| 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. |
- Bonaglia, Stefano, et al.
(författare)
-
Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments
- 2020
-
Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 248
-
Tidskriftsartikel (refereegranskat)abstract
- Biodegradation by microorganisms is a useful tool that helps alleviating hydrocarbon pollution in nature. Microbes are more efficient in degradation under aerobic than anaerobic conditions, but the majority of sediment by volume is generally anoxic. Incubation experiments were conducted to study the biodegradation potential of naphthalene-a common polycyclic aromatic hydrocarbon (PAH)-and the diversity of microbial communities in presence/absence of activated carbon (AC) under aerobic/anaerobic conditions. Radio-respirometry experiments with endogenous microorganisms indicated that degradation of naphthalene was strongly stimulated (96%) by the AC addition under anaerobic conditions. In aerobic conditions, however, AC had no effects on naphthalene biodegradation. Bioaugmentation tests with cultured microbial populations grown on naphthalene showed that AC further stimulated (92%) naphthalene degradation in anoxia. Analysis of the 16S rRNA gene sequences implied that sediment amendment with AC increased microbial community diversity and changed community structure. Moreover, the relative abundance of Geobacter, Thiobacillus, Sulfuricurvum, and methanogenic archaea increased sharply after amendment with AC under anaerobic conditions. These results may be explained by the fact that AC particles promoted direct interspecies electron transfer (DIET) between microorganisms involved in PAH degradation pathways. We suggest that important ecosystem functions mediated by microbes-such as hydrocarbon degradation-can be induced and that AC enrichment strategies can be exploited for facilitating bioremediation of anoxic oil-contaminated sediments and soils.
|
|
| 3. |
- Broman, Elias, et al.
(författare)
-
Active DNRA and denitrification in oxic hypereutrophic waters
- 2021
-
Ingår i: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 194
-
Tidskriftsartikel (refereegranskat)abstract
- Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen mi- croniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15 N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated ( > 224 μM O 2 ). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sedi- ment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA accord- ing to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides ) and Proteobac- teria (genus Wolinella ), while denitrification was mainly associated with proteobacterial genera Pseu- domonas, Achromobacter , and Brucella . The metagenomic and microscopy data suggest that these anaero- bic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix . By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.
|
|
| 4. |
- 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.
|
|
| 5. |
- 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.
|
|
| 6. |
- Broman, Elias, et al.
(författare)
-
Denitrification responses to increasing cadmium exposure in Baltic Sea sediments
- 2019
-
Ingår i: Aquatic Toxicology. - : Elsevier. - 0166-445X .- 1879-1514. ; 217
-
Tidskriftsartikel (refereegranskat)abstract
- Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline and industrial metal contamination. One of the most toxic metals is Cadmium (Cd), which is lethal to many aquatic organisms already at low concentrations. Denitrification by facultative anaerobic microorganisms is an essential process to transform, but also to remove, excess nitrate in eutrophied systems. Cd has been shown to decrease denitrification and sequester free sulfide, which is available when oxygen is scarce and generally inhibits complete denitrification (i.e. N2O to N2). In polluted sediments, an interaction between oxygen and Cd may influence denitrification and this relationship has not been studied. For example, in the Baltic Sea some sediments are double exposed to both Cd and hypoxia. In this study, we examined how the double exposure of Cd and fluctuations in oxygen affects denitrification in Baltic Sea sediment. Results show that oxygen largely regulated N2O and N2 production after 21 days of exposure to Cd (ranging from 0 to 500 μg/L, 5 different treatments, measured by the isotope pairing technique (IPT)). In the high Cd treatment (500 μg/L) the variation in N2 production increased compared to the other treatments. Increases in N2 production are suggested to be an effect of 1) enhanced nitrification that increases NO3 − availability thus stimulating denitrification, and 2) Cd successfully sequestrating sulfide (yielding CdS), which allows for full denitrification to N2. The in situ field sediment contained initially high Cd concentrations in the pore water (∼10 μg/L) and microbial communities might already have been adapted to metal stress, making the effect of low Cd levels negligible. Here we show that high levels of cadmium pollution might increase N2 production and influence nitrogen cycling in marine sediments. © 2019 The Authors
|
|
| 7. |
- 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.
|
|
| 8. |
- 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.
|
|
| 9. |
- 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.
|
|
| 10. |
- 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’.
|
|
