Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa.

Animal gut mycobiota, the community of fungi that reside within the gastrointestinal tract, make an important contribution to host health. Accordingly, there is an emerging interest to quantify the gut mycobiota of wild animals. However, many studies of wild animal gut mycobiota do not distinguish between the fungi that likely can reside within animal gastrointestinal tracts from the fungal taxa that are non-residents, such as macrofungi, lichens or plant symbionts/pathogens that can be ingested as part of the host's diet. Confounding the non-resident and resident gut fungi may obscure attempts to identify processes associated with the authentic, resident gut mycobiota per se. To redress this problem, we propose some strategies to filter the taxa identified within an apparent gut mycobiota based on an assessment of host ecology and fungal traits. Consideration of the different sources and roles of fungi present within the gastrointestinal tract should facilitate a more precise understanding of the causes and consequences of variation in wild animal gut mycobiota composition.

Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

Examining transmission of gut bacteria to preserved carcass via anal secretions in Nicrophorus defodiens.

Direct transmission of bacteria to subsequent generations highlights the beneficial nature of host-bacteria relationships. In insects, this process is often mediated by the production of microbe-containing secretions. The objective of this study was to determine if the burying beetle, Nicrophorus defodiens, utilizes anal secretions to transmit adult digestive tract bacteria onto a small vertebrate carcass; thus creating the potential to aid in carcass preservation or pass digestive tract bacteria to their larval offspring. Using high-throughput Illumina sequencing of the 16S rRNA gene, we characterized bacterial communities of adult beetle digestive tracts, their anal secretions, and prepared mouse carcasses. We also examined unprepared carcass bacterial communities as a means to interpret community shifts that take place during carcass preservation. We found a vast reduction in diversity on prepared carcasses after anal secretion application. Overall, there was little similarity in bacterial communities among adult digestive tracts, anal secretions, and prepared carcasses, suggesting bacterial communities found in adult digestive tracts do not successfully colonize and achieve dominance on prepared carcasses by way of beetle anal secretions. We concluded that N. defodiens does not transmit their digestive tract bacterial communities to prepared carcasses in a wholesale manner, but may transmit key microbes, including core microbiome members, to preserved carcasses that may ultimately act to sustain larvae and serve as inocula for larval digestive tracts.

rMyCoPortal - an R package to interface with the Mycology Collections Portal.

The understanding of the biodiversity and biogeographical distribution of fungi is still limited. The small number of online databases and the large effort required to access existing data have prevented their use in research articles. The Mycology Collections Portal was established in 2012 to help alleviate these issues and currently serves data online for over 4.3 million fungal records. However, the current process for accessing the data through the web interface is manual, therefore slow, and precludes the extensive use of the existing datasets. Here we introduce the software package rMyCoPortal, which allows users rapid, automated access to the data. rMyCoPortal makes data readily available for further computations and analyses in the open source statistical programming environment R. We will demonstrate the core functions of the package, and how rMyCoPortal can be employed to obtain fungal data that can be used to address basic research questions. rMyCoPortal is a free and open-source R package, available via GitHub.

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats.

The gut microbiome of herbivorous animals consists of organisms that efficiently digest the structural carbohydrates of ingested plant material. Green turtles (Chelonia mydas) provide an interesting model of change in these microbial communities because they undergo a pronounced shift from a surface-pelagic distribution and omnivorous diet to a neritic distribution and herbivorous diet. As an alternative to direct sampling of the gut, we investigated the cloacal microbiomes of juvenile green turtles before and after recruitment to neritic waters to observe any changes in their microbial community structure. Cloacal swabs were taken from individual turtles for analysis of the 16S rRNA gene sequences using Illumina sequencing. One fecal sample was also obtained, allowing for a preliminary comparison with the bacterial community of the cloaca. We found significant variation in the juvenile green turtle bacterial communities between pelagic and neritic habitats, suggesting that environmental and dietary factors support different bacterial communities in green turtles from these habitats. This is the first study to characterize the cloacal microbiome of green turtles in the context of their ontogenetic shifts, which could provide valuable insight into the origins of their gut bacteria and how the microbial community supports their shift to herbivory.

Loss of functional diversity and network modularity in introduced plant-fungal symbioses.

The introduction of alien plants into a new range can result in the loss of co-evolved symbiotic organisms, such as mycorrhizal fungi, that are essential for normal plant physiological functions. Prior studies of mycorrhizal associations in alien plants have tended to focus on individual plant species on a case-by-case basis. This approach limits broad scale understanding of functional shifts and changes in interaction network structure that may occur following introduction. Here we use two extensive datasets of plant-fungal interactions derived from fungal sporocarp observations and recorded plant hosts in two island archipelago nations: New Zealand (NZ) and the United Kingdom (UK). We found that the NZ dataset shows a lower functional diversity of fungal hyphal foraging strategies in mycorrhiza of alien as compared with native trees. Across species this resulted in fungal foraging strategies associated with alien trees being much more variable in functional composition compared with native trees, which had a strikingly similar functional composition. The UK data showed no functional difference in fungal associates of alien and native plant genera. Notwithstanding this, both the NZ and UK data showed a substantial difference in interaction network structure of alien trees compared with native trees. In both cases, fungal associates of native trees showed strong modularity, while fungal associates of alien trees generally integrated into a single large module. The results suggest a lower functional diversity (in one dataset) and a simplification of network structure (in both) as a result of introduction, potentially driven by either limited symbiont co-introductions or disruption of habitat as a driver of specificity due to nursery conditions, planting, or plant edaphic-niche expansion. Recognizing these shifts in function and network structure has important implications for plant invasions and facilitation of secondary invasions via shared mutualist populations.

Forecasting the Effects of Fertility Control on Overabundant Ungulates: White-Tailed Deer in the National Capital Region.

Overabundant populations of ungulates have caused environmental degradation and loss of biological diversity in ecosystems throughout the world. Culling or regulated harvest is often used to control overabundant species. These methods are difficult to implement in national parks, other types of conservation reserves, or in residential areas where public hunting may be forbidden by policy. As a result, fertility control has been recommended as a non-lethal alternative for regulating ungulate populations. We evaluate this alternative using white-tailed deer in national parks in the vicinity of Washington, D.C., USA as a model system. Managers seek to reduce densities of white-tailed deer from the current average (50 deer per km2) to decrease harm to native plant communities caused by deer. We present a Bayesian hierarchical model using 13 years of population estimates from 8 national parks in the National Capital Region Network. We offer a novel way to evaluate management actions relative to goals using short term forecasts. Our approach confirms past analyses that fertility control is incapable of rapidly reducing deer abundance. Fertility control can be combined with culling to maintain a population below carrying capacity with a high probability of success. This gives managers confronted with problematic overabundance a framework for implementing management actions with a realistic assessment of uncertainty.

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils.

Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide.

Aboveground-belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m(2) plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Aurantioporthe corni gen. et comb. nov., an endophyte and pathogen of Cornus alternifolia.

Cryptodiaporthe corni is the causal agent of a destructive disease called golden canker, which affects Cornus alternifolia, known as the pagoda or alternate-leaved dogwood. Due to the association between Cr. corni and pagoda dogwood, we sought to determine whether this fungus was capable of living as an endophyte in pagoda dogwood and causing this disease. Forty asymptomatic stems of plants growing in nature were sampled from five sites across Minnesota. Cryptodiaporthe corni was present in more than half (62.5%) of the stems. Asymptomatic nursery material also was sampled, and the fungus was isolated from a small percentage (20%) of them. Inoculations carried out in the field and greenhouse suggested the endophytic isolates of Cr. corni were capable of causing disease. Asymptomatic stems of trees in the field inoculated with non-colonized (control) grain seed developed golden canker as frequently as those inoculated with grain seed colonized by Cr. corni, suggesting that the fungus was already present in these plants. In greenhouse pathogenicity trials an isolate of Cr. corni obtained from an asymptomatic stem was capable of causing golden canker disease, thus demonstrating causality, fulfilling Koch's postulates. The taxonomic placement of Cr. corni within Cryphonectriaceae was determined. Phylogenetic analysis of the ITS rDNA and ß-tubulin gene regions, along with morphological characteristics, suggested Cr. corni is distinct from other genera within this family. Therefore, we propose a new genus, Aurantioporthe, as well as the new combination, A. corni, to accommodate this species within Cryphonectriaceae.

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally.

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of above-ground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity. Despite high variability across the Park, below-ground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographic patterns. Further, Central Park soils harboured nearly as many distinct soil microbial phylotypes and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents.

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times.

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Towards a unified paradigm for sequence-based identification of fungi.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

Visitor assessment of the mandatory alternative transportation system at Zion National Park.

Transportation infrastructure in national parks has historically been designed for the automobile. With more vehicles in the parks, visitors found themselves in circumstances more reminiscent of a city than a park. Traffic jams, overcrowding, illegal parking, horn honking, and idling vehicles became common, creating stress and contributing to air and noise pollution, the very things visitors were hoping to get away from. Park managers began searching for alternatives, including shuttle systems. Many national parks have implemented optional shuttle systems, but relatively few have completely closed roads to vehicles, transporting visitors on mandatory shuttles. Zion National Park instituted a mandatory shuttle system in May 2000 to relieve crowding and congestion in the main canyon and to protect natural resources. Taking a longitudinal approach, attributes of the shuttle (e.g., crowding, accessibility, freedom, efficiency, preference, and success) were assessed with experiential park factors (e.g., scenic beauty, naturalness, solitude, tranquility, air quality, and soundscape) in 2000, 2003, and 2010 by surveying shuttle-riding park visitors. While visitors initially reported a few reservations about the shuttle system, by 2003, the majority rated the system successful. Ratings of all shuttle-related variables, except crowding, improved over the decade. Improvements were greatest for freedom, accessibility, and efficiency. Multiple regression found overall shuttle success to be mediated by preference, freedom, accessibility, efficiency, and comfort. Experiential variables assessing park conditions followed a similar pattern, with improved ratings as the decade progressed. Results provide important insights into the visitor experience with mandatory alternative shuttle systems in national parks.

Meeting report: fungal its workshop (october 2012).

This report summarizes a meeting held in Boulder, CO USA (19-20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the primary goal of supporting collaboration among researchers for improving fungal ITS sequence resources and developing recommendations for standard ITS primers for the research community.

Some hospitals are falling behind in meeting 'meaningful use' criteria and could be vulnerable to penalties in 2015.

With nearly $30 billion in incentives available, it is critical to know to what extent US hospitals have been able to respond to those incentives by adopting electronic health record (EHR) systems that meet Medicare's criteria for their "meaningful use." Medicare has provided aggregate incentive payment data, but still missing is an understanding of how these payments are distributed across hospital types and years. Our analysis of Medicare data found a substantial increase in the percentage of hospitals receiving EHR incentive payments between 2011 (17.4 percent) and 2012 (36.8 percent). However, this increase was not uniform across all hospitals, and the overall proportion of hospitals receiving a payment for meaningful use was low. Critical-access, smaller, and publicly owned or nonprofit hospitals appeared to be at particular risk for failing to meet Medicare's meaningful-use criteria, and the overall proportion of hospitals receiving a payment for meaningful use was low. Starting in 2015, hospitals that fail to meet the criteria will be subject to financial penalties. To address the needs of institutions in danger of incurring these penalties, policy makers could implement targeted grant programs and provide additional information technology workforce support. In addition, the capacity of EHR system vendors should be carefully monitored to ensure that these institutions have access to the technology they need.

Diversity, distribution and sources of bacteria in residential kitchens.

Bacteria readily colonize kitchen surfaces, and the exchange of microbes between humans and the kitchen environment can impact human health. However, we have a limited understanding of the overall diversity of these communities, how they differ across surfaces and sources of bacteria to kitchen surfaces. Here we used high-throughput sequencing of the 16S rRNA gene to explore biogeographical patterns of bacteria across > 80 surfaces within the kitchens of each of four households. In total, 34 bacterial and two archaeal phyla were identified, with most sequences belonging to the Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Genera known to contain common food-borne pathogens were low in abundance but broadly distributed throughout the kitchens, with different taxa exhibiting distinct distribution patterns. The most diverse communities were associated with infrequently cleaned surfaces such as fans above stoves, refrigerator/freezer door seals and floors. In contrast, the least diverse communities were observed in and around sinks, which were dominated by biofilm-forming Gram-negative lineages. Community composition was influenced by conditions on individual surfaces, usage patterns and dispersal from source environments. Human skin was the primary source of bacteria across all kitchen surfaces, with contributions from food and faucet water dominating in a few specific locations. This study demonstrates that diverse bacterial communities are widely distributed in residential kitchens and that the composition of these communities is often predictable. These results also illustrate the ease with which human- and food-associated bacteria can be transferred in residential settings to kitchen surfaces.

Global biogeography of highly diverse protistan communities in soil.

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States.

Molecular methodologies were used to investigate fungal assemblages of biological soil crusts (BSCs) from arid lands in the southwestern United States. Fungal diversity of BSCs was assessed in a broad survey that included the Chihuahuan and Sonoran deserts as well as the Colorado Plateau. At selected sites samples were collected along kilometer-scale transects, and fungal community diversity and composition were assessed based on community rRNA gene fingerprinting using PCR-denaturing gradient gel electrophoresis (DGGE). Individual phylotypes were characterized through band sequencing. The results indicate that a considerable diversity of fungi is present within crusted soils, with higher diversity being recovered from more successionally mature BSCs. The overwhelming majority of crust fungi belong to the Ascomycota, with the Pleosporales being widespread and frequently dominant. Beta diversity patterns of phylotypes putatively representing dominant members of BSC fungal communities suggest that these assemblages are specific to their respective geographic regions of origin.