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While the complexity of prokaryotic communities in soil is relatively well understood, we are currently ignorant of the role of viruses in influencing their ecology. Viruses infect every living organism and affect rates of biogeochemical processes by killing active cells via cell lysis, or augmenting function through the transfer of auxiliary metabolic genes. The microbially-mediated process of nitrification is central to nitrogen losses and emissions of the greenhouse gas nitrous oxide, contributing to global warming and stratospheric ozone depletion, and viruses may impact this central step of the global N cycle. However, challenges remain in identifying active interactions with specific host or functional groups and virus populations within structurally complex and diverse soil environments. To address this, discrete active interactions between individual hosts and viruses in soil microcosms were examined using the transfer of assimilated carbon from autotrophic prokaryotes to viruses. Microcosms were established with amendments of urea to fuel nitrification and 13C carbon dioxide, followed by DNA stable-isotope probing (SIP) combined with metagenomic analyses. Hybrid analysis of GC mol% fractionation and 13C-DNA-SIP resulted in the identification of active ammonia oxidizing archaea (AOA) hosts and viruses only. To enable characterization of viruses actively infecting all active ammonia- and nitrite oxidizing bacteria (AOB, NOB), a second approach was used where incubations were performed using filtration of virus-like particles to increase the recovery of virus metagenomes. This included differential inhibition of specific nitrifier groups to alleviate competition and potentially increase the abundance of viruses infecting non-inhibited groups. Applications of DMPP or octyne were added to preferentially inhibit AOB and encourage growth of AOA, or acetylene to inhibit all ammonia oxidizing activity as a negative control. This approach dramatically increased the recovery of high-quality virus contigs, with 225 contigs associated with those infecting AOA, AOB or NOB including 69 complete or near-complete genomes. Viruses of ammonia-oxidizers contained auxiliary metabolic genes involved in central metabolic pathways, and analysis of viral hallmark genes revealed that they were distinct from previously cultivated viruses. Results demonstrate that virus infection of nitrifiers and propagation of viruses is a dynamic process during soil nitrification, providing insights into potential impacts of viruses on a specific functional process in soil.

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived13C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of13C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of13C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in13C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.

Intensively managed agriculture land is a significant contributor to nitrous oxide (N2O) emissions, which adds to global warming and the depletion of the ozone layer. Recent studies have suggested that fungal dominant N2O production may be promoted by pathogenic fungi under high nitrogen fertilization and continuous cropping. Here, we measured the contribution of fungal communities to N2O production under intensively managed strawberry fields of three continuous cropping years (1, 5, and 10 years) and compared this adjacent bare soil. Higher N2O emission was observed from the 10-year field, of which fungi and prokaryotes accounted for 79.7% and 21.3%, respectively. Fungal population density in the 10-year field soil (4.25 × 105 colony forming units per g (CFU/g) of air-dried soil) was greater than the other cropping years. Illumina MiSeq sequencing of the nirK gene showed that long-term continuous cropping decreased the diversity of the fungal denitrifier community, but increased the abundance of Fusarium oxysporum. Additionally, F. oxysporum produced large amounts of N2O in culture and in sterile 10-year field soil. A systemic infection displayed by bioassay strawberry plants after inoculation demonstrated that F. oxysporum was a pathogenic fungus. Together, results suggest that long-term intensively managed monocropping significantly influenced the denitrifying fungal community and increased their biomass, which increased fungal contribution to N2O emissions and specifically by pathogenic fungi. KEY POINTS: • Distinguishing the role of fungi in long-term continuous cropping field. • Identifying the abundant fungal species with denitrifying ability.

Peatlands contain a significant fraction of global soil carbon, but how these reservoirs will respond to the changing climate is still relatively unknown. A global picture of the variations in peat organic matter chemistry will aid our ability to gauge peatland soil response to climate. The goal of this research is to test the hypotheses that 1) peat carbohydrate content, an indicator of soil organic matter reactivity, will increase with latitude and decrease with mean annual temperatures (MAT), 2) while peat aromatic content, an indicator of recalcitrance, will vary inversely, and 3) elevation will have a similar effect to latitude. We used Fourier Transform Infrared Spectroscopy (FTIR) to examine variations in the organic matter functional groups of 1034 peat samples collected from 10-20, 30-40, and 60-70 cm depths at 165 individual sites across a latitudinal gradient of 79˚N to 65˚S and from elevations of 0 to 4773 meters. Carbohydrate contents of high latitude peat were significantly greater than peat originating near the equator, while aromatic content showed the opposite trend. For peat from similar latitudes but different elevations, the carbohydrate content was greater and aromatic content was lower at higher elevations. Higher carbohydrate content at higher latitudes indicates a greater potential for mineralization, whereas the chemical composition of low latitude peat is consistent with their apparent relative stability in the face of warmer temperatures. The combination of low carbohydrates and high aromatics at warmer locations near the equator suggests the mineralization of high latitude peat until reaching recalcitrance under a new temperature regime.

Small genes (40,000 small-gene families in ~2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil virus communities. In this study, prokaryotic and viral communities were characterized in soils sampled from the extremes of a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations were compared to those in a variety of soil ecosystems ranging in pH (4.0 – 7.5). Prokaryotic and viral community structure were significantly influenced by soil pH at the local scale. Of 1,910 viral operational taxonomic units (vOTUs), 99% were restricted to pH 4.5 or 7.5 soil only. These were compared in gene sharing networks of populations from six other European and North American soil systems. A selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. Results indicate that as with prokaryotes, soil pH is a factor structuring viral communities at the local and global scale.

International audience; The concentration of atmospheric methane (CH 4 ) continues to increase with microbial communities controlling soil–atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH 4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH 4 -fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH 4 -derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of 13 C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH 4 -fueled microbial food networks.

Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species- rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.

Intensively managed agriculture land is a significant contributor to nitrous oxide (N

Potential rate assays are used in soil microbial ecology to determine the rates of a functional process in environmental samples under a defined set of conditions. While they can be used appropriately to provide mechanistic insights, potential rates are also often used to estimate the abundance of specific taxonomic groups and their in situ activity. These estimates incorrectly assume that all contributing organisms in a community are active at a maximum rate under one set of ‘optimal’ incubation conditions and that potential rates reflect activity in the soil. While investigators now recognise that populations within communities are physiologically diverse, they often ignore the consequent suboptimal activity, or even inactivity, of the majority of community members performing that function. In this short perspective article, we discuss when potential assays can be informative and highlight the underlying conceptual problems under circumstances where potential assays are misused, using potential nitrification rate (PNR) as an example. PNR was originally developed to estimate the size of active ammonia oxidising communities in environmental samples. It is routinely determined in short-term shaken slurry incubations by measuring assumed maximum rates of nitrate or nitrite production under optimal, non-substrate-limiting conditions. As with other functional processes, it is now recognised that a broad diversity of organisms contribute to aerobic ammonia oxidation in terrestrial and other habitats, and this diversity represents a substantial range of physiologies, including variation in substrate affinity, ammonia tolerance, cell specific activity and substrate preference. Despite this, PNR, and other potential rate assays, are often inappropriately used in an attempt to determine an ecologically relevant measurement of activity in soil. As with any potential assay, PNR has inherent biases towards particular functional groups and its use in investigating the ecology of ammonia oxidisers in natural systems should be carefully considered.

Contents Summary 1122 I. Introduction 1122 II. Are there consistent patterns in diversity of mycorrhizal fungal genotypes and species across space? 1125 III. What is the variation in functional traits and genes of mycorrhizal fungi at different taxonomic scales? 1125 IV. How will environmental change impact the relationships between genotypic and species diversity of mycorrhizal fungi and ecosystem function? 1126 V. Conclusions: considerations for future MEF research 1127 Acknowledgements 1127 References 1127 SUMMARY: Both genotypes and species of mycorrhizal fungi exhibit considerable variation in traits, and this variation can result in their diversity regulating ecosystem function. Yet, the nature of mycorrhizal fungal diversity-ecosystem function (MEF) relationships for both genotypes and species is currently poorly defined. New experiments should reflect the richness of genotypes and species in nature, but we still lack information about the extent to which fungal populations in particular are structured. Sampling designs should quantify the diversity of mycorrhizal fungal genotypes and species at three key broad spatial scales (root fragment, root system and interacting root systems) in order to inform manipulation experiments and to test how mycorrhizal fungal diversity both responds, and confers resilience to, environmental drivers.

A major gap in our understanding of biodiversity–ecosystem function relationships concerns the role of intra- and interspecific diversity of mycorrhizal fungi, which are critical for plant fitness, biogeochemical cycling and other processes. Here, we test the hypothesis that the identity and richness of ectomycorrhizal (ECM) fungi at the intra- and interspecific levels affect ecosystem multifunctionality by regulating plant and fungal productivity, soil CO2 efflux and nutrient retention. Microcosms containing Scots pine (Pinus sylvestris) seedlings colonized by different ECM fungal isolates, in monocultures and mixtures, enabled us to test for both intra- and interspecific identity and richness effects, and transgressive overyielding. Intra- and interspecific identity had modest but significant effects on plant and fungal productivity and nutrient retention, but no effect on CO2 efflux. Intraspecific richness increased plant root productivity and ECM root tips but decreased hyphal length, whereas interspecific richness had no effects. Interspecific mixtures outperformed the most productive monocultures in only 10% of the cases, compared with 42% for the intraspecific mixtures. Both intra- and interspecific identity and richness of ECM fungi regulate ecosystem multifunctionality, but their effects on the direction and magnitude of individual variables differ. Transgressive overyielding suggests that positive niche complementarity effects are driving some of the responses to intraspecific richness.

Landspreading of biosolids (treated sewage sludge) in agroecosystems is a common waste management practice worldwide. Evidence suggests biosolids may be detrimental to arbuscular mycorrhizal fungi (AMF); however, previous studies focused on arable systems and often unrealistically high biosolids application levels. We investigated the effects of biosolids on AMF communities in grassland and arable agroecosystems, in the context of the natural seasonal dynamics of AMF community composition and diversity. A pasture and arable system under commercial farming management were amended annually with two different types of biosolids, applied at levels meeting current European Union regulations, in a factorial, replicated field-scale plot experiment. AMF root colonisation and community composition were measured in Lolium perenne roots from the pasture and Trifolium repens roots growing in arable soil across the seasons of two years. AMF community compositions were assessed by terminal-restriction fragment length polymorphism analyses. Biosolids had no significant effect on AMF root colonisation or community composition in either agroecosystem. Soil chemical analyses indicated several changes in the top 0–5 cm layer of the pasture soil, including small increases in heavy metal concentrations in biosolids relative to control plots. Temporal AMF dynamics were detected in soils from both agroecosystem indicating that the effect of seasonality outweighed that of biosolids application.

The first species of Rhizopogon subgenus Amylopogon identified from eastern North America is described here as Rhizopogon kretzerae Grubisha, Dowie, & Mill. sp. nov. In nature, R. kretzerae has been identified only from DNA sequences of the nuclear ribosomal internal transcribed spacer region (ITS) from mycorrhizal roots of Pinus strobus L. and Pterospora andromedea Nutt. Phylogenetic analyses and nucleotide divergence estimates of Rhizopogon ITS sequences from Pterospora roots from Quebec, Michigan, New York, and New Hampshire combined with ITS sequences of Rhizopogon subgenus Amylopogon species type collections suggest R. kretzerae is a sister-group to Rhizopogon salebrosus A.H. Sm. An absence of shared mutations, two informative sequence gaps, and 12 fixed nucleotide differences differentiate R. kretzerae and R. salebrosus. Furthermore, ITS sequences of 40 Pterospora root samples from five populations in the province of Quebec provided the first record of the distribution of R. kretzerae, a potentially rare to endangered species, in eastern Canada.

Important steps in developing reliable bioindicators for soil quality are characterising soil biodiversity and determining the response of its components to environmental factors across a range of land uses and soil types. Baseline data from a national survey in Ireland were used to explore relationships between diversity and composition of micro-organisms (bacteria, fungi, mycorrhiza), and micro-, meso- and macro-fauna (nematodes; mites; earthworms, ants) across a general gradient representing dominant land uses (arable, pasture, rough-grazing, forest and bogland). These diversity data were also linked to soil physico-chemical properties. Differences in diversity and composition of meso- and macro-fauna, but not microbes, were clear between agriculturally-managed (arable and pasture) and extensively-managed (rough-grazing and bogland) soils corresponding to a broad division between ‘mineral’ and ‘organic’ soils. The abundance, richness and composition of nematode and earthworm taxa were significantly congruent with a number of the other groups. Further analysis, using significant indicator species from each group, identified potential target taxa and linked them to soil environmental gradients. This study suggests that there is potential surrogacy between the diversity of key soil taxa groups and that different sets of bioindicators may be most effective under agricultural and extensive land use.

Lisa C. Grubisha, Nicholas J. Dowie, Steven L. Miller, Christina Hazard, Steven M. Trowbridge, Thomas R. Horton, Matthew R. Klooster (2014): Rhizopogon kretzerae sp. nov.: the rare fungal symbiont in the tripartite system with Pterospora andromedea and Pinus strobus. Botany 92: 526-534, DOI: 10.1139/cjb-2013-0309

Rhizopogon kretzerae Grubisha, Dowie, & Mill. sp. nov. and. INDEX FUNGORUM REGISTRATION NUMBER : IF 550254 DIAGNOSIS : Known only from ectomycorrhizal symbioses with Pinus strobus and monotropoid mycorrhizal symbioses with the mycoheterotrophic plant Pterospora andromedea in eastern North America. Rhizopogon kretzerae can be distinguished from R. salebrosus, presently the closest identified species, by two indels found in the ITS1 and 12 fixed nucleotide differences, three in the ITS1 and nine in the ITS2. HOLOTYPE : DAOM 242738 LOCATION : United States of America, Michigan, Ottawa National Forest, 46.64271��N, 89.17873��W. Collection number: Miller 207, Collected: 4 August 2011 by N.J. Dowie and S.L. Miller. DAOM 242738 is a specimen from silica-dried, dead culture isolated from Pterospora andromedea roots, stored with silica. ETYMOLOGY : Named in honor of Dr. Annette Kretzer (State Univer- sity of New York, Syracuse, New York, USA), whose pioneering work on the population genetics of Rhizopogon vinicolor A.H. Sm. and Rhizopogon vesiculosus A.H. Sm. advanced our understanding of Rhizopogon evolutionary biology and provided inspiration to many mycologists and students. DESCRIPTION : Macroscopic and microscopic observations were made from a live culture of isolate Miller 207 but not the dried specimen that was deposited as the holotype because these notes were made after the dried holotype specimen was deposited at DAOM. MACROSCOPIC CHARACTERISTICS : Mycelial mat whitish at first (circa one week), aerial hyphae developing shades of pale brownish grey, older cultures (circa three weeks) pale reddish grey to gray- ish red, brownish orange, light brown or brown, often with patches of lighter color scattered across the colony (). Under U.V. light, light purple with dark purple patches; reverse brown, uniform, with radiating fans at the margin; mycelial mat floccose when first isolated, becoming low, dense, felty with age and with repeated transfers; margin irregular, whispy, aerial mycelium sparser toward edge, hyphae submerged at edge of colony when younger, submerged area overgrown on surface with fine hyphae in age, darker brown-like reverse appearing as a dark halo sur- rounding mycelial mat, minute knots of hyphae scattered to abundant at margin and throughout colony, concolorous with mycelium or lighter in color; maximum growth rate 3.0���3.4 cm in one month at 25 ��C; odor strong, sweet, and pleasant. MICROSCOPIC CHARACTERISTICS : Hyphae of interior of mycelial mat mostly 3���7 um, thick-walled, smooth, frequently swollen at sep- tations or forming vesciculose, catenulate cells, 6���33 ��m wide, thin-walled, easily collapsing; branching mostly simple, dendritic hyphae common; septae simple; clamps absent. Hyphae of ex- terior of mycelial mat mostly 3���10 ��m, cylindrical, branching simple, dendritic hyphae common, few swollen catenulate cells present, moderately thick-walled, heavily encrusted overall or in discreet patches with granular, pale brown pigment in KOH, in Melzer's Reagent pigment darker brown (dextriniod), soluble and floating free from the hyphal wall and appearing large globular or amorphous; septae simple; clamps absent. ECOLOGY AND DISTRIBUTION : Rhizopogon kretzerae appears to be re- stricted to areas with Pinus strobus and Pterospora andromedea or P. strobus alone in Northern Michigan, New York, New Hampshire, and southern Quebec. identified R. kretzerae from P. strobus roots within a P. andromedea rootball from Keweenaw County, Michigan. A soil bioassay study has shown that the frequency of R. kretzerae propagules in soil increases in P. strobus areas where P. andromedea is reproductively active with R. kretzerae occurring at a frequency from 6% of soil samples from sites with P. strobus to 14% to 25% (site vs. plot) in soils with both P. strobus and P. andromedea (). COMMENTS : Rhizopogon kretzerae is the first record of a Rhizopogon subgenus Amylopogon species that occurs in eastern North Amer- ica (i.e., east of the Mississippi River in US;;). Presently, there are no known annotated herbarium collections of the basidiocarp. Monotropoid mycorrhizal rootballs of eastern P. andromedea and R. kretzerae have diameters reaching a maximum of approximately 1.5 inches and are substantially smaller than rootballs of P. andromedea and R. salebrosus in western North America (). Ultrastructure of P. andromedea monotropoid roots has been described in detail by . OTHER SPECIMENS EXAMINED : Pterospora andromedea monotropoid mycorrhizal roots DAOM 242739, Location: Canada, province of Quebec, 45.4947��N, 76.3786��W; Collection number: Quebec A21, Collected: 26 July 2012 by M.R. Klooster and L.C. Grubisha; DAOM 242740, Location: Canada, province of Quebec, 45.4947��N, 76.3786��W; Collection number: Quebec A22, Collected: 26 July 2012 by M.R. Klooster and L.C. Grubisha; DAOM 242741, Location: Canada, province of Quebec, 47.2900��N, 79.4566��W, Collection number: Quebec D16, Collected 27 July 2012 by M.R. Klooster and L.C. Grubisha; DAOM 242742, Location: Canada, province of Quebec, 47.3166��N, 79.4533��W, Collection number: Quebec E22, Collected: 27 July 2012 by M.R. Klooster and L.C. Grubisha; DAOM 242743, Location: Canada, province of Quebec, 45.4672��N, 75.8069��W, Collection number: Quebec H11, Collected: 27 July 2012 by M.R. Klooster and L.C. Grubisha. All root samples were dried in silica gel. Discussion In this study, Rhizopogon kretzerae Grubisha, Dowie, & Mill., sp. nov. was described. This is also the first report of the distribution of this rare fungus in Quebec from five locations covering approximately 430 km. Since there are no known basidiocarp collections, the species description was based on ITS sequence data, ecological information, and a morphological description of the culture isolated from P. andromedea roots. The results from phylogenetic analyses presented here and in previous studies (;) are strong evidence that R. kretzerae is a species according to the phylogenetic species concept. If a basidiocarp is collected at some future time, the present description should be amended. Prior to this study, two GenBank environmental sequences (AF442136, DQ426677) had a>99% identity and both came to be known by some variation of the cumbersome phrase ���the unnamed species of Rhizopogon subgenus Amylopogon that associates with P. andromedea in the east��� (;), which can now be referred to as R. kretzerae. Furthermore, now it is possible to communicate ecological information about R. kretzerae if this species is found in environmental samples not associated with Pterospora in future studies of pines in eastern North America. Likewise, identification of R. kretzerae from soil near P. strobus may indicate the presence of potential candidate sites for Pterospora restoration efforts. Nucleotide divergence estimates provided a quantitative measure for comparing how sequences between species differ at the molecular level. In previous fungal studies, these statistics provided additional molecular evidence in support of speciation events in the Amanita muscaria complex (), Tricholoma scalpturatum complex (), and in identifying two lineages of cryptic species in Tricholoma populinum ( ). In this study, R. kretzerae and R. salebrosus are separated by the fewest number of fixed nucleotide differences (12) that support an apparent sister-group relationship in the unrooted phylogeny (). A phylogeny with an outgroup was not shown due to the large number of gaps and ambiguously aligned positions that needed to be removed for analyses, which would have removed too many informative positions within the ingroup. Phylogenetic assessments of species in Rhizopogon subgenus Amylopogon based on multiple nuclear loci are currently underway (N.J. Dowie, unpublished data). The lack of historic collections of basidiocarps in herbaria or collection by contemporary researchers of Pterospora or Rhizopogon may stem from a variety of reasons. This species may no longer reproduce sexually in nature due to severely altered environmental conditions (e.g., fire suppression), or alternatively, basidiocarps are produced but (1) at a time when no one has searched for them (e.g., early or late in the fruiting season); (2) are deeper in the soil profile than is typical for finding Rhizopogon basidiocarps; or (3) at a very low frequency and less likely to be collected. Hypothesis 3 is supported by the low frequency in which R. kretzerae has been identified in soil bioassays () when compared with similar studies on western North America Rhizopogon species (;). In this study, two strategies were implemented to avoid naming an already described species. First, 22 ITS holotype and paratype sequences of Rhizopogon subgenus Amylopogon were retrieved from GenBank for phylogenetic comparison to R. kretzerae (). Second, partial to entire ITS sequences were determined from four Rhizopogon holotypes collected in Michigan that were associated with Pinus spp., but subsequently shown to belong to Rhizopogon subgenera other than subgenus Amylopogon. These results support who had synonymized R. superiorensis with R. succossus. In the case of R. baxteri, Zeller had originally identified the collection Baxter2578 as R. rubescens (see original herbarium card; ). Owing to the high similarity of Baxter2578 with R. rubescens and R. roseolus sequences, it is unclear whether R. baxteri is a unique species; however, this, along with determining the taxonomic status of R. gelatinosus MICH 3268 and holotypes R. gelatinosus MICH 12392 and R. pinicola MICH 12404 will be left for investigation in future studies as it is beyond the scope of the current study. The ITS2 primers introduced here (R370F and R536R) may be useful in future studies of historic Rhizopogon collections. Pterospora andromedea populations in Quebec were reproductively active in July 2012 despite a widespread drought in southeastern Canada. We found plants at five out of seven sites visited based on 10 historic Pterospora locations listed on the collecting permit provided by Quebec's provincial government. Four of five sites had more than 10 plants, but only one site had more than 20 plants. Stems from 2011 were present at all sites that had flowering plants in 2012, but were equal or fewer in number to those counted in 2012. However, the total number of stems present in 2012 at these five sites was lower than in previous records (24���270) provided on the collecting permit. The low number to complete absence of plants observed in 2012 could have been the result of: (i) the severe drought, (ii) a simple reflection of the sporadic nature of the flowering pattern in Pterospora, in which the plant is abundant in some years and completely absent in others, similar to the fruiting pattern of some fungi, or (iii) an indication that the Quebec populations are in serious decline, as has been shown in other eastern populations. Continued monitoring of Pterospora sites, historic and contemporary, is necessary to gain a better understanding of the ecology and reproductive biology of this species. This work is the first installment of a series of conservation genetics and phylogeographic studies of eastern and western populations of Pterospora andromedea and Rhizopogon symbionts. Conservation management plans and scientific studies may now refer to this potentially rare fungal species as Rhizopogon kretzerae, instead of the formerly used name ���the undescribed Rhizopogon subgenus Amylopogon species that associates with Pterospora andromedea in the east���., Published as part of Lisa C. Grubisha, Nicholas J. Dowie, Steven L. Miller, Christina Hazard, Steven M. Trowbridge, Thomas R. Horton & Matthew R. Klooster, 2014, Rhizopogon kretzerae sp. nov.: the rare fungal symbiont in the tripartite system with Pterospora andromedea and Pinus strobus, pp. 526-534 in Botany 92 on pages 531-533, DOI: 10.1139/cjb-2013-0309, http://zenodo.org/record/246791

Culture-independent molecular studies have provided new insights into the diversity of fungi associating with ericaceous plant roots. However, there is little understanding of the distribution of these fungi across landscapes, or the effects of environmental heterogeneity on ericoid mycorrhizal (ERM) fungal diversity and distribution. Terminal-restriction fragment length polymorphism and selective sequence analyses of the internal transcribed spacer regions of rDNA were used to infer fungal diversity of bait Vaccinium macrocarpon grown in soils from nine peatland sites in Ireland, representing three different land uses (bog, rough grazing and forest plantation) and the fungal communities of field-collected Calluna vulgaris for five of these nine sites. A diverse range of potential ERM fungi were found, and the sampling approach significantly affected the diversity of the fungal community. Despite significant site groupings of the fungal communities associated with V. macrocarpon and C. vulgaris, fungal communities were significantly dissimilar between sites with different land uses. Soil nitrogen content significantly explained 52% of the variation in the V. macrocarpon fungal communities. Evidence suggests that environmental heterogeneity has a role in shaping ERM fungal community composition at the landscape scale.

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects’) was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.

Like other myco-heterotrophic plants, Pterospora andromedea (pinedrops) is dependent upon its specific fungal symbionts for survival. The rarity of pinedrops fungal symbiont was investigated in the eastern United States where pinedrops are rare. Wild populations of eastern pinedrops were sampled, and the plant haplotypes and fungal symbionts were characterized with molecular techniques; these data were compared to those from the West with phylogenetic analyses. The frequency of the fungal symbiont in eastern white pine forests was assessed using a laboratory soil bioassay and in situ pinedrops seed baiting. Only one plant haplotype and fungal symbiont was detected. The plant haplotype was not unique to the East. The fungal symbiont appears to be a new species within the genus Rhizopogon, closely related to the western symbionts. This fungal species was not frequent in soils with or without pinedrops, but was less frequent in the latter and in comparison to the fungal symbionts in western forests. Seed baiting resulted in few germinants, suggesting that mycelial networks produced by the eastern fungal symbiont were rare. Results suggest that eastern pinedrops rarity is influenced by the distribution and rarity of its fungal symbiont.

KELSALL, N., C. HAZARD, AND D. J. LEOPOLD (Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, 1 Forestry Drive Syracuse, New York 13210). Influence of climate factors on demographic changes in the New York populations of the federally-listed Phyllitis scolopendrium (L.) Newm. var. americana J. Torrey Bot. Soc. 131:161-168. 2004.-Approximately 92% of the U.S. population of American hart's-tongue fern (Phyllitis scolopendrium var. americana) is found in Onondaga and Madison counties, New York, in 17 distinct colonies. All New York colonies have been periodically censused since 1916, though rarely in the same year. This study examines census data of the total New York population during and following the severe drought of 1999 and during the summers of 2000 and 2002. Additionally, the long-term (1922-2002) census data of seven colonies are examined relative to climate data for the same period. The total New York population has declined overall since the last previous census in 1995. No climate variables explained more than 23% of variation in population size of any growth phase. The lack of controlling, largescale climate factors suggests that the distribution of hart's-tongue fern in New York is determined mostly by the occurence of habitat capable of buffering climatic fluctuations. Future work should combine small-scale habitat and large-scale climate factors in any analysis.