Biology subjects

Nilsson, R. H.

Publications and source records attributed to Nilsson, R. H..

3 recordsLinked to original sources

bioRxiv2026

Metabarcoding reveals that bacterial and fungal microbiomes are perturbed by micropollutants in a fjord system (Hakefjorden and Askerofjorden) at the Swedish west coast

Fjord systems are susceptible to anthropogenic pressures, including discharges from wastewater treatment plants (WWTPs), which introduce micropollutants into coastal waters. We investigated the impact of micropollutants on bacteria and fungi within a fjord system adjacent to a significant petrochemical industry hub on the Swedish west coast. We characterised microbial assemblages along a land-to-sea transect, encompassing freshwater streams receiving agricultural and urban runoff, as well as the direct effluent from a WWTP. Our findings revealed elevated concentrations and a diverse array of micropollutants in the WWTP effluent and the stream running through the urban/industrial zone, highlighting these areas as major sources of pollution to the fjord. Bacterial and fungal communities inhabiting the WWTP effluent and the receiving marine waters near the marine outflow exhibited distinct structural compositions, indicating a selective pressure exerted in part by the micropollutant load. While freshwater sites generally displayed higher overall microbial diversity compared to marine sites, the WWTP effluent showed reduced diversity in both bacterial and fungal communities, likely due to the impact of micropollutants. Interestingly, marine sites far from the WWTP discharges exhibited a recovery in bacterial diversity, suggesting a potential response or adaptation. In contrast, fungal diversity remained comparable to that observed in other marine locations. Multivariate analyses identified physicochemical parameters and nutrients, alongside with summed fungicides and antibiotic stress as key factors driving the community dissimilarities across the fjord. Significant disruptions in potential bacterial metabolism and fungal ecological functions were evident at the WWTP discharge point, underscoring the ecological consequences of wastewater pollution. HighlightsO_LIWWTP discharge is the primary source of complex micropollutants in the fjord. C_LIO_LIAntibiotics and fungicides significantly shape bacterial and fungal communities. C_LIO_LIWastewater impacts reduce microbial diversity and disrupt functional potential. C_LIO_LIMarine sites show microbial recovery and enrichment away from discharge points. C_LIO_LIeDNA and toxic unit modeling link chemical stress to microbiome restructuring. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/711609v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1751e5forg.highwire.dtl.DTLVardef@1d0d78org.highwire.dtl.DTLVardef@15f446aorg.highwire.dtl.DTLVardef@184bb0a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus

BackgroundRecent evidence shows that arbuscular mycorrhizal (AM) symbiosis is established by two distinct fungal groups, with the distinctive fine root endophyte morphotype formed by fungi from the sub-phylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While Mucoromycotina AM fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts. ResultsWe used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis. ConclusionThese differences highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina AM fungi with their host plant and the environment which could support niche differentiation and complementary ecological functions.

microbiology↗

bioRxiv2018

Introducing ribosomal tandem repeat barcoding for fungi

Sequence analysis of the various ribosomal genetic markers is the dominant molecular method for identification and description of fungi. However, there is little agreement on what ribosomal markers should be used, and research groups utilize different markers depending on what fungal groups are targeted. New environmental fungal lineages known only from DNA data reveal significant gaps in the coverage of the fungal kingdom both in terms of taxonomy and marker coverage in the reference sequence databases. In order to integrate references covering all of the ribosomal markers, we present three sets of general primers that allow the amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers (ETS, SSU, ITS1, 5.8S, ITS2, LSU, and IGS) from the 5 end of the ribosomal operon all the way to the 3 end. We coupled these primers successfully with third generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens. In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the need for a large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85 %, which is comparable with the 99.78 % accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.

genetics↗