SwePub - sökning: WFRF:(Broman Elias 1985 )

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1.	Berggren, Hanna, et al. (författare) Fish skin microbiomes are highly variable among individuals and populations but not within individuals 2022 Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12 Tidskriftsartikel (refereegranskat)abstract Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.
2.	Broman, Elias, 1985-, et al. (författare) Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments 2024 Ingår i: The ISME journal. - 1751-7370 .- 1751-7362. ; 18:1 Tidskriftsartikel (refereegranskat)abstract Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial-temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment-water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH4. We show that macrofauna increases CH4 fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH4 flux reduces CH4 pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH4 emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.
3.	Broman, Elias, 1985-, et al. (författare) Cyanophage Diversity and Community Structure in Dead Zone Sediments 2021 Ingår i: mSphere. - : American Society for Microbiology. - 2379-5042. ; 6:2 Tidskriftsartikel (refereegranskat)abstract Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N-2 fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient-representing oxic, hypoxic, and anoxic conditions-in one of the world's largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium. RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N-2 fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments. IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.
4.	Broman, Elias, 1985-, et al. (författare) Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments 2017 Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society Publishing. - 0962-8452 .- 1471-2954. ; 284:1864 Tidskriftsartikel (refereegranskat)abstract An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.
5.	Broman, Elias, 1985-, et al. (författare) Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter 2019 Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 10, s. 1-15 Tidskriftsartikel (refereegranskat)abstract Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.
6.	Broman, Elias, 1985- (författare) Ecology and evolution of coastal Baltic Sea 'dead zone' sediments 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Since industrialization and the release of agricultural fertilizers began, coastal and open waters of the Baltic Sea have been loaded with nutrients. This has increased the growth of algal blooms and because a portion of the algal organic matter sinks to the sea floor, hypoxia has increased. In conjunction to this, natural stratification of the water column makes the bottom zones especially prone to oxygen depletion due to microbes using oxygen and organic matter to grow. Hypoxia (<2 mg/L O2) and anoxia (no oxygen) are deadly for many organisms and only specialists (typically some microorganisms) are able to survive. Due to the harsh conditions these bottom zones are commonly referred to as 'dead zones'. The focus of this thesis was to look closer at the microbial community changes upon degradation of algal organic matter and the effect of oxygenating coastal Baltic Sea 'dead zone' sediments on chemistry fluxes, phyto- and zooplankton, the microbial community structure, and microbial metabolic responses. Results from field sampling and incubation experiments showed that degradation of algal biomass in nutrient rich oxic sediment was partly related to the growth of archaea; that oxygenation of anoxic sediments decreased stored organic matter plus triggered hatching of zooplankton eggs increasing the benthic-pelagic coupling; and resting diatoms buried in hypoxic/anoxic sediment were alive and triggered to germinate by light rather than oxygen. Changes in the microbial community structures to oxygen shifts were dependent on the historical exposure to oxygen and that microbial generalists adapted to episodic oxygenation were favored during oxygen shifts. Facultative anaerobic sulfur/sulfide oxidizing bacterial genera were favored upon oxygenation of hypoxic/anoxic sediment plus sulfur cycling and nitrogen fixation genes were abundant. Finally, it was discovered that oxygenation regulates metabolic processes involved in the sulfur and methane cycles, especially by metabolic processes that results in a decrease of toxic hydrogen sulfide as well as the potent greenhouse gas methane. This thesis has explored how 'dead zones' change and develop during oxygen shifts and that re-oxygenation of ‘dead zones’ could bring favorable conditions in the sediment surface for reestablishment of new micro- and macroorganism communities.
7.	Broman, Elias, 1985-, et al. (författare) Eutrophication induced early stage hypoxic ‘dead zone’ sediment releases nitrate and stimulates growth of archaea Annan publikation (övrigt vetenskapligt/konstnärligt)abstract In the Baltic Sea, two annual algal blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water column, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen, referred to as ‘dead zones’). These zones prevent the establishment of benthic communities and result in fish mortality. The aim of the study was to determine how the sediment chemistry and microbial community composition changed due to phytoplankton biomass degradation by adding cyanobacterial or diatom biomass to sediment cores from an all-year round oxic coastal Baltic Sea bay. After biomass addition, some typical anaerobic microbial processes were observed such as a decrease in NO2-+NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2-+NO3- was observed in the water phase in all incubations (including controls without addition of phytoplankton biomass). The combination of NO2-+NO3- diffusion from the sediment plus nitrification of the available NH4+ could not account for this increase. Potential nitrogen sources that could at least partially explain this discrepancy included microbial nitrogen fixation and cycling of nitrogen compounds from deeper layers of the sediment. Based on 16S rRNA gene sequences, the addition of diatom biomass caused minor changes in the relative abundance of microbial community members while cyanobacterial biomass caused a large increase in ferrous iron-oxidizing archaea. Considering that OTUs sharing lineages with acidophilic microorganisms were present, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling in oxic sediments and early microbial community changes in the sediment surface due to sinking phytoplankton before major hypoxia events occur. The release of nitrate into the water could potentially enhance algal blooms and facilitate the development of ‘dead zones’.
8.	Broman, Elias, 1985-, et al. (författare) Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities 2023 Ingår i: Microbial Ecology. - : Elsevier. - 0095-3628 .- 1432-184X. ; 86, s. 2357-2372 Tidskriftsartikel (refereegranskat)abstract Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.
9.	Broman, Elias, 1985-, et al. (författare) Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor 2017 Ingår i: Biodegradation. - : Springer. - 0923-9820 .- 1572-9729. ; 28:4, s. 287-301 Tidskriftsartikel (refereegranskat)abstract Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH < 3) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8 °C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.
10.	Broman, Elias, 1985-, et al. (författare) No evidence of light inhibition on aerobic methanotrophs in coastal sediments using eDNA and eRNA 2023 Ingår i: Environmental DNA. - 2637-4943. ; 5:4, s. 766-781 Tidskriftsartikel (refereegranskat)abstract It is estimated that up to half of global methane (CH4) emissions are derived from microbial processes in aquatic ecosystems. However, it is not fully understood which factors explain the spatial and temporal variability of these emissions. For example, light has previously been shown to both inhibit and stimulate aerobic methane-oxidizing bacteria (i.e., methanotrophs) in the water column. These contrasting results indicate that the mechanisms that light has on CH4 oxidation are not yet clearly known, even less so for benthic aerobic methanotrophs. Here, we tested whether light reaching the seafloor can inhibit methanotrophic activity on the sediment surface. We sampled and distributed over 40 intact sediment cores from two coastal sites (illuminated 10 m, and a dark site at 33 m water depth) into 0, 50, and 100 PAR light treatments. After 10 days, we found no difference between treatments for each site in pore-water CH4 concentrations, relative abundance of aerobic methanotrophs, or the number of RNA transcripts related to methane oxidation. Our results suggest that light attenuation in coastal waters does not significantly affect aerobic methanotrophs in coastal sediments.
11.	Broman, Elias, 1985-, et al. (författare) Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism 2017 Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8 Tidskriftsartikel (refereegranskat)abstract The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.
12.	Broman, Elias, 1985-, et al. (författare) Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. 2017 Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5:1, s. 96- Tidskriftsartikel (refereegranskat)abstract BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.RESULTS: Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.CONCLUSIONS: These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.
13.	Broman, Elias, 1985-, et al. (författare) Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure 2019 Ingår i: Microbial Ecology. - : Springer. - 0095-3628 .- 1432-184X. ; 77:2, s. 288-303 Tidskriftsartikel (refereegranskat)abstract Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2− + NO3− in the sediment surface (0–1 cm) and iron in the underlying layer (1–2 cm). In addition, an increase in NO2− + NO3− was observed in the overlying benthic water in all amended and control incubations. The combination of NO2− + NO3− diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.
14.	Garrison, Julie A., 1993-, et al. (författare) Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica 2022 Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 17:11 Tidskriftsartikel (refereegranskat)abstract Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.
15.	Lopez-Fernandez, Margarita, et al. (författare) Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling 2018 Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 94:8 Tidskriftsartikel (refereegranskat)abstract The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligo trophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modem marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligo trophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoauto trophic deep biosphere.
16.	Lopez-Fernandez, Margarita, et al. (författare) Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters 2019 Ingår i: mBio. - : American Society of Microbiology. - 2161-2129 .- 2150-7511. ; 10:4, s. 1-6 Tidskriftsartikel (refereegranskat)abstract Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H-2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases." IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omits studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.
17.	Lopez-Fernandez, Margarita, et al. (författare) Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield 2023 Ingår i: npj Biofilms and Microbiomes. - : Nature Publishing Group. - 2055-5008. ; 9:1 Tidskriftsartikel (refereegranskat)abstract Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the aspo Hard Rock Laboratory, Sweden. Metatranscriptomes showed Thiobacillus, Sideroxydans, and Desulforegula to be abundant and together accounted for 31% of the transcripts in the biofilm communities. Differential expression analysis highlighted Thiobacillus to have a principal role in biofilm formation in these oligotrophic groundwaters by being involved in relevant processes such as the formation of extracellular matrix, quorum sensing, and cell motility. The findings revealed an active biofilm community with sulfur cycling as a prominent mode of energy conservation in the deep biosphere.
18.	Maciute, Adele, et al. (författare) Reconciling the importance of meiofauna respiration for oxygen demand in muddy coastal sediments 2023 Ingår i: Limnology and Oceanography. - 0024-3590 .- 1939-5590. ; 68:8, s. 1895-1905 Tidskriftsartikel (refereegranskat)
19.	Ni, Gaofeng, et al. (författare) A novel inorganic sulfur compound metabolizing Ferroplasma-like population is suggested to mediate extracellular electron transfer 2018 Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. Tidskriftsartikel (refereegranskat)abstract Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbemineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-likepopulation had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylylsulfate released electrons and the extracellular electrontransfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganicsulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.
20.	Ni, Gaofeng, et al. (författare) Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells 2018 Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9 Tidskriftsartikel (refereegranskat)abstract Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the 'cyanate' degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.
21.	Roman, Pawel, et al. (författare) Selection and Application of Sulfide Oxidizing Microorganisms Able to Withstand Thiols in Gas Biodesulfurization Systems 2016 Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 50:23, s. 12808-12815 Tidskriftsartikel (refereegranskat)abstract After the first commercial applications of a new biological process for the removal of hydrogen sulfide (H2S) from low pressure biogas, the need arose to broaden the operating window to also enable the removal of organosulfur compounds from high pressure sour gases. In this study we have selected microorganisms from a full-scale biodesulfurization system that are capable of withstanding the presence of thiols. This full-scale unit has been in stable operation for more than 10 years. We investigated the microbial community by using high-throughput sequencing of 16S rRNA gene amplicons which showed that methanethiol gave a competitive advantage to bacteria belonging to the genera Thioalkalibacter (Halothiobacillaceae family) and Alkalilimnicola (Ectothiorhosdospiraceae family). The sulfide-oxidizing potential of the acclimatized population was investigated under elevated thiol loading rates (4.5–9.1 mM d–1), consisting of a mix of methanethiol, ethanethiol, and propanethiol. With this biomass, it was possible to achieve a stable bioreactor operation at which 80% of the supplied H2S (61 mM d–1) was biologically oxidized to elemental sulfur. The remainder was chemically produced thiosulfate. Moreover, we found that a conventionally applied method for controlling the oxygen supply to the bioreactor, that is, by maintaining a redox potential set-point value, appeared to be ineffective in the presence of thiols.
22.	Roth, Florian, et al. (författare) Methane emissions offset atmospheric carbon dioxide uptake in coastal macroalgae, mixed vegetation and sediment ecosystems 2023 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 14 Tidskriftsartikel (refereegranskat)abstract Coastal ecosystems can efficiently remove carbon dioxide (CO2) from the atmosphere and are thus promoted for nature-based climate change mitigation. Natural methane (CH4) emissions from these ecosystems may counterbalance atmospheric CO2 uptake. Still, knowledge of mechanisms sustaining suchCH4 emissions and their contribution to net radiative forcing remains scarce for globally prevalent macroalgae, mixed vegetation, and surrounding depositional sediment habitats. Here we show that these habitats emit CH4 in the range of 0.1 – 2.9 mg CH4 m−2 d−1 to the atmosphere, revealing in situ CH4 emissions from macroalgae that weresustained by divergent methanogenic archaea in anoxic microsites. Over an annual cycle, CO2-equivalent CH4 emissions offset 28 and 35% of the carbon sink capacity attributed to atmospheric CO2 uptake in the macroalgae and mixed vegetation habitats, respectively, and augment net CO2 release of unvegetated sediments by 57%. Accounting for CH4 alongside CO2 sea-air fluxes and identifying the mechanisms controlling these emissions is crucial to constrain the potential of coastal ecosystems as net atmospheric carbon sinks and develop informed climate mitigation strategies.
23.	Rydin, Emil, et al. (författare) Contrasting distribution and speciation of sedimentary organic phosphorus among different basins of the Baltic Sea 2023 Ingår i: Limnology and Oceanography. - : John Wiley & Sons. - 0024-3590 .- 1939-5590. ; 68:4, s. 767-779 Tidskriftsartikel (refereegranskat)abstract Recycling of phosphorus (P) from deoxygenated sediments perpetuates eutrophic conditions in parts of the Baltic Sea. Sedimentary organic P is a major source of dissolved P to the water column, but also a sink for permanent P burial. The mechanisms behind these two pathways are, however, largely unknown. Using new methods, we determined P in DNA and phospholipids, which are both found in all organisms. We also identified inositol phosphates that are particularly important in eukaryotes. Sediment cores were collected from contrasting basins in the Baltic Sea to study their relative contribution to the total P pool. We found high DNA-P/phospholipid-P ratios in surface sediments from the Bothnian Bay and Bothnian Sea. However, these ratios were low throughout profiles in euxinic Baltic Proper sediments. The elevated ratios present in sediments overlain by oxic bottom waters might indicate the presence of a microbial community stimulated by bioturbation, whereas the low DNA-P/phospholipid-P ratios in Baltic Proper sediments likely indicate an energy-limited microbial community, typical to the "deep biosphere" environment. Inositol-P was almost absent in euxinic Baltic Proper sediments that had a low total P amount compared to those in the other basins. We suggest that variability in the composition of sedimentary microbial communities among the Baltic Sea basins might cause differences in organic P forms that in turn affects its turnover.
24.	Seidel, Laura, 1989-, et al. (författare) Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities 2023 Ingår i: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 17, s. 855-869 Tidskriftsartikel (refereegranskat)abstract 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.
25.	Seidel, Laura, et al. (författare) Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history 2021 Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1 Tidskriftsartikel (refereegranskat)abstract 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.

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