Corrigendum: Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre
- 1College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
- 2Flathead Lake Biological Station, University of Montana, MT, United States
by Gradoville, M. R., Crump, B. C., Church, M. J., Letelier, R. M., and White, A. E. (2017). Front. Microbiol. 8:1122. doi: 10.3389/fmicb.2017.01122
In the original article, there were two errors. First, an incorrect NCBI accession number was provided. A correction has been made to Methods, Bioinformatic Analyses, Paragraph 4:
“All raw sequences are available from NCBI (accession SRP095769). Assemblies and annotation data are available from IMG/M ER (http://img.jgi.doe.gov/mer; Taxon OIDs 3300009572, 3300009536, and 3300010936).”
Additionally, in the original article, the two primer sets used for nested nifH PCR were listed in the incorrect order and included an incorrect reference. A correction has been made to Methods, Nucleic Acid Extraction, Amplification, and Sequencing, Paragraph 3:
“The nifH gene was amplified using nested degenerate nifH primers (Zehr and McReynolds, 1989; Zani et al., 2000). The first round contained 1X PCR buffer, 0.1U Platinum High Fidelity Taq polymerase (Invitrogen), 200 μmol L−1 dNTPs, 3% BSA, 4 mmol L−1 Mg2+, 1 μL DNA or cDNA, and 1 μmol L−1 nifH3 and nifH4 primers (Zani et al., 2000). Reaction conditions were: 94°C for 7 min, followed by 30 cycles of 94°C for 1 min, 57°C for 1 min, and 72°C for 1 min, and a final 72°C extension for 7 min. The second round of nifH PCR used the same components and thermocycling conditions as the first round, except the DNA extract was replaced with 1 μL of the amplified product generated during the first round PCR reaction, and custom primers were used, consisting of gene-specific sites (nifH1 and nifH2), dual- indexed barcodes, Illumina linkers, and a sequencing primer binding region, similar to those described by Kozich et al. (2013; Table S1). PCR negative controls and filter blank samples were included in PCR reactions.”
Finally, there was a mistake in the legend for Supplementary Table 1 as published. This table listed the incorrect nifH primer names. The correct legend appears below.
Table S1: Dual-index barcoded, forward and reverse nifH primers (5′ -> 3′) used in this study. Sample barcodes are shown in bold. Forward and reverse nifH PCR primers are indicated by nifH1 (TGYGAYCCNAARGCNGA) and nifH2 (ADNGCCATCATYTCNCC; note the misprint of this primer in the original manuscript by Zani et al., 2000). NNNN indicate Illumina linker regions: AATGATACGGCGACCACCGAGATCTACAC (forward) and CAAGCAGAAGACGGCATACGAGAT (reverse). Blue text indicates the binding site for sequencing primers, which were designed to optimize melting temperature during sequencing, as described by Kozich et al. (2013).
The authors apologize for these errors and state that they do not change the scientific conclusions of the article in any way.
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., and Schloss, P. D. (2013). Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120. doi: 10.1128/AEM.01043-13
Zani, S., Mellon, M. T., Collier, J. L., and Zehr, J. P. (2000). Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl. Environ. Microbiol. 66, 3119–3124. doi: 10.1128/AEM.66.7.3119-3124.2000
Keywords: Trichodesmium, marine microbiome, nifH diversity, heterotrophic marine diazotrophs, metagenomics, 16S rRNA, nitrogen fixation
Citation: Gradoville MR, Crump BC, Letelier RM, Church MJ and White AE (2017) Corrigendum: Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre. Front. Microbiol. 8:1780. doi: 10.3389/fmicb.2017.01780
Received: 14 August 2017; Accepted: 01 September 2017;
Published: 19 September 2017.
Edited and reviewed by: Sophie Rabouille, Centre National de la Recherche Scientifique (CNRS), France
Copyright © 2017 Gradoville, Crump, Letelier, Church and White. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Mary R. Gradoville, firstname.lastname@example.org
†Present Address: Mary R. Gradoville, Ocean Sciences Department, University of Santa Cruz, Santa Cruz, CA, United States