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Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Changes in Marsh Elevation, Edaphic Conditions and Plant Host Species

  • Environmental Microbiology
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Abstract

An important source of new nitrogen in salt marsh ecosystems is microbial diazotrophy (nitrogen fixation). The diazotroph assemblages associated with the rhizospheres (sediment directly affected by the roots) of salt marsh plants are highly diverse, somewhat stable, and consist mainly of novel organisms. In Crab Haul Creek Basin, North Inlet, SC, the distribution of plant types into discrete zones is dictated by relatively minor differences in marsh elevation and it was hypothesized that the biotic and abiotic properties of the plant zones would also dictate the composition of the rhizosphere diazotroph assemblages. Over a period of 1 year, rhizosphere sediments were collected from monotypic stands of the black needlerush, Juncus roemerianus, the common pickleweed, Salicornia virginica, the short and tall growth forms of the smooth cordgrass Spartina alterniflora, and a mixed zone of co-occurring S. virginica and short form, S. alterniflora. DNA was extracted, purified and nifH sequences PCR amplified for denaturing gradient gel electrophoresis (DGGE) analysis to determine the composition of the diazotroph assemblages. The diazotroph assemblages were strongly influenced by season, abiotic environmental parameters and plant host. Sediment chemistry and nitrogen fixation activity were also significantly influenced by seasonal changes. DGGE bands that significantly affected seasonal and zone specific clustering were identified and most of these sequences were from novel diazotrophs, unaffiliated with any previously described organisms. At least one third of the recovered nifH sequences were from a diverse assemblage of Chlorobia, and γ-, α-, β- and δ-Proteobacteria. Diazotrophs that occurred throughout the growing season and among all zones (frequently detected) were also mostly novel. These significant sequences indicated that diazotrophs driving the structure of the assemblages were diverse, versatile, and some were ubiquitous while others were seasonally responsive. Several ubiquitous sequences were closely related to sequences of actively N2 fixing diazotrophs previously recovered from this system. These sequences from ubiquitous and versatile organisms likely indicate the diazotrophs in these rhizosphere assemblages that significantly contribute to ecosystem function.

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Acknowledgements

We acknowledge the Belle W. Baruch Institute for Coastal and Marine Sciences for access to sampling sites and for logistical support and the Environmental Genomics Core facility at the University of South Carolina for assistance with DNA sequencing. We also acknowledge Xiaobo Zhou for collection of elevation data and site mapping. This research was supported by the National Science Foundation award MCB-0237854 to C.R.L. Contribution 1619 to the Belle W. Baruch Institute for Coastal and Marine Sciences.

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Author notes

  1. Christopher E. Bagwell

    Present address: Environmental Sciences and Biotechnology, Savannah River National Laboratory, Aiken, SC, 29803, USA

  2. Peter W. Bergholz

    Present address: Crop and Soil Sciences, Cornell University, Ithaca, NY, 14853, USA

Authors and Affiliations

  1. Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA

    Debra A. Davis, Megan D. Gamble, Christopher E. Bagwell, Peter W. Bergholz & Charles R. Lovell

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  1. Debra A. Davis
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  2. Megan D. Gamble
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Correspondence to Charles R. Lovell.

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Figure 1

a PCA results for dates June (SS, JP, S and T) and September 2000 (SV, SS, S and T). Circles denote significance (p < 0.001) for clustering. For June 2000 axis 1 represents 28.4% of the variance and axis 2 represents 14.7% of the variance. For September 2000 axis 1 represents 31.5% of the variance and axis 2 represents 11.5% of the variance (GIF 67 kb). b PCA results for April 2001 (JS, SV, SS, S and T). Circles denote significance (p < 0.001) for clustering. For April 2001 axis 1 represents 25.9% of the variance and axis 2 represents 21.2% of the variance (GIF 28 kb)

High-resolution image (EPS 912 kb)

High-resolution image (EPS 574 kb)

Figure 2

a PCA results for Salicornia virginica and mixed (S. virginica/Short form S. alterniflora—SS) plant zone on all dates. Circles denote significance (p < 0.001) for clustering. For S. virginica axis 1 represents 33.6% of the variance and axis 2 represents 26.4% of the variance. For S. virginica/Short form S. alterniflora axis 1 represents 24.5% of the variance and axis 2 represents 17.3% of the variance (GIF 66 kb). b PCA results for Juncus roemerianus patch (JP) and short form S. alterniflora (S) for all dates. Circles denote significance (p < 0.001) for clustering. For J. roemerianus patch axis 1 represents 24.7% of the variance and axis 2 represents 22.1% of the variance. For short form S. alterniflora, axis 1 represents 25.8% of the variance and axis 2 represents 12.6% of the variance (GIF 71 kb)

High-resolution image (EPS 912 kb)

High-resolution image (EPS 912 kb)

Figure 3

a, b Phylogram of sequences from rhizosphere samples, frequently detected (FD) and longest eigenvector (LV) sequences, nifH mRNA sequences, and seasonally responsive and non-responsive sequences (nucleotide sequences, neighbor-joining, Jukes–Cantor correction, 1,000 bootstrap replicates, complete deletion of gaps and missing data). Sequences with GenBank accession numbers beginning with AY are nifH mRNA sequences from Brown et al. [16] and accession numbers beginning with FJ are seasonally responsive and non-responsive sequences from Gamble et al. [20] a (GIF 61 kb), b (GIF 135 kb)

High-resolution image (EPS 1642 kb)

High-resolution image (EPS 2133 kb)

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Davis, D.A., Gamble, M.D., Bagwell, C.E. et al. Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Changes in Marsh Elevation, Edaphic Conditions and Plant Host Species. Microb Ecol 61, 386–398 (2011). https://doi.org/10.1007/s00248-010-9757-8

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