Jimmy H.W. Saw

George Washington University | GW · Department of Biological Sciences

The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic featu...

The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2, 3, 4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are un...

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of /`Lok...

Our knowledge of archaeal diversity and evolution has expanded rapidly in the past decade. However, hardly any genomes of the phylum Korarchaeota have been obtained due to the difficulty in accessing their natural habitats and – possibly – their limited abundance. As a result, many aspects of Korarchaeota biology, physiology and evolution remain en...

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...

Bald sea urchin disease (BSUD) is most likely a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages. The disease has a variety of additional symptoms, which may be the result of the many bacteria that are associated with BSUD. Previous studies have investigated causative agents of BSUD, ho...

In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes¹. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukar...

In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and euka...

We report the draft genome sequences of three bacterial species isolated from freshwater ponds or features around monuments in Washington, DC, during a semester-long microbiology lab course at the George Washington University. Two of the isolates belong to potentially novel species but lost their viability and could not be revived.

Strain 5675061T was isolated from a deep-sea microbial mat near hydrothermal vents within the Axial Seamount caldera on the Juan de Fuca Ridge (NE Pacific Ocean) and was taxonomically evaluated using a polyphasic approach. Morphological and chemotaxonomic properties are consistent with characteristics of the genus Streptomyces: aerobic Gram-stain-p...

Clade-based taxonomy has become a recognised means of classifying members of the family Vibrionaceae. A multilocus sequence analysis (MLSA) approach based on eight housekeeping genes can be used to infer phylogenetic relationships, which then groups species into monophyletic clades. Recent work on the Vibrionaceae clades added newly described speci...

Strain OCN044T was isolated from the homogenised tissue and mucus of an apparently healthy Acropora cytherea coral fragment collected from the western reef terrace of Palmyra Atoll in the Northern Line Islands and was taxonomically evaluated with a polyphasic approach. The morphological and chemotaxonomic properties are consistent with characterist...

Bacteria belonging to the Candidate Phyla Radiation/Patescibacteria are known for their relatively small genome sizes and their potential for co‐metabolism interdependencies. Patescibacteria are often found in low abundances and are considered to be part of the “microbial dark matter”. Here, we have identified uncharacterized lineages of the phylum...

Hawaii is a biodiversity hotspot known for its diverse endemic species of birds and other animals. For evolutionary biologists and ecologists, it is a great place to study adaptive radiation of species and island biogeography. However, very little is known about microbial diversity in geothermal features of Hawaii. Previous studies that focused on...

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...

Bacteria belonging to the class Vampirovibrionia are interesting because they are closest non-photosynthetic members of the phylum Cyanobacteria and their diversity, ecology, and evolution are poorly understood. None of them have so far been successfully cultivated in a pure culture to date and they are exclusively detected through metagenomic stud...

The bacterium Vibrio coralliilyticus has been implicated in mass mortalities of corals and shellfish larvae. However, using corals for manipulative infection experiments can be logistically difficult compared to other model organisms, so we aimed to establish oyster larvae infections as a proxy model. Therefore, this study assessed the virulence of...

Aestuariibacter halophilus strain JC2043, a Gram-negative gammaproteobacterium, is often used as a reference organism for assigning taxonomy within the family Alteromonadaceae . Isolates of this species have also been investigated for compound degradation (e.g., phthalates and oil) and biofilm association. Presented here is the draft genome sequenc...

Planctobacterium marinum strain K7 is a Gram-negative gammaproteobacterium of the Alteromonadaceae family and is the sole type strain in the genus Planctobacterium . Presented here is the draft whole-genome sequence of P. marinum strain K7.

Only two complete genomes of the cyanobacterial genus Gloeobacter from two very different regions of the world currently exist. Here we present the complete genome sequence of a third member of the genus isolated from a waterfall cave in Mexico. Analysis of the average nucleotide identities (ANI) between published Gloeobacter genomes revealed that...

Microbial communities are frequently numerically dominated by just a few species. Often, the long "tail" of the rank-abundance plots of microbial communities constitutes the so-called "rare biosphere," microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has on...

Vibrio ostreicida is a Gram-negative gammaproteobacterium that has been shown to cause disease in bivalve larvae. Presented here is the draft genome of the type strain Vibrio ostreicida strain PP-203, which was isolated from the inner surface of an Ostrea edulis (European flat oyster) spat container with recorded deaths at a hatchery in Galicia, Sp...

The draft genome of Streptomyces sp. strain ventii, an environmental isolate recovered from deep-sea hydrothermal vents in the Pacific Ocean, is presented along with the resequenced draft genomes of the type strains Streptomyces bohaiensis 11A07 and Streptomyces lonarensis NCL 716.

Vibrio sp. strain OCN044 is a Gram-negative gammaproteobacterium found in marine environments. Presented here is the whole-draft genome sequence of nonpathogenic Vibrio sp. strain OCN044, isolated from a healthy Acropora cytherea colony off the western reef terrace of Palmyra Atoll.

The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathw...

It has been hypothesized that abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolism for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metab...

In vast, warm regions of the oceans, phytoplankton face the problem of arsenic poisoning. Arsenate is toxic because it is chemically similar to phosphate, a scarce nutrient that phytoplankton cells need for growth. Many phytoplankton, including the commonest phytoplankton type in warm oceans, Prochlorococcus , detoxify arsenate by adding methyl gro...

In Spang et al. [1], we reported the discovery of Lokiarchaeum (Loki1) and two related lineages (Loki2 and Loki3, now referred to as Heimdallarchaeote LC_2 and LC_3). These were the first known representatives of the subsequently described Asgard superphylum [2], which branches as a sister clade to the TACK archaea [3]. We provided extensive phylog...

Nature Microbiology 1 , 16002 (2016); published 15 February 2016; corrected 6 June 2016. This Letter should have been published under a Creative Commons licence according to the Nature policy on publishing the primary sequence of an organism's genome for the first time.

The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these player...

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...

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Loki...

The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics app...

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.

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...

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-...

The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel,...

Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plas...

##Assembly-Data-START## Assembly Method :: Seqman in DNAStar Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Transformation plasmid-derived insert number and insert site sequence in 55-1 line papaya derivatives Rainbow and SunUp was determined as part of a larger petition to allow its import into Japan (Suzuki et al., 2007, 2008). Three insertions were detected by Southern analysis and their corresponding sequences determined by clones (Fermín, 2002) or v...

Locations of 268 single copy genes, conserved among Flavobacteria (CSCGs), on the genomes of Gramella forsetii KT0803 (A), Flavobacterium johnsoniae UW101 (B), and Flavobacterium psychrophilum JIP02/86 (C). The outermost two circles indicate start sites of genes and assigned functional categories: forward-strand gene products (circle 1) and reverse...

Principal component analysis of nucleotide tetramer frequency in Sanger reads of MS024-2A (A) and MS024-3C (B). The taxonomic origins of the reads were inferred by blastx against GenBank nr database and summarized by MEGAN. Outliers I (0.7% of all reads) were identified as proteobacterial contamination, which may have been introduced during the seq...

Maximum likelihood phylogenetic tree of 16S rRNA genes. Included are Flavobacteria isolates undergoing whole genome sequencing, single amplified genomes (SAGs) from the same environmental sample as MS024-2A and MS024-3C, as well as those sequences in Genbank that are ≥97% identical to MS024-2A and MS024-3C. Black circles indicate ≥70% neighbor-join...

Genome size estimates. A: Number of conserved single copy genes (CSCGs) in Flavobacteria family genomes. The pre-computed COG function distribution from 16 genomes was retrieved from the IMG database, and the number of SCSGs was calculated through an iterative re-sampling of these genomes (see Materials and Methods). Provided are means and standard...

The total and genome size (Mbp)-normalized number of hydrolytic enzymes, TonB dependent/ligand-gated channels and SusD homologs. Included in the analysis are MS024-2A, MS024-3C and other Bacteroidetes genomes with high hydrolytic potential (Flavobacterium johnsoniae UW101, Gramella forsetii KT0803, Cytophaga hutchinsonii ATCC 33406, Bacteroides the...

Putative sugar uptake and degradation pathways in MS024-2A. (0.05 MB PDF)

MS024-2A and MS024-3C genome coverage as a function of the sequencing effort (A); and the impact of 454 and Sanger sequence on the number of contigs (B), assembly size (C) and the number of scaffolds (D) for MS024-2A. For panel A, genome size estimates were based on conserved single copy gene (CSCG) analysis (see Materials and Methods). The curves...

Multiple displacement amplification bias (A) and GC content (B) in MS024-2A and MS024-3C shotgun sequence products. Significant MDA bias is evident from the sequence depth distribution plots for MS024-2A and MS024-3C (A). The contigs for the SAGs were aligned by length and contig breaks, indicated by the tic marks along each top panel. The GC conte...

Global Ocean Sampling metagenome fragment recruitment by MS024-2A and MS024-3C and the three best GOS fragment recruiters: Synechococcus sp. WH8102, Prochlorococcus marinus strain MIT 9312 and 9312 and “Candidatus Pelagibacter ubique” HTCC1062. Fragment recruitment was performed with MUMMER and only ≥400 bp alignments were counted. For the two SAGs...

Genes and domains with a potential role in adhesion. (0.05 MB PDF)

Neighbor-joining tree of DNA photolyase-like genes from all available Flavobacteria genomes. Indicated are IMG gene object identifiers and strain or SAG names. Colors represent marine organisms with rhodopsins (red), marine organisms without rhodopsins (blue), and non-marine organisms (green). (0.40 MB TIF)

Chimeric rearrangements in SAG DNA. To identify chimeric reads and clones, reads were Q20 quality trimmed and Blast-aligned against the SAG draft assemblies with an alignment minimum of 25 bp. On average, we detected one chimera per 13–27 Kbp of single cell whole genome multiple displacement amplification products. No notable reduction in chimeric...

The structure of the rsb operon in MS024-2A (A) and a model for the regulation of σ24 in MS024-2A (B). In panel B, σ24 is held inactive in unstressed MS024-2A as a complex with an anti-sigma factor RsbW. The σ24 is freed from RsbW when a release factor, RsbV, binds to RsbW. In other words, RsbW forms mutually exclusive complexes with either the Rsb...

Key enzymes and metabolic pathways in the uptake and metabolism of N, P, S and Fe. Two pathways for ammonium assimilation were detected in MS024-3C, Gln synthetase (GS)/Glu synthase (GOGAT), and Glu dehydrogenase (GDH) pathways. MS024-2A only contains the GDH pathway. Genes involved in nitrate or nitrite utilization were not found. Polyphosphate ki...

The Oral Pathogen Genome Sequence Database (ORALGEN) is funded by the National Institute of Craniofacial and Dental Research (NIDCR) of NIH. Objective: It is a specialized sequence database managed at the Los Alamos National Laboratory in support of oral pathogen research. Methods: The database currently encompasses primary and derived molecular...

The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality g...

Inserts and insert sites in transgenic, papaya ringspot virus (PRSV)-resistant commercial papaya Rainbow and SunUp, were characterized as part of a petition to Japan to allow import of fresh fruit of these cultivars from the U.S. and to provide data for a larger study aimed at understanding the global impact of DNA transformation on whole genome st...

Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability o...

Figure S1: phylogenetic distribution of the best BLAST hits of A. flavithermus proteins. Figure S2: the tree of the phylum Firmicutes based on similarity of the phyletic patterns in COGs. Figure S3: two-dimensional gels comparing expression of A. flavithermus proteins from cells grown with or without silica. Figure S4: SDS-PAGE analysis of purified...

Supplementary Figures 1–6 and Supplementary Tables 1–3.

Supplementary Figures added in the course of the Open Review. Supplementary Figures 7–9

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but conta...

The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultiv...

Sex chromosomes in flowering plants, in contrast to those in animals, evolved relatively recently and only a few are heteromorphic. The homomorphic sex chromosomes of papaya show features of incipient sex chromosome evolution. We investigated the features of paired X- and Y-specific bacterial artificial chromosomes (BACs), and estimated the time of...

Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active...

A high-density genetic map of papaya (Carica papaya L.) was constructed using microsatellite markers derived from BAC end sequences and whole-genome shot gun sequences. Fifty-four F(2) plants derived from varieties AU9 and SunUp were used for linkage mapping. A total of 707 markers, including 706 microsatellite loci and the morphological marker fru...