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Amplicon Sequence Collections

16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary

Eugenia Naro-Maciel, Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald
Frank J. Stewart, Editor
Eugenia Naro-Maciel
aLiberal Studies, New York University, New York, New York, USA
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Melissa R. Ingala
bSackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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Irena E. Werner
cBiology Department, College of Staten Island, City University of New York, Staten Island, New York, USA
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Allison M. Fitzgerald
dNew Jersey City University, Jersey City, New Jersey, USA
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Frank J. Stewart
Georgia Institute of Technology
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DOI: 10.1128/MRA.00182-20
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ABSTRACT

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

ANNOUNCEMENT

With increased urbanization comes the recommendation to monitor disrupted ecological communities and maintain sustainable environments. Much of the biodiversity in New York City, New York, remains to be described, including cryptic prokaryotic communities in the South Bronx River Estuary. Here, 16S rRNA gene amplicons from 33 samples collected at Hunts Point Riverside Park (nsediment, 9; nwater, 8) and Soundview Park (nsediment, 8; nwater, 8) are presented. Soundview (40.81N, 73.87W) is among the successful regional oyster restoration sites (1), and Hunts Point (40.82N, 73.88W) is a former illegal dump area being revitalized as a Bronx River Greenway component.

Sampling occurred between August 2015 and September 2016, monthly from May to October during low tide. Soundview samples were collected along the restored oyster reef, an area containing live Crassostrea virginica. Surface water samples were obtained by horizontally submerging a 1-liter autoclaved jar. Core sediment samples weighing approximately 100 g were collected from the surface sediment layer with a polyvinyl chloride pipe and a pallet shovel (2). Samples were placed in a cooler and then a laboratory refrigerator and were processed within 24 h of collection. Water samples were filtered using Whatman cellulose nitrate sterile filters, and a randomly selected 0.25-g soil subsample was used for extraction. DNA was extracted with the PowerWater and PowerSoil kits for water and soil, respectively (Qiagen, USA), and quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). Samples were stored at −20° C until transfer to MR DNA (Shallowater, TX), where the bacterial V4 hypervariable region segment was amplified with the 16S primers 515F-Y (3) and R806 (4) using the HotStarTaq Plus master mix kit (Qiagen, USA) under standard conditions and controls (5). After agarose gel checks, 3 replicates of the same DNA extract were pooled in equal proportions and purified with calibrated Ampure XP beads (Agencourt Bioscience, USA) (5). A DNA library was created following the Illumina TruSeq protocol, and 16S sequencing was performed using v. 3 chemistry (2 × 250 bp) on the Illumina MiSeq platform.

In total, 4,673,520 raw reads (Hunts Point: nsediment, 1,130,030, and nwater, 1,200,424; Soundview: nsediment, 1,363,728, and nwater, 979,338) were sequenced and then processed with QIIME2 using default parameters unless otherwise specified (v. 2019.10) (6). The DADA2 plugin was used to quality filter, denoise, and join paired-end reads (6, 7). Sequences were truncated at 260 bp for quality purposes and trimmed to remove primers. After DADA2 filtering, 2,585,025 (per-sample average, 78,334; standard error, 73,923) or 58% of reads were retained across all samples (Table 1). The QIIME2 naive Bayesian q2 classifier was used for taxonomic classification in comparison to the SILVA 16S rRNA database (8, 9). The amplicon sequence variant (ASV) feature table, taxonomy, and sample metadata were exported to BIOM format for analysis in R (v. 3.6.1) with default parameters (https://www.r-project.org/) using the phyloseq v. 1.29.0 (10), vegan v. 2.5-6 (https://cran.r-project.org/package=vegan), and ggplot2 v. 3.2.1 (11) packages.

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TABLE 1

Summary of sample data

After removal of contaminant mitochondria and chloroplast sequences, 508,352 sequences and 16,165 unique ASVs were recovered, and rarefaction analysis showed sufficient sampling depth. The mean diversity indices were higher in sediment (observed ASVs: Hunts Point, 1,283.3, and Soundview, 1,646.5; Shannon diversity: Hunts Point, 6.33, and Soundview, 6.14; Pielou’s evenness: Hunts Point, 0.876, and Soundview, 0.848) than in water samples (observed ASVs: Hunts Point, 612.6, and Soundview, 734.1; Shannon diversity: Hunts Point, 4.69, and Soundview, 5.08; Pielou’s evenness: Hunts Point, 0.732, and Soundview, 0.763). The communities were dominated mostly by the bacterial phyla Proteobacteria, Epsilonbacteraeota, Cyanobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria, but other phyla were present in significant proportions (Fig. 1). These analyses provide a baseline for further characterizing and monitoring the microbial biodiversity in a complex urban estuary.

FIG 1
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FIG 1

Relative abundance bar plot of the top 10 microbial phyla obtained from 16S rRNA sequencing of water (W) and sediment (S) samples at Hunts Point Riverside (HP) Park or Soundview (BRO, SVP) Park. Each color shade represents a different phylum of bacteria or archaea, and sample type is indicated by bars below the graph. Samples collected in 2016 have “16” included in the name, while all other samples were collected in 2015. All organisms belong to the domain Bacteria, except for the Nanoarchaeota, which is classified in Archaea.

Data availability.The 16S rRNA amplicon gene sequences from this study have been uploaded to the GenBank Sequence Read Archive (SRA) under the BioProject accession number PRJNA606795 (Table 1).

ACKNOWLEDGMENTS

We thank the New York University Research Challenge Fund (to E.N.-M.) and Experiment.com private donors (to I.E.W.) for funding the research.

Special thanks are extended to Brendan Reid, as well as to student assistants Christian Bojorquez, NaVonna Turner, Sean Thomas, Jennifer Servis, and Patrick Shea. We thank the NY/NJ Baykeeper and NYC Parks (Natural Resources Group) for access to Soundview Park and Hunts Point Riverside Park, as well as for field assistance.

E.N.-M. and I.E.W. developed the research question. I.E.W. and A.M.F. collected the samples and prepared them for sequencing. E.N.-M. and M.R.I. analyzed the data and wrote the paper. All the authors edited and revised the paper.

FOOTNOTES

    • Received 20 February 2020.
    • Accepted 4 May 2020.
    • Published 28 May 2020.
  • Copyright © 2020 Naro-Maciel et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Grizzle R,
    2. Ward K,
    3. Lodge J,
    4. Suszkowski D,
    5. Mosher-Smith K,
    6. Kalchmayr K,
    7. Malinowski P
    . 2012. Oyster Restoration Research Project (ORRP) final technical report. Hudson River Foundation. http://www.hudsonriver.org/download/ORRP_Phase1.2013.pdf.
  2. 2.↵
    1. Fitzgerald AM
    . 2013. The effects of chronic habitat degradation on the physiology and metal accumulation of eastern oysters (Crassostrea virginica) in the Hudson Raritan Estuary. PhD thesis. The City University of New York, New York, NY.
  3. 3.↵
    1. Parada AE,
    2. Needham DM,
    3. Fuhrman JA
    . 2016. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol 18:1403–1414. doi:10.1111/1462-2920.13023.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Apprill A,
    2. McNally S,
    3. Parsons R,
    4. Weber L
    . 2015. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol 75:129–137. doi:10.3354/ame01753.
    OpenUrlCrossRef
  5. 5.↵
    1. Dowd SE,
    2. Sun Y,
    3. Wolcott RD,
    4. Domingo A,
    5. Carroll JA
    . 2008. Bacterial tag–encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis 5:459–472. doi:10.1089/fpd.2008.0107.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Bolyen E,
    2. Rideout JR,
    3. Dillon MR,
    4. Bokulich NA,
    5. Abnet CC,
    6. Al-Ghalith GA,
    7. Alexander H,
    8. Alm EJ,
    9. Arumugam M,
    10. Asnicar F,
    11. Bai Y,
    12. Bisanz JE,
    13. Bittinger K,
    14. Brejnrod A,
    15. Brislawn CJ,
    16. Brown CT,
    17. Callahan BJ,
    18. Caraballo-Rodríguez AM,
    19. Chase J,
    20. Cope EK,
    21. Da Silva R,
    22. Diener C,
    23. Dorrestein PC,
    24. Douglas GM,
    25. Durall DM,
    26. Duvallet C,
    27. Edwardson CF,
    28. Ernst M,
    29. Estaki M,
    30. Fouquier J,
    31. Gauglitz JM,
    32. Gibbons SM,
    33. Gibson DL,
    34. Gonzalez A,
    35. Gorlick K,
    36. Guo J,
    37. Hillmann B,
    38. Holmes S,
    39. Holste H,
    40. Huttenhower C,
    41. Huttley GA,
    42. Janssen S,
    43. Jarmusch AK,
    44. Jiang L,
    45. Kaehler BD,
    46. Kang KB,
    47. Keefe CR,
    48. Keim P,
    49. Kelley ST,
    50. Knights D, et al
    . 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. doi:10.1038/s41587-019-0209-9.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Callahan BJ,
    2. McMurdie PJ,
    3. Rosen MJ,
    4. Han AW,
    5. Johnson AJA,
    6. Holmes SP
    . 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. doi:10.1038/nmeth.3869.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Bokulich NA,
    2. Kaehler BD,
    3. Rideout JR,
    4. Dillon M,
    5. Bolyen E,
    6. Knight R,
    7. Huttley GA,
    8. Gregory Caporaso J
    . 2018. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6:90. doi:10.1186/s40168-018-0470-z.
    OpenUrlCrossRefPubMed
  9. 9.↵
    1. Karst SM,
    2. Dueholm MS,
    3. McIlroy SJ,
    4. Kirkegaard RH,
    5. Nielsen PH,
    6. Albertsen M
    . 2018. Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nat Biotechnol 36:190–195. doi:10.1038/nbt.4045.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. McMurdie PJ,
    2. Holmes S
    . 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. doi:10.1371/journal.pone.0061217.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Ginestet C
    . 2011. ggplot2: elegant graphics for data analysis. J R Stat Soc Ser A Stat Soc 174:245–246. doi:10.1111/j.1467-985X.2010.00676_9.x.
    OpenUrlCrossRefPubMed
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16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary
Eugenia Naro-Maciel, Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald
Microbiology Resource Announcements May 2020, 9 (22) e00182-20; DOI: 10.1128/MRA.00182-20

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16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary
Eugenia Naro-Maciel, Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald
Microbiology Resource Announcements May 2020, 9 (22) e00182-20; DOI: 10.1128/MRA.00182-20
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