Designer diatom episomes delivered by bacterial conjugation.

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research

Nanoplankton : the dominant vector for carbon export across the Atlantic Southern Ocean in spring

DATA AND MATERIAL AVAILABILITY : The data used in this manuscript are available in the Zenodo data repository: 10.5281/zenodo.7820428. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.SUPPLEMENTARY MATERIAL : Supplementary Text; Figs. S1 to S4; Tables S1 and S2.Across the Southern Ocean, large (≥20 μm) diatoms are generally assumed to be the primary vector for carbon export, although this assumption derives mainly from summertime observations. Here, we investigated carbon production and export potential during the Atlantic Southern Ocean’s spring bloom from size-fractionated measurements of net primary production (NPP), nitrogen (nitrate, ammonium, urea) and iron (labile inorganic iron, organically complexed iron) uptake, and a high-resolution characterization of phytoplankton community composition. The nanoplankton-sized (2.7 to 20 μm) diatom, Chaetoceros spp., dominated the biomass, NPP, and nitrate uptake across the basin (40°S to 56°S), which we attribute to their low iron requirement, rapid response to increased light, and ability to escape grazing when aggregated into chains. We estimate that the spring Chaetoceros bloom accounted for >25% of annual export production across the Atlantic Southern Ocean, a finding consistent with recent observations from other regions highlighting the central role of the phytoplankton “middle class” in carbon export.The South African National Research Foundation, South African National Antarctic Programme, University of Cape Town Science Faculty Fellowship, University of Cape Town Vice-Chancellor Doctoral Research Scholarship, University of Cape Town Vice-Chancellor Future Leaders 2030 Award, European Union’s Horizon 2020 Research and Innovation Programme No. 844733, Academy of Finland, and Funds from an Anonymous Charitable Donor Trust as part of Whales and Climate Change Program.https://www.science.org/journal/sciadvhj2024GeneticsSDG-14:Life below wate

Iron, ice and advection: how the physiology and distribution of marine organisms is influenced by the extremes of the Antarctic environment

The Southern Ocean is a key driver of biogeochemical processes and the earth’s climate, influencing the global distribution of water masses, nutrients, and drawdown rates of atmospheric carbon dioxide. The physical and geochemical environment of the Southern Ocean influences and is in turn influenced by the plankton of the euphotic zone. One of the key controlling factors which limits the growth and productivity of phytoplankton is the availability of the micronutrient iron. In the first chapter, I characterize a novel high affinity iron binding phytotransferrin in the diatom Phaeodactyulum tricornutum, which reveals that carbonate-coordinated ferric iron binding evolved independently and convergently from metazoan transferrin. Biochemical manipulations of the seawater carbonate system demonstrate that the concentration of the carbonate ion co-limits uptake rates of unchelated ferric iron. As phytotransferrin sequences have broad taxonomic distribution and are abundant in marine environmental genomic datasets, this suggests that ocean acidification will negatively impact a globally important eukaryotic iron acquisition mechanism. In the second chapter, I analyze a metagenomic survey of the distribution and genomic capacity of planktonic organisms in the continental shelf regions of East Antarctica and demonstrate an advective connection between surface and deep populations of ammonia oxidizing Archaea. In the third chapter, I use environmental transcriptomics (metatranscriptomics) to evaluate cellular- and ecosystem-level responses of an ice algae community living and fixing carbon on the underside of Antarctic sea ice. Taken together, these three chapters reveal some of the remarkable adaptations which marine plankton have used to adapt to life in one of the Earth’s most extreme environments, the Southern Ocean

A Metagenomic Framework for the Study of Airborne Microbial Communities

<div><p>Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.</p></div

Abundances of KEGG functional categories.

<p>Abundances of KEGG functional categories.</p

Taxonomic classification and diversity of the NYC 16S data.

<p>In the stacked barcharts, only those taxonomic groups that have ≥2% abundance in at least one of the samples is reported. The rarefaction curves along with the richness and diversity estimates were calculated using mothur and were based on averages of 25 random samples of 10,000 sequences from each dataset.</p

DNA yields after amplification.

<p> The MDA products for the NYC samples were quantified by UV spectroscopy and the linker amplification products for the SD samples were quantified by fluorescence spectroscopy.</p

Taxonomic classification of metagenomic reads.

<p>Taxonomic classification of metagenomic reads.</p

Taxonomic classification of metagenomic reads.

<p><i>Mixed</i> refers to a read that had matches to multiple kingdoms and could not be definitively assigned to one kingdom. <i>Other</i> refers to sequences that could not be identified (NCBI taxonomy ID 32644), mostly synthetic constructs. <i>Unclassified</i> refers to a read that could not be assigned to any kingdom (i.e. had no match in the reference databases). Kingdom taxonomy: </p

Ordination of the six metagenomic samples by principal component analysis based on KO abundance profiles.

<p>The first three principal components (PC1, PC2, and PC3) account for 83.1% of the total variation. The dashed lines in the 3D plot shows the height (PC3) of the sample points when projected on to the PC1-PC2 plane.</p