Biology subjects

Broman, E.

Publications and source records attributed to Broman, E..

4 recordsLinked to original sources

bioRxiv2026

Benchmarking the quantitative performance of metabarcoding and shotgun sequencing using mock communities of marine nematodes

High-throughput sequencing has transformed biodiversity assessment and ecological monitoring, yet its quantitative reliability remains unclear. Here, we assembled two experiments of nematode mock communities: one based on extracted DNA and one on individual specimens. Although DNA extraction was required in both experiments to assess the quantitative performance of the sequencing approaches, we essentially evaluated whether this performance was influenced by differences in the start material used to constructed the mock communities. Each community was analyzed using 18S and 28S metabarcoding and shotgun sequencing to evaluate their ability to resolve quantitative information. Across datasets, the number of observed taxa increased with sequencing depth despite controlled input, indicating that higher read numbers primarily revealed intragenomic variation in nematodes than true diversity. Community composition was more accurately recovered by 18S metabarcoding and shotgun sequencing than by 28S. Both sequencing approaches reflected DNA input reasonably well; however, shotgun sequencing provided more consistent abundance estimates relative to individual counts, particularly for nematodes with relatively large-bodied size. In contrast, all methods showed limited ability to accurately quantify taxa with low DNA input or small body size. Comparisons between mock community types showed strong correspondence between read abundance and DNA input, but weaker relationships with individual counts. Overall, both metabarcoding and shotgun sequencing effectively detected community-level patterns and within-taxon abundance, but shotgun sequencing was more reliable for cross-taxon quantitative comparisons. Our findings demonstrate how input material, primer choice, and sequencing approach influence the accuracy of nematode abundance estimates, and provide guidance for improving quantitative applications in nematode-based bioindication and, more broadly environmental DNA biomonitoring.

ecology↗

bioRxiv2026

Pollutant biodegradation profile mediated by multi-trophic microbial dynamics in rivers

Microbial communities and environmental conditions are closely linked to ecosystem functions and directly govern the biodegradation of pollutants in aquatic environments. However, the role of multi-trophic interactions and their spatiotemporal dynamics in these processes remains poorly understood. Here, we examined how seasonal and spatial variations, mediated by trophic interactions within benthic microbial communities, influence their composition, functional capacity, and collective potential to degrade a diverse array of organic pollutants in rivers. By characterizing both prokaryotic (i.e., archaea and bacteria) and eukaryotic taxa (i.e., algae, fungi, protists, and metazoans), and inferring metabolic pathways, we explored the connections between community composition and pollutant degradation in wastewater-receiving rivers across four seasons. Mediation analysis revealed that multi-trophic communities mediate the total effect of environmental factors on the biodegradation of 96 organic pollutants. Prokaryotic communities explained 60% of the total environmental influence on pollutant biodegradation. Additionally, eukaryotic groups had significant indirect mediation effects, with fungal, protistan, algal, and metazoan communities responsible for 56%, 53%, 26%, and 38%, respectively. Notably, fungal and protist communities mediated approximately 83% and 73% of the environmental impacts on prokaryotic community composition, respectively. Across the two rivers studied, spatial variation (at the river and reach scales) explained more variance in community composition than seasonality over the sampled year. Our findings improve understanding of ecosystem resilience and support the development of predictive models and sustainable water management strategies in dynamic aquatic environments.

microbiology↗

bioRxiv2025

Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem

BackgroundThe Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds. ResultsKnown hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (>10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea. ConclusionsUsing metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/657333v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1ba6e59org.highwire.dtl.DTLVardef@a2c000org.highwire.dtl.DTLVardef@eb7bd2org.highwire.dtl.DTLVardef@e4dce_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2025

Environmental drivers of the resistome across the Baltic Sea

BackgroundAntimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions. ResultsWe analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition. ConclusionsWe presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems.

microbiology↗