and temporal scales are often complex and remain controversial. Here, we reconstructed one‐century...
Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may...
Since the seminal paper in 1998 (Coolen and Overmann), sedimentary ancient DNA (sedaDNA) has become a powerful tool in paleoecology to reconstruct past changes in terrestrial and aquatic biodiversity. Still, sedaDNA is an emerging tool and there is a need for calibrations and validations to ensure the reliability of sedaDNA as a proxy to reconstruc...
Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we pre...
On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However , the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we appl...
To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic...
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building...
Microorganisms play a significant role in regulating the form and fate of mercury (Hg) in aquatic and terrestrial ecosystems. Microbes with the hgcAB gene pair can produce a more toxic, and bioaccumulative form of Hg, methylmercury (MeHg). Microbes that possess the mer operon can demethylate and/or reduce Hg species as part of a detoxification mech...
Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Balt...
Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine rela...
Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this gap of knowledge, we used the B...
Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populatio...
The quantification of the abundance of aquatic organisms via the use of environmental
DNA (eDNA) molecules present in water is potentially a useful tool for efficient
and noninvasive population monitoring. However, questions remain about the reliability
of molecular methods. Among the factors that can hamper the reliability of the
eDNA quantificati...
The temporal trajectory of lake microbial communities is still rarely investigated over
timescales that encompass the full history of an aquatic ecosystem and, therefore, its response
to global or local long-term environmental changes. Thanks to the development of molecularbased
procedures in paleoecology, it is today possible to assess changes in...
To assess the sensitivity of lakes to anthropogenically-driven environmental changes (e.g., nutrient supply, climate change), it is necessary to first isolate the effects of between-year variability in weather conditions. This variability can strongly impact a lake's biological community especially in boreal and arctic areas where snow phenology pl...
Climate change is a key driver of changes in lakes, especially in northern ecosystems. The structure, composition and metabolism of aquatic communities may be highly sensitive to climate-driven weather variability with possible negative effects on lake functioning and ecosystem services. Ice-covered lakes are particularly interesting because of the...
Paleogenetics provides a powerful framework to reconstruct the long-term temporal dynamics of various biological groups from aquatic sediments. However, validations are still required to ensure the authenticity of the molecular signal obtained from sedimentary DNA. Here, we investigated the effects of early diagenesis on the DNA signal from micro-e...
High-throughput sequencing of sedimentary DNA (sed-DNA) was utilized to reconstruct the temporal dynamics of microbial eukaryotic communities (MECs) at a centennial scale in two re-oligotrophicated lakes that were exposed to different levels of phosphorus enrichment. The temporal changes within the MECs were expressed in terms of richness, composit...
The emergence of DNA analyses of lake sediments has opened up many new areas of inquiry, including the study of taxa that were traditionally not considered in paleolimnology because they do not leave distinct morphological fossils. Here, we discuss the potential and challenges associated with the study of DNA in paleolimnology to address critical r...
L’eutrophisation et le réchauffement climatique sont reconnus comme des forçages majeurs du fonctionnement des lacs. Toutefois les connaissances concernant la réponse des communautés microbiennes eucaryotes à ces forçages sont encore très lacunaires, alors même que les microbes eucaryotes, porteurs d’une vaste diversité taxonomique et fonctionnelle...
Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive paleolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of 2...
Based on the coupling between paleoecology and high-throughput sequencing of DNA, we analyzed the sedimentary records from two lakes (Lake Annecy and Lake Bourget, French Alps) in order to reconstruct the temporal dynamics of their microbial eukaryotes communities. We aimed to reveal the effects of environmental changes in these two lakes both simi...
Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do...
Questions
Question (1)
Nowodays, there are many papers published in the field of sedimentary DNA. Some provide new strategies for the authentication of the past signal of biological communities, others provide interesting findings about population/community ecology or human migrations. Please cite one or several sed-DNA based papers that made major contributions in ecology.
