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Ryan Moore edited this page Jul 13, 2018 · 1 revision

ZetaHunter introduction

Taxonomic groups with limited cultivated representatives are often lumped into a single taxonomic label, which includes multiple distinct ecological units. This makes it difficult to dis- cuss these groups in an ecological context and is particularly problematic within the extensive uncultivated microbial groups in the Candi- date Phyla Radiation (CPR) as well as other poorly represented taxa [1]. One class with few cultivated representatives is the Zetaproteobacteria, from which only three distinct genera have been isolated [2, 3, 4]. Researchers using standard 16S rRNA classification tools (SILVA, RDP, Greengenes) are shown the classification to the nearest defined taxonomy, which only exists for genus Mariprofundus and is found to represent a limited proportion (3.8%) of Zetaproteobacteria sequences found in the environment [5]. As a result of this taxonomy, re- searchers can only accurately classify the group at the class level.

OTU comparisons are often difficult to repro- duce between researchers and over multiple studies. As a result, OTU definitions are usu- ally abandoned. However, using a dataset with a defined, high-resolution taxonomy, those def- initions can be preserved and reproduced, al- lowing for ecological comparisons across stud- ies. Here, we introduce the ZetaHunter pro- gram, which can reproducibly assign novel 16S rRNA sequences to any curated taxonomic framework. The program was designed for and comes with a curated database to identify the members of the Zetaproteobacteria, though it may be used with any curated 16S rRNA database. The use of this program will allow researchers to explicitly discuss ZOTU abun- dance, significance, and niche preference be- tween studies for the Zetaproteobacteria and other microbes with poorly defined taxonomy. Indeed, ZetaHunter has already been used by researchers for classifying Zetaproteobacteria isolates [3, 6], classifying Zetaproteobacteria within 16S rRNA surveys [7, 8], classifying Zetaproteobacteria ecotypes determined from minimum entropy decomposition [9, 10], and in a review of Zetaproteobacteria physiology, ecology, and genomics [5].

References

  1. Hug, LA, BJ Baker, K Anantharaman, CT Brown, AJ Probst, CJ Castelle, CN Butterfield, AW Hernsdorf, Y Amano, K Ise, Y Suzuki, N Dudek, DA Relman, KM Finstad, R Amundson, BC Thomas, and JF Banfield. 2016. A new view of the tree of life. Nat. Microbiol., 1:16048. doi:10.1038/nmicrobiol.2016.48
  2. Emerson, D, and CL Moyer. 2002. Neutrophilic Fe-oxidizing Bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Appl. Environ. Microbiol., 68:3085–3093. doi:10.1128/AEM.68.6.3085- 3093.2002
  3. Mori, JF, JJ Scott, KW Hager, CL Moyer, K Küsel, and D Emerson. 2017. Phys- iological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov. ISME J., 11:2624–2636. doi:10.1038/ismej.2017.132
  4. Beam, JP, JJ Scott, SM McAllister, CS Chan, J McManus, FJR Meysman, and D Emerson. 2017. A biological source of marine sedimentary iron oxides. bioRxiv, 108621. doi:10.1101/108621
  5. McAllister, SM, RM Moore, A Gartman, GW Luther III, and CS Chan. In prep. The marine Fe(II)-oxidizing Zetaproteobacteria.
  6. Chiu, BK, S Kato, SM McAllister, EK Field, and CS Chan. 2017. Novel pelagic iron-oxidizing Zetaproteobacteria from the Chesapeake Bay oxic-anoxic transition zone. Front. Microbiol., 8:1280. doi:10.3389/fmicb.2017.01280
  7. Hager, KW, H Fullerton, DA Butterfield, and CL Moyer. 2017. Community structure of lithotrophically-driven hydrothermal microbial mats from the Mariana Arc and Back-Arc. Front. Microbiol., 8:1578. doi:10.3389/fmicb.2017.01578
  8. Vander Roost, J, IH Thorseth, and H Dahle. 2017. Microbial analysis of Zetaproteobacteria and co-colonizers of iron mats in the Troll Wall Vent Field, Arctic Mid-Ocean Ridge. PLoS ONE, 12:e0185008. doi:10.1371/journal.pone.0185008
  9. Scott, JJ, BT Glazer, and D Emerson. 2017. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lo'ihi Seamount. Environ. Microbiol., 19:301–316. doi:10.1111/1462-2920.13607
  10. Emerson, D, JJ Scott, A Leavitt, E Fleming, and C Moyer. 2017. In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Lo'ihi Seamount. Deep Sea Res. Pt. I, 126:31–39. doi:10.1016/j.dsr.2017.05.011

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