Biology subjects

Bertilsson, S.

Publications and source records attributed to Bertilsson, S..

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bioRxiv2021

mOTUpan: a robust Bayesian approach to leverage metagenome assembled genomes for core-genome estimation

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 available for core-genome estimation are overly sensitive to genome completeness. Consequently a major portion of the huge phylogenetic diversity uncovered by environmental genomics approaches remain excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core-genome for sets of genomes of highly diverse completeness range. The likelihood for each gene-cluster to belong to core- or accessory-genome is estimated by computing the probability of its presence/absence pattern in the target set of genomes. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates as state-of-the-art tools Roary and PPanGGoLiN for high-quality genomes and outperforms them at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.

bioinformatics↗

bioRxiv2021

Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies

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. To understand the complex changes associated with allochthonous inputs, experiments are needed. However, manipulative studies, especially at ecosystem scales, require large amounts of dissolved organic matter with optical and chemical properties resembling indigenous organic matter. Here we compared the chemical and biological impacts of two leonardite products (HuminFeed (HF) and SuperHume (SH)) and a freshly derived reverse osmosis concentrate of organic matter (RO) in a set of comprehensive mesocosm- and laboratory-scale experiments and analyses. The chemical properties of RO concentrate and the leonardite products were very different with leonardite products being low and RO being high in carboxylic functional groups. Light had a strong impact on the properties of leonardite products, including loss of color and increased particle formation. Furthermore, HF had drastic impacts on bacteria as light stimulated bacterial production and modified community composition, while dark conditions appeared to inhibit bacterial processes. While none of the browning agents inhibited the growth of the tested phytoplankton, Gonyostomum semen, leonardite products had detrimental effects on zooplankton abundance and Daphnia reproduction. We conclude that the effects of browning agents extracted from leonardite are in sharp contrast to those originating from terrestrially-derived DOM. Hence, they should be used with great caution in experimental studies on the consequences of terrestrial carbon for aquatic systems.

ecology↗

bioRxiv2020

Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds

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 metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

ecology↗

bioRxiv2020

Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations

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 their functional ecology and local adaptations came from isolates and merely 26 sequenced genomes that are poor representatives of natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-cell genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs) or "species". Of the 71 mOTUs, 57 were classified as genus Chlorobium and these mOTUs varied in relative abundance up to ~60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many were lacking genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian Chlorobium clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insights into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. ImportanceThe reconstruction of genomes from metagenomes has enabled unprecedented insights into the ecology and evolution of environmental microbiomes. We applied this powerful approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and pinpoint nutrients that likely fuel their electron chains. Being photoautotrophs, these Chlorobia organisms also have the potential to serve as carbon sources that support metalimnetic and hypolimnetic food webs.

ecology↗

bioRxiv2020

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Extremely oligotrophic deep groundwaters host organisms attuned to the low-end of the bioenergetics spectrum. While all domains of life along with viruses are active in this habitat, the evolutionary and ecological constraints on colonization and niche shifts and their consequences for the microbiome convergence are unknown. Here we provide a comparative genome-resolved analysis of the prokaryotic community in disconnected fracture fluids of the Fennoscandian Shield. The data show that the oligotrophic deep groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common deep groundwater core microbiome. Based on this high resolution "multi-omics" enabled understanding of the underlying mechanisms via functional expression analysis, we conclude that deep groundwater ecosystems foster highly diverse, yet cooperative microbial communities adapted to this setting. The fitness of primary energy producers is increased by ecological traits such as aggregate or biofilm formation. This also facilitates reciprocal promiscuous partnerships with diverse and prevalent epi-bionts, alleviating the "tragedy of common goods". Hence, instead of a lifestyle where microbes predominantly invest in functions related to maintenance and survival, an episodic and cooperative lifestyle ensures the subsistence of the deep groundwater microbiome. We suggest the name "halt and catch fire" for this way of life.

microbiology↗

bioRxiv2020

Streamlined freshwater bacterioplankton Nanopelagicales (acI) and Ca. Fonsibacter (LD12) thrive in functional cohorts

While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or non-reciprocal, and expensive (Black Queen hypothesis) or costless (byproduct). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture dependent (minimalist mixed cultures) and culture independent (SSU rRNA gene time series and environmental metagenomics) methods we independently identified the primary cohorts of Actinobacterial genera "Ca. Planktophila" (acI-A) and "Ca. Nanopelagicus" (acI-B), and the Proteobacterial genus "Ca. Fonsibacter" (LD12). While "Ca. Planktophila" and "Ca. Fonsibacter" had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bi-functional catalase-peroxidase enzyme KatG (a common good which "Ca. Planktophila" is dependent upon) and its most likely providers in the lake. Further we found that while ecotype and community cooperation combined may explain "Ca. Planktophila" population abundance, the success of "Ca. Nanopelagicus" and "Ca. Fonsibacter" is better explained as a community byproduct. Ecotype differentiation of "Ca. Fonsibacter" as a means of escaping predation was supported but not for overcoming auxotrophies. IMPORTANCEThis study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: "Ca. Planktophila" (acI-A), "Ca. Nanopelagicus" (acI-B), and "Ca. Fonsibacter" (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide and this study adds a layer of understanding to how seemingly competing clades of bacteria can co-exist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.

microbiology↗

bioRxiv2020

Marine snow as a habitat for microbial mercury methylators in the Baltic Sea

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 Baltic Sea Reference Metagenome (BARM) dataset to study the distribution of the genes involved in Hg methylation (the hgcAB gene cluster). We determined the relative abundance of the hgcAB genes and their taxonomic identity in 81 brackish metagenomes that cover spatial, seasonal and redox variability in the Baltic Sea water. The hgcAB genes were predominantly detected in anoxic water, but some hgcAB genes were also detected in hypoxic and normoxic waters. Higher relative quantities of hgcAB genes were found in metagenomes from marine snow compared to free-living communities in anoxic water, suggesting that marine snow are hotspot habitats for Hg methylators in oxygen-depleted seawater. Phylogenetic analysis identified well-characterized Hg methylators such as Deltaproteobacteria in oxygen-depleted water, but also uncovered Hg methylators within the Spirochaetes and Lentisphaerae phyla. Altogether, our work unveils the diversity of the microorganisms mediating MeHg production in the Baltic Sea and pinpoint the ecological niches of these microorganisms within the marine water column.

microbiology↗

bioRxiv2019

Effects of long-term warming and enhanced nitrogen and sulfur deposition on microbial communities in a boreal peatland

With ongoing environmental change, it is important to understand ecosystem responses to multiple perturbations over long time scales at in situ conditions. Here, we investigated the individual and combined effects of 18 years of warming and enhanced nitrogen and sulfate deposition on peat microbial communities in a nutrient-poor boreal mire. The three perturbations individually affected prokaryotic community composition, where nitrogen addition had the most pronounced effect, and its combination with the other perturbations led to additive effects. The functional potential of the community, characterized by shotgun metagenomics, was strongly affected by the interactive effects in the combined treatments. The responses in composition were also partly reflected in the functional gene repertoire and in altered carbon turnover, i.e. an increase of methane production rates as a result of nitrogen addition and a decrease with warming. Long-term nitrogen addition and warming-induced changes caused a shift from Sphagnum-dominated plant communities to vascular plant dominance, which likely transact with many of the observed microbial responses. We conclude that simultaneous perturbations do not always lead to synergistic effects, but can also counteract and even neutralize one another, and thus must be studied in combination when attempting to predict future characteristics and services of peatland ecosystems.

microbiology↗

bioRxiv2018

Connections between freshwater carbon and nutrient cycles revealed through reconstructed population genomes

Metabolic processes at the microbial scale influence ecosystem functions because microbes are responsible for much of the carbon and nutrient cycling in freshwater. One approach to predict the metabolic capabilities of microbial communities is to search for functional marker genes in metagenomes. However, this approach does not provide context about co-occurrence with other metabolic traits within an organism or detailed taxonomy about those organisms. Here, we combine a functional marker gene analysis with metabolic pathway prediction of microbial population genomes (MAGs) assembled from metagenomic time series in eutrophic Lake Mendota and humic Trout Bog to identify how carbon and nutrient cycles are connected in freshwater. We found that phototrophy, carbon fixation, and nitrogen fixation pathways co-occurred in Cyanobacteria MAGs in Lake Mendota and in Chlorobiales MAGs in Trout Bog. Cyanobacteria MAGs also had strong temporal correlations to functional marker genes for nitrogen fixation in several years. Genes encoding steps in the nitrogen and sulfur cycles varied in abundance and taxonomy by lake, potentially reflecting the availability and composition of inorganic nutrients in these systems. We were also able to identify which populations contained the greatest density and diversity of genes encoding glycoside hydrolases. Populations with many glycoside hydrolases also encoded pathways for sugar degradation. By using both MAGs and marker genes, we were better able to link functions to specific taxonomic groups in our metagenomic time series, enabling a more detailed understanding of freshwater microbial carbon and nutrient cycling.

microbiology↗

bioRxiv2018

Mercury methylating microbial communities of boreal forest soils

The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is linked to the composition of also non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.\n\nImportanceDespite a global state of awareness that mercury, and methylmercury in particular, is a neurotoxin that millions of people continue to be exposed to, there are sizable gaps in our fundamental understanding of the processes and organisms involved in methylmercury formation. In the present study we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal forest soils. All the microorganisms identified have a relevant role on the processing of organic matter in soils. Moreover, our results show that the formation of methylation formation is not only linked to mercury methylating microorganisms but also to the presence of non-mercury methylating bacterial communities that contribute to methylmercury formation by the appropriate substrate to the microorganisms responsible for the actual methylation process. This study improves current knowledge on the diversity of organisms involved in methylmercury formation in soils.

microbiology↗

bioRxiv2018

Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom

In Antarctica, summer is a time of extreme environmental shifts resulting in large coastal phytoplankton blooms fueling the food web. Despite the importance of the microbial loop in remineralizing biomass from primary production, studies of how microzooplankton communities respond to such blooms in the Southern Ocean are rather scarce. Microzooplankton (ciliates and dinoflagellates) communities were investigated combining microscopy and 18S rRNA sequencing analyses in the Amundsen Sea Polynya during an extensive summer bloom of Phaeocystis antarctica. The succession of microzooplankton was further assessed during a 15-day induced bloom microcosm experiment. Dinoflagellates accounted for up to 58% the microzooplankton biomass in situ with Gymnodinium spp., Protoperidium spp. and Gyrodinium spp. constituting 87% of the dinoflagellate biomass. Strombilidium spp., Strombidium spp. and tintinids represented 90% of the ciliates biomass. Gymnodinium, Gyrodinium and tintinnids are known grazers of Phaeocystis, suggesting that this prymnesiophyte selected for the key microzooplankton taxa. Availability of other potential prey, such as diatoms, heterotrophic nanoflagellates and bacteria, also correlated to changes in microzooplankton community structure. Overall, both heterotrophy and mixotrophy appeared to be key trophic strategies of the dominant microzooplankton observed, suggesting that they influence carbon flow in the microbial food web through top-down control on the phytoplankton community.

ecology↗

bioRxiv2017

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

BackgroundProkaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.\n\nResultsWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.\n\nConclusionsThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

bioinformatics↗

bioRxiv2017

Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics

Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions, and greatly expand the known genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide-degraders in freshwater, uncovered interesting genomic features for this life style, and suggested their adaptation to nutrient availabilities in their environments. Between the two lakes, Verrucomicrobia populations differ significantly in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially-derived allochthonous carbon sources of the two ecosystems respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humic-rich environment. Notably, most epilimnion genomes have large numbers of so-called \"Planctomycete-specific\" cytochrome c-containing genes, which exhibited nearly opposite distribution patterns with glycoside hydrolase genes, probably associated with the different environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes are a major step towards understanding the role, ecophysiology and distribution of Verrucomicrobia in freshwater.\n\nIMPORTANCEFreshwater Verrucomicrobia are cosmopolitan in lakes and rivers, yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia are restricted to one subdivision of this phylum. Here, we greatly expand the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia as potential (poly)saccharide-degraders, and suggested their adaptation to carbon source of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called \"Planctomycete-specific\" cytochrome c-containing genes, and found their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

microbiology↗

bioRxiv2017

Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic condition

Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance1. Using micro-manipulation combined with shotgun metagenomic approaches, we disentangled the genomes of complex consortia inside a short chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes of this study, encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature in the consortia. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership2. Our study uncovers the complexity of interactomes within microbial consortia mediating hydrocarbon transformation under anaerobic conditions.

microbiology↗

bioRxiv2017

High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage

An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the \"seed set framework\", which computes the set of compounds that an organism must acquire from its environment (1), enables computational analysis of metabolic reconstructions, while providing new insights into a microbes metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater Actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support to the hypothesis that members of the acI are photoheterotrophs.\n\nImportanceThe metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organisms metabolic pathways, or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more intensive metabolic reconstruction efforts, and also provide new hypotheses about the specific contributions microbes make to ecosystem-scale metabolic processes.

microbiology↗