Correction: De Vogel, F.A., et al. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021, 9, 186
by
,
Fons A. de Vogel
1,2
,
Cathleen Schlundt
3,†,
Robert E. Stote
4,
Jo Ann Ratto
4 and
Linda A. Amaral-Zettler
1,3,5,*
1
Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands
2
Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.115, 3508 TC Utrecht, The Netherlands
3
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
4
U.S. Army Combat Capabilities Development Command Soldier Center, 10 General Greene Avenue, Natick, MA 01760, USA
5
Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands
*
Author to whom correspondence should be addressed.
†
Current address: GEOMAR, Helmholtz Center for Ocean Research, Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
Microorganisms 2021, 9(4), 744; https://doi.org/10.3390/microorganisms9040744
Submission received: 22 March 2021
/
Accepted: 23 March 2021
/
Published: 2 April 2021
(This article belongs to the Special Issue Microbes on Plastics, Close Encounters of the Fourth Kind)
The authors wish to make the following corrections to this paper [1]:
1. Change to Section 3.1. Isolate Identification
The 16S rRNA gene sequences are deposited under GenBank accession numbers MW435594-MW435596 and in CPXXXXXXX-CPXXXXX. Associated metadata are specified in Supplementary Tables S9 and S10.
To the correct version, as follows:
The 16S rRNA gene sequences are deposited under GenBank accession numbers MW435594-MW435596 and in JAFKOK000000000, JAFKOJ000000000, JAFKOI000000000, and JAFKOH000000000. Associated metadata are specified in Supplementary Tables S9 and S10.
2. Change to Section 3.4. Whole-Genome Sequencing
The RASTtk annotated genomes are available online via https://rast.nmpdr.org/ by logging in as guest and can be found under ID numbers 6666666.521526 (Rhodobacter sp. NTK016B), 6666666.521528 (Bacillus sp. NTK034), 6666666.521530 (Bacillus sp. NTK071) and 6666666.521531 (Bacillus sp. NTK074B). The raw sequence reads are deposited in the NCBI Sequence Read Archive under BioProject PRJNA649735 with sample accession numbers SRR12354198 to SRR12354201. Annotated genomes are also deposited in INSDC under references CPXXXXXX-CPXXXXXX, and associated metadata are specified in Supplementary Table S10.
To the correct version, as follows:
The RASTtk annotated genomes are available online via https://rast.nmpdr.org/ by logging in as guest and can be found under ID numbers 6666666.521526 (Rhodobacter sp. NTK016B), 6666666.521528 (Bacillus sp. NTK034), 6666666.521530 (Bacillus sp. NTK071), and 6666666.521531 (Bacillus sp. NTK074B). The raw sequence reads are deposited in the NCBI Sequence Read Archive under BioProject PRJNA649735 with sample accession numbers SRR12354198 to SRR12354201. Assembled genomes are deposited in INSDC under references JAFKOK000000000, JAFKOJ000000000, JAFKOI000000000, and JAFKOH000000000, and associated metadata are specified in Supplementary Table S10.
3. Change to Data Availability Statement
The genome data obtained in this study can be found there under BioProject number PRJNA649735. More specifically, the raw genome sequence reads are deposited in the NCBI Sequence Read Archive with accession numbers SRR12354198-SRR12354201 and annotated genomes are deposited in INSDC under accession numbers CPXXXXXX-CPXXXXXX. The annotated genomes are also available online at RAST via https://rast.nmpdr.org/, when logging in with a guest-account. They can be found under ID numbers 6666666.521526, 6666666.521528, 6666666.521530, and 6666666.521531.
To the correct version, as follows:
The genome data obtained in this study can be found there under BioProject number PRJNA649735. More specifically, the raw genome sequence reads are deposited in the NCBI Sequence Read Archive with accession numbers SRR12354198-SRR12354201 and assembled genomes are deposited in INSDC under accession numbers JAFKOK000000000, JAFKOJ000000000, JAFKOI000000000, and JAFKOH000000000. The annotated genomes are available online at RAST via https://rast.nmpdr.org/, when logging in with a guest-account. They can be found under ID numbers 6666666.521526, 6666666.521528, 6666666.521530, and 6666666.521531.
4. Addition to Supplementary Table S8
| Protein | NCBI Protein Accession | Species | Signal Peptide | Oxyanion Hole | Lipase Box | Catalytic Triad (S-H-A) | Reference |
| Hypothetical protein ◄ | XXXXXX | Bacillus sp. NTK074B | 1-22 | 57-57 | 119-123 | 121-223-256 | This study |
| Hypothetical protein sed_3530 | ABV38134 | Shewanella sediminis HAW-EB3 | 1-23 | 67-73 | 160-164 | 162-269-331 | [84] |
| Lipase A | P37957 | Bacillus subtilisstrain 168 | 1-31 | 36-42 | 106-110 | 108-164-187 | [85] |
| Lipase class 2 | ABZ77296 | Shewanella halifaxensis HAW-EB4 | 1-23 | 67-73 | 160-164 | 162-269-331 | [84] |
| Lipase precursor ◄ | XXXXXX | Vibrio alginolyticus ATCC 33787 | 1-23 | 33-39 | 104-108 | 106-253-275 | This study |
| Lipase precursor ◄ | XXXXXX | Vibrio proteolyticus NBRC 13287 | 1-23 | 35-41 | 106-110 | 108-255-277 | This study |
| PhaZ7 | Q939Q9 | Paucimonas lemoignei | 1-38 | 80-86 | 172-176 | 174-280-344 | [86–88] |
| Thermostable lipase | Q842J9 | Geobacillus zalihaeT1 | 1-28 | 37-43 | 139-143 | 141-345-386 | [89,90] |
| Triacylglycerol lipase | WP_005101273 | Acinetobacter multispecies | 1-29 | 50-56 | 125-129 | 127-280-302 | [91] |
| Triacylglycerol lipase | WP_005101276 | Acinetobacter multispecies | 1-23 | 44-50 | 120-124 | 122-267-289 | [91] |
| Triacylglycerol lipase | WP_064094572 | Acinetobacter multispecies | 1-21 | 42-48 | 117-121 | 119-266-288 | [91] |
| Triacylglycerol lipase | P22088 | Burkholderia cepacianATCC 21808 | 1-44 | 54-60 | 129-133 | 131-308-330 | [92,93] |
| Triacylglycerol lipase | Q05489 | Burkholderia glumaeATCC 6918 | 1-39 | 49-55 | 124-128 | 126-302-324 | [94,95] |
| Triacylglycerol lipase | P26876 | Pseudomonas aeruginosaPAO1 | 1-26 | 35-41 | 106-110 | 108-255-277 | [96,97] |
To the correct version, as follows:
| Protein | NCBI Protein Accession | Species | Signal Peptide | Oxyanion Hole | Lipase Box | Catalytic Triad (S-H-A) | Reference |
| Hypothetical protein ◄ | MBN8191285 | Bacillus sp. NTK074B | 1-22 | 57-57 | 119-123 | 121-223-256 | This study |
| Hypothetical protein sed_3530 | ABV38134 | Shewanella sediminis HAW-EB3 | 1-23 | 67-73 | 160-164 | 162-269-331 | [84] |
| Lipase A | P37957 | Bacillus subtilisstrain 168 | 1-31 | 36-42 | 106-110 | 108-164-187 | [85] |
| Lipase class 2 | ABZ77296 | Shewanella halifaxensis HAW-EB4 | 1-23 | 67-73 | 160-164 | 162-269-331 | [84] |
| Lipase precursor ◄ | ALR91050 | Vibrio alginolyticus ATCC 33787 | 1-23 | 33-39 | 104-108 | 106-253-275 | Direct Submission (08-DEC-2015) |
| Lipase precursor ◄ | GAD66740 | Vibrio proteolyticus NBRC 13287 | 1-23 | 35-41 | 106-110 | 108-255-277 | Direct submission (10-SEP-2013) |
| PhaZ7 | Q939Q9 | Paucimonas lemoignei | 1-38 | 80-86 | 172-176 | 174-280-344 | [86–88] |
| Thermostablelipase | Q842J9 | Geobacillus zalihaeT1 | 1-28 | 37-43 | 139-143 | 141-345-386 | [89,90] |
| Triacylglycerol lipase | WP_005101273 | Acinetobacter multispecies | 1-29 | 50-56 | 125-129 | 127-280-302 | [91] |
| Triacylglycerol lipase | WP_005101276 | Acinetobacter multispecies | 1-23 | 44-50 | 120-124 | 122-267-289 | [91] |
| Triacylglycerol lipase | WP_064094572 | Acinetobacter multispecies | 1-21 | 42-48 | 117-121 | 119-266-288 | [91] |
| Triacylglycerollipase | P22088 | Burkholderia cepacianATCC 21808 | 1-44 | 54-60 | 129-133 | 131-308-330 | [92,93] |
| Triacylglycerollipase | Q05489 | Burkholderia glumaeATCC 6918 | 1-39 | 49-55 | 124-128 | 126-302-324 | [94,95] |
| Triacylglycerollipase | P26876 | Pseudomonas aeruginosaPAO1 | 1-26 | 35-41 | 106-110 | 108-255-277 | [96,97] |
5. Addition to Table S10 (only Partly Shown):
| NCBI BioProject number | PRJNA649735 | PRJNA649735 | PRJNA649735 | PRJNA649735 |
| NCBI BioSample number | SAMN15677905 | SAMN15677906 | SAMN15677907 | SAMN15677908 |
| NCBI SRA accession number | SRR12354201 | SRR12354200 | SRR12354199 | SRR12354198 |
| NCBI Genome accession number |
To the correct version, as follows:
| NCBI BioProject number | PRJNA649735 | PRJNA649735 | PRJNA649735 | PRJNA649735 |
| NCBI BioSample number | SAMN15677905 | SAMN15677906 | SAMN15677907 | SAMN15677908 |
| NCBI SRA accession number | SRR12354201 | SRR12354200 | SRR12354199 | SRR12354198 |
| NCBI Genome accession number | JAFKOK000000000 | JAFKOJ000000000 | JAFKOI000000000 | JAFKOH000000000 |
The authors would like to apologize to the readers for any inconvenience caused by these changes.
Conflicts of Interest
The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
Reference
- De Vogel, F.A.; Schlundt, C.; Stote, R.E.; Ratto, J.A.; Amaral-Zettler, L.A. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021, 9, 186. [Google Scholar] [CrossRef] [PubMed]
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de Vogel, F.A.; Schlundt, C.; Stote, R.E.; Ratto, J.A.; Amaral-Zettler, L.A. Correction: De Vogel, F.A., et al. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021, 9, 186. Microorganisms 2021, 9, 744. https://doi.org/10.3390/microorganisms9040744
AMA Style
de Vogel FA, Schlundt C, Stote RE, Ratto JA, Amaral-Zettler LA. Correction: De Vogel, F.A., et al. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021, 9, 186. Microorganisms. 2021; 9(4):744. https://doi.org/10.3390/microorganisms9040744
Chicago/Turabian Stylede Vogel, Fons A., Cathleen Schlundt, Robert E. Stote, Jo Ann Ratto, and Linda A. Amaral-Zettler. 2021. "Correction: De Vogel, F.A., et al. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021, 9, 186" Microorganisms 9, no. 4: 744. https://doi.org/10.3390/microorganisms9040744
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