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Symbiotic N2-Fixer Community Composition, but Not Diversity, Shifts in Nodules of a Single Host Legume Across a 2-Million-Year Dune Chronosequence

Abstract

Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N2)-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient. We collected nodules from plants grown in soils from five chronosequence stages ranging from very young (10s of years; associated with strong N limitation for plant growth) to very old (> 2,000,000 years; associated with strong P limitation), and sequenced the nifH gene in root nodules to determine the composition and diversity of N2-fixing bacterial symbionts. A total of 335 unique nifH gene operational taxonomic units (OTUs) were identified. Community composition of N2-fixing bacteria within nodules, but not diversity, changed with increasing soil age. These changes were attributed to pedogenesis-driven shifts in edaphic conditions, specifically pH, exchangeable manganese, resin-extractable phosphate, nitrate and nitrification rate. A large number of common N2-fixing bacteria genera (e.g. Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium) belonging to the Rhizobiaceae family (α-proteobacteria) comprised 70% of all raw sequences and were present in all nodules. However, the oldest soils, which show some of the lowest soil P availability ever recorded, harboured the largest proportion of unclassified OTUs, suggesting a unique set of N2-fixing bacteria adapted to extreme P limitation. Our results show that N2-fixing bacterial composition varies strongly during long-term ecosystem development, even within the same host, and therefore rhizobia show strong edaphic preferences.

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Acknowledgements

We thank Yvette Hill who provided comments and information of rhizobia nodulating A. rostellifera. We appreciate the cooperation by the Western Australian Department of Parks and Wildlife (DPaW) with acquiring permits to sample the field soils. We are grateful for the hard work of Yuphin Khentry and Ghulam Abbas during the soil collections and glasshouse measurements.

Funding

This research was made possible by research grants from the Australian Research Council (DE120100352 and DP130100016) and the Hermon Slade Foundation to E.L.

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Contributions

FPT and EL designed the experiment. FPT supervised and maintained the experiment. CB conducted the DNA extractions. CB performed statistical analyses with assistance from all authors. AB conducted the bioinformatics work. CB led the writing of the manuscript and all authors contributed to revisions.

Corresponding author

Correspondence to Christina Birnbaum.

Electronic Supplementary Material

Online resource 1

List of 30 soil variables, sampling levels and methods used in dbRDA analyses. (XLSX 13 kb)

Online resource 2

Means and ± S.E. of 30 soil variables used in the dbRDA analysis. (XLSX 13 kb)

ESM 1

(DOCX 21 kb)

Online resource 5

Phylogenetic tree showing the 335 OTUs based on nifH gene amplified from A. rostellifera nodules’ DNA after growing in the greenhouse in soils collected across five chronosequence stages in Jurien Bay, Western Australia. The tree is based on the neighbour joining tree of Gaby et al. (2014) to which 335 OTU sequences were added using the ARB parsimony tool. Three phylogenetically distinct clusters are shown. In blue are marked the 12 most common OTUs based on Table 2. In green are marked OTUs that associated significantly with dune stage 5 (the oldest) based on Table 3. (attached separately) (PDF 50 kb)

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Birnbaum, C., Bissett, A., Teste, F.P. et al. Symbiotic N2-Fixer Community Composition, but Not Diversity, Shifts in Nodules of a Single Host Legume Across a 2-Million-Year Dune Chronosequence. Microb Ecol 76, 1009–1020 (2018). https://doi.org/10.1007/s00248-018-1185-1

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Keywords

  • Acacia rostellifera
  • Rhizobia
  • Ecosystem development
  • Illumina sequencing
  • nifH