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Publication N6-methyladenosine modification of a parvovirus-encoded small noncoding RNA facilitates viral DNA replication through recruiting Y-family DNA polymerases(PNAS, 2024-06-14) Ning, Kang; Zhao, Junxing; Feng, Zehua; Park, Soo Yeun; McFarlin, Shane; Cheng, Fang; Yan, Ziying; Wang, Jingxin; Qiu, JianmingHuman bocavirus 1 (HBoV1) is a human parvovirus that causes lower respiratory tract infections in young children. It contains a single-stranded (ss) DNA genome of ~5.5 kb that encodes a small noncoding RNA of 140 nucleotides known as bocavirus-encoded small RNA (BocaSR), in addition to viral proteins. Here, we determined the secondary structure of BocaSR in vivo by using DMS-MaPseq. Our findings reveal that BocaSR undergoes N6-methyladenosine (m6A) modification at multiple sites, which is critical for viral DNA replication in both dividing HEK293 cells and nondividing cells of the human airway epithelium. Mechanistically, we found that m6A-modified BocaSR serves as a mediator for recruiting Y-family DNA repair DNA polymerase (Pol) η and Pol κ likely through a direct interaction between BocaSR and the viral DNA replication origin at the right terminus of the viral genome. Thus, this report represents direct involvement of a viral small noncoding RNA in viral DNA replication through m6A modification.Publication Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California(BMC, 2023-11-23) Swift, Joel F.; Migicovsky, Zoë; Trello, Grace E; Miller, Allison J.Background Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose ‘terroir’, the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions. Results To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. Conclusions These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California. Supplementary Information The online version contains supplementary material available at 10.1186/s40793-023-00539-0.Publication Parartemiopsis shangrilaensis, a new species of fairy shrimp (Branchiopoda, Anostraca) from Yunnan, with a key to the Chirocephalidae of China(Pensoft Publishers, 2023-07-04) Shu, Shu-Sen; Chen, Xiao-Yong; Rogers, D. Christopher; Sanoamuang, LaorsriThe fairy shrimp genus Parartemiopsis Rogers, 2005 currently contains a single species reported from Russia and Mongolia. In 2013, an unidentified Parartemiopsis population was reported from the eastern margin of the Tibetan Plateau in China’s Yunnan Province, from Patatson National Park in Shangri-La County. Here, we describe the Chinese populations as a new species, Parartemiopsis shangrilaensis sp. nov. This new species is distinguished from its congener, P. longicornis (Smirnov, 1930), by the form of the male second antennae and the gonopod. The discovery of P. shangrilaensis sp. nov. extends the known distribution of the genus, and more Parartemiopsis species may be found in the future. We present a key to the genera and species of Chirocephalidae in China as an aid to future research.Publication A Mixed Model for Assessing the Effect of Numerous Plant Species Interactions on Grassland Biodiversity and Ecosystem Function Relationships(Springer, 2022-09-01) McDonnell, Jack; McKenna, Thomas; Yurkonis, Kathryn A.; Hennessy, Deirdre; de Andrade Moral, Rafael; Brophy, CarolineIn grassland ecosystems, it is well known that increasing plant species diversity can improve ecosystem functions (i.e., ecosystem responses), for example, by increasing productivity and reducing weed invasion. Diversity-Interactions models use species proportions and their interactions as predictors in a regression framework to assess biodiversity and ecosystem function relationships. However, it can be difficult to model numerous interactions if there are many species, and interactions may be temporally variable or dependent on spatial planting patterns. We developed a new Diversity-Interactions mixed model for jointly assessing many species interactions and within-plot species planting pattern over multiple years. We model pairwise interactions using a small number of fixed parameters that incorporate spatial effects and supplement this by including all pairwise interaction variables as random effects, each constrained to have the same variance within each year. The random effects are indexed by pairs of species within plots rather than a plot-level factor as is typical in mixed models, and capture remaining variation due to pairwise species interactions parsimoniously. We apply our novel methodology to three years of weed invasion data from a 16-species grassland experiment that manipulated plant species diversity and spatial planting pattern and test its statistical properties in a simulation study. Supplementary materials accompanying this paper appear online.Publication Dietary overlap and selectivity among mountain steppe river fish in the United States and Mongolia(Wiley Open Access, 2023-05-21) Minder, Mario; Arsenault, Emily R.; Pyron, Mark; Otgonganbat, Amarbat; Mendsaikhan, BudLotic systems in mountain regions have historically provided secure habitat for native fish populations because of their relative isolation from human settlement and lack of upstream disturbances. However, rivers of mountain ecoregions are currently experiencing heightened levels of disturbance due to the introduction of nonnative species impacting endemic fishes in these areas. We compared the fish assemblages and diets of mountain steppe fishes of the stocked rivers in Wyoming with rivers in northern Mongolia where stocking is absent. Using gut content analysis, we quantified the selectivity and diets of fishes collected in these systems. Nonnative species had more generalist diets with lower levels of selectivity than most native species and native species had high levels of dietary specificity and selectivity. High abundances of nonnative species and high levels of dietary overlaps in our Wyoming sites is a cause of concern for native Cutthroat Trout and overall system stability. In contrast, fish assemblages characterizing Mongolia mountain steppe rivers were composed of only native species with diverse diets and higher selectivity values, suggesting low probability for interspecific competition.Publication Native Microbes Amplify Native Seedling Establishment and Diversity While Inhibiting a Non-Native Grass(MDPI, 2023-03-06) Koziol, Liz; McKenna, Thomas P.; Bever, James D.Although several studies have shown increased native plant establishment with native microbe soil amendments, few studies have investigated how microbes can alter seedling recruitment and establishment in the presence of a non-native competitor. In this study, the effect of microbial communities on seedling biomass and diversity was assessed by seeding pots with both native prairie seeds and a non-native grass that commonly invades US grassland restorations, Setaria faberi. Soil in the pots was inoculated with whole soil collections from ex-arable land, late successional arbuscular mycorrhizal (AM) fungi isolated from a nearby tallgrass prairie, with both prairie AM fungi and ex-arable whole soil, or with a sterile soil (control). We hypothesized (1) late successional plants would benefit from native AM fungi, (2) that non-native plants would outcompete native plants in ex-arable soils, and (3) early successional plants would be unresponsive to microbes. Overall, native plant abundance, late successional plant abundance, and total diversity were greatest in the native AM fungi+ ex-arable soil treatment. These increases led to decreased abundance of the non-native grass S. faberi. These results highlight the importance of late successional native microbes on native seed establishment and demonstrate that microbes can be harnessed to improve both plant community diversity and resistance to invasion during the nascent stages of restoration.Publication Phylogenetic Signal, Root Morphology, Mycorrhizal Type, and Macroinvertebrate Exclusion: Exploring Wood Decomposition in Soils Conditioned by 13 Temperate Tree Species(MDPI, 2022-03-30) Malik, Rondy J.; Bruns, Mary Ann V.; Bell, Terrence H.; Eissenstat, David M.Woodlands are pivotal to carbon stocks, but the process of cycling C is slow and may be most effective in the biodiverse root zone. How the root zone impacts plants has been widely examined over the past few decades, but the role of the root zone in decomposition is understudied. Here, we examined how mycorrhizal association and macroinvertebrate activity influences wood decomposition across diverse tree species. Within the root zone of six predominantly arbuscular mycorrhizal (AM) (Acer negundo, Acer saccharum, Prunus serotina, Juglans nigra, Sassafras albidum, and Liriodendron tulipfera) and seven predominantly ectomycorrhizal (EM) tree species (Carya glabra, Quercus alba, Quercus rubra, Betula alleghaniensis, Picea rubens, Pinus virginiana, and Pinus strobus), woody litter was buried for 13 months. Macroinvertebrate access to woody substrate was either prevented or not using 0.22 mm mesh in a common garden site in central Pennsylvania. Decomposition was assessed as proportionate mass loss, as explained by root diameter, phylogenetic signal, mycorrhizal type, canopy tree trait, or macroinvertebrate exclusion. Macroinvertebrate exclusion significantly increased wood decomposition by 5.9%, while mycorrhizal type did not affect wood decomposition, nor did canopy traits (i.e., broad leaves versus pine needles). Interestingly, there was a phylogenetic signal for wood decomposition. Local indicators for phylogenetic associations (LIPA) determined high values of sensitivity value in Pinus and Picea genera, while Carya, Juglans, Betula, and Prunus yielded low values of sensitivity. Phylogenetic signals went undetected for tree root morphology. Despite this, roots greater than 0.35 mm significantly increased woody litter decomposition by 8%. In conclusion, the findings of this study suggest trees with larger root diameters can accelerate C cycling, as can trees associated with certain phylogenetic clades. In addition, root zone macroinvertebrates can potentially limit woody C cycling, while mycorrhizal type does not play a significant role.Publication Role of plant relatedness in plant–soil feedback dynamics of sympatric Asclepias species(Wiley Open Access, 2023-01-24) Duell, Eric B.; Bever, James D.; Wilson, Gail W. T.Plants affect associated biotic and abiotic edaphic factors, with reciprocal feedbacks from soil characteristics affecting plants. These two-way interactions between plants and soils are collectively known as plant–soil feedbacks (PSFs). The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of PSFs, although the strength and direction of feedbacks among sympatric congeners are not well-understood. We examined plant–soil feedback responses of Asclepias syriaca, a common clonal milkweed species, with several sympatric congeners across a gradient of increasing phylogenetic distances (A. tuberosa, A. viridis, A. sullivantii, and A. verticillata, respectively). Plant–soil feedbacks were measured through productivity and colonization by arbuscular mycorrhizal (AM) fungi. Asclepias syriaca produced less biomass in soils conditioned by the most phylogenetically distant species (A. verticillata), relative to conspecific-conditioned soils. Similarly, arbuscular mycorrhizal (AM) fungal colonization of A. syriaca roots was reduced when grown in soils conditioned by A. verticillata, compared with colonization in plants grown in soil conditioned by any of the other three Asclepias species, indicating mycorrhizal associations are a potential mechanism of observed positive PSFs. This display of differences between the most phylogenetically distant, but not close or intermediate, paring(s) suggests a potential phylogenetic threshold, although other exogenous factors cannot be ruled out. Overall, these results highlight the potential role of phylogenetic distance in influencing positive PSFs through mutualists. The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of plant–soil feedbacks (PSFs), although the strength and direction of feedbacks among sympatric congeners are not well-understood. Congeneric, sympatric milkweeds typically generated positive PSFs in terms of productivity and AM fungal colonization, suggesting the low likelihood of coexistence among tested pairs, with a strength of feedback increasing as the phylogenetic distance increases.Publication The complete mitogenome of an undescribed clam shrimp of the genus Gondwanalimnadia (Branchiopoda: Spinicaudata), from a temporary wetland in Central District, Botswana(Taylor and Francis, 2020-02-28) Tladi, Murphy; Dalu, Tatenda; Rogers, D. Christopher; Nyamukondiwa, Casper; Emami-Khoyi, Arsalan; Oliver, Jody C.; Teske, Peter R.; Wasserman, Ryan J.Clam shrimps (Spinicaudata) are a widespread and diverse crustacean group that frequent temporary aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of an undescribed Gondwanalimnadia species from Botswana. Raw sequences were assembled into a single circular genome with a total length of 15,663 bp. Thirteen protein-coding genes, 22 tRNAs, and 2 rRNAs were identified using the MITOS pipeline. The mitogenome’s GC content is 33.52%. Phylogenetic analysis using protein-coding genes confirmed that Gondwanalimnadia sp. is closely related to another member of the Limnadiidae, Limnadia lenticularis.Publication The complete mitogenome of the fairy shrimp Streptocephalus cafer (Lovén, 1847) (Crustacea: Branchiopoda: Anostraca) from an ephemeral pond in Botswana, southern Africa(Taylor and Francis, 2020-01-14) Tladi, Murphy; Dalu, Tatenda; Rogers, D. Christopher; Nyamukondiwa, Casper; Parbhu, Shilpa Pradeep; Teske, Peter R.; Emami-Khoyi, Arsalan; Wasserman, Ryan JohnFairy shrimps (Anostraca) constitute an important component of seasonally aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of a common southern African species, Streptocephalus cafer, from Botswana (accession number: MN720104). Low-coverage shotgun sequencing recovered two contigs 15653 bp and 1347 bp in length that are separated by a repetitive region of unknown length within the non-coding control region. The mitogenome’s GC content is 31.80%. Phylogenetic analysis using protein-coding genes confirms the sister taxon relationship of S. cafer with the only other congener whose mitogenome has been reconstructed to date, the Asian S. sirindhornae.Publication Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress(American Society for Microbiology, 2022-04-20) Sarkar, Soumyadev; Kamke, Abigail; Ward, Kaitlyn; Rudick, Aoesta K.; Baer, Sara G.; Ran, QingHong; Feehan, Brandi; Thapa, Shiva; Anderson, Lauren; Galliart, Matthew; Jumpponen, Ari; Johnson, Loretta; Lee, Sonny T. M.Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species’ range in Colby, Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after 10 years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western Kansas as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after 10 years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought.Publication Global Probable Maximum Precipitation (PMP) Dataset(2022-05-05) Ekpetere, Kenneth Okechukwu; Coll, James; Li, Xingong; Kastens, Jude; Mechem, David B.Publication Geomorphology variables predict fish assemblages for forested and endorheic rivers of two continents(Wiley Open Access, 2021-11-26) Shields, Robert; Pyron, Mark; Arsenault, Emily R.; Thorp, James H.; Minder, Mario; Artz, Caleb; Costello, John; Otgonganbat, Amarbat; Mendsaikhan, Bud; Altangerel, Solongo; Maasri, AlainStream fishes are restricted to specific environments with appropriate habitats for feeding and reproduction. Interactions between streams and surrounding landscapes influence the availability and type of fish habitat, nutrient concentrations, suspended solids, and substrate composition. Valley width and gradient are geomorphological variables that influence the frequency and intensity that a stream interacts with the surrounding landscape. For example, in constrained valleys, canyon walls are steeply sloped and valleys are narrow, limiting the movement of water into riparian zones. Wide valleys have long, flat floodplains that are inundated with high discharge. We tested for differences in fish assemblages with geomorphology variation among stream sites. We selected rivers in similar forested and endorheic ecoregion types of the United States and Mongolia. Sites where we collected were defined as geomorphologically unique river segments (i.e., functional process zones; FPZs) using an automated ArcGIS-based tool. This tool extracts geomorphic variables at the valley and catchment scales and uses them to cluster stream segments based on their similarity. We collected a representative fish sample from replicates of FPZs. Then, we used constrained ordinations to determine whether river geomorphology could predict fish assemblage variation. Our constrained ordination approach using geomorphology to predict fish assemblages resulted in significance using fish taxonomy and traits in several watersheds. The watersheds where constrained ordinations were not successful were next analyzed with unconstrained ordinations to examine patterns among fish taxonomy and traits with geomorphology variables. Common geomorphology variables as predictors for taxonomic fish assemblages were river gradient, valley width, and valley slope. Significant geomorphology predictors of functional traits were valley width-to-floor width ratio, elevation, gradient, and channel sinuosity. These results provide evidence that fish assemblages respond similarly and strongly to geomorphic variables on two continents.Publication Community structure of soil fungi in a novel perennial crop monoculture, annual agriculture, and native prairie reconstruction(Public Library of Science, 2020-01-30) McKenna, Thomas P.; Crews, Timothy E.; Kemp, Laura; Sikes, Benjamin A.The use of perennial crop species in agricultural systems may increase ecosystem services and sustainability. Because soil microbial communities play a major role in many processes on which ecosystem services and sustainability depend, characterization of soil community structure in novel perennial crop systems is necessary to understand potential shifts in function and crop responses. Here, we characterized soil fungal community composition at two depths (0–10 and 10–30 cm) in replicated, long-term plots containing one of three different cropping systems: a tilled three-crop rotation of annual crops, a novel perennial crop monoculture (Intermediate wheatgrass, which produces the grain Kernza®), and a native prairie reconstruction. The overall fungal community was similar under the perennial monoculture and native vegetation, but both were distinct from those in annual agriculture. The mutualist and saprotrophic community subsets mirrored differences of the overall community, but pathogens were similar among cropping systems. Depth structured overall communities as well as each functional group subset. These results reinforce studies showing strong effects of tillage and sampling depth on soil community structure and suggest plant species diversity may play a weaker role. Similarities in the overall and functional fungal communities between the perennial monoculture and native vegetation suggest Kernza® cropping systems have the potential to mimic reconstructed natural systems.Publication The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana(Taylor & Francis Open Access, 2021-02-17) Emami-Khoyi, Arsalan; Tladi, Murphy; Dalu, Tatenda; Teske, Peter R.; van Vuuren, Bettine Jansen; Rogers, D. Christopher; Nyamukondiwa, Casper; Wasserman, Ryan J.Spinicaudatan clam shrimp are a widespread and diverse group of branchiopod crustaceans, yet few mitochondrial genomes have been published for this taxonomic group. Here, we present the mitogenome of Leptestheria brevirostris from a rock pool ecosystem in Botswana. Massively parallel sequencing of a single specimen facilitated the reconstruction of the species’ 15,579 bp circularized mitogenome. The reconstructed phylogenetic tree confirms that L. brevirostris forms a monophyletic group with other diplostracan branchiopods, and that these are the sister taxon to Notostraca. The mitogenome reconstructed here is the first to be reported from a leptestherid clam shrimp.Publication A guide to preservation techniques for amphibians and reptiles(Society for the Study of Amphibians and Reptiles, 1973) Pisani, George R.Publication Review of: Dinosaurs, Asteroids and Superstars: Why the Dinosaurs Disappeared(Society for the Study of Amphibians and Reptiles, 1983-09) Pisani, George R.Publication Notes on early Spring parasites and pathologies of Oklahoma Crotalus atrox.(Society for the Study of Amphibians and Reptiles, 1991-09) Stephenson, Barbara R.; Pisani, George R.Publication Notes on Ameiva exsul (Cope) from Culebra Island, Puerto Rico(Philadelphia Herpetological Society, 1968) Pisani, George R.Publication Anonymous Reviews: A response to Wilson and McCranie(Society for the Study of Amphibians and Reptiles, 1994-09) Pisani, George R.
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