Stuart P Donachie

Stuart P Donachie
University of Hawaiʻi at Mānoa | UH Manoa · School of Life Sciences

GIBiol, PhD

About

184
Publications
18,139
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2,085
Citations
Additional affiliations
November 1988 - May 1995
Polish Academy of Sciences
Position
  • PhD Student
August 2018 - present
University of Hawaiʻi at Mānoa
Position
  • Professor

Publications

Publications (184)
Article
Full-text available
Early Mars was likely habitable, but could life actually have started there? While cellular life emerged from prebiotic chemistry through a pre-Darwinian selection process relevant to both Earth and Mars, each planet posed unique selection ‘hurdles’ to this process. We focus on drivers of selection in prebiotic chemistry generic to Earth-like world...
Article
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Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students a...
Article
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Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we ana...
Article
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A Gram-negative, rod-shaped and filamentous bacterium designated MD30BT was isolated from a biofilm hanging in water flowing from an air conditioner condensate drain line in Honolulu, Hawai'i. Based on 1517 nucleotides of the strain's 16S rRNA gene, its nearest neighbours are Chitinophaga rhizosphaerae T16R-86T (96.7 %), Chitinophaga caseinilytica...
Article
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Here, we report the genome sequence of bacteriophage KeAlii, a Siphoviridae that infects Arthrobacter globiformis strain B-2979, from Honolulu, Hawaiʻi. The 41,850-bp genome contains 66 predicted protein-coding genes and 1 gene that encodes a tRNA for tryptophan. Genome comparisons suggest KeAlii is closely related to actinobacteriophage Adolin.
Article
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Lava caves, tubes, and fumaroles in Hawai'i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare th...
Article
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The term "microbiome" is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, "microbiome" is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communitie...
Article
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A Gram-negative, rod-shaped bacterium, designated KH87(T), was isolated from a fishing hook that had been baited and suspended in seawater off O'ahu, Hawai'i. Based on a comparison of 1524 nt of the 16S rRNA gene sequence of strain KH87(T), its nearest neighbours were the GammaproteobacteriaRheinheimera nanhaiensis E407-8(T) (96.2 % identity), Rhei...
Article
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A methylene group in the fluorinated carbon backbone of 1H,1H,2H,2H,8H,8H–perfluorododecanol (degradable telomer fluoroalcohol, DTFA) renders the molecule cleavable by microbial degradation into two fluorinated carboxylic acids. Several biodegradation products of DTFA are known, but their rates of conversion and fates in the environment have not be...
Article
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Most of the 24 known Chitinophaga species were originally isolated from soils. We report the draft genome sequence of a putatively novel Chitinophaga sp. from a biofilm in an air conditioner condensate pipe. The genome comprises 7,661,303 bp in one scaffold, 5,694 predicted protein-coding sequences, and a G+C content of 47.6%.
Article
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Bacterial cooperative associations and dynamics in the biofilm microenvironments are of special interest in recent years. Knowledge of localized gene-expression and corresponding bacterial behaviors within the biofilm architecture at a global scale has been limited, due to a lack of robust technology to study limited number of cells in stratified l...
Poster
Full-text available
Investigation of the microbial diversity of Kawainui Marsh, the second largest historical fishpond on O’ahu, and Ulupo Lo’i, a native Hawaiian historical site actively producing taro for our community. We are examining links between pathogenicity, water quality, community composition, and gene expression.
Article
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A Gram-stain-negative, motile, rod-shaped bacterium designated OCN003T was cultivated from mucus taken from a diseased colony of the coral Montipora capitata in Kāne'ohe Bay, O'ahu, Hawai'i. Colonies of OCN003T were pale yellow, 1-3 mm in diameter, convex, smooth and entire. The strain was heterotrophic, strictly aerobic and strictly halophilic. Ce...
Poster
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Investigation of the diversity of microbes in lava caves from the Big Island, Hawaii, using culturing techniques and next generation sequencing.
Poster
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Preliminary results of microbial diversity in a tropical estuarine system, Hawaii. This project is a joint effort between the University of Hawaii Manoa and the Pacific American Foundation WIRED program (http://www.thepaf.org/portfolio-items/wired/).
Article
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Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their clos...
Data
Table of genome structure statistics, from the data-set of eukaryotic genomes used in the study.Includes genome size and portion of the genome covered by genes, exons, introns and intergenic regions. Used in Figures 1, 3 and 4.DOI: http://dx.doi.org/10.7554/eLife.26036.004
Data
BVD57 phylogenomic dataset (see (Torruella et al., 2015)), including 87 unaligned protein domains (with PFAM accession number) per species.Used in Figure 2.DOI: http://dx.doi.org/10.7554/eLife.26036.009
Data
Reconstruction of intron site evolutionary histories, using a rates-across-sites Markov model for intron evolution, with branch-specific gain and loss rates (Csurös, 2008).Used in Figures 5 and 6.DOI: http://dx.doi.org/10.7554/eLife.26036.021
Data
Reconstruction of the evolutionary histories of protein domain pairs gains within orthogroups, using a phylogenetic birth-and-death probabilistic model that accounts for gains, losses and duplications (Csurös, 2010).Used in Figures 7, 8, 9 and 10.DOI: http://dx.doi.org/10.7554/eLife.26036.029
Data
Annotated repetitive sequences from 10 unicellular Holozoa genomes.Includes transposable elements, simple repeats, low complexity regions and small RNAs. Used in Figure 3.DOI: http://dx.doi.org/10.7554/eLife.26036.012
Data
Reconstruction of the evolution of the NMD machinery (He and Jacobson, 2015) and key SR splicing factors (Plass et al., 2008).Used in Figure 5.DOI: http://dx.doi.org/10.7554/eLife.26036.022
Data
List of genome and transcriptome assemblies and annotations, including abbreviations, taxonomic classification and data sources.DOI: http://dx.doi.org/10.7554/eLife.26036.008
Data
List of annotated transposable element families in 10 unicellular Holozoa genomes, with copy counts.Used in Figure 3.DOI: http://dx.doi.org/10.7554/eLife.26036.013
Data
Reconstruction of the evolutionary histories of individual protein domains, using Dollo parsimony and accounting for gains and losses (Csurös, 2010).Used in Figures 7, 8, 9 and 10.DOI: http://dx.doi.org/10.7554/eLife.26036.030
Data
Rates of gain and loss of orthogroups for extant and ancestral eukaryotes, using a phylogenetic birth-and-death probabilistic model that accounts for gains, losses and duplications.Used in Figure 1.DOI: http://dx.doi.org/10.7554/eLife.26036.005
Data
List of annotated transposable element families shared between the genomes of 10 unicellular holozoans and 11 animals, including the number of species where the TE family is present.Three lists are included: all TE families present in any holozoan, a list restricted to the most abundant TE families accounting for 75% of all copies in each holozoan...
Data
Rates of gain and loss of intron sites for extant and ancestral eukaryotes, calculated for a rates-across-sites Markov model for intron evolution with branch-specific gain and loss rates (Csurös, 2008).Used in Figure 5.DOI: http://dx.doi.org/10.7554/eLife.26036.020
Data
Rates of gain and loss of protein domain pairs within a given orthogroup for extant and ancestral eukaryotes, calculated for a phylogenetic birth-and-death probabilistic model that accounts for gains, losses and duplications (Csurös, 2010).Used in Figures 7, 8 and 9.DOI: http://dx.doi.org/10.7554/eLife.26036.028
Data
Probability of emergence of protein domain combinations present in the LCA of Metazoa in previous ancestral nodes (from LCA of Metazoa to LCA of Unikonta/Amorphea).Only protein domain combinations with >90% presence probability in the LCA of Metazoa were included. Protein domain combinations that are not gained with >90% probability in any of the s...
Article
Full-text available
Rheinheimera salexigens KH87T is an obligately halophilic gammaproteobacterium. The strain’s draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%.
Article
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Marinobacter sp. strain X15-166B T was cultivated from sediment in Honolulu Harbor, Hawai‘i. The X15-166B T draft genome of 3,490,661 bp encodes 3,115 protein-coding open reading frames. We anticipate that the genome will provide insights into the strain’s lifestyle and the evolution of Marinobacter .
Article
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One species of Piscirickettsia , a pathogen of salmonid fish, has been described. The genome sequence of a putative second and free-living species may provide insights into the evolution of pathogenicity in the genus.
Article
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Luteimonas sp. strain JM171 was cultivated from mucus collected around the coral Porites lobata . The JM171 draft genome of 2,992,353 bp contains 2,672 protein-coding open reading frames, 45 tRNA coding regions, and encodes a putative globin-coupled diguanylate cyclase, Jm GReg.
Article
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The genus Terasakiispira hosts only Terasakiispira papahanaumokuakeensis PH27A T , cultivated from an anchialine pond on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The strain’s genome sequence may provide insights into the evolution of free-living Oceanospirillaceae .
Article
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A putatively novel basidiomycetous fungus termed Moniliella wahieum Y12T was isolated from a 20% biodiesel blend. The strain maximally degraded biodiesel at a rate of 3.56 × 10-2 mg/h during log phase growth. Induction of metal corrosion by the strain in a mass loss procedure using 1018 metal coupons showed total mass reduction exceeded that in con...
Article
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Flavobacterium spp. have been cultivated from diverse aquatic and terrestrial habitats. F. akiainvivens IK-1 T was cultivated from decaying wood of Wikstroemia oahuensis , an endemic Hawaiian shrub. The strain’s genome sequence may provide insights into niche adaptation and evolution of the genus in a mid-ocean archipelago.
Article
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Graphical Abstract Highlights d Taxon-rich phylogenomics provides an evolutionary framework for the opisthokonts d Specialized osmotrophy evolved independently in fungi and animal relatives d Opisthokonts underwent independent secondary losses of the flagellum d The last opisthokont common ancestor had a complex repertoire of chitin synthases Corre...
Article
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A Gram-negative helical bacterium designated PH27A was cultivated from an anchialine pool on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The obligately halophilic strain is motile by bipolar tufts of flagella, grows optimally at pH 7, and microaerobically or aerobically. Closest neighbors based on 16S rRNA gene nucleotide sequence identi...
Article
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Most Pantoea spp. have been isolated from plant sources or clinical samples. However, we cultivated Pantoea anthophila 11-2 from hypersaline water from the lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2 provides a molecular basis for studies in evolution and pathogenicity in Pantoea spp.
Chapter
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Lakes in the craters of active volcanoes and their related streams are often characterised by conditions considered extreme for life, such as high temperatures, low pH and very high concentrations of dissolved metals and minerals. Such lakes tend to be transient features whose geochemistry can change markedly over short time periods. They might als...
Article
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The ancestor of Gloeobacter violaceus PCC 7421(T) is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cya...
Article
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Strain IK-1T was isolated from decaying Wikstroemia oahuensis collected on Oahu, Hawaii. Cells are rods that stain Gram-negative. Gliding motility was not observed. The strain is oxidase-negative and catalase-positive. Zeaxanthin is the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-...
Article
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We present evidence that a clade of bacteria in the Oceanospirillaceae is widely distributed in Porites spp. and other hermatypic corals. Bacteria 16S rDNA clone libraries were prepared from community genomic DNA extracted from Porites compressa and Porites lobata surface mucus and adjacent seawater collected along a line transect off Maui. Phyloge...
Data
##Assembly-Data-START## Assembly Method :: Seqman in DNAStar Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
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Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material, the lack of poly(A)-tails, and the fact that the messages can be polycistronic. Here, we describe a novel method for single-bacterium TTA...
Article
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We report a ribosomal tag pyrosequencing study of the phylogenetic diversity of Archaea, Bacteria and Eucarya over a depth profile at the Hawaii Ocean Time-Series Station, ALOHA. The V9 region of the SSU rRNA gene was amplified from samples representing the epi- (10 m), meso- (800 m) and bathy- (4400 m) pelagia. The primers used are expected to amp...
Article
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A previously unknown basidiomycetous yeast is described for which the name Sympodiomycopsis lanaiensis is proposed. The type strain, LM418(T), was isolated from driftwood collected on a beach on Lana'i (Hawai'i). On the basis of ribosomal DNA sequence analysis [large subunit (LSU), internal transcribed spacer (ITS) 1 & 2, and 18S], LM418(T) belongs...
Article
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The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
Article
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We investigated the phylogenetic diversity of microorganisms in a microbial mat in the entrance of a lava cave in Kilauea Crater, Hawai'i Volcanoes National Park, Hawai'i. Diversity among the Bacteria was very high, with 53 distinct phylotypes (defined at the 97% nucleotide identity level) detected from only 120 non-chimeric, full length 16S rRNA g...
Article
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The fine-scale phylogeny of the deeply branching Deltaproteobacteria Marine Group B/SAR324 (MGB/SAR324) bacterioplankton clade was analyzed using partial 16S rRNA gene sequence and internal transcribed spacer (ITS) sequences. Both sets of analyses revealed considerable sequence variation, which, along with bootstrap calculations, strongly support t...
Article
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A Gram-negative bacterium, designated LA33B(T), was isolated from water collected from a hypersaline lake on uninhabited Laysan Atoll in the Northwestern Hawaiian Islands. Cells of strain LA33B(T) are motile, straight rods that grow between 4 and 45 degrees C and in media containing 1-17.5% (w/v) NaCl. The strain oxidizes carbohydrates, nucleosides...
Article
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A Gram-negative bacterium, designated LA31B(T), was isolated from water collected from a hypersaline lagoon on Laysan Atoll in the north-western Hawaiian Islands. Single cells of LA31B(T) were slightly curved but became helical as their length increased. Preliminary characterization based on 16S rRNA gene sequence analysis showed that LA31B(T) shar...
Article
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We report the complete genome sequence of the deep-sea gamma-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii. The I. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comp...
Article
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The marine psychrophilic and endemic Antarctic yeast Leucosporidium antarc− ticum strain 171 synthesizes intracellular −fructofuranosidase, and intra− and extracellular −glucosidases. Each enzyme is maximally produced at 5C, while the strain's optimum growth temperature is 15C. Invertase biosynthesis appeared regulated by catabolic repres− sion, an...
Article
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The Hawaiian Archipelago is a "biodiversity hotspot" where significant endemism among eukaryotes has evolved through geographic isolation and local topography. To address the absence of corresponding region-wide data on Hawaii's microbiota, we compiled the first 16S SSU rDNA clone libraries and cultivated bacteria from five Hawaiian lakes, an anchi...
Article
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A Gram-negative bacterium designated LA1(T) was isolated from water collected in hypersaline Lake Laysan on Laysan Island in the Northwestern Hawaiian Islands. Cells occurred singly as fine rods to short filaments. Growth in 50 % strength marine broth occurred optimally when the medium contained 7.5-10 % (w/v) NaCl. The major fatty acids in LA1(T)...
Article
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During an investigation of bacterial diversity at hydrothermal vents on the Lō'ihi Seamount, Hawai'i, a novel bacterium (designated L2-TR(T)) was cultivated, which shares 99.9 % 16S rRNA gene sequence similarity over 1415 nt with an uncultured eubacterium from sediment at a depth of 11 000 m in the Mariana Trench. The nearest cultivated neighbour o...
Article
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We report the first description of the microbial community in a stream of acidic hydrothermal waters on volcanically active White Island, New Zealand, using both molecular and microbiological methods. alpha- and beta-Proteobacteria, green-sulfur bacteria, and uncultured Firmicutes were identified from the community DNA-based 16s rRNA gene library....