02899nas a2200265   4500008004100000245012000041210006900161300001200230490000600242520206400248653001302312653001702325653002602342653001502368653002502383653002202408653001802430653002202448100001702470700001602487700001502503700002002518700001702538856007802555       2013                        eng d00aLong-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie0 aLongterm nitrogen amendment alters the diversity and assemblage   a67884 -0 v83 a<p>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.</p>10aBacteria10aBiodiversity10aEcosystem functioning10aGrasslands10aMicrobial ecosystems10aPlant communities10aRibosomal RNA10aSequence analysis1 aCoolon, J.D.1 aJones, K.L.1 aTodd, T.C.1 aBlair, John, M.1 aHerman, M.A.  uhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.006788403078nas a2200169   4500008004100000245008200041210006900123260004300192490002100235520251000256653002702766653002402793653002002817653001802837100001702855856003602872       2008                        eng d00aEcological genomics of nematode responses to different bacterial environments0 aEcological genomics of nematode responses to different bacterial  aManhattan, KSbKansas State University0 vPhD Dissertation3 a<p>Determining the genetic mechanisms involved in organismal response to environmental change is essential for understanding the effects of anthropogenic disturbance. The composition of the bacterial-feeding nematode community is an excellent biological indicator of disturbance, particularly in grassland ecosystems. We have previously shown that grassland soil nematodes are responsive to perturbations in the field including the addition of nitrogen fertilizer. We are interested in how this perturbation affects the microbial community and downstream effects on the next trophic level, the bacterial-feeding nematodes. To determine the effects of disturbance on soil bacterial communities we used massively parallel sequencing and found that chronic nitrogen addition on tallgrass prairie significantly impacts overall bacterial community diversity and the abundance of specific bacterial taxa. Because native soil nematodes lack well developed genomic tools, we employed Caenorhabditis elegans as a model for native soil nematode taxa and used transcriptional profiling to identify 204 candidate genes regulated in response to altered bacterial diets isolated from grassland soils. To biologically validate our results we used mutations that inactivate 21 of the identified genes and showed that most contribute to fitness or lifespan in a given bacterial environment. Although these bacteria may not be natural C. elegans food sources, this study aimed to show how changes in food source, as can occur in environmental disturbance, has large effects on gene expression and those genes whose expression are affected, contribute to fitness. Furthermore, we identified new functions for genes of unknown function as well as previously well-characterized genes, demonstrating the utility of this approach to further describe C. elegans genome. We also investigated the function of previously well-characterized C. elegans defense pathways in our grassland soil bacterial environments and found that some are environment specific. Additionally, we found that cuticular collagen genes are important for lifespan, and appear to function downstream of known defense pathways. Overall, our results suggest that anthropogenic disturbance in grasslands alters the most basal components of the soil food web, bacteria and bacterial-feeding nematodes through the genes they possess and how they are expressed, and resultant bottom-up effects could have profound consequences on ecosystem health and function.</p>10aCaenorhabditis elegans10aEcological genomics10aInnate immunity10aSoil bacteria1 aCoolon, J.D.  uhttp://hdl.handle.net/2097/275002631nas a2200181   4500008004100000245014300041210006900184300001500253490000700268520194700275100001602222700001502238700002002253700001702273700002002290700001702310856012202327       2006                        eng d00aMolecular approach for assessing responses of microbial-feeding nematodes to burning and chronic nitrogen enrichment in a native grassland0 aMolecular approach for assessing responses of microbialfeeding n  a2601 -26090 v153 aA 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.1 aJones, K.L.1 aTodd, T.C.1 aWall-Beam, J.L.1 aCoolon, J.D.1 aBlair, John, M.1 aHerman, M.A.  uhttp://knz.lternet.edu/content/molecular-approach-assessing-responses-microbial-feeding-nematodes-burning-and-chronic