scholarly journals Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea

2017 ◽  
Author(s):  
Petter Thureborn ◽  
Yue O.O. Hu ◽  
Andrea Franzetti ◽  
Sara Sjöling ◽  
Daniel Lundin
Keyword(s):  
Protein Synthesis ◽  
Microbial Community ◽  
Baltic Sea ◽  
High Protein ◽  
Community Members ◽  
The Baltic Sea ◽  
Anoxic Sediment ◽  
Metabolic Potential ◽  
Deep Sediment ◽  
The Baltic

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms in the Landsort Deep sediment. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.

scholarly journals Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea

2017 ◽  
Author(s):  
Petter Thureborn ◽  
Yue O.O. Hu ◽  
Andrea Franzetti ◽  
Sara Sjöling ◽  
Daniel Lundin
Keyword(s):  
Protein Synthesis ◽  
Microbial Community ◽  
Baltic Sea ◽  
High Protein ◽  
Community Members ◽  
The Baltic Sea ◽  
Anoxic Sediment ◽  
Metabolic Potential ◽  
Deep Sediment ◽  
The Baltic

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms in the Landsort Deep sediment. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.

scholarly journals Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea

2016 ◽  
Author(s):  
Petter Thureborn ◽  
Yue O.O. Hu ◽  
Andrea Franzetti ◽  
Sara Sjöling ◽  
Daniel Lundin
Keyword(s):  
Protein Synthesis ◽  
Microbial Community ◽  
Baltic Sea ◽  
Active Role ◽  
High Protein ◽  
Community Members ◽  
The Baltic Sea ◽  
Anoxic Sediment ◽  
Metabolic Potential ◽  
The Baltic

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.

scholarly journals Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1593 ◽  
Author(s):  
Petter Thureborn ◽  
Andrea Franzetti ◽  
Daniel Lundin ◽  
Sara Sjöling
Keyword(s):  
Microbial Community ◽  
Baltic Sea ◽  
Oxygen Depletion ◽  
Ecosystem Functions ◽  
The Baltic Sea ◽  
Anoxic Sediment ◽  
Expression Of Genes ◽  
The Baltic ◽  
Deep Sediments ◽  
Insight Into

Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning.

scholarly journals Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics

2018 ◽  
Vol 5 ◽  
Author(s):  
Carlo Berg ◽  
Chris L. Dupont ◽  
Johannes Asplund-Samuelsson ◽  
Narin A. Celepli ◽  
Alexander Eiler ◽  
...  
Keyword(s):  
Microbial Community ◽  
Baltic Sea ◽  
Cyanobacterial Bloom ◽  
The Baltic Sea ◽  
The Baltic

scholarly journals Shifts in the microbial community in the Baltic Sea with increasing CO<sub>2</sub>

2016 ◽  
Author(s):  
K .J. Crawfurd ◽  
C .P. D. Brussaard ◽  
U. Riebesell
Keyword(s):  
Carbon Dioxide ◽  
Microbial Community ◽  
Ocean Acidification ◽  
Baltic Sea ◽  
Community Dynamics ◽  
The Other ◽  
The Baltic Sea ◽  
Viral Lysis ◽  
Large Shift ◽  
The Baltic

Abstract. Ocean acidification, due to dissolution of anthropogenically produced carbon dioxide is considered a major threat to marine ecosystems. The Baltic Sea, with extremely low salinity and thus low pH buffering capacity, is likely to experience stronger variation in pH than the open ocean with increasing atmospheric carbon dioxide. We examined the effects of ocean acidification on the microbial community during summer using large volume in situ mesocosms to simulate present to future and far future scenarios. We saw distinct trends with increasing CO2 in each of the 6 groups of phytoplankton with diameters below 20 μm that we enumerated by flow cytometry. Of these groups two picoeukaryotic groups increased in abundance whilst the other groups, including prokaryotic Synechococcus spp., decreased with increasing CO2. Gross growth rates increased with increasing CO2 in the dominant picoeukaryote group sufficient to double their abundances whilst reduced grazing allowed the other picoeukaryotes to flourish at higher CO2. Significant increases in lysis rates were seen at higher CO2 in these two picoeukaryote groups. Converting abundances to particulate organic carbon we saw a large shift in the partitioning of carbon between the size fractions which lasted throughout the experiment. The heterotrophic prokaryotes largely followed the algal biomass with responses to increasing CO2 reflecting the altered phytoplankton community dynamics. Similarly, higher viral abundances at higher CO2 seemed related to increased prokaryote biomass. Viral lysis and grazing were equally important controlling prokaryotic abundances. Overall our results point to a shift towards a more regenerative system with potentially increased productivity but reduced carbon export.

scholarly journals Metagenome-assembled genomes uncover a global brackish microbiome

2015 ◽  
Author(s):  
Luisa W Hugerth ◽  
John Larsson ◽  
Johannes Alneberg ◽  
Markus V Lindh ◽  
Catherine Legrand ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Evolutionary History ◽  
Seasonal Succession ◽  
Integrated Analysis ◽  
The Baltic Sea ◽  
Metabolic Potential ◽  
Bacterial Populations ◽  
History Of ◽  
The Baltic ◽  
Genome Context

Microbes are main drivers of biogeochemical cycles in oceans and lakes. Yet an understanding of the regulation of such processes is hampered by limited genome-context insight into the metabolic potential of bacterial populations. Here we explored an automatic binning approach to reconstruct representative bacterioplankton genomes from metagenomic samples across a time-series in the Baltic Sea. The 30 unique genomes assembled represent novel species within typical marine and freshwater clades. Analysis of the first genomes for abundant lineages entirely lacking reference genomes, such as OM182, acIV and LD19, uncovered divergent ecological adaptations. While phylogenetic patterns in the seasonal succession of the investigated genomes were evident, closely related genomes sometimes displayed distinct seasonal patterns, that could to some extent be explained by gene content. Signs of streamlining were evident in most genomes; and genome sizes correlated with abundance variation across filter size fractions. Comparisons of 86 aquatic metagenomes against the assembled genomes revealed significant fragment recruitment from brackish waters in North America, but little from lakes or oceans, suggesting the existence of a global brackish microbiome. Current estimates of evolutionary rates imply brackish bacteria diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 ya), markedly contrasting the evolutionary history of Baltic Sea macro-organisms, which are locally adapted populations of nearby meta-populations. We have thus demonstrated how metagenome-assembled genomes enable an integrated analysis of ecological patterns, functional potential and evolutionary history of several relevant genomes at a time in natural communities.

scholarly journals Evaluation of Community Involvement in Participatory Process – Lessons Learned in the Baltic Sea Region

2020 ◽  
Vol 16 (1) ◽  
pp. 56-65
Author(s):  
Sanda Geipele ◽  
Antra Kundzina ◽  
Edgars Pudzis ◽  
Andrejs Lazdins
Keyword(s):  
Baltic Sea ◽  
Community Involvement ◽  
Local Governance ◽  
Community Planning ◽  
Lessons Learned ◽  
Participatory Process ◽  
Community Members ◽  
The Baltic Sea ◽  
Baltic Sea Region ◽  
The Baltic

Abstract For exploring and discovering the main knowledge, experience and practices, four main issues were analyzed: what were the goals of the involved participants regarding the community involvement in the spatial and community planning; what methods were used to extend the involvement of community members; what problems and obstacles did the project participants face, and what were the main lessons learned. This study provides reflections (analysis, comparison and evaluation) on community involvement in participatory process in coastal areas of the Baltic Sea Region by investigating the methods, which were used in community involvement in project participating countries; and its influence in improving local governance of the local territory development.

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