The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Metagenome-assembled genomes uncover a global brackish microbiome
Open accessAbstract
BACKGROUND: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. RESULTS: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. CONCLUSIONS: We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.
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Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
Herlemann, D. P. R., Labrenz, M., Jürgens, K., Bertilsson, S., Waniek, J. J., & Andersson, A. F. (2011) · The ISME Journal · doi:10.1038/ismej.2011.41 · Cited by 2,885
Self-citationCommunity structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324
Unusual biology across a group comprising more than 15% of domain Bacteria
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · cited 3×
“More recently, coverage variation across multiple samples has been used, allowing binning down to species and sometimes strain level [24, 29, 32–35].”
Status of biodiversity in the Baltic Sea
Ojaveer, H., Jaanus, A., MacKenzie, B. R., Martin, G., Olenin, S., Radziejewska, T., Telesh, I., Zettler, M. L., & Zaiko, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012467 · Cited by 362
Cited by
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Uritskiy, G. V., DiRuggiero, J., & Taylor, J. (2018) · Microbiome · doi:10.1186/s40168-018-0541-1 · Cited by 2,642
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
Tully, B. J., Graham, E. D., & Heidelberg, J. F. (2018) · Scientific Data · doi:10.1038/sdata.2017.203 · Cited by 508
Lindemann, S. R., Mobberley, J. M., Cole, J. K., Markillie, L. M., Taylor, R. C., Huang, E., Chrisler, W. B., Wiley, H. S., Lipton, M. S., Nelson, W. C., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01020 · Cited by 346
Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
Marine Bacterioplankton Seasonal Succession Dynamics
Bunse, C., & Pinhassi, J. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2016.12.013 · Cited by 284
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Metadata
- Authors
- Hugerth, L. W., Larsson, J., Alneberg, J., Lindh, M. V., Legrand, C., Pinhassi, J., & Andersson, A. F.
- Venue
- Genome Biology
- Published
- 2015-12
- Volume
- 16
- Issue
- 1
- Pages
- 279-279
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2952673498
- Cited by
- 249
- References
- 10
- FWCI
- 14.86
- Type
- journal article
- Language
- en
- Open access
- gold
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