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© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Faktorova, D., Nisbet, R. E. R., Robledo, J. A. F., Casacuberta, E., Sudek, L., Allen, A. E., Ares, M., Jr., Areste, C., Balestreri, C., Barbrook, A. C., Beardslee, P., Bender, S., Booth, D. S., Bouget, F., Bowler, C., Breglia, S. A., Brownlee, C., Burger, G., Cerutti, H., Cesaroni, R., Chiurillo, M. A., Clemente, T., Coles, D. B., Collier, J. L., Cooney, E. C., Coyne, K., Docampo, R., Dupont, C. L., Edgcomb, V., Einarsson, E., Elustondo, P. A., Federici, F., Freire-Beneitez, V., Freyria, N. J., Fukuda, K., Garcia, P. A., Girguis, P. R., Gomaa, F., Gornik, S. G., Guo, J., Hampl, V., Hanawa, Y., Haro-Contreras, E. R., Hehenberger, E., Highfield, A., Hirakawa, Y., Hopes, A., Howe, C. J., Hu, I., Ibanez, J., Irwin, N. A. T., Ishii, Y., Janowicz, N. E., Jones, A. C., Kachale, A., Fujimura-Kamada, K., Kaur, B., Kaye, J. Z., Kazana, E., Keeling, P. J., King, N., Klobutcher, L. A., Lander, N., Lassadi, I., Li, Z., Lin, S., Lozano, J., Luan, F., Maruyama, S., Matute, T., Miceli, C., Minagawa, J., Moosburner, M., Najle, S. R., Nanjappa, D., Nimmo, I. C., Noble, L., Vanclova, A. M. G. N., Nowacki, M., Nunez, I., Pain, A., Piersanti, A., Pucciarelli, S., Pyrih, J., Rest, J. S., Rius, M., Robertson, D., Ruaud, A., Ruiz-Trillo, I., Sigg, M. A., Silver, P. A., Slamovits, C. H., Smith, G. J., Sprecher, B. N., Stern, R., Swart, E. C., Tsaousis, A. D., Tsypin, L., Turkewitz, A., Turnsek, J., Valach, M., Verge, V., von Dassow, P., von der Haar, T., Waller, R. F., Wang, L., Wen, X., Wheeler, G., Woods, A., Zhang, H., Mock, T., Worden, A. Z., & Lukes, J. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods, 17, (2020): 481-494, doi:10.1038/s41592-020-0796-x., Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways., We thank M. Salisbury and D. Lacono, C. Poirier, M. Hamilton, C. Eckmann, H. Igel, C. Yung and K. Hoadley for assistance; V.K. Nagarajan, M. Accerbi and P.J. Green who carried out Agrobacterium studies in Heterosigma akashiwo, and N. Kraeva, C. Bianchi and V. Yurchenko for the help with designing the p57-V5+NeoR construct. We are also grateful to the protocols.io team (L. Teytelman and A. Broellochs) for their support. This collaborative effort was supported by the Gordon and Betty Moore Foundation EMS Program of the Marine Microbiology Initiative (grant nos. GBMF4972 and 4972.01 to F.-Y.B.; GBMF4970 and 4970.01 to M.A. and A.Z.W.; GBMF3788 to A.Z.W.; GBMF 4968 and 4968.01 to H.C.; GBMF4984 to V.H.; GBMF4974 and 4974.01 to C. Brownlee; GBMF4964 to Y. Hirakawa; GBMF4961 to T. Mock; GBMF4958 to P.S.; GBMF4957 to A.T.; GBMF4960 to G.J.S.; GBMF4979 to K.C.; GBMF4982 and 4982.01 to J.L.C.; GBMF4964 to P.J.K.; GBMF4981 to P.v.D.; GBMF5006 to A.E.A.; GBMF4986 to C.M.; GBMF4962 to J.A.F.R.; GBMF4980 and 4980.01 to S.L.; GBMF 4977 and 4977.01 to R.F.W.; GBMF4962.01 to C.H.S.; GBMF4985 to J.M.; GBMF4976 and 4976.01 to C.H.; GBMF4963 and 4963.01 to V.E.; GBMF5007 to C.L.D.; GBMF4983 and 4983.01 to J.L.; GBMF4975 and 4975.01 to A.D.T.; GBMF4973 and 4973.01 to I.R.-T. and GBMF4965 to N.K.), by The Leverhulme Trust (RPG-2017-364) to T. Mock and A. Hopes, and by ERD funds (16_019/0000759) from the Czech Ministry of Education to J.L.

The work is made available under the Creative Commons CCO public domain dedication.. The definitive version was published in PLoS Biology 16 (2018): e2006333, doi:10.1371/journal.pbio.2006333., Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models. The development of new models faces many barriers, some technical and others institutional, and this often discourages the risky, long-term effort that may be required. To lower these barriers and tackle the complexity of this effort, a highly collaborative community-based approach was taken. Herein, we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research., The research efforts, connections, and collaborations described in this paper and protocols.io (https://www.protocols.io/) were supported by the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative.

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 15 (2018): 4923-4942, doi:10.5194/bg-15-4923-2018., Phaeocystis antarctica is an important phytoplankter of the Ross Sea where it dominates the early season bloom after sea ice retreat and is a major contributor to carbon export. The factors that influence Phaeocystis colony formation and the resultant Ross Sea bloom initiation have been of great scientific interest, yet there is little known about the underlying mechanisms responsible for these phenomena. Here, we present laboratory and field studies on Phaeocystis antarctica grown under multiple iron conditions using a coupled proteomic and transcriptomic approach. P. antarctica had a lower iron limitation threshold than a Ross Sea diatom Chaetoceros sp., and at increased iron nutrition (>120pM Fe') a shift from flagellate cells to a majority of colonial cells in P. antarctica was observed, implying a role for iron as a trigger for colony formation. Proteome analysis revealed an extensive and coordinated shift in proteome structure linked to iron availability and life cycle transitions with 327 and 436 proteins measured as significantly different between low and high iron in strains 1871 and 1374, respectively. The enzymes flavodoxin and plastocyanin that can functionally replace iron metalloenzymes were observed at low iron treatments consistent with cellular iron-sparing strategies, with plastocyanin having a larger dynamic range. The numerous isoforms of the putative iron-starvation-induced protein (ISIP) group (ISIP2A and ISIP3) had abundance patterns coinciding with that of either low or high iron (and coincident flagellate or the colonial cell types in strain 1871), implying that there may be specific iron acquisition systems for each life cycle type. The proteome analysis also revealed numerous structural proteins associated with each cell type: within flagellate cells actin and tubulin from flagella and haptonema structures as well as a suite of calcium-binding proteins with EF domains were observed. In the colony-dominated samples a variety of structural p, Support for this study was provided by an Investigator grant to Mak A. Saito from the Gordon and Betty Moore Foundation (GBMF3782), National Science Foundation grants NSF-PLR 0732665, OCE-1435056, OCE-1220484, and ANT-1643684, the WHOI Coastal Ocean Institute, and a CINAR Postdoctoral Scholar Fellowship provided to Sara J. Bender through the Woods Hole Oceanographic Institution. Support was provided to Andrew E. Allen through NSF awards ANT-0732822, ANT-1043671, and OCE-1136477 and Gordon and Betty Moore Foundation grant GBMF3828. Additional support was provided to GRD through NSF award OPP-0338097.

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters., Gordon and Betty Moore Foundation, Agouron Institute, University of Hawaii and Manoa School of Ocean and Earth Science and Technology, National Science Foundation (U.S.). Science and Technology Center (Award EF0424599)

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Phycology 52 (2016): 716–731, doi:10.1111/jpy.12441., Diatoms are highly productive single-celled algae that form an intricately patterned silica cell wall after every cell division. They take up and utilize silicic acid from seawater via silicon transporter (SIT) proteins. This study examined the evolution of the SIT gene family to identify potential genetic adaptations that enable diatoms to thrive in the modern ocean. By searching for sequence homologs in available databases, the diversity of organisms found to encode SITs increased substantially and included all major diatom lineages and other algal protists. A bacterial-encoded gene with homology to SIT sequences was also identified, suggesting that a lateral gene transfer event occurred between bacterial and protist lineages. In diatoms, the SIT genes diverged and diversified to produce five distinct clades. The most basal SIT clades were widely distributed across diatom lineages, while the more derived clades were lineage-specific, which together produced a distinct repertoire of SIT types among major diatom lineages. Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among SITs. Both laboratory cultures and natural communities changed transcription of each SIT clade in response to experimental or environmental growth conditions, with distinct transcriptional patterns observed among clades. Together, these data suggest that the diversification of SITs within diatoms led to specialized adaptations among diatoms lineages, and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions., Gordon and Betty Moore Foundation Grant Numbers: GBMF2637, GBMF3776; University of Washington; National Science Foundation Grant Number: OCE-1205233

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 632-645, doi:10.4056/sigs.4998989., Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters., We gratefully acknowledge the support of the Gordon and Betty Moore Foundation, which funded the sequencing of this genome. Annotation was performed as part of the 2011 C-MORE Summer Course in Microbial Oceanography (http://cmore.soest.hawaii.edu/summercourse/2011/index.htm), with support by the Agouron Institute, the Gordon and Betty Moore Foundation, the University of Hawaii and Manoa School of Ocean and Earth Science and Technology (SOEST), and the Center for Microbial Oceanography: Research and Education (C-MORE), a National Science Foundation-funded Science and Technology Center (award No. EF0424599).

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.