An Evolutionary Mosaic Challenges Traditional Monitoring of a Foundation Species in a Coastal Environment-The Baltic Fucus vesiculosus.

During periods of environmental change, genetic diversity in foundation species is critical for ecosystem function and resilience, but it remains overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates. Ecological distribution models predict a significant loss of Baltic F.

Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.

Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample.

Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions.

Diatoms can survive long periods in dark, anoxic sediments by forming resting spores or resting cells. These have been considered dormant until recently when resting cells of Skeletonema marinoi were shown to assimilate nitrate and ammonium from the ambient environment in dark, anoxic conditions. Here, we show that resting cells of S.

Strain-specific metabarcoding reveals rapid evolution of copper tolerance in populations of the coastal diatom Skeletonema marinoi.

Phytoplankton have short generation times, flexible reproduction strategies, large population sizes and high standing genetic diversity, traits that should facilitate rapid evolution under directional selection. We quantified local adaptation of copper tolerance in a population of the diatom Skeletonema marinoi from a mining-exposed inlet in the Baltic Sea and in a non-exposed population 100 km away. We hypothesized that mining pollution has driven evolution of elevated copper tolerance in the impacted population of S.

Phenomics reveals a novel putative chloroplast fatty acid transporter in the marine diatom Skeletonema marinoi involved in temperature acclimation.

Diatoms are the dominant phytoplankton in temperate oceans and coastal regions and yet little is known about the genetic basis underpinning their global success. Here, we address this challenge by developing the first phenomic approach for a diatom, screening a collection of randomly mutagenized but identifiably tagged transformants. Based upon their tolerance to temperature extremes, several compromised mutants were identified revealing genes either stress related or encoding hypothetical proteins of unknown function.

Whole Genome Sequence of Strain SMR5, Shown to Promote Growth in its Diatom Host.

Attempts to obtain axenic cultures of the marine diatom often result in poor growth, indicating the importance of the microbiome to the growth of its host. In order to identify the precise roles played by these associated bacteria, individual strains were isolated, cultured and sequenced. We report the genome of one such strain - SMR5, isolated from a culture of strain R05AC sampled from top layer sediments of the Swedish west coast.

Friends With Benefits: Exploring the Phycosphere of the Marine Diatom .

Marine diatoms are the dominant phytoplankton in the temperate oceans and coastal regions, contributing to global photosynthesis, biogeochemical cycling of key nutrients and minerals and aquatic food chains. Integral to the success of marine diatoms is a diverse array of bacterial species that closely interact within the diffusive boundary layer, or phycosphere, surrounding the diatom partner. Recently, we isolated seven distinct bacterial species from cultures of , a chain-forming, centric diatom that dominates the coastal regions of the temperate oceans.

Complete Genome Sequence of the Diatom-Associated Bacterium sp. Strain SMR4y.

The bacterial strain SMR4y belongs to the diverse microbiome of the marine diatom strain R05AC. After assembly of its genome, presented here, and subsequent analyses, we placed it in the genus This strain has a 3,479,724-bp circular chromosome (with 3,340 coding sequences) and no known plasmids.

Genome Sequence of sp. Strain SMS9 Identified in a Non-Axenic Culture of the Diatom .

Initial efforts to sequence the genome of the marine diatom were hampered by the presence of genetic material from bacteria, and there was sufficient material from some of these bacteria to enable the assembly of full chromosomes. Here, we report the genome of strain SMS9, one such bacterial species identified in a non-axenic culture of strain ST54. Its 5,482,391 bp circular chromosome contains 4,641 CDSs, and has a G+C content of 35.

Skeletonema marinoi as a new genetic model for marine chain-forming diatoms.

Diatoms are ubiquitous primary producers in marine ecosystems and freshwater habitats. Due to their complex evolutionary history, much remains unknown about the specific gene functions in diatoms that underlie their broad ecological success. In this study, we have genetically transformed the centric diatom Skeletonema marinoi, a dominant phytoplankton species in temperate coastal regions.

Complete Genome Sequence of Novel Strain SMR1, Isolated from a Culture of the Marine Diatom .

When studying diatoms, an important consideration is the role of associated bacteria in the diatom-microbiome holobiont. To that end, bacteria isolated from a culture of strain R05AC were sequenced, one of which being bacterial strain SMR1, presented here. The genome consists of a circular chromosome and seven circular plasmids, totalling 5,121,602 bp.

Genome Sequence of Strain SMS7, Found in Association with the Marine Diatom .

Arenibacter algicola strain SMS7 was isolated from a culture of the marine diatom Skeletonema marinoi strain ST54, sampled from top-layer sediments in Kosterfjord, Sweden. Here, we present its 5,857,781-bp genome, consisting of a circular chromosome and one circular plasmid, in all containing 4,932 coding sequences.

Whole-Genome Sequence of the Novel Strain SMS3, Found in Association with the Marine Diatom .

As part of an ongoing investigation into the microbiome of the marine diatom , the bacterial strain SMS3 was isolated from a culture of strain ST54, which had been propagated from a sample of top layer marine sediments taken from the Swedish west coast. We present here the sequenced genome of this bacterium, which we place in the taxon , based on a phylotaxonomic analysis and its high 16S rRNA sequence similarity to the type strain DSM 11445. Its 5,331,190 bp genome consists of a circular chromosome and three circular plasmids, and contains 5,019 CDSs.

Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi.

We report here the genome sequence of strain SMR4r, isolated from the marine diatom strain RO5AC. Its 3,987,360-bp genome consists of a circular chromosome and two circular plasmids, one of which appears to be shared with an -associated species.

Genome Sequence of Strain SMR3, Isolated from a Culture of the Diatom .

We present the genome of strain SMR3, a marine bacterium isolated from the diatom strain RO5AC sampled from top layer sediments at 14 m depth. Its 4,381,426 bp genome consists of a circular chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).