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Diversity of Assimilatory Nitrate Reductase Genes From Plankton and Epiphytes Associated with a Seagrass Bed

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Abstract

Assimilatory nitrate reductase gene fragments were isolated from epiphytes and plankton associated with seagrass blades collected from Tampa Bay, Florida, USA. Nitrate reductase genes from diatoms (NR) and heterotrophic bacteria (nasA) were amplified by polymerase chain reaction (PCR) using two sets of degenerate primers. A total of 129 NR and 75 nasA clones from four clone libraries, two from each of epiphytic and planktonic components, were sequenced and aligned. In addition, genomic DNA sequences for the NR fragment were obtained from Skeletonema costatum and Thalassiosira weissflogii diatom cultures. Rarefaction analysis with an operational taxonomic unit cut-off of 6% indicated that diversity of the NR and nasA clone libraries were similar, and that sequencing of the clone libraries was not yet saturated. Phylogenetic analysis indicated that 121 of the 129 NR clones sequenced were similar to diatom sequences. Of the eight non-diatom sequences, four were most closely related to the sequence of Chlorella vulgaris. Introns were found in 8% of the Tampa Bay NR sequences; introns were also observed in S. costatum, but not T. weissflogii. Introns from within the same clone library exhibited close similarity in nucleotide sequence, position and length; the corresponding exon sequences were unique. Introns from within the same component were similar in position and length, but not in nucleotide sequence. These findings raise questions about the function of introns, and mechanisms or time evolution of intron formation. A large cluster of 14 of the 75 nasA sequences was similar to sequences from Vibrio species; other sequences were closely related to sequences from Alteromonas, alpha-proteobacteria and Marinomonas-like species. Biogeographically consistent patterns were observed for the nasA Tampa Bay sequences compared with sequences from other locations: for example, Tampa Bay sequences were similar to those from the South Atlantic Bight, but not the Barents Sea. The Tampa Bay NR clone libraries contained sequences that exhibited phylogenetic similarity with sequences from coastal New Jersey and Monterey Bay, USA. For both NR and nasA, the sequences formed phylogenetic clusters containing nitrate reductase gene fragments that were common to both plankton and epiphyte components, and sequences that were unique to just one component. The implication that some organisms may be differentially represented in epiphytic versus planktonic components of the community suggests that local environmental conditions may have ramifications for regulation of nitrate assimilation processes, community composition, and ecosystem function.

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Acknowledgments

The authors thank Sean Kinane, Mark Driscoll, and Alison Meyers for field assistance; Bongkeun Song for providing Thalassiosira weissflogii DNA; and Andrew Allen for assistance with NR and nasA database sequences. This work was supported by NSF grant OCE9981482 to BBW, NSF grants and OCE-0424978 and OCE-0337052 to FIMT, and USGS cooperative agreement 04ERAAG0050 to FIMT.

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Authors and Affiliations

  1. Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA

    Anita Adhitya & Bess B. Ward

  2. Hawaii Institute of Marine Biology, University of Hawaii, PO Box 1346, Kaneohe, HI, 96744, USA

    Florence I. M. Thomas

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  1. Anita Adhitya
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  2. Florence I. M. Thomas
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  3. Bess B. Ward
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Correspondence to Anita Adhitya.

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Adhitya, A., Thomas, F.I.M. & Ward, B.B. Diversity of Assimilatory Nitrate Reductase Genes From Plankton and Epiphytes Associated with a Seagrass Bed. Microb Ecol 54, 587–597 (2007). https://doi.org/10.1007/s00248-006-9175-0

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  • DOI: https://doi.org/10.1007/s00248-006-9175-0

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