Papers by Stephanie Connon
Applied and Environmental Microbiology, May 1, 2004
Since their initial discovery in samples from the north Atlantic Ocean, 16S rRNA genes related to... more Since their initial discovery in samples from the north Atlantic Ocean, 16S rRNA genes related to the environmental gene clone cluster known as SAR202 have been recovered from pelagic freshwater, marine sediment, soil, and deep subsurface terrestrial environments. Together, these clones form a major, monophyletic subgroup of the phylum Chloroflexi. While members of this diverse group are consistently identified in the marine environment, there are currently no cultured representatives, and very little is known about their distribution or abundance in the world's oceans. In this study, published and newly identified SAR202-related 16S rRNA gene sequences were used to further resolve the phylogeny of this cluster and to design taxon-specific oligonucleotide probes for fluorescence in situ hybridization. Direct cell counts from the Bermuda Atlantic time series study site in the north Atlantic Ocean, the Hawaii ocean time series site in the central Pacific Ocean, and along the Newport hydroline in eastern Pacific coastal waters showed that SAR202 cluster cells were most abundant below the deep chlorophyll maximum and that they persisted to 3,600 m in the Atlantic Ocean and to 4,000 m in the Pacific Ocean, the deepest samples used in this study. On average, members of the SAR202 group accounted for 10.2% (؎5.7%) of all DNA-containing bacterioplankton between 500 and 4,000 m.
Applied and Environmental Microbiology, Aug 1, 2002
Microbial diversity studies based on the cloning and sequencing of DNA from nature support the co... more Microbial diversity studies based on the cloning and sequencing of DNA from nature support the conclusion that only a fraction of the microbial diversity is currently represented in culture collections. Out of over 40 known prokaryotic phyla, only half have cultured representatives. In an effort to culture the uncultured phylotypes from oligotrophic marine ecosystems, we developed high-throughput culturing procedures that utilize the concept of extinction culturing to isolate cultures in small volumes of low-nutrient media. In these experiments, marine bacteria were isolated and cultivated at in situ substrate concentrations-typically 3 orders of magnitude less than common laboratory media. Microtiter plates and a newly developed procedure for making cell arrays were employed to raise the throughput rate and lower detection sensitivity, permitting cell enumeration from 200-l aliquots of cultures with densities as low as 10 3 cells/ml. Approximately 2,500 extinction cultures from 11 separate samplings of marine bacterioplankton were screened over the course of 3 years. Up to 14% of the cells collected from coastal seawater were cultured by this method, which was 14-to 1,400-fold higher than the numbers obtained by traditional microbiological culturing techniques. Among the microorganisms cultured were four unique cell lineages that belong to previously uncultured or undescribed marine Proteobacteria clades known from environmental gene cloning studies. These cultures are related to the clades SAR11 (␣ subclass), OM43 ( subclass), SAR92 (␥ subclass), and OM60/OM241 (␥ subclass). This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries.
Springer eBooks, Sep 2, 2008
... For example, several B. anthracis strains have been found to have resistance to gamma phage a... more ... For example, several B. anthracis strains have been found to have resistance to gamma phage and some rare B. cereus strains are sensitive to gamma phage and penicillin and are nonhemolytic (Schuch, Nelson and Fischetti 2002; Marston et al. 2006) (Fig. 19.6). ...
Environmental Microbiology, Jul 26, 2018
Applied and Environmental Microbiology, Jun 14, 2022
Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large... more Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood.
AGU Fall Meeting Abstracts, Dec 1, 2012
AGU Fall Meeting Abstracts, Dec 14, 2015
AGU Fall Meeting Abstracts, Dec 19, 2014
bioRxiv (Cold Spring Harbor Laboratory), Aug 2, 2021
Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic an... more Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physico-chemical data and 16S rRNA amplicons to characterize the diversity, temperature optima, and biogeographic distribution of sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California, the deepest known hydrothermal vent field in the Pacific Ocean. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 1/3 of the currently known phylum diversity, showing the microbial community in Auka hydrothermal sediments is highly diverse. Large scale 16S rRNA amplicon screening of 227 sediment samples across the vent field indicates that the MAGs are largely representative of the microbial community. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota (Tharpobacteria) suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison of the average nucleotide identity of the Auka MAGs with MAGs from the Guaymas Basin vent field, found 400 km to the Northwest, revealed a remarkable 20% species-level overlap between vent sites, suggestive of long-distance species transfer and sediment colonization. An adapted version of a recently developed model for predicting optimal growth temperature to the Auka and Guaymas MAGs indicates several of these uncultured microorganisms could grow at temperatures exceeding the currently known upper limit of life. Extending this analysis to reference data shows that thermophily is a trait that has evolved frequently among Bacteria and Archaea. Combined, our results show that Auka vent field offers new perspectives on our understanding of hydrothermal vent microbiology. 2 .
The ISME Journal, Mar 28, 2022
Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic an... more Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.
Environmental Microbiology Reports, Jan 29, 2013
Nature microbiology, Jan 13, 2022
T o chronicle the emergence of evolutionary innovation is a long-standing pursuit in biology. Due... more T o chronicle the emergence of evolutionary innovation is a long-standing pursuit in biology. Due to scant record of reliable microscale fossils, resolving evolutionary history at the cellular scale relies primarily on molecular comparisons across present-day life, provided that phylogenetic relatives can be well delineated. Culture-independent metagenomics has substantially expanded our access to the Earth's diverse biomes 1 , including lineages carrying genetic imprints of critical evolutionary events through deep time. The Heimdallarchaeota, previously referred to as the ancient archaea group (AAG) 2 , are one such group and the closest known relative of eukaryotes as suggested by phylogenomics 3-5. Heimdallarchaeotes and their related lineages collectively called the Asgard archaea contain a sizeable repertoire of eukaryotic signature proteins (ESPs) 3,6,7. However, the genetic make-up of Heimdallarchaeotes has so far only been inferred from a few metagenome-assembled genomes (MAGs), which are fragmented and suffer from uncertainty in their completeness and accuracy 3,7-12. Mobile (genetic) elements, including transposons, viruses and plasmids, which are known to play dominant roles in evolution 13 , are frequently misassembled, omitted or misassigned during MAG assembly and binning 14. These drawbacks propagate into uncertainties in the resolution of archaeal lineages related to eukaryotes and can obscure the drivers of evolutionary crosstalk and divergence between eukaryotes and their prokaryotic relatives. Results Circular Heimdallarchaeota genomes. Recovering contiguous genomes from environmental samples is notoriously challenging due to their enormous biodiversity and strain-level heterogeneity, while most known lineages have been hard to isolate due to their unresolved metabolism and/or poorly understood partner-dependent growth. We overcame these limitations by combining cultivation methods with molecular community profiling to progressively dissect environmental microbial enrichment cultures where a clonal expansion of our species of interest was accompanied by a reduction in diversity (Extended Data Fig. 1 and Methods). Using anaerobic cultivation methods, we enriched a member of the Heimdallarchaeota AAG clade from a barite-rich rock retrieved in 2017 from the Auka hydrothermal vent field (23° 57′ N, 108° 51′ W) located in the southern Pescadero Basin near the southern tip of the Gulf of California at a water depth of 3,674 m (ref. 15). While initially below detection, this rock-associated AAG phylotype emerged at 1-4% of the 16S ribosomal RNA gene relative abundance in 3 lactate-supplemented, anaerobic enrichment cultures incubated at 40 °C after 7 months (Extended Data Fig. 1, Supplementary Tables 1-3 and Supplementary Note 1). In an independent set of enrichments inoculated with sediments collected from the Auka site in 2018 (23° 53′ N, 108° 48′ W), alkane-supplemented anaerobic incubations at 37 °C additionally yielded a second AAG phylotype that increased in 16S rRNA gene relative abundance from 0.03 to 4-7% after 9 months (Supplementary Tables 4 and 5 and Supplementary Note 1). De novo assembly 16-18 of Nanopore long-read and Illumina paired-end sequencing of genomic DNA recovered from these enrichments (Supplementary Table 6) resulted in complete circularized genomes of the two AAG species from the barite and sediment enrichment cultures, with genome sizes of 3.32 and 3.08 million
Applied and Environmental Microbiology, Sep 15, 2007
Frontiers in Microbiology, Aug 17, 2018
The capability of microorganisms to alter metal speciation offers potential for the development o... more The capability of microorganisms to alter metal speciation offers potential for the development of new strategies for immobilization of toxic metals in the environment. A metal-reducing microbe, "Pelosinus lilae" strain UFO1, was isolated under strictly anaerobic conditions from an Fe(III)-reducing enrichment established with uncontaminated soil from the Department of Energy Oak Ridge Field Research Center, Tennessee. "P. lilae" UFO1 is a rod-shaped, spore-forming, and Gram-variable anaerobe with a fermentative metabolism. It is capable of reducing the humic acid analog anthraquinone-2,6-disulfonate (AQDS) using a variety of fermentable substrates and H 2. Reduction of Fe(III)-nitrilotriacetic acid occurred in the presence of lactate as carbon and electron donor. Ferrihydrite was not reduced in the absence of AQDS. Nearly complete reduction of 1, 3, and 5 ppm Cr(VI) occurred within 24 h in suspensions containing 10 8 cells mL −1 when provided with 10 mM lactate; when 1 mM AQDS was added, 3 and 5 ppm Cr(VI) were reduced to 0.1 ppm within 2 h. Strain UFO1 is a novel species within the bacterial genus Pelosinus, having 98.16% 16S rRNA gene sequence similarity with the most closely related described species, Pelosinus fermentans R7 T. The G+C content of the genomic DNA was 38 mol%, and DNA-DNA hybridization of "P. lilae" UFO1 against P. fermentans R7 T indicated an average 16.8% DNA-DNA similarity. The unique phylogenetic, physiologic, and metal-transforming characteristics of "P. lilae" UFO1 reveal it is a novel isolate of the described genus Pelosinus.
FEMS Microbiology Ecology, Mar 25, 2010
Two different versions of the 16S rRNA gene, one of which contained an unusual 100-bp insertion i... more Two different versions of the 16S rRNA gene, one of which contained an unusual 100-bp insertion in helix 6, were detected in isolate UFO1 acquired from the Oak Ridge Integrated Field-Research Challenge (ORIFRC) site in Tennessee. rRNA was extracted from UFO1 and analyzed by reverse transcriptase-quantitative PCR with insert-and non-insert-specific primers; only the noninsert 16S rRNA gene sequence was detected. Similarly, PCR-based screening of a cDNA library (190 clones) constructed from reverse-transcribed rRNA from UFO1 did not detect any clones containing the 100-bp insert. Examination of cDNA with primers specific to the insert-bearing 16S rRNA gene, but downstream of the insert, suggests that the insert was excised from rRNA. Inspection of other 16S rRNA genes in the GenBank database revealed that a homologous insert sequence, also found in helix 6, has been reported in other environmental clones, including those acquired from ORIFRC enrichments. These findings demonstrate the existence of widely divergent copies of the 16S rRNA gene within the same organism, which may confound 16S rRNA gene-based methods of estimating microbial diversity in environmental samples.
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Papers by Stephanie Connon