Biology subjects

Andersson, A. F.

Publications and source records attributed to Andersson, A. F..

14 recordsLinked to original sources

bioRxiv2026

A streamlined and abundant Nitrosopumilus population retains vitamin biosynthesis under high purifying selection in the Baltic Sea

Genome streamlining is expected to favor the loss of costly biosynthetic functions, raising the question of what benefit justifies the continued maintenance of complex pathways in small genomes. Here, we investigated this question in an abundant Nitrosopumilus population from the Baltic Sea that combined a streamlined genome (1.4 Mbp) with substantial biosynthetic capacity for vitamins B1, B7, and B12. We found three lines of evidence that support the biological significance of this retention. First, phylogenomic analysis of 1,077 archaeal species representatives showed that B-vitamin biosynthesis is broadly conserved across ammonia-oxidizing archaea (AOA), indicating maintenance over deep evolutionary timescales. Second, genes associated with B-vitamin biosynthesis tended to be under stronger purifying selection than the genomic background across Baltic Sea metagenomes, consistent with selection preserving these functions in current environmental populations. Third, measurements in the cultured relative Nitrosopumilus maritimus showed B-vitamins and related precursors in both intracellular and extracellular fractions, providing a potential route through which these retained functions could influence metabolite availability beyond the producing cell. Together, our findings suggest that retained biosynthetic pathways in highly streamlined microorganisms reveal functions that are beneficial for the success of a natural population, while also pointing to their potential importance for other community members coexisting within the same environment.

microbiology↗

bioRxiv2026

The marine microbiome can accurately predict its chemical and biological environment

The microbiome responds to physicochemical changes in the environment, making it a sensitive indicator of ecosystem status. Monitoring microbial communities in aquatic systems is therefore essential for understanding ecosystem health and responses to change. Traditionally reliant on microscopy, monitoring programmes are increasingly incorporating DNA-based approaches leveraging on advances in high-throughput sequencing. In this study, we evaluate the potential of using DNA metabarcoding to predict abiotic and biotic parameters across the spatiotemporal gradients of the Baltic Sea. The dataset comprises 397 seawater samples integrating prokaryotic (16S rRNA gene) and eukaryotic (18S rRNA gene) metabarcoding data with environmental measurements and plankton microscopy counts. Random Forest models based on metabarcoding data accurately predicted a range of physicochemical parameters and showed performance comparably to more complex machine learning algorithms. Models based on 16S rRNA gene data tended to perform better than those based on 18S rRNA gene data, with amplicon sequence variant-level data yielding the best results. Metabarcoding outperformed plankton microscopy in predicting abiotic factors and effectively predicted the presence of phytoplankton and zooplankton genera using [≤]1 L of water. Models trained on independent datasets accurately predicted several of the physicochemical parameters, but performed weaker on others, highlighting the potential and challenges for their transferability. Furthermore, our predictions closely matched the observed HELCOM indicator values for assessing good environmental status, suggesting the utility of microbiome-based approaches in regional marine monitoring frameworks. These findings underscore the potential of environmental DNA as a tool for ecosystem monitoring and management in dynamic coastal systems.

microbiology↗

bioRxiv2025

Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system

Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible, and metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesizing that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict protein-coding genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularized regression, which allowed filtering out irrelevant features even when the number of features was much larger than the number of samples. Taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations, both when analyzing separate studies as well as when analyzing the combined data of the studies. Our hypothesis that functional metagenomics would outperform taxonomic metagenomics was therefore not supported. Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/658511v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@43aaeforg.highwire.dtl.DTLVardef@8b5d27org.highwire.dtl.DTLVardef@190e737org.highwire.dtl.DTLVardef@3c0206_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Microbial model communities reveal widespread auxotrophies in abundant bacteria

Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity - ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than 3 species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, biosynthetic genes were distributed across genomes within the same model community, indicating metabolic interdependencies. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.

microbiology↗

bioRxiv2024

Distinct bacterial and protist plankton diversity dynamics uncovered through DNA-based monitoring in the Baltic Sea area

Planktonic microorganisms in coastal waters form the base of food web and biogeochemical cycles. The Baltic Sea area, with its pronounced environmental gradients, serves as a model coastal environment. Yet, microbial diversity assessment across these environmental gradients has so far lacked either taxonomic scope or the integration of spatial and temporal scales. Here, we analyzed protist and bacterial diversity using DNA metabarcoding across 398 samples synchronized with national monitoring of the Baltic Sea and the Kattegat-Skagerrak. We show that salinity, unlike other environmental factors, had a stronger effect on bacterial than on protist community composition. Likewise, Bayesian modeling showed that bacterial lineages were less likely than protists to occur in both lower (<9 PSU) and higher (>15 PSU) brackish salinities. Nonetheless, protist alpha diversity increased with salinity. Changes in bacterial alpha diversity were primarily seasonal and linked to influx of deepwater taxa through vertical mixing in winter. We propose that protists are ecologically less sensitive to salinity because compartmentalization allows them to disconnect basic metabolic processes from the cell membrane. Additionally, further and more frequent dispersal of bacteria might impede local adaptation. Ultimately, DNA-based environmental monitoring expands our understanding of microbial diversity patterns and the underlying factors.

microbiology↗

bioRxiv2023

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we optimized a microarray single-cell sequencing (MASC-seq) technology that generates microscope images of cells in parallel with capturing their transcriptomes. We tested the method on three species representing important plankton groups with different cell structures, the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum and the dinoflagellate Heterocapsa sp.. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.

genomics↗

bioRxiv2022

Genome size variation between pelagic and benthic communities across prokaryotic taxonomy and environmental gradients in the Baltic Sea

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.

microbiology↗

bioRxiv2022

Optimizing insect metabarcoding using replicated mock communities

Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundances, and biomass. Here we use mock community experiments and a simple probabilistic model to evaluate the performance of different metabarcoding protocols. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization?; and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Tiny insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalizes better across species for homogenates. We conclude that a non-destructive, mild lysis approach shows the highest promise for presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.

ecology↗

bioRxiv2021

Evaluating metagenomic assembly approaches for biome-specific gene catalogues

For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene-calling on the assembled contigs. The assembly can be conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is likely preferable. Thus, both approaches have pros and cons and it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: 1) assembly on individual samples followed by clustering of the resulting genes, 2) co-assembly on all samples, and 3) mix-assembly, combining individual and co-assembly. The mix-assembly approach resulted in a more extensive non-redundant gene set than the other approaches, and with more genes predicted to be complete and that could be functionally annotated. The mix-assembly consists of 67 million genes (Baltic Sea gene set; BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (<95% amino acid identity) to the Tara Oceans gene dataset, and hence BAGS represents a valuable resource for brackish water research. IMPORTANCESeveral ecosystem types, such as soils and oceans, are studied through metagenomics. It allows the analysis of genetic material of the microbes within a sample without the need for cultivation. When performing the DNA sequencing with an instrument that generates short sequence reads, these reads need to be assembled in order to obtain more complete gene sequences. In this paper, we have evaluated three strategies for assembling metagenome sequences using a large metagenomic dataset from the Baltic Sea. The method that we call mix-assembly generated the greatest number of non-redundant genes and the largest fraction of genes that were predicted to be complete. The resulting gene catalogue will serve as an important resource for brackish water research. We believe this method to be efficient also for generating gene catalogs for other biomes.

bioinformatics↗

bioRxiv2020

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

BackgroundBacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. However, difficulties in culturing the majority of aquatic prokaryotic species have complicated the study of their microdiversity. Here, we present POGENOM, a software that quantifies population genomic indices from metagenome data, enabling comparative analysis of genomic diversity and differentiation in multiple species in parallel. We demonstrate POGENOM on metagenome-assembled genomes from the Baltic Sea and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. ResultsThe majority of the investigated species, representing several major bacterioplankton clades, displayed population structure correlating significantly with environmental factors such as salinity, temperature, nutrients and oxygen, both over horizontal and vertical dimensions. Population differentiation was more pronounced over spatial than temporal scales, although some species displayed population structure correlating with season. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations existence along the salinity range. ConclusionsWe provide a new tool for high-throughput population genomics analysis based on metagenomics data. From an evolutionary point of view, our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species, despite their seemingly unlimited dispersal potential. This is of central importance when learning about how species have adapted to new environmental conditions and what their adaptive potential is in the face of Global Change.

genomics↗

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

Genome Sequence of Segmented Filamentous Bacteria Present in the Human Intestine

Segmented filamentous bacteria (SFB) colonize the small intestine of a variety of animals in a host-specific manner. SFB are physically attached to the hosts intestinal epithelium and affect several functions related to the immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome had been described. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with the SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the other genomes, and is tentatively unique for the human small intestine. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB-genome. We thus conclude that a unique SFB variant exists in humans and we foresee a renewed interest in the elucidation of SFB functionality in this environment.

microbiology↗

bioRxiv2018

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

Insect metabarcoding has been mainly based on PCR amplification of short fragments within the barcoding region of the gene COI. However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ECOPRIMERS and DEGEPRIME) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.

bioinformatics↗

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↗