A New Perspective on Sustainable Soil Remediation—Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants

Deciding upon a cost effective and sustainable method to address soil pollution is a challenge for many remedial project managers. High pressure to quickly achieve cleanup goals pushes for energy‐intensive remedies that rapidly address the contaminants of concern with established technologies, often leaving little room for research and development especially for slower treatment technologies, such as bioremediation, for the more heavily polluted sites. In this case study, new genomic approaches have been leveraged to assess fungal biostimulation potential in soils polluted with particularly persistent hydrophobic contaminants. This new approach provides insights into the genetic functions available at a given site in a way never before possible. In particular, this article presents a case study where next‐generation sequencing has been used to categorize fungi in soils from the Atlantic Wood Industries Superfund site in Portsmouth, Virginia. Data suggest that original attempts to harness fungi for bioremediation may have focused on fungal genera poorly suited to survive under heavily polluted site conditions, and that more targeted approaches relying on native indigenous fungi which are better equipped to survive under site‐specific conditions may be more appropriate. ©2016 Wiley Periodicals, Inc.     

Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival

Host-specific mortality driven by natural enemies is a widely discussed mechanism for explaining plant diversity. In principle, populations of plant species can be regulated by distinct host-specific natural enemies that have weak or nonexistent effects on heterospecific competitors, preventing any single species from becoming dominant and thus promoting diversity. Two of the first steps in exploring the role of natural enemies in diversity regulation are to (1) identify potential enemies and (2) evaluate their levels of host specificity by determining if interactions between any one host and its enemy have equivalent survival impacts on co-occurring host species. We developed a bioinformatics framework to evaluate impacts of potential pathogens on seedling survival, for both single and multiple infections. Importantly, we consider scenarios not only if there are specialist pathogens for each plant, but also when generalist pathogens have differential effects on multiple host species, and when co-infection has species-specific effects. We then applied this analytical framework to a field experiment using molecular techniques to detect potential fungal pathogens on co-occurring tree seedling hosts. Combinatorial complexity created by 160 plant-fungus interactions was reduced to eight combinations that affect seedling survival. Potential fungal pathogens had broad host ranges, but seedling species were each regulated by different combinations of fungi or by generalist fungi that had differential effects on multiple plant species. Soil moisture can have the potential to shift the nature of the interactions in some plant-fungal combinations from neutral to detrimental. Reassessing the assumption of single-enemy-single-host interactions broadens the mechanisms through which natural enemies can influence plant diversity.     

CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities

Ectomycorrhizal fungi (EMF), a phylogenetically and physiologically diverse guild, form symbiotic associations with many trees and greatly enhance their uptake of nutrients and water. Elevated CO2, which increases plant carbon supply and demand for mineral nutrients, may change the composition of the EMF community, possibly altering nutrient uptake and ultimately forest productivity. To assess CO2 effects on EMF communities, we sampled mycorrhizae from the FACTS-I (Forest-Atmosphere Carbon Transfer and Storage) research site in Duke Forest, Orange County, North Carolina, USA, where Pinus taeda forest plots are maintained at either ambient or elevated CO2 (200 ppm above ambient) concentrations. Mycorrhizae were identified by DNA sequence similarity of the internal transcribed spacer ribosomal RNA gene region. EMF richness was very high; 72 distinct phylotypes were detected from 411 mycorrhizal samples. Overall EMF richness and diversity were not affected by elevated CO2, but increased CO2 concentrations altered the relative abundances of particular EMF taxa colonizing fine roots, increased prevalence of unique EMF species, and led to greater EMF community dissimilarity among individual study plots. Natural variation among plots in mean potential net nitrogen (N) mineralization rates was a key determinant of EMF community structure; increasing net N mineralization rate was negatively correlated with EMF richness and had differential effects on the abundance of particular EMF taxa. Our results predict that, at CO2 concentrations comparable to that predicted for the year 2050, EMF community composition and structure will change, but diversity will be maintained. In contrast, high soil N concentrations can negatively affect EMF diversity; this underscores the importance of considering CO2 effects on forest ecosystems in the context of background soil chemical parameters and other environmental perturbations such as acid deposition or fertilizer runoff.