Soil fungal and prokaryotic community structure exhibits differential short-term responses to timber harvest in the Pacific Northwest

doi:10.1016/S1002-0160(19)60827-1

Pedosphere

Volume 30, Issue 1, February 2020, Pages 109-125

https://doi.org/10.1016/S1002-0160(19)60827-1 Get rights and content

Abstract

Conventional clear-cut timber harvest is a widespread industrial practice across the Pacific Northwest; however, information regarding how these practices impact soil microbial community structure at the regional scale is limited. With evidence of consistent and substantial impact of harvest on soil microbial functional profiles across the region (despite a range of environmental conditions), the objective of this study was to determine the extent to which harvest also influences the structure of prokaryotic and fungal soil microbial communities, and how generalized these trends are throughout the geographic region. Paired soil samples were collected one year before and after harvest across nine second-growth Douglas-fir forests in the Pacific Northwest. Total community DNA was extracted from the soils, and high-throughput targeted gene sequencing of the 16S rRNA gene for prokaryotes and the internal transcribed spacer (ITS) gene for fungi was performed. Alpha diversity was consistently and significantly higher after harvest; it was moderately so for fungal communities (+14.6%), but only marginally so for prokaryotic communities (+2.0%). Similarly, on average, a greater proportion of the variation in the community structure of fungi (20.1%) at each site was associated with forest harvest compared to that of prokaryotes (13.2%). Overall, the greatest influence of timber harvest on soil microbial communities appeared to be a relative depletion of ectomycorrhizal fungi, with a concomitant enrichment of saprotrophic fungi. Understanding the short-term responses of soil microbial communities across the region, particularly those of tree root-associated symbionts, may aid our understanding of the role soil microbial communities play in ecological succession.

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^*: Present address: Department of Land, Air, and Water Resources, University of California, Davis CA 95616, USA.

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Soil fungal and prokaryotic community structure exhibits differential short-term responses to timber harvest in the Pacific Northwest

Abstract

For Ecol Manage

Soil Biol Biochem

Appl Soil Ecol

For Ecol Manage

Fungal Ecol

Soil Biol Biochem

Soil Biol Biochem

Soil Biol Biochem

For Ecol Manage

Soil Biol Biochem

Soil Biol Biochem

Fungal Ecol

Resistance, resilience, and redundancy in microbial communities

Proc Natl Acad Sci USA

The functioning of ectomycorrhizal fungi in the field: Linkages in space and time

Plant Soil

Reduction of native mycorrhizae reduce growth of Douglas-fir seedlings

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Methods Ecol Evol

Trimmomatic: A flexible trimmer for Illumina sequence data

Bioinformatics

Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon

Environ Microbiol

Ectomycorrhizas of lodgepole pine (Pinus contorta) seedlings originating from seed in southwestern Alberta cut blocks

Can J Bot

QIIME allows analysis of high-throughput community sequencing data

Nat Methods

Ultrahigh-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

ISME J

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

Proc Natl Acad Sci USA

Forest harvesting reduces the soil metagenomic potential for biomass decomposition

ISME J

Growing-season microclimatic gradients from clearcut edges into old-growth douglas-fir forests

Ecol Appl

Mycorrhizal Fungus Communities of Douglas-fir (Pseudotsuga menziesii) Seedlings and Trees: Effects of Proximity to Residual Trees

Does proximity to mature trees influence ectomycorrhizal fungus communities of Douglas-fir seedlings?

New Phytol

Predicting the responsiveness of soil biodiversity to deforestation: A cross-biome study

Glob Change Biol

Harvesting douglas-fir stands shifts soil microbial activity and biogeochemical cycling

Soil Sci Soc Am J

Increasing biomass demand enlarges negative forest nutrient budget areas in wood export regions

Sci Rep

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

Appl Environ Microbiol

Species richness of ectomycorrhizal fungi in cutblocks of different sizes in the Interior Cedar-Hemlock forests of northwestern British Columbia: Sporocarps and ectomycorrhizae

Can J For Res

Usearch. Lawrence Berkeley National Lab

Wood decay community of raised bogs in West Siberia

Environ Dyn Glob Climate Change