skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

Abstract

Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar inmore » community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Univ. of Michigan, Ann Arbor, MI (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1200903
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; metatranscriptomics; nitrogen deposition; soil fungal community; soil bacterial community; carbohydrate active enzymes; soil RNA

Citation Formats

Hesse, Cedar N., Mueller, Rebecca C., Vuyisich, Momchilo, Gallegos-Graves, La Verne, Gleasner, Cheryl D., Zak, Donald R., and Kuske, Cheryl R. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. United States: N. p., 2015. Web. https://doi.org/10.3389/fmicb.2015.00337.
Hesse, Cedar N., Mueller, Rebecca C., Vuyisich, Momchilo, Gallegos-Graves, La Verne, Gleasner, Cheryl D., Zak, Donald R., & Kuske, Cheryl R. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. United States. https://doi.org/10.3389/fmicb.2015.00337
Hesse, Cedar N., Mueller, Rebecca C., Vuyisich, Momchilo, Gallegos-Graves, La Verne, Gleasner, Cheryl D., Zak, Donald R., and Kuske, Cheryl R. Thu . "Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests". United States. https://doi.org/10.3389/fmicb.2015.00337. https://www.osti.gov/servlets/purl/1200903.
@article{osti_1200903,
title = {Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests},
author = {Hesse, Cedar N. and Mueller, Rebecca C. and Vuyisich, Momchilo and Gallegos-Graves, La Verne and Gleasner, Cheryl D. and Zak, Donald R. and Kuske, Cheryl R.},
abstractNote = {Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.},
doi = {10.3389/fmicb.2015.00337},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 13 works
Citation information provided by
Web of Science

Save / Share:

Works referencing / citing this record:

Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi
journal, February 2018

  • Entwistle, Elizabeth M.; Zak, Donald R.; Argiroff, William A.
  • Ecological Monographs, Vol. 88, Issue 2
  • DOI: 10.1002/ecm.1288

Anthropogenic N deposition, fungal gene expression, and an increasing soil carbon sink in the Northern Hemisphere
journal, July 2019

  • Zak, Donald R.; Argiroff, William A.; Freedman, Zachary B.
  • Ecology, Vol. 100, Issue 10
  • DOI: 10.1002/ecy.2804

Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments
journal, January 2020


Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands
journal, January 2017

  • Kyaschenko, Julia; Clemmensen, Karina E.; Hagenbo, Andreas
  • The ISME Journal, Vol. 11, Issue 4
  • DOI: 10.1038/ismej.2016.184

Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil
journal, December 2018

  • Levy-Booth, David J.; Giesbrecht, Ian J. W.; Kellogg, Colleen T. E.
  • The ISME Journal, Vol. 13, Issue 4
  • DOI: 10.1038/s41396-018-0334-3

Mycobiome diversity: high-throughput sequencing and identification of fungi
journal, November 2018

  • Nilsson, R. Henrik; Anslan, Sten; Bahram, Mohammad
  • Nature Reviews Microbiology, Vol. 17, Issue 2
  • DOI: 10.1038/s41579-018-0116-y

Nitrogen additions stimulate litter humification in a subtropical forest, southwestern China
journal, December 2018


The known and the unknown in soil microbial ecology
journal, January 2019


Forest microbiome: diversity, complexity and dynamics
journal, November 2016


Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium
journal, April 2019

  • Chen, Ko‐Hsuan; Liao, Hui‐Ling; Bellenger, Jean‐Philippe
  • Environmental Microbiology, Vol. 21, Issue 7
  • DOI: 10.1111/1462-2920.14605

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures
journal, February 2019

  • Thorn, Camilla E.; Bergesch, Christian; Joyce, Aoife
  • Molecular Ecology Resources, Vol. 19, Issue 2
  • DOI: 10.1111/1755-0998.12979

Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria)
journal, November 2019

  • Dumack, Kenneth; Fiore‐Donno, Anna Maria; Bass, David
  • Molecular Ecology Resources, Vol. 20, Issue 2
  • DOI: 10.1111/1755-0998.13112

Long‐term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil
journal, August 2019

  • Tian, Jing; Dungait, Jennifer A. J.; Lu, Xiankai
  • Global Change Biology, Vol. 25, Issue 10
  • DOI: 10.1111/gcb.14750

Gene expression of indoor fungal communities under damp building conditions: Implications for human health
journal, April 2018

  • Hegarty, B.; Dannemiller, K. C.; Peccia, J.
  • Indoor Air, Vol. 28, Issue 4
  • DOI: 10.1111/ina.12459

Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil
journal, May 2018

  • Albright, Michaeline B. N.; Johansen, Renee; Lopez, Deanna
  • Applied and Environmental Microbiology, Vol. 84, Issue 15
  • DOI: 10.1128/aem.00598-18

Anthropogenic N Deposition Alters the Composition of Expressed Class II Fungal Peroxidases
journal, February 2018

  • Entwistle, Elizabeth M.; Romanowicz, Karl J.; Argiroff, William A.
  • Applied and Environmental Microbiology, Vol. 84, Issue 9
  • DOI: 10.1128/aem.02816-17

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil
journal, September 2017


Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses
journal, March 2016

  • Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.00259

Fungal Biodiversity and Their Role in Soil Health
journal, April 2018


Belowground Microbiota and the Health of Tree Crops
journal, June 2018

  • Mercado-Blanco, Jesús; Abrantes, Isabel; Barra Caracciolo, Anna
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.01006

How to normalize metatranscriptomic count data for differential expression analysis
journal, January 2017


Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest
journal, January 2018

  • Vivanco, Lucía; Rascovan, Nicolás; Austin, Amy T.
  • PeerJ, Vol. 6
  • DOI: 10.7717/peerj.4754