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This report presents results from a project investigating the use of microbes as indicators of mercury (Hg) pollution in sediments. Microbes respond rapidly to environmental change, making them excellent bioindicators. However, to ensure reliable results, it is essential to analyze microbial communities soon after sampling to prevent degradation or loss of activity.

To address this, a portable molecular sequencing laboratory, OmiBox, was developed, enabling near in situ analysis of microbial taxonomic composition and gene expression. Additionally, microbial community composition was studied in Hg-contaminated fiber banks in the Gulf of Bothnia. The results revealed that certain taxonomic groups, such as bacteria from the phyla Campylobacterota and Desulfobacterota, were enriched in fiber-rich, Hg-polluted sediments.

The study also included tolerance experiments comparing bacteria from clean and contaminated sediments in response to Hg addition. Bacteria from polluted sites exhibited significantly greater tolerance, suggesting evolved resistance and retained microbial functionality. Nonetheless, Hg-contaminated sediments pose ecological risks, as methylmercury (MeHg) can bioaccumulate and magnify through the food web.

This project contributes a framework for understanding how bacterial community structure and function respond to Hg pollution in sediments, offering valuable tools for environmental monitoring and assessment.

Kemiska föroreningar orsakar problem världen över. Miljögifter som hamnat i akvatiska miljöer ackumuleras ofta till nivåer som har skadliga effekter på organismerna och hela ekosystemen. Inom EU-lagstiftningen används biomarkörer för att analysera statusen på naturliga miljöer. Mikroorganismer skulle kunna vara väl lämpade som bioindikator, eftersom de i stort sett finns överallt på jorden och snabbt svarar på miljöförändringar.

Målsättningen med detta projekt var att klarlägga om bakterier kan användas som indikator för kontaminerade sediment. Vi fokuserade på kvicksilver, som är ett vanligt förekommande miljögift i fiberrika sediment i Bottniska viken. Inom projektet utvecklades ett portabelt molekylärt sekvenseringslaboratorium (Omibox), experiment utfördes för att testa effekter av terrestra organiska ämnen samt mikroorganismers toleransnivåer för kvicksilverbelastning. Därutöver utfördes fältstudier i gradienter av kvicksilverbelastade områden i Bottniska viken för att hitta möjliga indikatorer i bakteriesamhället.

Rehmannia glutinosa, an extensively utilized Chinese herbal medicine, is highly valued for its medicinal properties. In this study, the complete mitochondrial genome (mitogenome) of R. glutinosa was sequenced and assembled for the first time. The mitogenome is 547,032 bp in length, with an overall GC content of 44.97%. The mitogenome contains 67 unique genes, comprising 43 protein-coding, three rRNA, and 21 tRNA genes, with six protein-coding and nine tRNA genes being chloroplast-derived. The phylogenetic analysis, based on the maximum-likelihood criterion, demonstrated that R. glutinosa is closely related to Aeginetia indica and Castilleja paramensis within the family Orobanchaceae.

Bacteria are major consumers of dissolved organic matter (DOM) in aquatic systems. In coastal zones, bacteria are exposed to a variety of DOM types originating from land and open sea. Climate change is expected to cause increased inflows of freshwater to the northern coastal zones, which may lead either to eutrophication or to increased inputs of refractory terrestrial compounds. The compositional and functional response of bacterial communities to such changes is not well understood. We performed a 2-day microcosm experiment in two bays in the coastal northern Baltic Sea, where we added plankton extract to simulate eutrophication and soil extract to simulate increased inputs of refractory terrestrial compounds. Our results showed that the bacterial communities responded differently to the two types of food substrates but responded in a similar compositional and functional way in both bays. Plankton extract addition induced a change of bacterial community composition, while no significant changes occurred in soil extract treatments. Gammaproteobacteria were promoted by plankton extract, while Alphaproteobacteria dominated in soil extract addition and in the non-amended controls. Carbohydrate metabolism genes, such as aminoglycan and chitin degradation, were enriched by plankton extract, but not soil extract. In conclusion, the coastal bacterial communities rapidly responded to highly bioavailable substrates, while terrestrial matter had minor influence and degraded slowly. Thus, in the northern Baltic Sea, if climate change leads to eutrophication, large changes of the bacterial community composition and function can be expected, while if climate change leads to increased inflow of refractory terrestrial organic matter the bacterial communities will not show fast compositional and functional changes. Degradation of terrestrial organic matter may instead occur over longer periods of time, e.g. years. These findings help to better understand the ability of bacterial communities to utilize different carbon sources and their role in the ecosystem.

Phytoplankton are used worldwide to monitor environmental status in aquatic systems. Long-time series of microscopy-analyzed phytoplankton are available from many monitoring stations. The microscopy-method is however time consuming and has short-comings. DNA metabarcoding has been suggested as an alternative method, but the consistency between different methods need further investigation. We performed a comparative study of microscopy and metabarcoding analyzing micro- and nanophytoplankton. For metabarcoding, 25-1000 ml seawater were filtered, DNA extracted and the 18S and 16S rRNA gene amplicons sequenced. For microscopy, based on the Utermöhl method we evaluated the use of three metrics: abundance, biovolume and carbon biomass. At the genus, species, and unidentified taxa level, metabarcoding generally showed higher taxonomic diversity than microscopy, and diversity was already captured at the lowest filtration volume tested, 25 ml. Metabarcoding and microscopy displayed relatively similar distribution pattern at the group level. The results showed that the relative abundances of the 18S rRNA amplicon at the group level best fitted the microscopy carbon biomass metric. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if databases would be improved and group level indexes could be applied to classify the environmental state of water bodies.

In northern marginal seas, like the northern Baltic Sea, climate change will lead to many alterations, for example increased inflows of nutrients and dissolved organic matter (DOM). Nutrients and DOM are fundamental drivers shaping marine microbial communities, including both bacterial and phytoplankton populations. Potentially microbial communities and their functions can be used as descriptors of environmental change in marine systems. 

Changed nutrient availability will affect the phytoplankton communities, which is widely used as descriptor of environmental state in aquatic systems. Traditionally phytoplankton is analyzed using microscopy in monitoring, while molecular methods holds a great potential for future development. I performed a comparative study between metabarcoding and microscopy. Metabarcoding and microscopy displayed relatively similar distribution pattern at the group level. The results showed that the relative abundances of the 18S rRNA amplicon at the group level best fitted the microscopy carbon biomass metric. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if databases would be improved and group level indexes could be applied to classify environmental state of water bodies.

Bacterioplankton are the main DOM processors in the marine food web. A shift in the quality and quantity of the DOM pool could affect the microbial community structure and alter their functioning. Presently it is poorly known how coastal bacteria respond compositionally and functionally to quality and quantity changes in DOM supply. To comprehensively address this question, there is a critical need for microcosm experimental studies as well as field studies. Thus, I used approaches from single species laboratory experiment to community levels in situ incubation experiments and community levels spatiotemporal field surveys to evaluate the impacts of climate shifts on microbial community. Intricate relationships between environmental factors and microbial communities, for example, links between key microbial functional genes and DOM conditions were identified. Results showed that bacteria isolated from coastal area harbor genes for the sequestration of autochthonously produced carbon substrates, while bacteria isolated from a river contained genes for the degradation of relatively refractive terrestrial organic matter. A field experiment showed that Gammaproteobacteria was promoted by plankton extract addition and the genes for chitin and cellulose catabolism are enriched by addition of autochthonous carbon sources. The field survey with comprehensive metagenomic investigation of microbial community composition indicated that the temporal variation is larger compare to spatial changes. Bacteroidia, Actinomycetia, Gammaproteobacteria, Acidimicrobiia, and Alphaproteobacteria were the dominant bacterial classes, with Bacteroidia being more abundant in inshore stations compared to offshore locations. The seasonal shift in the relative abundance of these bacterial classes suggests that environmental factors and ecological processes drive changes in the abundance of different bacterial classes over time. Overall, these studies strengthen our understanding of the relationships between microbial composition and biogeochemical processes in coastal areas.

Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.

Global warming scenarios indicate that in subarctic regions, the precipitation will increase in the future. Coastal bacteria will thus receive increasing organic carbon sources from land runoff. How such changes will affect the function and taxonomic composition of coastal bacteria is poorly known. We performed a 10-day experiment with two isolated bacteria: Shewanella baltica from a seaside location and Duganella sp. from a river mouth, and provided them with a plankton and a river extract as food substrate. The bacterial growth and carbon consumption were monitored over the experimental period. Shewanella and Duganella consumed 40% and 30% of the plankton extract, respectively, while the consumption of the river extract was low for both bacteria, ∌1%. Shewanella showed the highest bacterial growth efficiency (BGE) (12%) when grown on plankton extract, while when grown on river extract, the BGE was only 1%. Duganella showed low BGE when grown on plankton extract (< 1%) and slightly higher BGE when grown on river extract (2%). The cell growth yield of Duganella was higher than that of Shewanella when grown on river extract. These results indicate that Duganella is more adapted to terrestrial organic substrates with low nutritional availability, while Shewanella is adapted to eutrophied conditions. The different growth performance of the bacteria could be traced to genomic variations. A closely related genome of Shewanella was shown to harbor genes for the sequestration of autochthonously produced carbon substrates, while Duganella contained genes for the degradation of relatively refractive terrestrial organic matter. The results may reflect the influence of environmental drivers on bacterial community composition in natural aquatic environments. Elevated inflows of terrestrial organic matter to coastal areas in subarctic regions would lead to increased occurrence of bacteria adapted to the degradation of complex terrestrial compounds with a low bioavailability.