Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

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From: PLoS ONE(Vol. 9, Issue 2)
Publisher: Public Library of Science
Document Type: Article
Length: 10,937 words
Lexile Measure: 1560L

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Author(s): Björn Hoppe 1,2,*, Tiemo Kahl 2, Peter Karasch 3, Tesfaye Wubet 1,5, Jürgen Bauhus 2, François Buscot 1,4,5, Dirk Krüger 1,*

Introduction

Dead wood is an important structural component of forest ecosystems. It influences numerous ecosystem functions [1], [2], including carbon (C) sequestration [3]-[6], nutrient cycling [7], and provision of habitats for wood-dwelling organisms [8], [9]. Although many investigations have focused on the diversity of fungi, particularly Agaricomycotina (basidiomycetes) and some Pezizomycotina (ascomycetes), in terms of assemblages [10]-[12] or their role in wood decomposition [13], the participation of bacteria in the processes involved is largely unexplored. It is known that substrate qualities, such as nutrient and water contents, strongly influence wood colonization by microbes [14]. The amount of nitrogen (N) available in wood is highly restricted [1], with carbon to nitrogen ratios generally ranging from ca. 350-800:1 [15], but wood-decaying fungi can completely mineralize and metabolize most wood residues such as cell wall lignocellulose complexes [16] and are capable of mobilizing enough N to produce not only their vegetative hyphae but also sporocarps and millions of spores. Cowling and Merrill [17] hypothesized that associations with N-fixing bacteria may enable wood-inhabiting fungi to meet their substantial N requirements. Nitrogen fixation, the energetically expensive reduction of atmospheric dinitrogen to two molecules of ammonia, is enabled by adenosine triphosphate (ATP) generated from the decomposition of cellulose [18]. This connects bacterial colonization of dead wood with fungal processes of wood decay. The presence and activity of N-fixing bacteria in both living and dead wood have been assessed by acetylene reduction assays in various studies [7], [15], [19]-[22]. However, with advances of molecular techniques in the 1980s, Zehr and McReynolds [23] were the first to establish oligonucleotide primers to amplify the nifH gene complex that encodes dinitrogenase reductase. NifH is still the standard target in studies on N-fixing prokaryotes in various natural environments [24]. Many investigations have been conducted on the molecular ecology of diazotrophic (N-fixing) communities in nitrogen-limited substrates, such as forest soils, salt marshes and oligotrophic marine sediments [25]. Wang et al. [26] recently reported on the distribution of nifH genes in four terrestrial climatic zones across the USA, where they surprisingly discovered an 80% overlap on the 95% amino acid identity threshold among their and already known genes. We are, however lacking information on nifH gene distribution in dead wood to date. In addition, several authors have investigated the diversity and community structure of bacteria in dead wood as well as functional traits related to white-rot fungi [27], [28], but without focusing on diazotrophic bacteria. The work presented here emanated from the initial idea to survey bacterial community structure on dead wood to gain information whether potential N-fixers are present or not. This prompted us to immediately investigate the presence and distribution of nifH genes in dead wood. The objectives of the present study were to: a) explore the diversity of nifH sequences in dead wood, b) test the hypothesis that the community composition of N-fixing bacteria correlates with the diversity...

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Gale Document Number: GALE|A478827733