Biology subjects

Tamminen, M.

Publications and source records attributed to Tamminen, M..

9 recordsLinked to original sources

bioRxiv2026

Culture-free single-cell transcriptomics shows short term functional and associative stability in non-model microeukaryotes under shading stress

Microeukaryotes are abundant, diverse, and morphologically and functionally complex. They represent one of the largest groups of primary producers and are involved in major ecosystem functions such as nutrient transformations and maintenance of food webs. Although ~74,000 species of microeukaryotes are estimated to exist, very few are available in culture and only ~3000 are represented by reference genomes and transcriptomes. This limited representation significantly hinders the study of microeukaryotes in their natural environments. Single-cell transcriptomics with sequencing of full-length transcripts has potential to bypass this limitation. In this study, we employ Smart-seq3xpress for taxonomic identification and functional characterization of non-model mixotrophic freshwater microeukaryotes in a culture-free and reference-free manner, while also enabling inferences to be made for their prokaryotic associations. Computational analyses revealed 22 distinct microeukaryote taxa upon sequencing of 1520 randomly sampled cells, with assemblies of 12 good quality de novo partial transcriptomes, followed by functional annotation using sequence and structure homology. Gene expression analysis of the transcriptome for the most abundant microeukaryote in the sample, Rhodomonas, revealed a transcriptomic dip a few hours after experimental shading, followed by a gradual recovery in the next few days. Compared to samples in illuminated conditions, there was widespread downregulation of photosynthesis-, lysosome-, and carbon metabolism-related pathways in the shade, but the prevailing associations with prokaryotic lineages was unaffected by the light conditions. The different microeukaryotes, all present in the same environmental sample, featured distinct prokaryotic associates that were consistent across illumination conditions. This reference-free and culture-free study of 22 different microeukaryotic taxa sets the stage for high-throughput single cell transcriptomics to study microeukaryotic diversity in complex natural ecosystems, for their population-level taxonomic identity, sub-population-level transcriptomic profiles and metabolic states, and individual-level prokaryotic associations.

microbiology↗

bioRxiv2026

Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation

Microbial communities frequently encounter recurrent antibiotic disturbance, yet how ecological, evolutionary, and environmental processes jointly shape the response remains unresolved. Here we experimentally disentangle these mechanisms using a 23-species bacterial community exposed to ampicillin pulses with pre-pulse and resistance priming. Pre-pulse priming preconditioned community composition toward resistant taxa, reducing compositional change during the main pulse. Resistance priming was the dominant determinant of community response, buffering compositional change, relaxing selection, and altering gene expression. This buffering arose from both evolution of higher resistance and accelerated ampicillin detoxification by a dominant degrader, which transiently reduced antibiotic effects and favoured non-degrading taxa. Yet buffering did not translate into better recovery: because resistance was coupled to competitive dominance, diversity remained comparable to or below that of ancestral communities, and dominance was reinforced. Together, we show that antibiotic history reshapes microbial disturbance response through coupled eco-evolutionary and environmental feedbacks, generating a trade-off between resistance and recovery.

evolutionary biology↗

bioRxiv2026

Application of the Nicking Loop™ targeted library preparation method to DNBSEQ™ sequencing

Nicking Loop is a PCR-free targeted library preparation method that combines conversion of linear target DNA into circular single-stranded DNA (CssDNA) library with early sample indexing in a single step. The resulting CssDNA libraries can be either directly sequenced or optionally amplified, offering maximum flexibility across sequencing applications. This study demonstrates the compatibility of Nicking Loop circular libraries with a MGIs DNBSEQ platform. Compatibility was evaluated against established linear Nicking Loop libraries sequenced on Illumina MiSeq platform. Using synthetic reference samples with defined variant allele frequencies, Nicking Loop method demonstrated matching performance across both library formats and sequencing platforms. Key quality metrics, including unique molecular identifier (UMI) distributions, error profiles and VAF detection, were all highly consistent. Both library types generated over 97% singleton UMIs, indicating uniform template sampling, and VAF measurements were strongly concordant across platforms (Spearmans {rho} = 0.939). Collectively, these findings demonstrate that Nicking Loop method is directly applicable to circular NGS platforms, such as DNBSEQ, strongly supporting its use as a platform-agnostic library preparation strategy for targeted sequencing applications.

molecular biology↗

bioRxiv2025

Polyacrylamide bead split-pool method for microbial community analysis

Understanding diverse microbial communities is important due to their ecological and medical significance. Bacterial cells are genetically and phenotypically heterogeneous, making their interactions in the communities complex. The heterogeneity and interactions of cells contribute to the formation of specific spatial structures, such as biofilms, and the spread of antibiotic resistance. Here, we describe a novel single-cell approach for studying the cellular heterogeneity and spatial interactions in microbial communities that combines polyacrylamide bead encapsulation of cells and split-pool-barcoding. We demonstrate the method by determining artificially imposed interactions and connecting the taxonomic information in a mock three-species bacterial community with a species-specific genomic target. The method can be utilised for the spatial analysis of microbial communities as well as, once fully optimised for single-cell resolution, linking genetic traits to single cells.

microbiology↗

bioRxiv2025

Nicking Loop™: An infinite amplification of single-stranded circular DNA

Circular single-stranded DNA (CssDNA) offers unique advantages for molecular diagnostics and next-generation sequencing (NGS) due to its nuclease resistance and compatibility with rolling circle amplification. We present the Nicking Loop, a novel and versatile method for converting both single- and double-stranded DNA into CssDNA and enabling robust, unbiased amplification. This technique preserves the original DNA template composition and outperforms PCR in reproducibility and sensitivity, particularly for low variant allele frequencies. We demonstrate that Nicking Loop-amplified CssDNA is directly compatible with NGS platforms utilizing circular DNA as a sequencing template and introduce a novel loop-based indexing strategy that enables efficient sample multiplexing. Furthermore, we confirm the methods compatibility with nanopore sequencing technologies, highlighting its broad applicability across sequencing platforms. Our results establish Nicking Loop as an alternative to conventional linear library preparation, streamlining workflows while enhancing sequencing accuracy and efficiency. Beyond its immediate application in NGS, the method holds promise for broader use in molecular biology, e.g. in DNA data storage. This proof-of-concept study highlights the transformative potential of Nicking Loop in enabling a shift toward circular DNA libraries for new generation of assay preps and precision sequencing applications.

molecular biology↗

bioRxiv2023

De novo assembled single-cell transcriptomes from aquatic phytoflagellates reveal a metabolically distinct cell population

Single-cell transcriptomics is a vital tool for unraveling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with growth phases. Unexpectedly, a third transcriptional state was identified, across both growth phases. Metabolic mapping revealed a down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism from fast to slow growth to the third transcriptional state. Using carry-over rRNA reads, taxonomic identity of Ochromonas triangulata was re-confirmed and distinct bacterial communities associated with transcriptional states were identified. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability for uncovering ecological roles, surpassing alternative methods like metagenomics or metatranscriptomics.

microbiology↗

bioRxiv2021

Prider - multiplexed primer design using linearly scaling approximation of set coverage

Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing primers and probes to complex, heterogeneous DNA data sets, an optimization problem arises where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking. Here we present Prider, an R package for designing primers and probes with a nearly optimal coverage for complex and large sequence sets. Prider initially prepares a full primer coverage of the input sequences, the complexity of which is subsequently reduced by removing components of high redundancy or narrow coverage. The primers from the resulting near-optimal coverage are easily accessible as data frames and their coverage across the input sequences can be visualized as heatmaps using Priders plotting function. Prider scales linearly to increasing sequence data and therefore permits efficient design of primers to large and highly diverse DNA datasets. Prider is available on GitHub under the permissive BSD-3-clause license: https://github.com/manutamminen/prider

bioinformatics↗

bioRxiv2019

The evolution of competitive ability for essential resources

Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered - to what extent are species competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposed Chlamydomonas reinhardtii for approximately 285 generations to seven environments in chemostats which differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.

evolutionary biology↗

bioRxiv2018

nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data

Advancements in DNA sequencing technologies rapidly change the landscape of modern biology. The novel next-generation sequencing (NGS) applications often have special requirements regarding experimental data processing. Software tools developed and used for novel applications are generally designed for specific use cases and as such may be difficult to adapt to new uses. Simultaneously, software tools designed to be general are often difficult to adapt to special use cases.\n\nHere, we present nsearch, a modern open source C++11 library and command-line tool for biological sequence data processing. nsearch offers commonly used components for handling of biological sequences including paired-end read merging, quality filtering and sequence similarity searching. nsearch can either be embedded natively into other C++ applications or be packaged as a standalone executable.\n\nFunctionality and performance of nsearch is shown using benchmark data created using the Rfam 13 database. Benchmarking against common general purpose tools USEARCH and VSEARCH demonstrates that nsearch delivers performance comparable these state-of-the-art tools.\n\nnsearch is available on GitHub under the permissive BSD-3-clause license: https://github.com/stevschmid/nsearch

bioinformatics↗