sh.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Publications (10 of 50) Show all publications
Espínola, F., Dionisi, H. M., Borglin, S., Brislawn, C. J., Jansson, J. K., Mac Cormack, W. P., . . . Lozada, M. (2018). Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microbial Ecology (1), 123-139
Open this publication in new window or tab >>Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes
Show others...
2018 (English)In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, no 1, p. 123-139Article in journal (Refereed) Published
Abstract [en]

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

Keywords
Anaerobic biodegradation, Biomarker genes, Cold environments, Community structure, Hydrocarbons, Metagenomics, Subtidal sediments
National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-33067 (URN)10.1007/s00248-017-1028-5 (DOI)000418740100012 ()28702706 (PubMedID)2-s2.0-85023166954 (Scopus ID)
Available from: 2017-07-20 Created: 2017-07-20 Last updated: 2018-07-05Bibliographically approved
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., . . . Zhao, H. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551, 457-463
Open this publication in new window or tab >>A communal catalogue reveals Earth’s multiscale microbial diversity
Show others...
2017 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 551, p. 457-463Article in journal (Refereed) Published
Abstract [en]

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-33742 (URN)10.1038/nature24621 (DOI)000416043700036 ()2-s2.0-85034804875 (Scopus ID)
Note

The Earth Microbiome Project Consortium includes principal investigators and scientists who were involved with the individual studies that make up the EMP. These individuals conceived of sampling regimes, collected samples, provided sample metadata, and published manuscripts about individual studies 

Available from: 2017-11-28 Created: 2017-11-28 Last updated: 2018-04-05Bibliographically approved
Aliyu, H., De Maayer, P., Sjöling, S. & Cowan, D. A. (2017). Metagenomic Analysis of Low-Temperature Environments. In: Rosa Margesin (Ed.), Psychrophiles: From Biodiversity to Biotechnology (pp. 389-421). Cham: Springer
Open this publication in new window or tab >>Metagenomic Analysis of Low-Temperature Environments
2017 (English)In: Psychrophiles: From Biodiversity to Biotechnology / [ed] Rosa Margesin, Cham: Springer, 2017, p. 389-421Chapter in book (Refereed)
Abstract [en]

The Earth’s permanently cold biosphere is known to harbour abundant microbial biomass and represents a rich resource for the discovery of novel cold-adapted microorganisms, many of which form part of the ‘microbial dark matter’ which cannot be analysed using traditional culture-dependent approaches. The recent development of metagenomics and related multi-omics strategies has provided a means by which entire microbial communities can be studied directly, without the prerequisite of culturing. The advancement of the ‘omic’ methods is directly linked to recent progress in high-throughput sequencing, robust data processing capabilities and the application of cutting-edge analytical tools for high-throughput detection of biomolecules. The combined application of these tools and strategies has provided an unprecedented access to the structure and potential function of microbial communities in cold environments, providing increasingly comprehensive insights into the taxonomic richness and functional capacity of the indigenous microorganisms. Applications of ‘omic’ strategies have enhanced our understanding of psychrophilic adaptation mechanisms, revealing the versatility and adaptability of life in the ‘cryosphere’. In addition to the predicted roles of psychrophiles in biogeochemical cycling, recent multi-omic studies have further emphasised the importance of the ‘cryosphere’ in influencing global atmospheric conditions. Finally, metagenomic bioprospecting of cold environments has yielded a variety of novel bioactive molecules including novel ‘psychrozymes’, with a wide range of potential industrial and biotechnological applications. Here, we have provided an overview of recent developments in metagenomic technologies and their application in the study of the cold biosphere.

Place, publisher, year, edition, pages
Cham: Springer, 2017
Keywords
Microbial ecology, Environmental Science, Low temperature
National Category
Biological Sciences Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-33586 (URN)10.1007/978-3-319-57057-0_16 (DOI)2-s2.0-85033981467 (Scopus ID)978-3-319-57056-3 (ISBN)
Projects
Metaexplore- metagenomics for bioexploration
Funder
The Foundation for Baltic and East European Studies, 47/42/2011
Available from: 2017-10-13 Created: 2017-10-13 Last updated: 2018-02-16Bibliographically approved
López, J. L., Golemba, M., Hernández, E., Lozada, M., Dionisi, H. M., Jansson, J., . . . Cormack, W. P. (2017). Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.. FEMS Microbiology Ecology, 93(1), Article ID fiw216.
Open this publication in new window or tab >>Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.
Show others...
2017 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 93, no 1, article id fiw216Article in journal (Refereed) Published
Abstract [en]

Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis. Viral rhodopsin genes were homologues of Phaeocystis globosa virus and Organic lake Phycodnavirus Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus as well as Cryptophyta and Fungi. A re-screening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 aminoacids). Phylogeographic analysis revealed a geographycal clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsins (PAVR) genes related to Actinobacteria and Chloroflexi This is the first report about the existence of a phylogeographic association of the viral rhodopsins sequences from marine sediments.

Keywords
polar/subpolar, marine sediment, metagenomes, microbial rhodopsin, viral rhodopsin, phylogeography
National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-31124 (URN)10.1093/femsec/fiw216 (DOI)000397429600015 ()27815287 (PubMedID)2-s2.0-85012054740 (Scopus ID)
Available from: 2016-11-11 Created: 2016-11-11 Last updated: 2017-05-24Bibliographically approved
Berini, F., Presti, I., Beltrametti, F., Pedroli, M., Vårum, K. M., Pollegioni, L., . . . Marinelli, F. (2017). Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome. Microbial Cell Factories, 16(1), Article ID 16.
Open this publication in new window or tab >>Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome
Show others...
2017 (English)In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 16, no 1, article id 16Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase-named Chi18H8 and belonging to family 18 glycosyl hydrolases-was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential.

RESULTS: We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca(2+)-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate.

CONCLUSIONS: Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies.

National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-31935 (URN)10.1186/s12934-017-0634-8 (DOI)000397718400001 ()28137256 (PubMedID)2-s2.0-85011032503 (Scopus ID)
Funder
EU, FP7, Seventh Framework Programme, 222625
Available from: 2017-02-03 Created: 2017-02-03 Last updated: 2017-11-29Bibliographically approved
Musumeci, M. A., Lozada, M., Rial, D. V., Mac Cormack, W. P., Jansson, J. K., Sjöling, S., . . . Dionisi, H. M. (2017). Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach. Marine Drugs, 15(4), Article ID 114.
Open this publication in new window or tab >>Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach
Show others...
2017 (English)In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 15, no 4, article id 114Article in journal (Refereed) Published
Abstract [en]

The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.

Keywords
Baeyer–Villiger monooxygenases, bacterial cytochrome P450, bioprospecting biocatalysts, molecular modeling, phylogenetic analysis
National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-32413 (URN)10.3390/md15040114 (DOI)000404228300030 ()28397770 (PubMedID)2-s2.0-85018661660 (Scopus ID)
Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2017-07-14Bibliographically approved
Thureborn, P., Hu, Y. O. O., Franzetti, A., Sjöling, S. & Lundin, D. (2016). A dark, anoxic mausoleum for DNA: perceived and actual community structure in the Landsort Deep sediment, the Baltic Sea. PeerJ
Open this publication in new window or tab >>A dark, anoxic mausoleum for DNA: perceived and actual community structure in the Landsort Deep sediment, the Baltic Sea
Show others...
2016 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359Article in journal (Other academic) Submitted
Abstract [en]

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.

Keywords
Anoxic accumulation sediment, Tag sequencing, Protein synthesis potential, Dormancy, Microbial activity, rDNA, rRNA, Amplicon
National Category
Environmental Sciences
Research subject
Environmental Studies; Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-30915 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-10-07 Created: 2016-09-28 Last updated: 2017-11-30Bibliographically approved
Nesme, J., Achouak, W., Agathos, S. N., Bailey, M., Baldrian, P., Brunel, D., . . . Simonet, P. (2016). Back to the Future of Soil Metagenomics. Frontiers in Microbiology, 7, Article ID 73.
Open this publication in new window or tab >>Back to the Future of Soil Metagenomics
Show others...
2016 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 73Article in journal (Refereed) Published
National Category
Microbiology
Identifiers
urn:nbn:se:sh:diva-29602 (URN)10.3389/fmicb.2016.00073 (DOI)000369839100001 ()26903960 (PubMedID)2-s2.0-84962046075 (Scopus ID)
Available from: 2016-02-26 Created: 2016-02-26 Last updated: 2017-11-30Bibliographically approved
Sjöling, S. & Thureborn, P. (2016). Livet i havets djup. HavsUtsikt- Om havsmiljön och Svensk havsforskning (2), 16-18
Open this publication in new window or tab >>Livet i havets djup
2016 (Swedish)In: HavsUtsikt- Om havsmiljön och Svensk havsforskning, ISSN 1104-0513, no 2, p. 16-18Article in journal (Other (popular science, discussion, etc.)) Published
Keywords
mikrobiell ekologi, Landsortsdjupet, samhälle, ekologiska interaktioner, havsbotten
National Category
Microbiology Environmental Sciences
Research subject
Environmental Studies; Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-33653 (URN)1169/42/2007:17 (Local ID)1169/42/2007:17 (Archive number)1169/42/2007:17 (OAI)
Funder
The Foundation for Baltic and East European Studies, 1169/42/2007:17
Available from: 2017-10-31 Created: 2017-10-31 Last updated: 2019-08-27Bibliographically approved
Matos, M. N., Lozada, M., Anselmino, L. E., Musumeci, M. A., Henrissat, B., Jansson, J. K., . . . Dionisi, H. M. (2016). Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environmental Microbiology, 18(12), 4471-4484
Open this publication in new window or tab >>Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments
Show others...
2016 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4471-4484Article in journal (Refereed) Published
Abstract [en]

Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-30655 (URN)10.1111/1462-2920.13433 (DOI)000392946900014 ()27348213 (PubMedID)2-s2.0-84994121145 (Scopus ID)
Available from: 2016-07-20 Created: 2016-07-20 Last updated: 2018-07-05Bibliographically approved
Projects
Anaerobid ammonia oxidation (anamox): a proposed missing piece in the Baltic Sea nitrogen cycle [A086-2007_OSS]; Södertörn University; Publications
Sjöling, S. & Thureborn, P. (2016). Livet i havets djup. HavsUtsikt- Om havsmiljön och Svensk havsforskning (2), 16-18Thureborn, P. (2016). Microbial Ecosystem Functions Along the Steep Oxygen Gradient of the Landsort Deep, Baltic Sea. (Doctoral dissertation). Huddinge: Södertörns högskolaThureborn, P., Franzetti, A., Lundin, D. & Sjöling, S. (2016). Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments. PeerJ, 4, Article ID e1593. Thureborn, P., Lundin, D., Plathan, J., Poole, A. M., Sjöberg, B.-M. & Sjöling, S. (2013). A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities. PLoS ONE, 8(9), Article ID e74983.
Response and recovery of benthic biodiversity and ecosystem functions to chemical pollution and eutrophication [77/2017_OSS]; Södertörn University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-5802-5126

Search in DiVA

Show all publications