Tolli John D.

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Tolli
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John D.
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  • Article
    Unexpected diversity of bacteria capable of carbon monoxide oxidation in a coastal marine environment, and contribution of the Roseobacter-cssociated clade to total CO oxidation
    (American Society for Microbiology, 2006-03) Tolli, John D. ; Sievert, Stefan M. ; Taylor, Craig D.
    The species diversity, phylogenetic affiliations, and physiological activity rates of carbon monoxide-oxidizing microorganisms were investigated, using new isolates from surface waters collected from the coast of New England and type strains from established collections. A direct isolation method allowed the simultaneous recovery of organisms with different growth rates and nutritional requirements and the identification of marine microorganisms that oxidize CO at an environmentally relevant concentration (42 nM CO). Isolates that oxidized CO at environmentally relevant rates (>4.5 x 10–11 nmol CO oxidized cell–1 h–1) were taxonomically diverse, with representatives in the alpha and gamma subclasses of the Proteobacteria and the phylum Bacteroidetes, and represent a hitherto unreported metabolic function for several diverse microbial types. Isolates and type strains having the greatest specific rates of CO metabolism (1.1 x 10–10 to 2.3 x 10–10 nmol CO oxidized cell–1 h–1) belonged to the Roseobacter-associated clade (RAC) of the alpha subclass of the Proteobacteria. By using triple-labeled slide preparations, differential counts of active CO-oxidizing RAC cells, total RAC cells, and total bacterial cell counts in environmental samples were obtained. RAC organisms were a major component of total cell numbers (36%). Based on the density of active CO-oxidizing RAC cells in natural samples and RAC-specific metabolic activities determined for pure cultures, active CO-oxidizing RAC cells may contribute up to 15% of the total CO oxidation occurring in coastal waters.
  • Preprint
    Biological CO oxidation in the Sargasso Sea and in Vineyard Sound, Massachusetts
    ( 2005) Tolli, John D. ; Taylor, Craig D.
    In situ dissolved carbon monoxide (CO) in oligotrophic waters follows a diel cycle varying from 0.3 to 0.5 nmol L-1 before dawn to 2.5 to 3 nmol L-1 in early afternoon, when photo-production of CO exceeds biological CO oxidation and other sinks. Coastal waters may contain up to 15 nmol L-1 [CO] in the daytime. Assays to measure the rate of CO bio-oxidation typically involve the addition of labeled CO to sealed samples, resulting in CO concentrations that are above ambient levels during incubation (up to 9 nmol L-1 CO). We find that biological oxidation of CO obeys first-order kinetics when incubated with up to 4 nmol L-1 [CO] in coastal water samples and up to between 4 and 10.8 nmol L-1 in oligotrophic waters. At higher [CO], kinetic behavior transitions to zero-order or saturation kinetics. CO–oxidation rate coefficients obtained in dark incubations were not representative of the entire diurnal period, as others have assumed. Biological CO–oxidation rate coefficients kco measured in dark incubations of Sargasso Sea surface water in summer were 0.020 ± 0.002 h-1 (mean ± standard deviation) and an order of magnitude greater than those measured in situ during daylight hours (0.002 ± 0.001 h-1). Dark and in situ rate coefficients in early spring were 0.006 ± 0.004 h-1 and 0.003 ± 0.001 h-1, respectively. In dark incubations of Vineyard Sound water, kco was 0.127 ± 0.038 h-1. The apparent half-saturation constant Kapp for CO ranged from 2.04 to 5.44 nmol L-1 CO in both environments.
  • Article
    Diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils
    (American Society for Microbiology, 2005-12) Tolli, John D. ; King, Gary M.
    Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5- bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) soils have been obtained from two sites in a Georgia agroecosystem (peanut and cotton plots) and an unmanaged pine stand (>50 years old). The extracts have been used in PCR amplifications of the cbbL gene for the rubisCO large subunit protein. cbbL PCR products were cloned, sequenced, and subjected to phylogenetic and statistical analyses. Numerous novel lineages affiliated with the form IC clade (one of four form I rubisCO clades), which is typified by facultative lithotrophs, comprised lithotrophic communities from all soils. One of the form IC clone sequences clustered with a form IC clade of ammonia-oxidizing Nitrosospira. Distinct assemblages were obtained from each of the sites and from surface and subsurface soils. The results suggest that lithotrophic populations respond differentially to plant type and land use, perhaps forming characteristic associations. The paucity of clone sequences attributed to ammonia-oxidizing bacteria indicates that even though ammonia oxidation occurs in the various soils, the relevant populations are small compared to those of facultative lithotrophs.
  • Thesis
    Identity and dynamics of the microbial community responsible for carbon monoxide oxidation in marine environments
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2003-09) Tolli, John D.
    As colored dissolved organic matter in seawater absorbs UV solar radiation, a variety of simple chemical species are produced, including carbon monoxide (CO). The ocean surface water is saturated with respect to CO, and is thus a source of CO to the atmosphere. CO reacts with and removes free-radical compounds, and may itself contribute to the 'greenhouse' gas content of the atmosphere. An important sink for CO in seawater is the biological oxidation of CO to CO2 by marine microorganisms. The objectives of this study are to identify component members of the microbial community responsible for the oxidation of CO in coastal marine environments through a combination of recent microbiological and molecular approaches, and to estimate their contributions to total in situ CO bio-oxidation. We utilize an enrichment method that involves cultivation of bacteria on membrane filters, subsequent incubation with radiolabeled CO, and the use of autoradiography to screen colonies with the desired phenotype. Cell-specific CO-oxidation activity is determined for selected purified strains with a time-series 14CO-oxidation method. Molecular phylogeny based on 16S-rDNA gene sequence information within the context of the large and growing 168 database determines the phylogenetic relatedness and identity of marine CO-oxidizing bacteria that result from our cultivation program. The CO oxidizing organisms isolated in this study with greatest activity are closely related to the Roseobacter and Paracoccus genera of the alpha-proteobacteria, collectively known as the "marine alpha group". Other microorganisms found to oxidize CO at environmentally relevant rates are members of beta- and gamma-proteobacteria, and one in the Cytophaga-Flavobacterium-Bacteroides group. A collective CO-oxidation activity was calculated from physiological measurements of purified isolates and abundance estimates of CO-oxidizing marine alpha group organisms. Relative proportions of CO-oxidizing Roseobacter and Paracoccus cells were resolved microscopically by microautoradiography in combination with DAPI and fluorescent-labeled oligonucleotide probes (Substrate Tracking AutoRadiography - Fluorescent In Situ Hybridization (STAR-FISH)). Marine alpha group organisms were a major component of total cell numbers (45.7%) at the time of sampling (March 2003), and CO-oxidizing members of the marine alpha group contributed up to 40.7% of total CO oxidation occurring in coastal waters.