Soil Fungal Cellobiohydrolase I Gene (
            <i>cbhI</i>
            ) Composition and Expression in a Loblolly Pine Plantation under Conditions of Elevated Atmospheric CO
            <sub>2</sub>
            and Nitrogen Fertilization

Weber, Carolyn F.; Balasch, M.; Gossage, Zachary; Porras-Alfaro, Andrea; Kuske, Cheryl R.

doi:10.1128/aem.08018-11

Cited by 14 publications

(11 citation statements)

References 46 publications

(28 reference statements)

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“…() found decreased abundance of functional markers associated with both cellulose and lignin degradation in response to nitrogen, and a study which targeted both DNA and RNA found no response of cbhI to nitrogen (Weber et al . ).…”

Section: Discussionmentioning

confidence: 97%

Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker

2014

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Human activities have resulted in increased nitrogen inputs into terrestrial ecosystems, but the impact of nitrogen on ecosystem function, such as nutrient cycling, will depend at least in part on the response of soil fungal communities. We examined the response of soil fungi to experimental nitrogen addition in a loblolly pine forest (North Carolina, USA) using a taxonomic marker (large subunit rDNA, LSU) and a functional marker involved in a critical step of cellulose degradation (cellobiohydrolase, cbhI) at five time points that spanned fourteen months. Sampling date had no impact on fungal community richness or composition for either gene. Based on the LSU, nitrogen addition led to increased fungal community richness, reduced relative abundance of fungi in the phylum Basidiomycota and altered community composition; however, similar shifts were not observed with cbhI. Fungal community dissimilarity of the LSU and cbhI genes was significantly correlated in the ambient plots, but not in nitrogen-amended plots, suggesting either functional redundancy of fungi with the cbhI gene or shifts in other functional groups in response to nitrogen addition. To determine whether sequence similarity of cbhI could be predicted based on taxonomic relatedness of fungi, we conducted a phylogenetic analysis of publically available cbhI sequences from known isolates and found that for a subset of isolates, similar cbhI genes were found within distantly related fungal taxa. Together, these findings suggest that taxonomic shifts in the total fungal community do not necessarily result in changes in the functional diversity of fungi.

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Section: Discussionmentioning

confidence: 97%

Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker

2014

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“…Based on the LSU, N addition increased fungal community richness, reduced the relative abundance of Basidiomycota fungi, and altered community composition, consistent with the present study. Weber et al (2012) provided evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in both DNA-and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of cbhI-containing, cellulolytic fungi that correlated with elevated CO 2 or N fertilization at the time of sampling (Entwistle et al 2013).…”

Section: Soil Acidification and Increasing Phmentioning

confidence: 80%

Simple measurements in a complex system: soil community responses to nitrogen amendment in a Pinus taeda forest

et al. 2019

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Microorganisms regulate the decomposition of soil organic matter and the flow of plant‐available nutrients. In a temperate pine forest in North Carolina, USA, where nitrogen (N) had been experimentally added for eight years, we combined DNA‐based measures of fungal and bacterial biomass and composition with measures of seven extracellular enzymes (ecoenzymes). These measures were then correlated with soil chemistry. Our goals were to evaluate the relative sensitivity and repeatability of multiple structural and functional measures of community organization to long‐term N deposition. Measurements were conducted at three litter/soil depths, corresponding to the litter, Oa, and mineral A horizons (max depth 10 cm) with ten spatial replicates per experimental plot. Soil chemistry differed significantly with soil depth and N amendment. Total biomass (soil DNA), as well as fungal and bacterial biomass (measured by qPCR), was greatest in the litter horizon and declined significantly with depth. Ecoenzyme activity patterns also changed with soil depth, transitioning from high levels of C, N, and P metabolizing activities in the litter horizon to increased oxidative activities at the lower depth. Under N amendment, soil pH decreased and nitrate concentrations increased in all three soil horizons. Correspondingly, the estimated microbial C use efficiency decreased in N‐amended soils at all depths, despite differences in microbial biomass, community composition, and soil chemistry. Overall, bacterial composition was most responsive to nitrogen amendment, but the taxonomic context of the response varied with soil horizons in conjunction with shifts in soil chemistry and enzyme activities. While a single measure that would incorporate all of the C, N, and P metabolizing activities did not emerge, many measures correlated with each other, and/or with depth and/or N amendment.

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“…Probably these are a relic of the supply of substrates, but as this is not measured here, we can only speculate. Earlier studies have found that GH7 composition or richness in soil or litter is not significantly affected by tree species (Edwards et al, 2008), genetic modification of potato leaves (Hannula et al, 2013), elevated CO 2 (Hassett et al, 2009), or N fertilization (Weber et al, 2012). Our results corroborate the lack of differentiation power of the GH7 gene to environmental disturbances.…”

Section: Discussionmentioning

confidence: 98%

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

Hannula

Veen

2016

Front. Microbiol.

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Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

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Soil Fungal Cellobiohydrolase I Gene ( cbhI ) Composition and Expression in a Loblolly Pine Plantation under Conditions of Elevated Atmospheric CO ₂ and Nitrogen Fertilization

Cited by 14 publications

References 46 publications

Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker

Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker

Simple measurements in a complex system: soil community responses to nitrogen amendment in a Pinus taeda forest

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

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Soil Fungal Cellobiohydrolase I Gene ( cbhI ) Composition and Expression in a Loblolly Pine Plantation under Conditions of Elevated Atmospheric CO 2 and Nitrogen Fertilization

Cited by 14 publications

References 46 publications

Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker

Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker

Simple measurements in a complex system: soil community responses to nitrogen amendment in a Pinus taeda forest

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

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Soil Fungal Cellobiohydrolase I Gene ( cbhI ) Composition and Expression in a Loblolly Pine Plantation under Conditions of Elevated Atmospheric CO ₂ and Nitrogen Fertilization