M. D. Johnston’s research while affiliated with The Ohio State University and other places

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Publications (13)


Supplementary Material 9
  • Data
  • File available

September 2017

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1 Read

R. E. Danczak

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M. D. Johnston

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C. Kenah

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[...]

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Fig. 5 nirK tree. A maximum-likelihood tree of nirK (nitrite reductase) amino acid sequences with bootstrap support indicated by the shaded circles on the nodes 
Fig. 6 Glycoside hydrolase (GH) heat map. A heat map illustrating the presence/absence of various different GH families with putative substrates illustrated by color. 
Map of Ohio and CPR relative abundance through time. a A map of Ohio with studied colors indicated by various colors; colored circles represent the approximate location of the Ohio Department of Natural Resources (ODNR) sampling wells and one private well. Columbus, OH, is indicated as the yellow dot for reference. b Stacked bar chart of CPR phyla relative abundances from the three ODNR sampling locations (Athens, Greene, and Licking). Oxidation-reduction potential (ORP) is plotted atop the abundance graphs as line graphs
CPR relative abundance derived from metagenomic rps3 sequences and bin counts. a Relative percentage of mapped rps3 sequence reads from a given metagenome presented as a stacked bar chart; Inset: a pie chart illustrating the relative percentage of mapped reads for the 0.1-μm filter from Greene 10/2014. b A count of the number of near-complete quality (NC; > 90% complete; solid colors) and incomplete (IC; 50–89% complete; dashed colors) bins from each metagenomic sample (71 total)
Sixteen-protein concatenated ribosomal tree. Concatenated ribosomal protein tree generated from 16 ribosomal proteins (rpL2, 3, 4, 5, 6, 14, 15, 16, 18, 22, 24, rpS3, 8, 10, 17, 19). Each of the major CPR classifications and phyla are provided as text. Each point represents a binned genome from a given location in Ohio, indicated by point shape and color. Newly proposed phyla are indicated by blue text

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Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

September 2017

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1,342 Reads

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135 Citations

Background: The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. Results: Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. Conclusions: CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life.








Citations (1)


... We speculate that its simple metabolic pathways and low-energy attachment mechanism facilitate adaptation to the optimal co-culture system; this also explains the increase in the relative abundance of Patescibacteria over the 3 d co-culture period. Similarly, many studies have shown that the relative abundance of ultra-small Patescibacteria lineages frequently exceed those of other bacteria in diversity surveys [63][64][65][66][67]. Proteobacteria was the second largest phylum of hydrogenogenic CO oxidizers [68], and the decrease in Proteobacteria after 3 days allowed the scallops and seaweed to maintain a good physiological state in the optimal co-culture system. ...

Reference:

Co-Culturing Seaweed with Scallops Can Inhibit the Occurrence of Vibrio by Increasing Dissolved Oxygen and pH
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities