Biology subjects

Turk-Kubo, K. A.

Publications and source records attributed to Turk-Kubo, K. A..

5 recordsLinked to original sources

bioRxiv2026

The Braarudosphaera bigelowii genome reveals cellular remodeling around a nitrogen-fixing organelle

Braarudosphaera bigelowii hosts the nitrogen-fixing cyanobacterial organelle UCYN-A, or the nitroplast, but the absence of a reference genome has limited investigation of the genomic features accompanying this association. Here, we present nuclear and organellar genome resources for the cultured B. bigelowii strain FR-21. The assembly comprises a 472.1-Mb nuclear genome together with representative nitroplast, chloroplast, and mitochondrial genomes of 1.49 Mb, 107 kb, and 44 kb, respectively. The four genomic compartments have strongly differentiated GC compositions, consistent with their distinct evolutionary origins. The large nuclear genome does not appear to reflect a corresponding expansion of protein-coding capacity. Repeat annotation indicates that approximately 77% of the nuclear assembly is repetitive, leaving approximately 108 Mb of nonrepetitive sequence containing roughly 16,000 predicted protein-coding genes. Phylogenomic analysis places B. bigelowii within the expected diversity of haptophytes, indicating that its unusual diazotrophic lifestyle is not associated with an anomalous phylogenetic position. Comparative analysis of nitrogen metabolism genes reveals extensive remodeling of host nitrogen acquisition and assimilation. B. bigelowii lacks major components required for nitrate and nitrite assimilation and has reduced capacity to use urea, cyanate, and several internally recycled nitrogen sources. In contrast, ammonium transport and the glutamine synthetase-glutamate synthase pathway are retained. This combination suggests reduced flexibility in nitrogen use and a host metabolism increasingly centered on ammonium supplied by the nitroplast. B. bigelowii also encodes an expanded set of flavodoxin and cryptochrome genes. Eleven of 14 flavodoxin candidates and 21 of 39 cryptochrome candidates contained motifs linked to nitroplast targeting. Together with previous evidence that some of these proteins are abundantly imported into the nitroplast, these expansions point to host-encoded roles in nitroplast redox metabolism and diel regulation. These genome resources establish a foundation for investigating nitroplast protein import, host-organelle metabolic integration, and the genomic consequences of acquiring an intracellular nitrogen-fixing compartment. They further show that the evolution of the B. bigelowii-UCYN-A relationship involved substantial remodeling of genome architecture and nitrogen metabolism in both partners.

genomics↗

bioRxiv2025

Characterizing organisms from three domains of life with universal primers from throughout the global ocean

We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003-2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (> 0.2{micro}m) seawater samples was amplified using the 515Y/926R universal three- domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S. Thus, the ratio between taxa in one sample is directly comparable to the ratio in any other GRUMP sample, regardless of gene copy number differences. This obviates a problem in prior global studies that used size-fractionation and different rRNA gene primers for bacteria, archaea, and eukaryotes, precluding comparisons across size fractions or domains. On average, bacteria contributed 71%, eukaryotes 19%, and archaea 8% to rRNA gene abundance, though eukaryotes contributed 32% at latitudes > 40{degrees}. GRUMP is publicly available on the Simons Collaborative Marine Atlas Project (CMAP), promoting the global comparison of marine microbial dynamics.

ecology↗

bioRxiv2024

Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow

Marine nitrogen (N) fixation is a globally significant biogeochemical process carried out by a specialized group of prokaryotes (diazotrophs), yet our understanding of their ecology is constantly evolving. Although marine dinitrogen (N2)-fixation is often ascribed to cyanobacterial diazotrophs, indirect evidence suggests that non-cyanobacterial diazotrophs (NCDs) might also be important. One widely used approach for understanding diazotroph diversity and biogeography is polymerase chain reaction (PCR)-amplification of a portion of the nifH gene, which encodes a structural component of the N2-fixing enzyme complex, nitrogenase. An array of bioinformatic tools exists to process nifH amplicon data, however, the lack of standardized practices has hindered cross-study comparisons. This has led to a missed opportunity to more thoroughly assess diazotroph biogeography, diversity, and their potential contributions to the marine N cycle. To address these knowledge gaps a bioinformatic workflow was designed that standardizes the processing of nifH amplicon datasets originating from high-throughput sequencing (HTS). Multiple datasets are efficiently and consistently processed with a specialized DADA2 pipeline to identify amplicon sequence variants (ASVs). A series of customizable post-pipeline stages then detect and discard spurious nifH sequences and annotate the subsequent quality-filtered nifH ASVs using multiple reference databases and classification approaches. This newly developed workflow was used to reprocess nearly all publicly available nifH amplicon HTS datasets from marine studies, and to generate a comprehensive nifH ASV database containing 7909 ASVs aggregated from 21 studies that represent the diazotrophic populations in the global ocean. For each sample, the database includes physical and chemical metadata obtained from the Simons Collaborative Marine Atlas Project (CMAP). Here we demonstrate the utility of this database for revealing global biogeographical patterns of prominent diazotroph groups and highlight the influence of sea surface temperature. The workflow and nifH ASV database provide a robust framework for studying marine N2 fixation and diazotrophic diversity captured by nifH amplicon HTS. Future datasets that target understudied ocean regions can be added easily, and users can tune parameters and studies included for their specific focus. The workflow and database are available, respectively, in GitHub (https://github.com/jdmagasin/nifH-ASV-workflow) and Figshare (https://doi.org/10.6084/m9.figshare.23795943.v1).

bioinformatics↗

bioRxiv2023

A novel, N2-fixing cyanobacterium present and active in the global oceans

Marine N2-fixing cyanobacteria, including the unicellular genus Crocosphaera, are considered keystone species in marine food webs. Crocosphaera are globally distributed and provide new sources of nitrogen (N) and carbon (C), which fuel oligotrophic microbial communities and upper trophic levels. Despite their ecosystem importance, only one species, Crocosphaera watsonii, has ever been identified and characterized as widespread in the oligotrophic oceans. Herein, we present a novel species, candidatus Crocosphaera waterburyi (C. waterburyi hereafter), enriched from the North Pacific Ocean, active in situ, and globally distributed in environmental datasets. C. waterburyi is morphologically, phylogenetically, and physiologically distinct from C. watsonii; therefore, description of this novel species provides a new window into previously uncharacterized diversity and ecology of unicellular N2-fixing cyanobacterial taxa and further highlights their importance in the global N cycle.

genomics↗

bioRxiv2021

Nitrogen fixation in mesoscale eddies of the North Pacific Subtropical Gyre: patterns and mechanisms

1.Mesoscale eddies have been shown to support elevated dinitrogen (N2) fixation rates (NFRs) and abundances of N2-fixing microorganisms (diazotrophs), but the mechanisms underlying these observations are not well understood. We explored relationships among NFRs and cyanobacterial diazotroph abundances in eddy pairs of opposite polarity sampled in the North Pacific Subtropical Gyre and compared our observations to seasonal trends from the Hawaii Ocean Time-series (HOT) program. Consistent with previous reports, we found that NFRs were anomalously high for this region (up to 3.7-fold above previous monthly HOT observations) in the centers of the sampled anticyclones, coinciding with elevated abundances of Crocosphaera in the summertime. We then coupled our field-based observations, together with transcriptomic analyses of nutrient stress marker genes and ecological models, to evaluate potential mechanisms controlling diazotroph abundance and activity at the mesoscale. Specifically, we evaluated the role of biological (via estimates of growth and grazing rates) and physical controls on populations of Crocosphaera, Trichodesmium, and diatom symbionts. Our results suggest that increased Crocosphaera abundances associated with summertime anticyclones resulted from the alleviation of phosphate limitation, allowing cells to grow at rates exceeding grazing losses. In contrast, distributions of larger, buoyant taxa (Trichodesmium and diatom symbionts) appeared less affected by eddy-driven biological controls. Instead, they appeared driven by physical dynamics along frontal boundaries that separate cyclonic and anticyclonic eddies. Together, the interplay of eddy-specific changes in bottom-up control, top-down control, and the physical accumulation of cells likely explains the elevated diazotroph abundances and NFRs associated with anticyclones and eddy fronts.

ecology↗