Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked. In this study, sediments were sampled from a heated (average 5°C increase over the whole year for over 50 years) and a control (contemporary conditions) Baltic Sea bay during four different seasons across a year. RNA transcript counts were then used to investigate eukaryotic community changes under long-term warming. The composition of active species in the heated and control bay sediment eukaryotic communities differed, which was mainly attributed to salinity and temperature. The family level RNA transcript alpha diversity in the heated bay was higher during May but lower in November, compared with the control bay, suggesting altered seasonal activity patterns and dynamics. In addition, structures of the active eukaryotic communities varied between the two bays during the same season. Hence, this study revealed that long-term warming can change seasonality in eukaryotic diversity patterns. Relative abundances and transcript expression comparisons between bays suggested that some taxa that now have lower mRNA transcripts numbers could be favored by future warming. Furthermore, long-term warming can lead to a more active metabolism in these communities throughout the year, such as higher transcript numbers associated with diatom energy production and protein synthesis in the heated bay during winter. In all, these data can help predict how future global warming will affect the ecology and metabolism of eukaryotic community in coastal sediments.

The world's oceans are challenged by climate change linked warming with typically highly populated coastal areas being particularly susceptible to these effects. Many studies of climate change on the marine environment use large, short-term temperature manipulations that neglect factors such as long-term adaptation and seasonal cycles. In this study, a Baltic Sea 'heated' bay influenced by thermal discharge since the 1970s from a nuclear reactor (in relation to an unaffected nearby 'control' bay) was used to investigate how elevated temperature impacts surface water microbial communities and activities. 16S rRNA gene amplicon based microbial diversity and population structure showed no difference in alpha diversity in surface water microbial communities, while the beta diversity showed a dissimilarity between the bays. Amplicon sequencing variant relative abundances between the bays showed statistically higher values for, e.g., Ilumatobacteraceae and Burkholderiaceae in the heated and control bays, respectively. RNA transcript-derived activities followed a similar pattern in alpha and beta diversity with no effect on Shannon's H diversity but a significant difference in the beta diversity between the bays. The RNA data further showed more elevated transcript counts assigned to stress related genes in the heated bay that included heat shock protein genes dnaKJ, the co-chaperonin groS, and the nucleotide exchange factor heat shock protein grpE. The RNA data also showed elevated oxidative phosphorylation transcripts in the heated (e.g., atpHG) compared to control (e.g., atpAEFB) bay. Furthermore, genes related to photosynthesis had generally higher transcript numbers in the control bay, such as photosystem I (psaAC) and II genes (psbABCEH). These increased stress gene responses in the heated bay will likely have additional cascading effects on marine carbon cycling and ecosystem services.

Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6–35 °C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (similar to 0.5 cm) to deeper sediments (similar to 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

Coastal marine ecosystems are some of the most diverse natural habitats while being highly vulnerable in the face of climate change. The combination of anthropogenic influence from land and ongoing climate change will likely have severe effects on the environment, but the precise response remains uncertain. This study compared an unaffected “control” Baltic Sea bay to a “heated” bay that has undergone artificial warming from cooling water release from a nuclear power plant for ~50 years. This heated the water in a similar degree to IPCC SSP5-8.5 predictions by 2100 as natural systems to study temperature-related climate change effects. Bottom water and surface sediment bacterial communities and their biogeochemical processes were investigated to test how future coastal water warming alters microbial communities; shifts seasonal patterns, such as increased algae blooming; and influences nutrient and energy cycling, including elevated respiration rates. 16S rRNA gene amplicon sequencing and geochemical parameters demonstrated that heated bay bottom water bacterial communities were influenced by increased average temperatures across changing seasons, resulting in an overall Shannon's H diversity loss and shifts in relative abundances. In contrast, Shannon's diversity increased in the heated surface sediments. The results also suggested a trend toward smaller-sized microorganisms within the heated bay bottom waters, with a 30% increased relative abundance of small size picocyanobacteria in the summer (June). Furthermore, bacterial communities in the heated bay surface sediment displayed little seasonal variability but did show potential changes of long-term increased average temperature in the interplay with related effects on bottom waters. Finally, heated bay metabolic gene predictions from the 16S rRNA gene sequences suggested raised anaerobic processes closer to the sediment-water interface. In conclusion, climate change will likely alter microbial seasonality and diversity, leading to prolonged and increased algae blooming and elevated respiration rates within coastal waters.

Climate Change is caused by the accelerated increase of anthropogenic greenhousegas emissions to the atmosphere and affects all ecosystems on our planet. A resultof higher CO2 uptake by the oceans as well as an increase of heat trapped in theatmosphere leads to, for example acidification, stratification, sea-level rise, oxygenloss, and temperature increase of the earth’s waterbodies. The IntergovernmentalPanel on Climate Change (IPCC) predicts the earth’s surface temperature to risebetween 1.0-5.7°C by the year 2100 and ocean temperatures are predicted to rise byup to 2.0°C.This thesis focuses on the effects of environmental changes on microbes and theirfunctions in coastal Baltic Sea sediments and overlying bottom-waters. The studiesexamine potential effects of ongoing climate change in combination with coastaleutrophication, as well as long-term warming due to e.g. climate change within anatural fluctuating system and a laboratory based incubation experiment.Investigation of coastal sediment and overlying bottom-waters showed thatpotential future changes on bacterial communities due to eutrophication incombination with climate change relies on the water depth and oxygen supply. Inaddition, the study of a natural seasonal fluctuating and long-term artificially heatedcoastal bay (compared to an unaffected control bay) gave insights into how theecosystem might react to future climate change. On one hand, bottom waters in theheated bay showed decreased bacterial diversity, suspended seasonal patterns pluselevated and prolonged cyanobacterial blooming. On the other hand, surfacesediment communities in the heated bay had an altered microbial community withdecreased seasonal variation and higher diversity likely due to a shallowing ofgeochemical layers. Furthermore, increased energy production occurred althoughhigher stress RNA transcripts suggested that the microbial community’stemperature optima were below that of the water. Nevertheless, incubationexperiments showed that exposure to short-term elevated temperatures shifted thecontrol bay microbial community closer to that of the heated bay with a similarresponse on RNA level at higher temperatures (28 °C).In summary, this thesis provides new insights into ongoing and likely future climatechange effects on coastal microbial communities, which are key players for nutrientandenergy cycling of the marine ecosystem.

De klimatförändringar som nu observeras orsakas av ökade utsläpp av växthusgaseroch förändringarna påverkar alla ekosystem på jorden. Uppvärmningen avatmosfären och upptaget av koldioxid i havet leder bland annat till havsförsurning,skiktning av vattenmassorna, ökad havsnivå, minskad syretillgång och ökadtemperatur i jordens vattensystem. Enligt IPCC:s (Intergovernmental Panel onClimate Change) prediktioner kommer luft- och vattentemperaturer att öka med1.0-5.7°C respektive 2.0°C till år 2100.Den här avhandlingen fokuserar på hur mikroorganismers diversitet och funktionpåverkas av klimatförändringar i kustnära sediment och bottenvatten i Östersjön. Ivissa av studierna undersöktes potentiella kombinationseffekter avklimatförändringar och eutrofiering. Medan andra studier fokuserade påklimateffekter i ett naturligt fluktuerande system som utsatts för långvariguppvärmning samt i laboratorieexperiment där mikroorganismerna utsattes för enmer tillfällig uppvärmning.Vid påverkan av eutrofiering och klimatförändringar visade undersökningarna isedimentet och i bottenvattnet att förändringar bland mikroorganismer vid dessaförhållanden regleras av vattendjup och syrgastillgång. Vidare gav studierna av enartificiellt långtidsuppvärmd men säsongsmässigt fluktuerande vik kunskap om hurekosystemet kommer påverkas av framtidens klimatförändringar (jämfört med enopåverkad referensvik). I bottenvattnet var diversiteten bland mikroorganismerlägre i den uppvärmda viken jämfört med i kontrollviken. Det var även mindresäsongsvariation och en ökad samt förlängd cyanobakterieblomning.Mikroorganismerna i sedimentet, å andra sidan, hade en förändradartsammansättning och minskad säsongsmässig variation samt en högre diversitetjämfört med mikroorganismerna i kontrollviken. Detta orsakas troligen av enförtätning av de geokemiska lagren i sedimentet. Vidare tyder resultaten på högreenergiproduktion i den uppvärmda viken och vissa RNA-transkript indikerar stressoch tillväxt i suboptimal temperatur bland mikroorganismerna i den uppvärmdaviken. Slutligen visade inkubationsexperimentet att det mikrobiella samhället frånkontrollviken förändrades till att mer likna samhället i den uppvärmda viken när deutsattes för uppvärmning med liknande RNA-signaler vid höga temperaturer.Mikroorganismer har en nyckelroll vad gäller närsalts- och energiflöden i det marinaekosystemet. Totalt sett illustrerar denna avhandling hur pågående och kommandeklimatförändringar påverkar kustnära mikrobiella samhällen och processer knutnatill dessa.

Der Klimawandel beeinflusst alle Ökosysteme unseres Planeten und wird durch den Anstiegder Konzentrationen an Treibhausgasen in der Atmosphäre verursacht und verstärkt. Diesresultiert zum Beispiel in der Versauerung des Wassers, Veränderung des Salzgehaltes,Stratifizierung des Wassers, Anstieg des Meeresspiegels, sowie Minderung desSauerstoffgehalts im Wasser. Das internationale Klimawandel Gremium (IPCC) berichtet,dass die Erdoberflächentemperatur bis zum Jahre 2100 zwischen 1.0-5.7 °C steigen wird,sowie ein Meerestemperatur Anstieg von bis zu 2 °C zu erwarten ist.In dieser Doktorarbeit wird der Effekt von Umweltveränderungen auf Mikroorganismen undderen Funktion in Küstensedimenten und den darüber liegenden Wasserschichten derOstsee untersucht. Die potentiellen Effekte von bereits auftretendem Klimawandel inKombination mit Eutrophierung, sowie der Effekt von Langzeiterwärmung in einem sichnatürlich saisonal wandelndem System und einem laborbasierten Inkubationsexperimentwerden analysiert.Im ersten Projekt wurden Sedimente untersucht, die zeigten, dass Veränderungen in dermikrobiellen Zusammensetzung in Kombination mit Eutrophierung und potentiellemKlimawandel abhängig von der Wassertiefe und dem Sauerstoffgehalt sind. Zusätzlichwurden Proben in einer künstlich erwärmten Bucht an der Küste der Ostsee genommen undmit einer Kontrollbucht verglichen, um Einsicht zu erlangen wie Küstenökosysteme auf denKlimawandel in Zukunft reagieren könnten. Einerseits haben die Untersuchungen dermikrobiellen Zusammensetzung des Wassers gezeigt, dass mit steigender Temperatur dieDiversität sinkt, die saisonale Zusammensetzung der Bakterien verschoben wird und eineverstärkte und länger anhaltende Cyanobakterienblüte auftritt. Andererseits konntenUntersuchungen des Oberflächensediments zeigen, dass die Diversität, sehr wahrscheinlichdurch eine Komprimierung der geochemischen Schichten, zunimmt. Des Weiteren war dieExpression von Genen des Energiemetabolismus erhöht, aber auch die der Gene, welche miterhöhtem Stress assoziiert sind. Das könnte darauf hindeuten, dass das Temperaturoptimumder Mikroorganismus unterhalb der Wassertemperatur lag. Die Inkubationsstudie konntezeigen, dass sogar kurze Temperaturanstiege in den Proben der Kontrollbucht zu einemWechsel in der mikrobiellen Zusammensetzung und der Exprimierung der Gene (mRNA)führten, sodass diese bei hohen Temperaturen (28 °C), die der künstlich erhitzten Buchtglichen.Zusammenfassend konnte diese Doktorarbeit einen Einblick geben, wie Mikroorganismenin Küstengewässern, die eine zentrale Rolle im Nährstoff- und Energiezyklus des marinenÖkosystems spielen, auf den Effekt des Klimawandels potentiell reagieren könnten.

Increased ocean temperature associated with climate change is especially intensified in coastal areas and its influence on microbialcommunities and biogeochemical cycling is poorly understood. In this study, we sampled a Baltic Sea bay that has undergone 50years of warmer temperatures similar to RCP5-8.5 predictions due to cooling water release from a nuclear power plant. The systemdemonstrated reduced oxygen concentrations, decreased anaerobic electron acceptors, and higher rates of sulfate reduction.Chemical analyses, 16S rRNA gene amplicons, and RNA transcripts all supported sediment anaerobic reactions occurring closer tothe sediment-water interface. This resulted in higher microbial diversities and raised sulfate reduction and methanogenesistranscripts, also supporting increased production of toxic sulfide and the greenhouse gas methane closer to the sediment surface,with possible release to oxygen deficient waters. RNA transcripts supported prolonged periods of cyanobacterial bloom that mayresult in increased climate change related coastal anoxia. Finally, while metatranscriptomics suggested increased energyproduction in the heated bay, a large number of stress transcripts indicated the communities had not adapted to the increasedtemperature and had weakened resilience. The results point to a potential feedback loop, whereby increased temperatures mayamplify negative effects at the base of coastal biochemical cycling.

Coastal aquatic systems suffer from nutrient enrichment, which results in accelerated eutrophication effects due to increased microbial metabolic rates. Climate change related prolonged warming will likely accelerate existing eutrophication effects, including low oxygen concentrations. However, how the interplay between these environmental changes will alter coastal ecosystems is poorly understood. In this study, we compared 16S rRNA gene amplicon based bacterial communities in coastal sediments of a Baltic Sea basin in November 2013 and 2017 at three sites along a water depth gradient with varying bottom water oxygen histories. The shallow site showed changes of only 1.1% in relative abundance of bacterial populations in 2017 compared to 2013, while the deep oxygen-deficient site showed up to 11% changes in relative abundance including an increase of sulfate-reducing bacteria along with a 36% increase in organic matter content. The data suggested that bacterial communities in shallow sediments were more resilient to seasonal oxygen decline, while bacterial communities in sediments subjected to long-term hypoxia seemed to be sensitive to oxygen changes and were likely to be under hypoxic/anoxic conditions in the future. Our data demonstrate that future climate changes will likely fuel eutrophication related spread of low oxygen zones.

Vanadium - a transition metal - is found in the ferrous-ferric mineral, magnetite. Vanadium has many industrial applications, such as in the production of high-strength low-alloy steels, and its increasing global industrial consumption requires new primary sources. Bioleaching is a biotechnological process for microbially catalyzed dissolution of minerals and wastes for metal recovery such as biogenic organic acid dissolution of bauxite residues. In this study, 16S rRNA gene amplicon sequencing was used to identify microorganisms in Nordic mining environments influenced by vanadium containing sources. These data identified gene sequences that aligned to the Gluconobacter genus that produce gluconic acid. Several strategies for magnetite dissolution were tested including oxidative and reductive bioleaching by acidophilic microbes along with dissimilatory reduction by Shewanella spp. that did not yield significant metal release. In addition, abiotic dissolution of the magnetite was tested with gluconic and oxalic acids, and yielded 3.99 and 81.31% iron release as a proxy for vanadium release, respectively. As a proof of principle, leaching via gluconic acid production by Gluconobacter oxydans resulted in a maximum yield of 9.8% of the available iron and 3.3% of the vanadium. Addition of an increased concentration of glucose as electron donor for gluconic acid production alone, or in combination with calcium carbonate to buffer the pH, increased the rate of iron dissolution and final vanadium recoveries. These data suggest a strategy of biogenic organic acid mediated vanadium recovery from magnetite and point the way to testing additional microbial species to optimize the recovery.

Several industrial processes produce toxic sulfide containing streams that are often scrubbed using caustic solutions. An alternative, cost effective sulfidetreatment method is bioelectrochemical sulfide removal. For the first time, a haloalkaliphilic sulfide-oxidizing microbial consortium was introduced to the anodic chamber of a microbial electrolysis cell operated at alkaline pH and with 1.0 M sodium ions. Under anode potential control, the highest sulfideremoval rate was 2.16 mM/day and chemical analysis supported that the electrical current generation was from the sulfide oxidation. Biotic operation produced a maximum current density of 3625 mA/m(2) compared to 210 mA/m2 while under abiotic operation. Furthermore, biotic electrical production was maintained for a longer period than for abiotic operation, potentially due to the passivation of the electrode by elemental sulfur during abiotic operation. The use of microorganisms reduced the energy input in this study compared to published electrochemical sulfide removal technologies. Sulfide-oxidizing populations dominated both the planktonic and electrode-attached communities with 16S rRNA gene sequences aligning within the genera Thioctikalivibrio, Thioalkaihnicrobium, and Desulfurivibrio. The dominance of the Desulfurivibrio-like population on the anode surface offered evidence for the first haloalkaliphilic bacterium able to couple electrons from sulfide oxidation to extracellular electron transfer to the anode.