@article {KNZ001635, title = {Tallgrass prairie soil fungal communities are resilient to climate change}, journal = {Fungal Ecology}, volume = {10}, year = {2014}, pages = {44 -57}, abstract = {

Climate models for central United States predict increasing temperatures and greater variability in precipitation. Combined, these shifts in environmental conditions impact many ecosystem properties and services. Long-term climate change experiments, such as the Rainfall Manipulation Plots (RaMPs), can be used to address soil community responses to simultaneous manipulation of temperature and temporal variability in precipitation. The RaMPs experiment is located in a native tallgrass prairie at the Konza Prairie Biological Station and has been operational since 1998 providing the potential to address responses to long-term environmental manipulations. To test whether community composition, richness, or diversity respond to environmental change, more than 40 000 fungal amplicons were analyzed from soil samples collected in 2006. The data suggest that soil fungal communities are compositionally resilient to predicted environmental change. This is the case both for the community composition overall as inferred from ordination analyses as well as analyses of variance for each of the most common Operational Taxonomic Units (OTUs). However, while this study suggests compositional resilience, further studies are required to address functional attributes of these communities and their responses to environmental manipulations.

}, keywords = {LTER-KNZ, Altered precipitation, Global warming, Soil fungi, tallgrass prairie}, doi = {10.1016/j.funeco.2013.11.003}, url = {https://www.sciencedirect.com/science/article/abs/pii/S1754504813001141?via\%3Dihub}, author = {A. Jumpponen and Jones, K.L.} } @article {KNZ001598, title = {Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie}, journal = {PLoS ONE}, volume = {8}, year = {2013}, pages = {67884 -}, abstract = {

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80\% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important implications for both managed and natural grassland ecosystems.

}, keywords = {LTER-KNZ, Bacteria, Biodiversity, Ecosystem functioning, Grasslands, Microbial ecosystems, Plant communities, Ribosomal RNA, Sequence analysis}, doi = {10.1371/journal.pone.0067884}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067884}, author = {Coolon, J.D. and Jones, K.L. and Todd, T.C. and John M. Blair and Herman, M.A.} } @article {KNZ001482, title = {Normalization and centering of array-based heterologous genome hybridization based on divergent control probes}, journal = {BMC Bioinformatics}, volume = {12}, year = {2011}, abstract = {

Background Hybridization of heterologous (non-specific) nucleic acids onto arrays designed for model-organisms has been proposed as a viable genomic resource for estimating sequence variation and gene expression in non-model organisms. However, conventional methods of normalization that assume equivalent distributions (such as quantile normalization) are inappropriate when applied to non-specific (heterologous) hybridization. We propose an algorithm for normalizing and centering intensity data from heterologous hybridization that makes no prior assumptions of distribution, reduces the false appearance of homology, and provides a way for researchers to confirm whether heterologous hybridization is suitable. Results Data are normalized by adjusting for Gibbs free energy binding, and centered by adjusting for the median of a common set of control probes assumed to be equivalently dissimilar for all species. This procedure was compared to existing approaches and found to be as successful as Loess normalization at detecting sequence variations (deletions) and even more successful than quantile normalization at reducing the accumulation of false positive probe matches between two related nematode species, Caenorhabditis elegans and C. briggsae. Despite the improvements, we still found that probe fluorescence intensity was too poorly correlated with sequence similarity to result in reliable detection of matching probe sequence. Conclusions Cross-species hybridizations can be a way to adapt genome-enabled tools for closely related non-model organisms, but data must be appropriately normalized and centered in a way that accommodates hybridization of nucleic acids with diverged sequence. For short, 25-mer probes, hybridization intensity alone may be insufficiently correlated with sequence similarity to allow reliable inference of homology at the probe level.

}, keywords = {LTER-KNZ}, doi = {10.1186/1471-2105-12-183}, url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-183}, author = {Darby, B.J. and Jones, K.L. and Wheeler, D. and Herman, M.A.} } @article {KNZ001278, title = {Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites}, journal = {Molecular Ecology}, volume = {19}, year = {2010}, pages = {41 -53}, abstract = {We analysed two sites within and outside an urban development in a rural background to estimate the fungal richness, diversity and community composition in Quercus spp. ectomycorrhizas using massively parallel 454-sequencing in combination with DNA-tagging. Our analyses indicated that shallow sequencing (\~{}150 sequences) of a large number of samples (192 in total) provided data that allowed identification of seasonal trends within the fungal communities: putative root-associated antagonists and saprobes that were abundant early in the growing season were replaced by common ectomycorrhizal fungi in the course of the growing season. Ordination analyses identified a number of factors that were correlated with the observed communities including host species as well as soil organic matter, nutrient and heavy metal enrichment. Overall, our application of the high throughput 454 sequencing provided an expedient means for characterization of fungal communities.}, keywords = {LTER-KNZ}, doi = {10.1111/j.1365-294X.2009.04483.x}, author = {A. Jumpponen and Jones, K.L. and Mattox, J.D. and Yeage, C.} } @article {KNZ001320, title = {Multi-element fingerprinting and high throughput sequencing identify multiple elements that affect fungal communities in Quercus macrocarpa foliage}, journal = {Plant Signaling and Behaviour}, volume = {5}, year = {2010}, pages = {1157 -1161}, abstract = {Diverse fungal mutualists, pathogens and saprobes colonize plant leaves. These fungi face a complex environment, in which stochastic dispersal interplays with abiotic and biotic filters. However, identification of the specific factors that drive the community assembly seems unattainable. We mined two broad data sets and identified chemical elements, to which dominant molecular operational taxonomic units (OTUs) in the foliage of a native tree respond most extremely. While many associations could be identified, potential complicating issues emerged. Those were related to unevenly distributed OTU frequency data, a large number of potentially explanatory variables, and the disproportionate effects of outlier observations.}, keywords = {LTER-KNZ}, doi = {10.4161/psb.5.9.12681}, author = {A. Jumpponen and Keating, K. and Gadbury, G.L. and Jones, K.L. and Mattox, J.D.} } @article {KNZ001307, title = {Seasonally dynamic fungal communities in Quercus macrocarpa phyllosphere differ among urban and nonurban environments}, journal = {New Phytologist}, volume = {186}, year = {2010}, pages = {496 -513}, abstract = {

\•The fungal richness, diversity and community composition in the Quercus macrocarpa phyllosphere were compared across a growing season in trees located in six stands within and outside a small urban center using 454-sequencing and DNA tagging. The approaches did not differentiate between endophytic and epiphytic fungal communities. \•Fungi accumulated in the phyllosphere rapidly and communities were temporally dynamic, with more than a third of the analyzed operational taxonomic units (OTUs) and half of the BLAST-inferred genera showing distinct seasonal patterns. The seasonal patterns could be explained by fungal life cycles or environmental tolerances. \•The communities were hyperdiverse and differed between the urban and nonurban stands, albeit not consistently across the growing season. Foliar macronutrients (nitrogen (N), potassium (K) and sulfur (S)), micronutrients (boron (B), manganese (Mn) and selenium (Se)) and trace elements (cadmium (Cd), lead (Pb) and zinc (Zn)) were enriched in the urban trees, probably as a result of anthropogenic activities. Because of correlations with the experimental layout, these chemical elements should not be considered as community drivers without further empirical studies. \•We suggest that a combination of mechanisms leads to differences between urban and nonurban communities. Among those are stand isolation and size, nutrient and pollutant accumulation plus stand management, including fertilization and litter removal.

}, keywords = {LTER-KNZ}, doi = {10.1111/j.1469-8137.2010.03197.x}, url = {https://nph.onlinelibrary.wiley.com/doi/full/10.1111/j.1469-8137.2010.03197.x}, author = {A. Jumpponen and Jones, K.L.} } @article {KNZ001302, title = {Vertical distribution of fungal communities in tallgrass prairie soil}, journal = {Mycologia}, volume = {102}, year = {2010}, pages = {1027 -1041}, abstract = {

We used 454 sequencing of the internal transcribed spacer region to characterize fungal communities in tallgrass prairie soils subdivided into strata 0\–10, 10\–20, 30\–40 and 50\–60 cm deep. The dataset included more than 14 000 fungal sequences distributed across Basidiomycota, Ascomycota, basal fungal lineages and Glomeromycota in order of decreasing frequency. As expected the community richness and diversity estimators tended to decrease with increasing depth. Although species richness was significantly reduced for samples from the deeper profiles, even the deepest stratum sampled contained richness of more than a third of that in the topmost stratum. More importantly, nonparametric multidimensional scaling (NMS) ordination analyses indicated that the fungal communities differed across vertical profiles, although only the topmost and deepest strata were significantly different when the NMS axis scores were compared by ANOVA. These results emphasize the importance of considering the fungal communities across the vertical strata because the deeper soil horizons might maintain a distinct community composition and thus contribute greatly to overall richness. The majority of operational taxonomic units (OTUs) declined in frequency with increasing depth, although a linear regression analysis indicated that some increased with increasing depth. The OTUs and BLAST-assigned taxa that showed increasing frequencies were mainly unculturable fungi, but some showed likely affinities to families Nectriaceae and Venturiaceae or to genus Pachnocybe. Although the ecological roles of the fungi in the deeper strata remain uncertain, we hypothesize that the fungi with preferences for deeper soil have adequate access to substrates and possess environmental tolerances that enable their persistence in those environments.

}, keywords = {LTER-KNZ, 454 sequencing, pyrosequencing, soil depth, Soil fungi, tallgrass prairie}, doi = {10.3852/09-316}, url = {https://www.tandfonline.com/doi/abs/10.3852/09-316?journalCode=umyc20}, author = {A. Jumpponen and Jones, K.L. and John M. Blair} } @article {KNZ001194, title = {Heteroduplex molecules cause sexing errors in a standard molecular protocol for avian sexing}, journal = {Molecular Ecology Resources}, volume = {9}, year = {2009}, pages = {61 -65}, abstract = {

Molecular methods are a necessary tool for sexing monomorphic birds. These molecular approaches are usually reliable, but sexing protocols should be evaluated carefully because biochemical interactions may lead to errors. We optimized laboratory protocols for genetic sexing of a monomorphic shorebird, the upland sandpiper (Bartramia longicauda), using two independent sets of primers, P2/P8 and 2550F/2718R, to amplify regions of the sex-linked CHD-Z and CHD-W genes. We discovered polymorphisms in the region of the CHD-Z intron amplified by the primers P2/P8 which caused four males to be misidentified as females (n = 90 mated pairs). We cloned and sequenced one CHD-W allele (370 bp) and three CHD-Z alleles in our population: Z\° (335 bp), Z\′ (331 bp) and Z\″ (330 bp). Normal (Z\°Z\°) males showed one band in agarose gel analysis and were easily differentiated from females (Z\°W), which showed two bands. However, males heterozygous for CHD-Z alleles (Z\′Z\″) unexpectedly showed two bands in a pattern similar to females. While the Z\′ and Z\″ fragments contained only short deletions, they annealed together during the polymerase chain reaction (PCR) process and formed heteroduplex molecules that were similar in size to the W fragment. Errors previously reported for molecular sex-assignment have usually been due to allelic dropout, causing females to be misidentified as males. Here, we report evidence that events in PCRs can lead to the opposite error, with males misidentified as females. We recommend use of multiple primer sets and large samples of known-sex birds for validation when designing protocols for molecular sex analysis.

}, keywords = {LTER-KNZ, 2550F/2718R, Bartramia longicauda, CHD-Z, molecular sexing, P2/P8, Upland Sandpiper}, doi = {10.1111/j.1755-0998.2008.02307.x}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1755-0998.2008.02307.x}, author = {Casey, A.E. and Jones, K.L. and Sandercock, B.K. and Wisely, S.M.} } @article {KNZ001277, title = {Massively parallel 454-sequencing of Quercus macrocarpa phyllosphere fungal communities indicates reduced richness and diversity in urban environments}, journal = {New Phytologist}, volume = {184}, year = {2009}, pages = {438 -448}, abstract = {

\•\ This study targeted the fungal communities in the phyllosphere of Quercus macrocarpa and compared the fungal species richness, diversity and community composition among trees located within and outside a small urban center using recently developed 454 sequencing and DNA tagging. \•\ The results indicate that the fungal phyllosphere communities are extremely diverse and strongly dominated by ascomycetes, with Microsphaeropsis [two Operational Taxonomic Units (OTUs); 23.6\%], Alternaria (six OTUs; 16.1\%), Epicoccum (one OTU; 6.0\%) and Erysiphe (two OTUs; 5.9\%) as the most abundant genera. \•\ Although the sequencing effort averaged 1000 reads per tree and detected nearly 700 distinct molecular OTUs at 95\% internal transcribed spacer 1 similarity, the richness of the hyperdiverse phyllosphere communities could not be reliably estimated as nearly one-half of the molecular OTUs were singletons. \•\ The fungal communities within and outside the urban center differed in richness and diversity, which were lower within the urban development. The two land-use types contained communities that were distinct and more than 10\% of the molecular OTUs differed in their frequency.

}, keywords = {LTER-KNZ}, doi = {10.1111/j.1469-8137.2009.02990.x}, url = {https://nph.onlinelibrary.wiley.com/doi/full/10.1111/j.1469-8137.2009.02990.x}, author = {A. Jumpponen and Jones, K.L.} } @article {KNZ001101, title = {Development of taxon-specific markers for high-throughput screening of microbial-feeding nematodes}, journal = {Molecular Ecology Notes}, volume = {6}, year = {2006}, pages = {712 -714}, abstract = {In an effort to assess the taxonomic identity of large-scale samplings of nematodes from the Konza Tallgrass Prairie, we sequenced a portion of the 18S rRNA gene and its associated internally transcribed spacer (ITS1) from 74 nematodes encompassing four taxonomic families. From these sequences, we have developed a series of molecular probes to distinguish 16 distinct microbivorous nematode taxa. Using a combination of low power microscopy and taxon-specific real-time probes, the 74 nematodes were correctly assigned to their respective taxonomic groups. This optimized method provides a high-throughput assay to determine nematode identities across larger data sets.}, keywords = {LTER-KNZ, 18S rRNA, 5' nuclease assaym, Nematoda, real-time PCR, Taqman}, doi = {10.1111/j.1471-8286.2006.01319.x}, author = {Jones, K.L. and Todd, T.C. and Herman, M.A.} } @article {KNZ001054, title = {Molecular approach for assessing responses of microbial-feeding nematodes to burning and chronic nitrogen enrichment in a native grassland}, journal = {Molecular Ecology}, volume = {15}, year = {2006}, pages = {2601 -2609}, abstract = {A substantial proportion of the primary productivity in grassland ecosystems is allocated belowground, sustaining an abundant and diverse community of microbes and soil invertebrates. These belowground communities drive many important ecosystem functions and are responsive to a variety of environmental changes. Nematodes, an abundant and diverse component of grassland soil communities, are particularly responsive to altered environmental conditions, such as those associated with reduced fire frequency and nitrogen enrichment, with the most consistent responses displayed by microbial-feeding nematodes. However, much of the available research characterizing nematode responses to environmental change has been carried out at the taxonomic level of family or by broad trophic categories (e.g. fungivores, bacterivores). The extent to which differential responses to environmental change occurs at the genus level or below is unclear. Therefore, the objective of this study was to use molecular methods to quantify the response of microbial-feeding nematodes, at the lowest levels of taxonomic resolution, to nitrogen enrichment and changes in fire frequency. Using sequencing and quantitative polymerase chain reaction (PCR) probes for the 18S ribosomal RNA gene and the ITS1 region, we identified 19 microbial-feeding nematode taxa across four families. When nematodes were sampled across treatments, we found that some nematode taxa within a family responded similarly to nitrogen and burning treatments, while other taxa within the same family respond quite differently. Additionally, although nematodes from different families on average responded differently to nitrogen enrichment and burning, similar responses were seen in nematode taxa that span three taxonomic families. Thus, if nematodes are to be used as indicators of environmental change, care should be taken to assess the response at the lowest taxonomic level possible.}, keywords = {LTER-KNZ}, doi = {10.1111/j.1365-294X.2006.02971.x}, author = {Jones, K.L. and Todd, T.C. and Wall-Beam, J.L. and Coolon, J.D. and John M. Blair and Herman, M.A.} }