DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones

Abstract

Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the efects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in fve ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profle variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment efects on gene profles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these efects varied among ecozones. Our results suggest that ecozone-specifc nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.

Authors:
ORCiD logo [1];  [2];  [2];  [1]
  1. Univ. of British Columbia, Vancouver, BC (Canada)
  2. Georgia Inst. of Technology, Atlanta, GA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Genome Canada; Genome British Columbia; TULA Foundation
OSTI Identifier:
1624382
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; science & technology - other topics; carbon cycle; element cycles; microbial ecology; soil microbiology

Citation Formats

Cardenas, Erick, Orellana, Luis H., Konstantinidis, Konstantinos T., and Mohn, William W. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. United States: N. p., 2018. Web. doi:10.1038/s41598-018-21197-0.
Cardenas, Erick, Orellana, Luis H., Konstantinidis, Konstantinos T., & Mohn, William W. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. United States. https://doi.org/10.1038/s41598-018-21197-0
Cardenas, Erick, Orellana, Luis H., Konstantinidis, Konstantinos T., and Mohn, William W. Fri . "Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones". United States. https://doi.org/10.1038/s41598-018-21197-0. https://www.osti.gov/servlets/purl/1624382.
@article{osti_1624382,
title = {Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones},
author = {Cardenas, Erick and Orellana, Luis H. and Konstantinidis, Konstantinos T. and Mohn, William W.},
abstractNote = {Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the efects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in fve ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profle variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment efects on gene profles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these efects varied among ecozones. Our results suggest that ecozone-specifc nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.},
doi = {10.1038/s41598-018-21197-0},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {2}
}

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

Citation Metrics:
Cited by: 12 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: Model of nitrogen cycle in forest soils. DNRA: dissimilatory nitrate reduction to ammonia. Nitrite (NO2−) appears twice since it is an intermediate in denitrification, nitrification, and DNRA. The four reactions in denitrification are shown in grey arrows. Significant differences in abundance for genes targeted in our database are shownmore » in blue (Anova p < 0.05, controlling for ecozone differences). Abundances for the IDF ecozone were not included in the calculation due to differences in the sequencing method for that ecozone.« less

Save / Share:

Works referenced in this record:

Forest soil carbon is threatened by intensive biomass harvesting
journal, November 2015

  • Achat, David L.; Fortin, Mathieu; Landmann, Guy
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep15991

The North American long-term soil productivity experiment: Findings from the first decade of research
journal, December 2005

  • Powers, Robert F.; Andrew Scott, D.; Sanchez, Felipe G.
  • Forest Ecology and Management, Vol. 220, Issue 1-3
  • DOI: 10.1016/j.foreco.2005.08.003

Effects of forest biomass harvesting on soil productivity in boreal and temperate forests — A review
journal, December 2011

  • Thiffault, Evelyne; Hannam, Kirsten D.; Paré, David
  • Environmental Reviews, Vol. 19, Issue NA
  • DOI: 10.1139/a11-009

Effects of organic matter removal, soil compaction and vegetation control on 10th year biomass and foliar nutrition: LTSP continent-wide comparisons
journal, August 2012


A meta-analysis of soil microbial biomass responses to forest disturbances
journal, January 2013


Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
journal, August 2012

  • Hartmann, Martin; Howes, Charles G.; VanInsberghe, David
  • The ISME Journal, Vol. 6, Issue 12
  • DOI: 10.1038/ismej.2012.84

Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands
journal, December 2009


Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils
journal, August 2015

  • Leung, Hilary T. C.; Maas, Kendra R.; Wilhelm, Roland C.
  • The ISME Journal, Vol. 10, Issue 2
  • DOI: 10.1038/ismej.2015.118

Forest harvesting reduces the soil metagenomic potential for biomass decomposition
journal, April 2015

  • Cardenas, Erick; Kranabetter, J. M.; Hope, Graeme
  • The ISME Journal, Vol. 9, Issue 11
  • DOI: 10.1038/ismej.2015.57

Nitrogen and Phosphorus Limitation over Long-Term Ecosystem Development in Terrestrial Ecosystems
journal, August 2012


The influence of the forest canopy on nutrient cycling
journal, November 2002


Nitrogen leaching following whole-tree and bole-only harvests on two contrasting Pacific Northwest sites
journal, March 2012


The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria
journal, January 2014


FunGene: the functional gene pipeline and repository
journal, January 2013


CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012


Fast and sensitive protein alignment using DIAMOND
journal, November 2014

  • Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3176

Random Forests
journal, January 2001


Feature Selection with the Boruta Package
journal, January 2010

  • Kursa, Miron B.; Rudnicki, Witold R.
  • Journal of Statistical Software, Vol. 36, Issue 11
  • DOI: 10.18637/jss.v036.i11

Integrative analysis of environmental sequences using MEGAN4
journal, June 2011

  • Huson, D. H.; Mitra, S.; Ruscheweyh, H. -J.
  • Genome Research, Vol. 21, Issue 9
  • DOI: 10.1101/gr.120618.111

Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012

  • Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
  • Nature Methods, Vol. 9, Issue 8
  • DOI: 10.1038/nmeth.2066

Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems
journal, December 2016


Impacts of forest harvesting on biological processes in northern forest soils
journal, August 2000


Harvest impacts on soil carbon storage in temperate forests
journal, February 2010

  • Nave, Lucas E.; Vance, Eric D.; Swanston, Christopher W.
  • Forest Ecology and Management, Vol. 259, Issue 5
  • DOI: 10.1016/j.foreco.2009.12.009

A meta-analysis of the effects of clearcut and variable-retention harvesting on soil nitrogen fluxes in boreal and temperate forests
journal, September 2011

  • Jerabkova, Lucie; Prescott, Cindy E.; Titus, Brian D.
  • Canadian Journal of Forest Research, Vol. 41, Issue 9
  • DOI: 10.1139/x11-087

Nitrate leaching in forest ecosystems is related to forest floor CN ratios
journal, January 1998


Microbial Potential for Ecosystem N Loss Is Increased by Experimental N Deposition
journal, October 2016


Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
journal, July 2011

  • Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina
  • The ISME Journal, Vol. 6, Issue 2
  • DOI: 10.1038/ismej.2011.95

Resistance and resilience of the forest soil microbiome to logging-associated compaction
journal, September 2013

  • Hartmann, Martin; Niklaus, Pascal A.; Zimmermann, Stephan
  • The ISME Journal, Vol. 8, Issue 1
  • DOI: 10.1038/ismej.2013.141

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013

  • Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
  • Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41
  • DOI: 10.1186/1754-6834-6-41

Risk analysis of effects of whole-tree harvesting on site productivity
journal, October 2012


Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
journal, June 2009

  • Lauber, C. L.; Hamady, M.; Knight, R.
  • Applied and Environmental Microbiology, Vol. 75, Issue 15
  • DOI: 10.1128/AEM.00335-09

Determinants of bacterial communities in Canadian agroforestry systems: Co-occurrence patterns of soil bacterial communities
journal, August 2015

  • Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N.
  • Environmental Microbiology, Vol. 18, Issue 6
  • DOI: 10.1111/1462-2920.12986

Soil properties and tree species drive ß-diversity of soil bacterial communities
journal, September 2014


Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale
journal, August 2010


Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees
journal, May 2015


Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil
journal, June 2001


Environmental pH as an important factor for the distribution of urease positive ammonia-oxidizing bacteria
journal, February 2005


Temporal and Spatial Distribution of the nifH Gene of N 2 Fixing Bacteria in Forests and Clearcuts in Western Oregon
journal, January 2000

  • Shaffer, B. T.; Widmer, F.; Porteous, L. A.
  • Microbial Ecology, Vol. 39, Issue 1
  • DOI: 10.1007/s002489900183

Temporal and Spatial Distribution of the nifH Gene of N 2 Fixing Bacteria in Forests and Clearcuts in Western Oregon
journal, January 2000

  • Shaffer, B. T.; Widmer, F.; Porteous, L. A.
  • Microbial Ecology, Vol. 39, Issue 1
  • DOI: 10.1007/s002489900183

Harvest impacts on soil carbon storage in temperate forests
journal, February 2010

  • Nave, Lucas E.; Vance, Eric D.; Swanston, Christopher W.
  • Forest Ecology and Management, Vol. 259, Issue 5
  • DOI: 10.1016/j.foreco.2009.12.009

Effects of organic matter removal, soil compaction and vegetation control on 10th year biomass and foliar nutrition: LTSP continent-wide comparisons
journal, August 2012


Risk analysis of effects of whole-tree harvesting on site productivity
journal, October 2012


Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees
journal, May 2015


Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems
journal, December 2016


Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale
journal, August 2010


Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
journal, July 2011

  • Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina
  • The ISME Journal, Vol. 6, Issue 2
  • DOI: 10.1038/ismej.2011.95

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
journal, August 2012

  • Hartmann, Martin; Howes, Charles G.; VanInsberghe, David
  • The ISME Journal, Vol. 6, Issue 12
  • DOI: 10.1038/ismej.2012.84

Resistance and resilience of the forest soil microbiome to logging-associated compaction
journal, September 2013

  • Hartmann, Martin; Niklaus, Pascal A.; Zimmermann, Stephan
  • The ISME Journal, Vol. 8, Issue 1
  • DOI: 10.1038/ismej.2013.141

Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012

  • Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
  • Nature Methods, Vol. 9, Issue 8
  • DOI: 10.1038/nmeth.2066

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
journal, January 2021


Forest soil carbon is threatened by intensive biomass harvesting
journal, November 2015

  • Achat, David L.; Fortin, Mathieu; Landmann, Guy
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep15991

CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012


A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria
journal, January 2014


The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

The influence of the forest canopy on nutrient cycling
journal, November 2002


Determinants of bacterial communities in Canadian agroforestry systems: Co-occurrence patterns of soil bacterial communities
journal, August 2015

  • Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N.
  • Environmental Microbiology, Vol. 18, Issue 6
  • DOI: 10.1111/1462-2920.12986

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea
journal, August 2012

  • Hatzenpichler, Roland
  • Applied and Environmental Microbiology, Vol. 78, Issue 21
  • DOI: 10.1128/aem.01960-12

A meta-analysis of the effects of clearcut and variable-retention harvesting on soil nitrogen fluxes in boreal and temperate forests
journal, September 2011

  • Jerabkova, Lucie; Prescott, Cindy E.; Titus, Brian D.
  • Canadian Journal of Forest Research, Vol. 41, Issue 9
  • DOI: 10.1139/x11-087

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013

  • Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
  • Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41
  • DOI: 10.1186/1754-6834-6-41

Nitrogen and Phosphorus Limitation over Long-Term Ecosystem Development in Terrestrial Ecosystems
journal, August 2012


Feature Selection with the Boruta Package
journal, January 2010

  • Kursa, Miron B.; Rudnicki, Witold R.
  • Journal of Statistical Software, Vol. 36, Issue 11
  • DOI: 10.18637/jss.v036.i11

Works referencing / citing this record:

Metagenomic analysis of relationships between the denitrification process and carbon metabolism in a bioaugmented full-scale tannery wastewater treatment plant
journal, September 2019

  • Emmanuel, S. Aalfin; Sul, Woo Jun; Seong, Hoon Je
  • World Journal of Microbiology and Biotechnology, Vol. 35, Issue 10
  • DOI: 10.1007/s11274-019-2716-8

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

Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests
journal, July 2019

  • Dukunde, Amélie; Schneider, Dominik; Schmidt, Marcus
  • Frontiers in Microbiology, Vol. 10
  • DOI: 10.3389/fmicb.2019.01519

Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.