Stefan Bertilsson

Swedish University of Agricultural Sciences | SLU · Department of Aquatic Sciences and Assessment

Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vi...

Deep groundwaters are among the most energy and nutrient-limited ecosystems on the planet. The limited resources are mainly due to the absence of photosynthesis-driven primary production (Kadnikov et al. 2020). These ecosystems do however host phylogenetically diverse and metabolically active microorganisms from all domains of life plus viruses (Ho...

Active microbial lineages inhabit the deep terrestrial subsurface (Fry et al. 1997, Lopez-Fernandez et al. 2018) with estimates suggesting deep subsurface ecosystems to host ca. 90% of the total bacterial and archaeal biomass on Earth and about 10-20% of all terrestrial biomass (McMahon and Parnell 2014, Bar-On et al. 2018, Magnabosco et al. 2018,...

General microbial patterns of biogeography can be established based on sedimentary DNA (sedDNA) retrieved from diverse inland aquatic ecosystems, provided that certain variable environmental factors are taken into consideration in order to trace the admixture of prokaryotic sedDNA preserved in lacustrine sediments from source to sink. These include...

Methylmercury (MeHg) produced in rice paddies is the main source of MeHg accumulation in rice, resulting in high risk of MeHg exposure to humans and wildlife. Net MeHg production is affected by Hg(II) reduction and MeHg demethylation, but it remains unclear to what extent these processes influence net MeHg production, as well as the role of the mic...

Scientific drilling expeditions offer a unique opportunity to characterize the microbial communities in the subsurface that have been long-term isolated from the surface. With subsurface microbial biomass being low in general, biological contamination from the drilling fluid, sample processing, or molecular work is a major concern. To address this,...

Single-cell transcriptomics have rapidly become a standard tool for decoding cell iden­tity, fate, and interactions in mammalian model organisms. Adopting these techniques to uncover functional dynamics in aquatic single-celled organisms holds huge potential, but evidence of their applicability to non-model, poorly understood microeukaryotes remain...

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...

Geographic separation is a principal factor for structuring populations of macroorganisms, with important consequences for evolution, by means of processes such as allopatric speciation. For free-living prokaryotes, implications of geographic separation on their evolution are more unclear. The limited phylogenetic resolution of commonly used marker...

Distinguishing the respective contributions of various microbes to methylmercury (MeHg) production is critical for predicting MeHg bioaccumulation and exposure risk. Metabolic inhibitors have been commonly used to block the activity of specific microbial groups and identify primary Hg methylating microbes. By reviewing literatures and our empirical...

At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic...

Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was design...

Per- and polyfluoroalkyl substances (PFAS) are widespread pollutants that can influence microorganisms. To unveil the effects of PFAS in natural microecosystems, a study that focused on the bacterial, fungal, and microeukaryotic communities around the PFAS point source was conducted in China. A total of 255 specific taxa were significantly differen...

The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater,...

Microeukaryote predation on bacteria is a fundamental phenomenon to understand energy and nutrient dynamics at the base of the aquatic food web. To date, the most prevalent way to estimate grazing rates is by using epifluorescence microscopy to enumerate ingestion events of fluorescently labelled tracers (FLTs) after short-term incubation experimen...

Background: Río Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study indicated that this color is not caused by dissolved chemical species, but by formation of light-scattering aluminosilicate particles at the...

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...

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...

Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.

Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our percept...

The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates their bacterial communities, but how these are related to brackish counterparts remains elusive, as are molecular adaptations facilitating cross-biome transitions. Here, we conduct large-scale phylogenomic analysis of freshwat...

The impact of perfluoroalkyl and polyfluoroalkyl substances on microbial communities is challenging to investigate in situ because of the complexity and dynamics of natural ecosystems. In the present study, four microcosms were established to explore the impact of perfluorooctanoate (PFOA) on bacterial communities in riverine and marine settings. P...

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...

Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages bet...

The turnover of microbial communities across space is dictated by local and regional factors. Locally, selection shapes community assembly through biological interactions between organisms and the environment, while regional factors influence microbial dispersion patterns. Methods used to disentangle the effects of local and regional factors typica...

Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-g...

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen. They mainly accumulate in oil reservoirs, but aromatic HCs can also have other sources and are widely distributed in the biosphere. Our perception of pathways for biotic degradation of major HCs and genetic information of key enzymes in these bioconversion processes ha...

Fungi are essential components in a wide range of ecosystems and while major efforts have been spent on disentangling the diversity and functional roles of fungi in terrestrial environments, our knowledge about aquatic fungi is lagging. To address this knowledge gap, we explored metagenomes from 25 lakes from the arctic and boreal zone and one trop...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning toward more sustainable practices. In particular, innovation...

Although development of microbiota in childhood has been linked to chronic immune-related conditions, early childhood determinants of microbiota development have not been fully elucidated. We used 16S rRNA sequencing to analyse faecal and saliva samples from 83 children at four time-points during their first 2 years of life and from their mothers....

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...

At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence of this, any individual genome or clonal population will contain merely a fraction of th...

Forest harvest might mobilize mercury (Hg) retained in soils and promote the transformation of inorganic Hg to its more bioavailable and toxic form methyl-Hg (MeHg). Previous studies, however, have revealed considerable variation in effects of forest harvest on the runoff of total Hg (THg) and MeHg between sites. This study addresses one factor tha...

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and fundamental for planetary processes and ecosystem functioning. While the link between microbial community composition and heterotrophic utilization of DOM has been recognized, the full diversity of organic compounds, their bioavailability, degradability and specific influences o...

Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal....

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...

The Collisional Orogeny in the Scandinavian Caledonides (COSC) scientific drilling project aims to characterise the structure and orogenic processes involved in a major collisional mountain belt by multidisciplinary geoscientific research. Located in western central Sweden, the project has drilled two fully cored deep boreholes into the bedrock of...

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...

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...

Río Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study suggested that this color is not caused by dissolved chemical species, but by precipitation of light-scattering aluminosilicate particles at the mixing...

The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial com- munities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRN...

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...

ARCTIC-BIODIVER is a large and multidisciplinary collaboration among research groups of Europe and North America that aims to facilitate development of biodiversity scenarios at national and circumpolar scales. In this poster, we present the extent and geographic distribution of a dataset of >100 lakes and streams covering broad latitudinal and eco...

Inland waters receive and process large amounts of colored organic matter from the terrestrial surroundings. These inputs dramatically affect the chemical, physical, and biological properties of water bodies, as well as their roles as global carbon sinks and sources. However, manipulative studies, especially at ecosystem scale, require large amount...

Background Intestinal Peyer’s patches (PPs) form unique niches for bacteria-immune cell interactions that direct host immunity and shape the microbiome. Here we investigate how peroral administration of probiotic bacterium Limosilactobacillus reuteri R2LC affects B lymphocytes and IgA induction in the PPs, as well as the downstream consequences on...

Ecological stability encompasses multiple dimensions of functional and compositional responses to environmental change. Though no single stability dimension used in isolation can fully reflect the overall response to environmental change, a common vulnerability assessment that integrates simultaneously across multiple stability components is highly...

Winter methane (CH4) accumulation in seasonally ice-covered lakes can contribute to large episodic emissions to the atmosphere during spring ice melt. Biological methane oxidation can significantly mitigate such CH4 emissions, but despite favorable CH4 and O2 concentrations, CH4 oxidation appears constrained in some lakes for unknown reasons. Here...

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities i...

Impoundment of rivers to construct reservoirs for hydropower and irrigation greatly increase the hydrostatic pressure acting on river sediments with potential repercussions for ecosystem-level microbial activity and metabolism. Understanding the functioning and responses of key biogeochemical cycles such as that of nitrogen cycling to shifting hydr...

Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome assembled genomes (MAGs) or single-cell assembled genomes (SAGs). While this expanded diversity can provide novel insights about microbial population structure, most tools ava...

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...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning towards more sustainable practices. In particular, innovatio...

A geographically constrained chronosequence of peatlands divided into three age classes (young, intermediate and old) was used to explore the role of biogeochemical influences, including electron donors and acceptors as well as chemical speciation of inorganic mercury (Hg(II)), on net formation of methylmercury (MeHg) as approximated by the fractio...

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun meta...

Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members ca...

For aquatic scientists mesocosm experiments are important tools for hypothesis testing as they offer a compromise between experimental control and realism. Here we present a new mesocosm infrastructure—SITES AquaNET—located in five lakes connected to field stations in Sweden that cover a ~760 km latitudinal gradient. SITES AquaNet overcomes major h...

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...

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenc...

• Reservoir sediments are subjected to highly variable hydrostatic pressures, but little is known about the direct impacts of this environmental variable on microbial communities and biogeochemical processes mediated by microbes in the numerous deep reservoirs (>100 m) scattered across our planet. • To address this gap, the organic matter degradati...