@article {KNZ001615, title = {High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure}, journal = {Molecular Ecology}, volume = {22}, year = {2013}, pages = {5456 -5471}, abstract = {

Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available.

}, keywords = {LTER-KNZ}, doi = {10.1111/mec.12480}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.12480}, author = {Darby, D.J. and Todd, T.C. and Herman, M.A.} } @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 {KNZ001483, title = {Several grassland soil nematodes species are insensitive to RNA-mediated interference}, journal = {Journal of Nematology}, volume = {44}, year = {2012}, pages = {92 -101}, abstract = {

Phenotypic analysis of defects caused by RNA mediated interference (RNAi) in Caenorhabditis elegans has proven to be a powerful tool for determining gene function. In this study we investigated the effectiveness of RNAi in four non-model grassland soil nematodes, Oscheius sp FVV-2., Rhabditis sp, Mesorhabditis sp., and Acrobeloides sp. In contrast to reference experiments performed using C. elegans and Caenorhabditis briggsae, feeding bacteria expressing dsRNA and injecting dsRNA into the gonad did not produce the expected RNAi knockdown phenotypes in any of the grassland nematodes. Quantitative reverse-transcribed PCR (qRT-PCR) assays did not detect a statistically significant reduction in the mRNA levels of endogenous genes targeted by RNAi in Oscheius sp., and Mesorhabditis sp. From these studies we conclude that due to low effectiveness and inconsistent reproducibility, RNAi knockdown phenotypes in non-Caenorhabditis nematodes should be interpreted cautiously.

}, keywords = {LTER-KNZ}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593264/}, author = {Wheeler, D. and Darby, B.J. and Todd, T.C. and Herman, M.A.} } @article {KNZ001266, title = {Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean, and sorghum}, journal = {Molecular Ecology}, volume = {19}, year = {2010}, pages = {79 -91}, abstract = {

Agricultural and wild ecosystems may interact through shared pathogens such as Macrophomina phaseolina, a generalist clonal fungus with more than 284 plant hosts that is likely to become more important under climate change scenarios of increased heat and drought stress. To evaluate the degree of subdivision in populations of M. phaseolina in Kansas agriculture and wildlands, we compared 143 isolates from maize fields adjacent to tallgrass prairie, nearby sorghum fields, widely dispersed soybean fields and isolates from eight plant species in tallgrass prairie. Isolate growth phenotypes were evaluated on a medium containing chlorate. Genetic characteristics were analysed based on amplified fragment length polymorphisms and the sequence of the rDNA-internal transcribed spacer (ITS) region. The average genetic similarity was 58\% among isolates in the tallgrass prairie, 71\% in the maize fields, 75\% in the sorghum fields and 80\% in the dispersed soybean fields. The isolates were divided into four clusters: one containing most of the isolates from maize and soybean, two others containing isolates from wild plants and sorghum, and a fourth containing a single isolate recovered from Solidago canadensis in the tallgrass prairie. Most of the sorghum isolates had the dense phenotype on media containing chlorate, while those from other hosts had either feathery or restricted phenotypes. These results suggest that the tallgrass prairie supports a more diverse population of M. phaseolina per area than do any of the crop species. Subpopulations show incomplete specialization by host. These results also suggest that inoculum produced in agriculture may influence tallgrass prairie communities, and conversely that different pathogen subpopulations in tallgrass prairie can interact there to generate \‘hybrids\’ with novel genetic profiles and pathogenic capabilities.

}, keywords = {LTER-KNZ}, doi = {10.1111/j.1365-294X.2009.04433.x}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2009.04433.x}, author = {Saleh, A.A. and Ahmed, H.U. and Todd, T.C. and Travers, S.E. and Zeller, K.A. and Leslie, J.F. and Garrett, K.A.} } @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.} } @article {KNZ001107, title = {Sentinel nematodes of land-use change and restoration in tallgrass prairie}, journal = {Journal of Nematology}, volume = {38}, year = {2006}, pages = {20 -27}, abstract = {Changes in land use and the associated changes in land cover are recognized as the most important component of human-induced global change. Much attention has been focused on deforestation, but grasslands are among the most endangered ecosystems on Earth. The North American tallgrass prairie is a dramatic example, exhibiting a greater than 95\% decline in historical area. Renewed interest in prairie conservation and restoration has highlighted the need for ecological indicators of disturbance and recovery in native systems, including the belowground component. The tallgrass prairie differs from the agricultural systems that have replaced it in having greater diversity and heterogeneity of resources, less physical soil disturbance (although other disturbances, such as fire and grazing, are prominent), and greater nitrogen limitation. Understanding the responses of nematode taxa to these characteristic differences is crucial to the development and improvement of community indices, but while knowledge of disturbance responses by individual taxa is accumulating, the level of necessary taxonomic resolution remains in question. Although nematode communities generally are better described for temperate grasslands than for other natural ecosystems, identification of sentinel taxa is further confounded by high levels of diversity, and both spatial and temporal heterogeneity.}, keywords = {LTER-KNZ}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19259426}, author = {Todd, T.C. and Powers, T.O. and Mullin, P.G.} } @article {KNZ00861, title = {Effects of fire, mowing and fertilization effects on density and biomass of macroinvertebrates in North American tallgrass prairie soils}, journal = {Soil Biology \& Biochemistry}, volume = {35}, year = {2003}, pages = {1079 -1093}, abstract = {The responses of tallgrass prairie plant communities and ecosystem processes to fire and grazing are well characterized. However, responses of invertebrate consumer groups, and particularly soil-dwelling organisms, to these disturbances are not well known. At Konza Prairie Biological Station, we sampled soil macroinvertebrates in 1994 and 1999 as part of a long-term experiment designed to examine the effects and interactions of annual fire, mowing, and fertilization (N and P) on prairie soil communities and processes. For nearly all taxa, in both years, responses were characterized by significant treatment interactions, but some general patterns were evident. Introduced European earthworms (Aporrectodea spp. and Octolasion spp.) were most abundant in plots where fire was excluded, and the proportion of the total earthworm community consisting of introduced earthworms was greater in unburned, unmowed, and fertilized plots. Nymphs of two Cicada genera were collected (Cicadetta spp. and Tibicen spp.). Cicadetta nymphs were more abundant in burned plots, but mowing reduced their abundance. Tibicen nymphs were collected almost exclusively from unburned plots. Treatment effects on herbivorous beetle larvae (Scarabaeidae, Elateridae, and Curculionidae) were variable, but nutrient additions (N or P) usually resulted in greater densities, whereas mowing usually resulted in lower densities. Our results suggest that departures from historical disturbance regimes (i.e. frequent fire and grazing) may render soils more susceptible to increased numbers of European earthworms, and that interactions between fire, aboveground biomass removal, and vegetation responses affect the structure and composition of invertebrate communities in tallgrass prairie soils.}, keywords = {LTER-KNZ, biomass, Cicadidae, Curculionidae, disturbance, earthworms, Elateridae, Fertilization, Fertilizer, fire, grassland, insect herbivores, nitrogen, Phosphorus, Scarabaeidae}, doi = {10.1016/S0038-0717(03)00153-6}, author = {Callaham, M.A. Jr. and John M. Blair and T.C. Todd and Kitchen, D.J. and M.R. Whiles} } @inbook {KNZ00721, title = {Responses of grassland soil invertebrates to natural and anthropogenic disturbances}, booktitle = {Invertebrates as Webmasters in Ecosystems}, year = {2000}, pages = {43 -71}, publisher = {CAB International Press}, organization = {CAB International Press}, address = {New York, NY}, abstract = {his chapter aims to (1) summarize the major factors influencing invertebrate abundance and distribution in tallgrass prairie soils, focusing on the responses of selected soil invertebrate groups to natural disturbances (such as fire, grazing and drought); (2) identify potential linkages between changes in soil communities and the effects of disturbances on key plant and soil characteristics or processes; and (3) to discuss potential effects of novel anthropogenic perturbations (altered amounts of precipitation, elevated CO2 and increased N inputs) on soil communities and processes. It focuses on North American tallgrass prairies and draws upon studies undertaken at the Konza Prairie Long-Term Ecological Research site, with results from other grasslands where appropriate.}, keywords = {LTER-KNZ}, doi = {10.1079/9780851993942.0043}, author = {John M. Blair and Todd, T.C. and Callaham, M.A.}, editor = {Coleman, D.C. and Hendrix, P.F.} } @article {KNZ00715, title = {Effects of altered soil water availability on a tallgrass prairie nematode community}, journal = {Applied Soil Ecology}, volume = {13}, year = {1999}, pages = {45 -55}, abstract = {Climate change predictions for the Great Plains region of North America include reduced growing season precipitation. The consequence of this prediction for soil fauna and belowground processes was investigated at two spatial scales by integrating experimental manipulation of soil moisture levels with natural variation in soil-water availability. Experiments consisted of (1) reciprocal core transplants across a regional precipitation gradient and (2) supplemental irrigation applied across a local topographic gradient. This report examines functional-level responses by the tallgrass prairie nematode community to differences in soil moisture levels over a four-year period. Effects on nematode community structure were complex and dependent upon nematode trophic habit and depth in the soil profile. The strongest and most consistent responses to changes in soil-water availability were displayed by herbivorous taxa, with 71\% higher densities observed under wetter soil conditions across experiments and years. Responses of microbial-feeding nematodes were more variable, with lower densities observed, in some cases, in the presence of experimentally-increased soil moisture levels. Effects of regional differences in soil-water availability on the nematode community were uniformly restricted to depths >20 cm. Community responses to short-term changes in soil moisture were not consistent with patterns in community structure developed under different natural moisture regimes, suggesting divergent short-term and long-term responses of belowground biota and processes to changes in soil-water availability.}, keywords = {LTER-KNZ, Climate change, community structure, Nematode, soil moisture, tallgrass prairie}, doi = {10.1016/S0929-1393(99)00022-0}, author = {Todd, T.C. and John M. Blair and Milliken, G.A.} } @inbook {KNZ00661, title = {Belowground biology and processes}, booktitle = {Grassland Dynamics: Long-Term Ecological Research in Tallgrass Prairie}, year = {1998}, pages = {244 -264}, publisher = {Oxford University Press}, organization = {Oxford University Press}, address = {New York}, keywords = {LTER-KNZ, tallgrass prairie}, author = {C. W. Rice and Todd, T.C. and John M. Blair and Seastedt, T.R. and Ramundo, R.A. and G.T. Wilson}, editor = {Alan K. Knapp and J. M. Briggs and D.C. Hartnett and Scott. L. Collins} } @inbook {KNZ00660, title = {Soils and soil biota}, booktitle = {Grassland Dynamics: Long-Term Ecological Research in Tallgrass Prairie}, year = {1998}, pages = {48 -66}, publisher = {Oxford University Press}, organization = {Oxford University Press}, address = {New York}, keywords = {LTER-KNZ, tallgrass prairie}, author = {Ransom, M.D. and C. W. Rice and Todd, T.C. and Wehmueller, W.A.}, editor = {Alan K. Knapp and J. M. Briggs and D.C. Hartnett and Scott. L. Collins} } @article {KNZ00572, title = {Effects of management practices on nematode community structure in tallgrass prairie}, journal = {Applied Soil Ecology}, volume = {3}, year = {1996}, pages = {235 -246}, abstract = {The effects of burning, mowing, and nitrogen (N) and phosphorus (P) fertilization on the trophic structure of a tallgrass prairie nematode community were examined in a long-term field experiment established in 1986. Nematode densities and trophic composition were determined in October of 1987, 1989, and 1994 following 2, 4, and 9 years of treatment, respectively. Total populations of obligate herbivores tended to increase with annual burning and N fertilization but responses by individual taxa were relative to the structure and composition of vegetation as determined by management practice. In contrast, mowing resulted in consistent reductions in herbivore densities. The family Tylenchidae, with species classified as both root and fungal feeders, exhibited short-term decreases in numbers due to burning and long-term increases in numbers due to mowing. Treatment responses by this group were more consistent with the behavior of known fungal-feeding than root-feeding nematodes. Microbivore densities increased with burning and N fertilization, while numbers of omnivores and predators declined with chronic N additions. The effects of P fertilization on nematode population densities varied with management practice, primarily N fertilization. Canonical discriminant analysis differentiated trophic groups based on their responses to mowing and P-fertilization. Measurements of the trophic composition of the nematode community, particularly the relative abundance of individual herbivore taxa and the proportion of fungivores to microbivores, were good indicators of ecosystem responses to management practices.}, keywords = {LTER-KNZ, disturbance, fire, Mowing, Nematode, nitrogen, tallgrass prairie, Trophic structure}, doi = {10.1016/0929-1393(95)00088-7}, author = {Todd, T.C.} } @article {KNZ00360, title = {Relationships of mycorrhizal symbiosis, rooting strategy and phenology among tallgrass prairie forbs}, journal = {Canadian Journal of Botany}, volume = {70}, year = {1992}, pages = {1521 -1528}, keywords = {LTER-KNZ, tallgrass prairie}, doi = {10.1139/b92-191}, author = {Hetrick, B.A.D. and G.T. Wilson and Todd, T.C.} } @article {KNZ00382, title = {Soil invertebrate and plant responses to mowing and Carbofuran application in a North American tallgrass prairie}, journal = {Plant and Soil}, volume = {144}, year = {1992}, pages = {117 -124}, keywords = {LTER-KNZ, tallgrass prairie}, doi = {10.1007/BF00018852}, author = {Todd, T.C. and James, S.W. and Seastedt, T.R.} } @article {KNZ00283, title = {Differential responses of C3 and C4 grasses to mycorrhizal symbiosis, phosphorus fertilization, and soil microorganisms}, journal = {Canadian Journal of Botany}, volume = {68}, year = {1990}, pages = {461 -467}, abstract = {

The responses of five C4, warm-season and five C3, cool-season tallgrass prairie grasses to phosphorus (P) fertilization, mycorrhizae, and soil microorganisms were compared in greenhouse studies. The warm-season grasses responded positively to mycorrhizae and to P fertilization, but mycorrhizal plants did not respond to P. The soil microflora reduced mycorrhizal plant dry weight and root colonization. In contrast, cool-season grasses did not respond to mycorrhizae or P fertilization. Soil microorganisms did not suppress cool-season plant growth, but root colonization was reduced in nonsterile soil. For the warm-season grasses there was an inverse relationship between mycorrhizal root colonization and P fertilization and a positive relationship between root colonization and plant dry weight. For the cool-season grasses there was also an inverse relationship between root colonization and P fertilization, but the relationship between root colonization and plant dry weight was negative. In both the warm-season and cool-season grasses, low levels of mycorrhizal root colonization persisted even when P fertilization was sufficient to eliminate mycorrhizal effects on plant growth. Thus, warm-and cool-season grasses display profoundly different strategies for nutrient acquisition. Key words: cool-season grasses, warm-season grasses, vesicular-arbuscular mycorrhizae

}, keywords = {LTER-KNZ, tallgrass prairie}, doi = {10.1139/b90-061}, author = {Hetrick, B.A.D. and G.T. Wilson and Todd, T.C.} } @article {KNZ00206, title = {Interactions among soil invertebrates, microbes and plant growth in tallgrass prairie}, journal = {Agriculture, Ecosystems, and Environment}, volume = {24}, year = {1988}, pages = {219 -228}, abstract = {

The tallgrass prairie of North American contains a diverse and abundant soil fauna well represented by earthworms, macro- and microarthopods and nematodes. A portion of this fauna representing a large fraction of the animal biomass has been introduced in the last 200 years, and functional roles and regulatory mechanisms may have been altered because of these introductions. Four years of experimental manipulations of plant and fauna variables have failed to establish a definitive net effect of the soil fauna on primary productivity. However, measurable effects of the fauna on nutrient dynamics of the grassland ecosystem have been observed. Experimental manipulations of plant root dynamics and addition of inorganic nitrogen and fixed carbon have demonstrated that both resources quality and resource quantity are factors limiting the size of soil fauna populations

}, keywords = {LTER-KNZ, tallgrass prairie}, doi = {10.1016/0167-8809(88)90067-9}, author = {Seastedt, T.R. and James, S.W. and Todd, T.C.} } @article {KNZ00161, title = {Experimental manipulations of soil arthropod, nematode, and earthworm communities in a North American tallgrass prairie}, journal = {Pedobiologia}, volume = {30}, year = {1987}, pages = {9 -17}, abstract = {An insecticide was applied to foliage and an insecticide-nematicide was applied to the soil surface of a North American tallgrass prairie site in an attempt to manipulate population densities of invertebrate consumers. The objectives of this study included 1) measurement of impacts of the dominant root herbivores, June beetle larvae (Phyllophaga spp.: Scarabaeidae) on plant root biomass and production; 2) to evaluate nematode and earthworm response to the chemicals and to correlate changes in these groups with changes in living or dead plant mass, and 3) to test if differences in densities of aboveground invertebrate consumer groups directly or indirectly affected population densities of the belowground groups. The last question resulted from an observation by Seastedt (1985) that moderate aboveground herbivory appears to increase population densities of soil nematodes and certain arthropod groups}, keywords = {LTER-KNZ, tallgrass prairie}, author = {Seastedt, T.R. and Todd, T.C. and James, S.J.} }