The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation

Danielle L. Rupp, Louis J. Lamit, Stephen M. Techtmann, Evan S. Kane, Erik A. Lilleskov, Merritt R. Turetsky

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae, were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae. IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens.

Original languageEnglish (US)
Pages (from-to)1-17
Number of pages17
JournalApplied and Environmental Microbiology
Issue number12
StatePublished - May 2021


  • archaea
  • bacteria
  • boreal ecosystems
  • carbon cycling
  • climate change
  • fungi
  • hydrology
  • in situ
  • iron
  • methanogen
  • peatland
  • plant functional group
  • plant functional type
  • root
  • subarctic
  • trace gas
  • vegetation

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Ecology
  • Applied Microbiology and Biotechnology


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