Great Lakes Cladophora harbors phylogenetically diverse nitrogen-fixing microorganisms

Muruleedhara N. Byappanahalli, Meredith B. Nevers, Katarzyna Przybyla-Kelly, Satoshi Ishii, Timothy L. King, Aaron W. Aunins

Research output: Contribution to journalArticlepeer-review

Abstract

Nitrogen-fixing microorganisms are among the epiphytic communities in Cladophora, potentially benefitting the algae in nutrient-deficient waters, but their abundance and diversity remain unexplored. In this study, we determined the abundance and taxonomic composition of these nitrogen-fixing microorganisms in Cladophora growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan (N = 33) during the summer 2015, using two complementary genomic techniques: quantitative PCR (qPCR) and shotgun metagenomic sequencing. Genomic DNA was extracted from processed algal pellets, and the nitrogen-fixing microbes were quantified by qPCR by targeting the nifH gene. Mean nifH concentrations (log10 copy numbers/gram algae fresh weight ± SE) were 5.54 ± 0.09, ranging from 4.31 to 6.57. Mean nifH concentrations in water samples (log10 copy numbers/milliliter of water ± SE) were: 3.25 ± 0.06, ranging from 2.41 to 3.90. Shotgun sequencing of a subset of algal samples representing the four sampling locations (N = 10) revealed as many as 267 nifH reads from among the sequences of the 10 shotgun metagenomes (averaging 27 reads per metagenome), ranging from 5 to 91 reads from Jeorse Park (September) and North Beach (September) locations. Taxonomic assignment of nifH sequences identified members from bacteria and archaea domains showing a clear separation of reads at domain and lower taxonomic levels. Bacteria were relatively more abundant than archaea. Anabaena, Bradyrhizobium, Geobacter, Methylocystis, Oscillatoria sp., and Skermanella (all bacteria), and Methanoregula, Methanothrix, and Methanosarcina (archaea) were among the nitrogen-fixing genera identified by the MEGAN Community Edition program. Collectively, these findings show that phylogenetically diverse nitrogen-fixing microbial communities are part of the Cladophora microbiome, likely contributing to the algal nitrogen needs.

Original languageEnglish (US)
Pages (from-to)186-195
Number of pages10
JournalEnvironmental DNA
Volume1
Issue number2
DOIs
StatePublished - Jul 2019

Bibliographical note

Funding Information:
This research was supported in part by funding from the U.S. Geological Survey's Ecosystems Mission Area. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The authors declare no competing financial interest. Dr. Timothy King, our beloved friend and a coauthor on this manuscript, sadly passed away during the preparation of this manuscript. Tim was instrumental in developing research concepts, designing experiments, and securing funding for the work reported in this study. Tim's untimely passing has been a huge loss to his friends and the scientific community in conservation biology and population genetics, where Tim's leadership was a constant source of inspiration. We thank Troy Janesheski, Rhiannon Ulatowski, USGS, and Julie Kinzelman and Stephan Kurdas, City of Racine, for sample collection; Ashley Spoljaric and Dawn Shively, USGS, for processing samples; and Kelly Duhn (University of Minnesota) for technical assistance.

Funding Information:
This research was supported in part by funding from the U.S. Geological Survey's Ecosystems Mission Area. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The authors declare no competing financial interest.

Publisher Copyright:
© 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd

Keywords

  • Lake Michigan
  • Proteobacteria
  • archaea
  • cyanobacteria
  • ecosystem
  • metagenome
  • metagenomics
  • nitrogen

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