James T Staley

James T Staley
University of Washington Seattle | UW · Department of Microbiology and Astrobiology Program

PhD

About

312
Publications
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24,373
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Additional affiliations
August 1971 - June 2010
University of Washington Seattle
Position
  • Professor Emeritus

Publications

Publications (312)
Article
Full-text available
N2 production by denitrification can occur in anoxic water or potentially inside organic particles. Here we compare data from the Black Sea, a permanently anoxic basin, during two organic matter regimes: suspended particulate organic matter concentrations were high in the oxycline after the spring bloom in March 2005 compared to lower organic matte...
Article
The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic‐wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of ce...
Article
Full-text available
In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured ‘Prokaryotes First’ hypotheses and another addressed ‘Eukaryotes First’ hypotheses. Those who propos...
Article
The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) Bacteria and the Eukarya. We propose that a grou...
Chapter
An.ca' lo.mi.cro' bi.um. Gr. masc. n. ancalos arm; Gr. adj. micros small; Gr. masc. n. bios life; M.L. neut. n. Ancalomicrobium arm (-producing) microorganism. Proteobacteria / Alphaproteobacteria / Rhizobiales / Hyphomicrobiaceae / Ancalomicrobium Unicellular bacterium with conical cells ~1.0 µm in diameter. Two to eight or more prosthecae produce...
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Pros.the' co.mi.cro.bi.um. Gr. fem. n. prosthece appendage; Gr. adj. micros small; Gr. masc. n. bios life; M.L. neut. n. Prosthecomicrobium appendage (-bearing) microbe. Proteobacteria / Alphaproteobacteria / Rhizobiales / Hyphomicrobiaceae / Prosthecomicrobium Unicellular bacterium with coccobacillary to rod-shaped cells ranging in diameter from 0...
Chapter
An' cy.lo.bac' ter. Gr. adj. ankylos sharply curved; Gr. n. bakterion rod; M.L. masc. n. Ancylobacter a curved rod. Proteobacteria / Alphaproteobacteria / Rhizobiales / Hyphomicrobiaceae / Ancylobacter Curved rods, 0.3–1.0 × 1.0–3.0 µm. Rings (0.9–3.0 µm outer diameter) occasionally formed prior to cell separation. Coiled, helical, and filamentous...
Chapter
Fu.so.bac.te'ri.a. N.L. neut. n. Fusobacterium genus of the phylum with ending -ia to denote phylum; N.L. neut. pl. n. Fusobacteriia the phylum of Fusobacterium. Fusobacteria
Chapter
Fu.so.bac.te.ri.a'les. N.L. neut. n. Fusobacterium type genus of the order; suff. -ales ending denoting order; N.L. fem. pl. n. Fusobacteriales the Fusobacterium order. Fusobacteria / Fusobacteriia / Fusobacteriales
Chapter
Fu.so.bac.te'ri.ia. N L. neut. n. Fusobacterium type genus of the order Fusobacteriales; suff. -ia ending proposed by Gibbons and Murray and by Stackebrandt et al. to denote class; N.L. neut. pl. n. Fusobacteriia the Fusobacterium class. Fusobacteria / Fusobacteriia
Chapter
Po.lar.i.bac'ter. N.L. adj. polaris pertaining to the geographic poles; N.L. masc. n. bacter from Gr. n. baktron rod or staff; N.L. masc. n. Polaribacter rod-shaped bacteria from polar habitats. Bacteroidetes / Flavobacteriia / Flavobacteriales / Flavobacteriaceae / Polaribacter Rods, curved rods, or filaments. Cell size varies between 0.8 and 48 µ...
Chapter
Taxonomy is the science of classification of organisms. Bacterial taxonomy consists of three separate, but interrelated areas: classification, nomenclature, and identification. Classification is the arrangement of organisms into groups (taxa) on the basis of similarities or relationships. Nomenclature is the assignment of names to the taxonomic gro...
Chapter
Fu.so.bac.te.ri.a.ce'a.e. N. L. neut. n. Fusobacterium type genus of the family; suff. -aceae ending denoting family; N.L. fem. pl. n. Fusobacteriaceae the Fusobacterium family. Fusobacteria / Fusobacteriia / Fusobacteriales / Fusobacteriaceae
Chapter
Aq' ua.bac.ter. L. n. aqua water; Gr. neut. n. bacter masc. form of Gr. neut. n. bacterion a rod; N.L. masc. n. Aquabacter aquatic rod. Proteobacteria / Alphaproteobacteria / Rhizobiales / Hyphomicrobiaceae / Aquabacter Rod-shaped cells, 0.5–1.0 × 1.5–3.0 µm. Unicellular. Encapsulated. Motile by flagella, but only under certain conditions. No resti...
Chapter
En.hy' dro.bac.ter. Gr. adj. enhydros aquatic Gr. neut. n. bacter masc. form of Gr. neut. n. bacterion a rod; N.L. masc. n. Enhydrobacter aquatic rod. Proteobacteria / Gammaproteobacteria / Pseudomonadales / incertae Sedis - Family III / Enhydrobacter Coccobacillary to rod-shaped cells, 0.5–0.7 × 1.0–5.0 µm. Unicellular; pairs and short chains occu...
Chapter
Lep.to.tri.chi.a.ce'a.e. N.L. fem. n. Leptotrichia type genus of the family; suff. -aceae ending to denote a family; N.L. fem. pl. n. Leptotrichiaceae the Leptotrichia family. Fusobacteria / Fusobacteriia / Fusobacteriales / Leptotrichiaceae
Chapter
Planc.to.my'ces. Gr. adj. planktos wandering, floating; Gr. masc. n. mukês fungus; N.L. masc. n. Planctomyces floating fungus. Planctomycetes / Planctomycetia / Planctomycetales / Planctomycetaceae / Planctomyces Cells are spherical, ovoid, ellipsoidal, teardrop-shaped, or bulbiform. Often relatively large (ignoring appendages and aggregations, ind...
Article
Full-text available
Ten well-annotated genomes of "Sulfolobus islandicus" strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis. To determine whether the ten strains meet the cri...
Chapter
The Planctomycetes phylum is a treasure trove of biology even though it is one of the most recently discovered bacterial groups. These organisms comprise one of the most divergent and innovative bacterial groups due to their (contested) phylogeny, complex life cycles, cell structure and metabolism. Here we trace the history of the planctomycetes fr...
Chapter
Continental Antarctica possesses a characteristic flora and fauna, which varies both qualitatively and quantitatively among the different habitats. Bacteria and other micro-organisms are usually present in numbers far lower than those encountered in temperature regions. In a few areas of the Taylor and Wright dry valleys, no microbes could be detec...
Article
Full-text available
The nuclear compartment commonality (NuCom) hypothesis posits that the Bacteria Domain and Eukarya- Archaea Domains share a major commonality in the process of DNA replication. The ancestors of both types of organisms used a similar or perhaps identical nuclear envelope platform and nuclear compartment to carry out DNA replication. The effects of t...
Article
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After the discovery of ANaerobic AMMonium OXidation (anammox) in the environment, the role of heterotrophic denitrification as the main marine pathway for fixed N loss has been questioned. A 3 part, 15 month time series investigating nitrite reductase (nirS) mRNA transcripts at a single location in the Black Sea was conducted in order to better und...
Article
Full-text available
Autotrophic denitrification was measured in the southwestern coastal Black Sea, where the Bosporus Plume injects oxidized chemical species (especially O2 and ) into the oxic, suboxic, and anoxic layers. Prominent oxygen intrusions caused an overlap of and sulfide at the same station where autotrophic denitrification activity was detected with incub...
Article
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We examined the distribution of uncultured Planctomycetes phylotypes along depth profiles spanning the redox gradient of the Black Sea suboxic zone to gain insight into their respective ecological niches. Planctomycetes phylogeny correlated with depth and chemical profiles, implying similar metabolisms within phylogenetic groups. A suboxic zone sam...
Article
The Black Sea is a permanently anoxic basin with a well-defined redox gradient. We combine environmental 16S rRNA gene data from clone libraries, terminal restriction fragment length polymorphisms, and V6 hypervariable region pyrosequences to provide the most detailed bacterial survey to date. Furthermore, this data set is informed by comprehensive...
Article
Full-text available
A collection of 79 bacterial isolates was obtained by plating scrapings and swabs from five rock varnish samples of the Negev Desert, Israel. Of the bacterial isolates which were obtained, 74 were able to oxidize manganese (MnII→MnIV) under laboratory conditions. The manganese-oxidizing bacteria were characterized and identified, when possible, to...
Chapter
The phylum Fusobacteria is described in part on the basis of phylogenetic analyses of the 16S rRNA gene sequences of its members. The phylum contains rod-shaped bacteria that stain Gram-negative. Described species are fermentative and produce a variety of organic acids when grown on carbohydrates, amino acids or peptides. Some species are pathogeni...
Article
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A total of 20 biogenic carboxylic acids, which contain one to three negatively charged -COO− group(s), were investigated as dispersion additives in the processing of ceramic particles. Only carboxylic acids containing one or more hydroxyl groups were able to disperse α-A12O3 particles in aqueous suspensions. Detailed studies of two carboxylic acids...
Article
Full-text available
Some acidic biopolymers serve as dispersants for colloidal processing of ceramics. One biopolymer we tested was alginate, a heteropolysaccharide containing two carboxylic sugar acids, D-mannuronic and D-guluronic. Kelp alginate was a suitable dispersant, provided that its viscosity was reduced by partial acid hydrolysis. Low molecular weight polyme...
Chapter
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IntroductionEarth is primarily a cold, marine planet with 90% of the ocean’s waters being at 5°C or lower. Frozen soils (permafrost), glaciers and ice sheets, polar sea ice, and snow cover make up 20% of the Earth’s surface environments (Deming and Eicken 2007). A great diversity of microorganisms has been found in these habitats. However, only tho...
Article
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Species of the genus Prosthecomicrobium are noted for their numerous cellular appendages or prosthecae that extend from the cells. This investigation confirms that the genus is polyphyletic based on an extensive analysis of the 16S rRNA gene sequences of several named species of the genus. The analyses indicate that some Prosthecomicrobium species...
Article
Traditionally, biologists exchange scientific materials with other scientists to enable the independent confirmation of their research. For example, in microbiology, cultures of bacteria and other microorganisms and viruses are commonly sent to other laboratories upon request. Apart from this, it is a requirement of the International Code of Nomenc...
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Here we present new information gleaned from cultures of Fe oxidizing bacteria and consider isotopic fractionation effects. This information may prove useful in understanding Fe as a biosignature in the natural environment.
Article
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Bergey's Manual Trust has formed a new international society for microbial taxonomists entitled Bergey's International Society for Microbial Systematics, or BISMiS. The major goals of the society are to comprehend the vast, undiscovered diversity of microbial life and to cultivate, describe, name and classify novel Bacteria and Archaea. The new soc...
Chapter
Cycloclasticus is a genus of marine bacteria that specializes in the aerobic breakdown of polycyclic aromatic hydrocarbon (PAH) compounds including naphthalene, phenanthrene, and pyrene. This bacterial genus contains a single validly described species, Cycloclasticus pugetii. Cycloclasticus is recognized as the predominant genus of PAH-degrading ba...
Book
Includes a revised taxonomic outline for the phyla Bacteroidetes, Planctomycetes, Chlamydiae, Spirochetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes based upon the SILVA project as well as a description of more than 153 genera in 29 families. Includes many medically important taxa.
Article
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The class Dothideomycetes (along with Eurotiomycetes) includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that tolerates surprisingly well harsh conditions prevailing on rock surfaces. Despite their convergent morphology and physiology, RIF are phylogenetically highly diverse in Dothideomycetes. However, the positions of main grou...
Article
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The Universal Tree of Life, which is based on phylogenetic analysis of the RNA sequence from the small ribosomal subunit, was a breakthrough in understanding the relatedness among all living organisms. The result has had a major impact on taxonomy by separating life into three domains: Eukarya, Bacteria, and Archaea. Indeed, microbiologists have us...
Article
Full-text available
An endophytic bacterium, wild poplar strain B (WPB), isolated from stems of wild cottonwood (Populus trichocarpa) was identified to Burkholderia vietnamiensis by analyzing the recA and rDNA genes. Phylogenetic analysis of the nifHDK cluster indicates that the WPB isolate shares high sequence similarity with known B. vietnamiensis strains. The nitro...
Article
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A gas-vacuolate bacterium, strain 174(T), was isolated from a sea-ice core collected from Point Barrow, Alaska, USA. Comparative analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to Psychromonas ingrahamii 37(T), with a similarity of >99 %. However, strain 174(T) could be clearly distinguished from closely rela...
Article
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Poplar and willow are economically-important, fast-growing tree species with the ability to colonize nutrient-poor environments. To initiate a study on the possible contribution of endophytes to this ability, we isolated bacteria from within surface-sterilized stems of native poplar (Populus trichocarpa) and willow (Salix sitchensis) in a riparian...
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The phylum Verrucomicrobia is a divergent phylum within domain Bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. At least one genus, Prosthecobacter, includes species with genes homologous to those encoding eukaryot...
Article
Bergey's Manual Trust is exploring interest among microbiologists in establishing an international society of microbial taxonomists. If you are interested in learning more about this or possibly becoming a charter member, please visit the Trust's Newsletter section (Volume 2, 2008 March and May issues) at our website www.bergeys.org and complete a...
Article
SUMMARYA microscope was adapted for immersion in natural aquatic habitats to make direct observations of attaching microorganisms. Using this technique the growth of several types of algae was followed. The algae observed exhibited a diurnal growth pattern. Most of the size increase occurred during the daylight hours, whereas most cellular division...
Data
Ping Correspodence Analysis. Correspondence analysis of amino acid content of Psychromonas ingrahamii proteins. Gene number, Cluster number, Product
Data
Ping Annotations 2. Further annotation of Psychromonas ingrahamii proteins. Gene number, Gi identifier, predicted protein product, type of product
Article
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The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Correspondence ana...
Article
By introducing the new term ‘organomineral’ to apply to minerals that are affected by organics, mostly life-related, but not directly produced by living cells, we hope to increase the accuracy of the terminology in present usage. We believe that the term ‘biomineral’ does not describe all mineral deposits precisely enough and offer case studies to...
Article
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The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes--bacterial septation and cell division in the case of FtsZ and in the case of tubulins t...
Article
Chemical profiles of the Black Sea suboxic zone show a distribution of nitrogen species which is traditionally associated with denitrification, i.e. a secondary nitrite maximum associated with nitrate depletion and a N(2) gas peak. To better understand the distribution and diversity of the denitrifier community in the Black Sea suboxic zone, we com...
Article
Full-text available
The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA-DNA hybri...
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Desert varnish, a widespread black manganese-rich rock coating, contains labile organic compounds, but a mechanism for its formation and for their preservation remains unproven. Using Raman spectroscopy, X-ray diffraction, and scanning transmission electron microscopy, we analyzed varnish and found amorphous hydrated silica (opal) and the silica mi...
Article
Full-text available
A gas vacuolate bacterium, designated strain 37T, was isolated from a sea ice core collected from Point Barrow, Alaska, USA. Cells of strain 37T were large (6-14 microm in length), rod-shaped, contained gas vacuoles of two distinct morphologies, and grew well at NaCl concentrations of 1-10 % and at temperatures of -12 to 10 degrees C. The DNA G+C c...
Article
Full-text available
Samples from six depths of the Black Sea's suboxic zone were analyzed for 16S rRNA gene sequence information. A gradient in phylotype diversity was found. The distributions of known anaerobic ammonium oxidation (anammox) bacteria, many unknown Planctomycetes, and other phylotypes were examined in relation to the local nutrient and redox conditions.
Article
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We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variati...
Article
Full-text available
Fifteen strains of polycyclic aromatic hydrocarbon (PAH)-catabolizing bacteria, identified as Pseudoalteromonas spp. were isolated from Eagle Harbor, Puget Sound, USA, using a most probable number procedure in which naphthalene or phenanthrene was the sole carbon and energy source. Despite having identical 16S rDNA sequences, some catabolized many...
Chapter
Full-text available
Taxonomy is the science of classification of organisms. Bacterial taxonomy consists of three separate, but interrelated areas: classification, nomenclature, and identification. Classification is the arrangement of organisms into groups (taxa) on the basis of similarities or relationships. Nomenclature is the assignment of names to the taxonomic gro...
Chapter
IntroductionGeneral Phylogeny and TaxonomyThe Verrucomicrobia were proposed as a new division within the bacterial domain by Hedlund et al. (1997) and more recently ranked as a phylum (Garrity and Holt, 2001). They represent a distinct lineage within the phylogenetic trees and contain a number of environmental species as well as a small number of c...
Article
Full-text available
Desert varnish is a black, manganese-rich rock coating that is widespread on Earth. The mechanism underlying its formation, however, has remained unresolved. We present here new data and an associated model for how desert varnish forms, which substantively challenges previously accepted models. We tested both inorganic processes (e.g. clays and oxi...