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Looney, Brian

Publications and source records attributed to Looney, Brian.

Global population structures and demographic history of Suillus luteus, a pine co‐introduced ectomycorrhizal fungus associated with exotic forestry and invasion

Human colonization since the 19th century has resulted in the global spread of pines beyond their original northern boreal distribution. Although the introduction history of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal (ECM) fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, whole genomes of 208 individuals collected across native and introduced ranges were sequenced to reveal the introduction history of pine co-introduced ECM fungi. Population genomics analyses showed that all introductions originated from Europe. With the exception of North America, introduced populations were genetically differentiated from the European population, with varying magnitudes of population expansion in different introduced regions. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial-genetic patterns of native vs exotic habitats. The spread of S. luteus is mediated by human activities accompanying pine introductions, with its demographic history linked to forestry practices. The spatial, temporal, and demographic patterns observed in S. luteus offer insight into the population genetics of a widely introduced ECM fungus and are likely applicable to other pine co-introduced ECM fungi.

Ke, Yi‐Hong↗

PacBio high‐throughput multi‐locus sequencing reveals high genetic diversity in mushroom‐forming fungi

Abstract Multi‐locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi‐locus pooled sequencing method using PacBio long‐read high‐throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein‐coding genesrpb1,rpb2 andtef1. Within‐sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants ofrpb2 andtef1 from corticioid Cantharellales. Our method is a cost‐effective approach for generating accurate multi‐locus sequence data coupled with recovery of alleles from polymorphic samples and multi‐organism specimens. These results have important implications for understanding intra‐individual genomic variation among genetic loci commonly used in species delimitation of fungi.

Biochemistry & Molecular Biology↗

A global phylogenomic analysis of the shiitake genus Lentinula

Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes . We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia–Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase ( lecsl ) and γ-glutamyl transpeptidase ( leggt ), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula . Paralogs of both genes that are unique to Lentinula ( lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes . The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.

59 BASIC BIOLOGICAL SCIENCES↗

Identifying Controlling Variables Related to Mercury Vapor Concentrations in Legacy Facilities: SRNL Technology Development For D&D

A suite of sensor packages has been installed in the Alpha-4 facility at Y-12 and preliminary data analysis to isolate the controlling variables has been performed after two months of data collection. In line with the conceptual model presented in Section 2.0, the preliminary analysis has demonstrated that temperature, barometric pressure, and relative humidity are the key controlling variables for mercury vapor releases within the building. The data analysis will continue to explore these controlling variables across the next several months to capture a more complete picture of the annual change in meteorological conditions at Y-12.

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Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungi

The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyperdiverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall-degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE ‘nests’, or dense aggregations of TEs. Here, some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of G. convolvens possesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.

59 BASIC BIOLOGICAL SCIENCES↗

Role of uncertainties in protecting ecological resources during remediation and restoration

Cleanup of contaminated waste sites is a National priority to protect human health and the environment, while restoring land to productive uses. While there are uncertainties with under standing risk to individuals from exposure, the aim of this study was to focus on uncertainties and complexities for ecological systems, complicated by hundreds of species occupying any remediation site which participate in multiple-interacting food webs. The ability to better predict the effectiveness of remediation in fostering future ecosystems might facilitate remedy selection and improve strategic environmental management. This investigation examined (1) uncertainties in ecosystem processes, (2) uncertainties in exposure from contamination before remediation, and (3) uncertainties during remediation. Two Department of Energy sites Hanford Site and Savannah River Site were used as case studies to illustrate how the uncertainties affect eco-receptors. Several types of ecological, physical, and human dimension uncertainties are defined. Ecological uncertainties include temporal, spatial, individual, developmental, and exogenous types. Physical uncertainties are weather-related, watershed variations, slope/aspect, soil/sediment structure and form, unforeseen events, and temporal patterns. Human dimension uncertainties include current land use, future land use, extractive and non-extractive recreation. The effects of remedial strategies varied between the two sites because Hanford is a primarily arid shrub-steppe ecotype, while Savannah River is a wet forest ecotype. Defining the associated ecological sensitivities and uncertainties and providing examples might help policy-makers, managers, planners, and contractors to be aware of issues to consider throughout planning, remediation, and restoration. Adding ecological uncertainty analysis to risk evaluations and remediation planning is analogous to using safety factors in human health risk assessment.

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Mercury Speciation via Diffusive Gradients Thin-Films Technology

Objectives: Develop and test various diffusive gradient in thin films (DGT) samplers for mercury - SRNL is developing reactive DGTS (rDGTs). Test chemistry to differentiate methylmercury from total and/or inorganic mercury in environmental samples. Fabricate and test rDGT samplers for deployment. Deploy the rDGTs in variable settings. Mercury is a persistent-bioaccumulative-toxic environmental pollutant. Mercury exists in different species such as elemental, inorganic, and methyl. Mercury speciation determine mercury behavior and toxicity. For example, methylmercury strongly accumulates in biota such as fish resulting in potential human health impacts. DGTs are innovative samplers to measure water concentration by diffusion and capture. Types of Hg DGTs used: Total Hg, Inorganic Hg, and Methyl Hg. Deployment Sites: Upper Three Runs, Lower Three Runs, Steele Creek, East Fork Poplar Creek (SRNL Sites), Horizons Creek, NOA Creek, Bruners Creek (ORNL Sites). DGT concentration estimates closely matched alternative measurements for soluble mercury at each Oak Ridge site - DGTs did not respond to particulate mercury. DGTs provide a representative measure for biota uptake since they are left out longer which allows for an average exposure concentration. DMA-80 provided an efficient and quick analysis. Variability in site location made a difference in Hg species. DGT preparations and sampling wasn't as quick and simple as microcolumn technology. Copper reagent degraded agarose gel - more work and cleaner data are needed to assess speciation in rDGTs. Future Work: Use cross-linked polyacrylamide for the collection layer for a stronger plastic. Make a copper diffusion layer without agarose. Test copper separation in lab using realistic stream conditions such as high organic carbon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Study of an Unrefined Humate Solution as a Possible Attenuation-based Remedy for Uranium Contamination in Acidic Groundwater - 20351

The Savannah River Site (SRS), joined the environmental cleanup program in 1981 after the Cold War, and was designated as a hazardous waste management facility. About 1.8 billion gallons of acid wastes were disposed into the F/H Area Seepage Basin that included many radionuclides and dissolved metals, resulting in highly contaminated groundwater plumes with pH of 3 - 5.5. The acidity of the plumes contributes to the mobility of several constituents of concern (COC) such as H-3, U-238, I-129, and Sr-90 for the F-Area plume and H-3, Sr-90 and mercury for the H-Area plume. An active treatment (pump-and-treat and re-injection) system was constructed and put in place in 1997 to address the removal of metals and radionuclides from the contaminated groundwater. As remediation projects advanced, active treatments were transitioned to more passive or enhanced-passive approaches such as the subsurface barrier with base injection system, which has been controlling the mobility of contaminants. However, new and more efficient attenuation-based remedies are always sought. Several studies have proposed that humic substances can be used to remediate sites contaminated with heavy metals by creating a permeable reactive barrier. Humic substances (HS) are major components of soil organic matter. HS are polyfunctional organic macromolecules formed by the chemo-microbiological decomposition of biomass or dead organic matter. These substances are usually divided into three main fractions: humin (insoluble at all pH values), humic acid (soluble at pH greater than 3.5), and fulvic acid (soluble at all pH values). Humic substances are major components of the soil at SRS and, in addition, are also helpful in the removal process of uranium. This research focuses on uranium (VI), which is a key contaminant of concern in the F-Area groundwater plume. The interaction of uranium with sediment in the presence or absence of humic substances involves complex mechanisms that are not yet well understood. The interaction of U(VI) with humic substances can affect the adsorption of U on sediment, altering its mobility in the subsurface. The objective of this study is to study the mobility of uranium in the presence of humic acid and to determine if sediments amended by humic acid can enhance the sorption of heavy metals onto sediments. In this research, experiments were conducted using background (clean) F-Area aquifer sediments to understand and predict uranium mobility. A blended material, humate, containing both humic and fulvic acids and a chemically modified humate (KW15 modified humic or mod-HA) was studied as a possible amendment for uranium remediation in SRS groundwater. Batch experiments were conducted in triplicates using 20 ml of aqueous suspension in DI water containing SRS sediment and mod-HA and studied the effect of pH, kinetics of humate sorption onto SRS sediment and also studied the sorption of uranium onto mod-HA amended SRS sediment. Results indicate that mod-HA amended sediment increases uranium removal significantly. (authors)

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