Field Methods: We propose to explore the effects of plant-microbial interactions on plasticity in flowering time and growth of populations from a broad latitudinal gradient. We will conduct experiments examining plasticity in these traits in response to temperature using Eastern Monkeyflowers (Mimulus alatus and Mimulus ringens) and their root microbial symbionts. We will collect one to two fruits per plant from up to 15 individuals per site, and we will sample from up to three sites within each of the North Carolina State Parks listed. In addition, we will collect up to six soil cores (2.5 x 30 cm) from each site. We will restrict our sampling to slopes of 15% or greater. Both Mimulus ringens and alatus are species of least concern, and our collection methods will not adversely affect these population’s survival or growth. We will collect fruits, seeds and soil cores between July 1 and August 31, 2019. The following members of the Sheth Laboratory will participate in collection: Erin Coughlin, Rachel Wooliver and Seema Sheth. Funding for this study has been requested by Rachel Wooliver from the National Science Foundation through a Postdoctoral Research Fellowship in Biology grant proposal, which is currently pending approval (Proposal # 1906426).

,Meta-data from over 100 studies that examined induction of plant phenolic compounds following colonization by insects or microbial organisms (both pathogens and beneficials). This meta-data was used in a meta-analysis to observe that both insects and microbes consistently induce phenolic production. The meta-data covers publications that range from 2008 to 2017.,,

,Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is largely unknown. Therefore, changes in soil bacterial community composition were assessed in response to cropping sequences and bio-covers at long-term no-tillage sites. Main effects of four different cropping sequences of corn (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean (Glycine max L.) were rotated in four year phases for 12-yrs at two Tennessee Research and Education Centers in a randomized complete block design with split-block treatments of four winter bio-covers: hairy vetch (Vicia villosa L.), wheat (Triticum aestivum L.), poultry litter, and a fallow control. Using Illumina high-throughput sequencing of 16S rRNA genes, bacterial community composition was determined. Composition, diversity, and relative abundance of specific taxa were correlated per cropping system, bio-cover, and their interaction. We found that i) richness and diversity varied temporally and spatially, coinciding with soil carbon, pH, nutrient levels, and climatic variability; ii) community composition varied by cropping system, with continuous corn, soybean, and the corn-soybean rotation presenting a hybrid of the continuous corn and soybean communities; however, continuous cotton resulted in the most varied assemblage; iii) bio-covers asserted the greatest influence on microbial communities; specifically poultry litter treatments differed from cover crops (all of which received inorganic-N). Consequently, microbial diversity was greatest under nutrient rich bio-covers (poultry litter) and high residue producing, less pesticide-intensive cropping sequences (soybean and corn compared to cotton), suggesting a more dynamic soil ecology under these no-till cropping systems. This suggests that nutrient management (inorganic fertilizers vs. animal manure) and greater crop rotations (within 4-yr phases) may directly drive phylogenetic community structure and subsequent ecosystem services across agricultural landscapes.,,

,Dataset that accompanies a research paper entitled, "Exploring soil ecology gradient concepts: Sensitivity of ecosystem properties to symbiotic fungi in semiarid prairie" to be submitted to a peer-reviewed journal. Journal information will be updated when paper is published. Files include a readme file, datasets, and the respective R script for analyzing the individual data files.,Results are relevant to arid and semiarid mixed-grass prairie ecosystems with calcareous and alkaline subsoils, especially sites with soils of Eapa loam soil series, frigid Aridic Argiustolls or Mollisols. The focal system was of northern mixed-grass prairie vegetation near Miles City, Montana which is in eastern Montana, USA (46.304583, -105.978050, elevation 849 m).,The study consisted of a five year field experiment and two complementary pot bioassays. The experiments were designed to improve understanding effects of mycorrhizal fungi on plant properties, soil structure, and soil hydrologic functioning. We performed experiments and evaluated evidence of AMF (arbuscular mycorrhizal fungi) effects on plants, plant-plant interactions, plant nutrient limitation, and nutrient acquisition strategy. First, we tested how AMF suppression affected plant biomass and composition; indicators of plant nutrient limitation (i.e. shoot nitrogen-to-phosphorus ratio, N:P) and P acquisition (i.e. shoot manganese concentration, [Mn]); and structure and function of soil with a five-year field experiment. This informed pot bioassays. Pot bioassays tested how dominant grass coexistence was affected by three pairs of soil treatments 1) field soil inoculant (FSI) versus FSI with AMF suppression, 2) FSI versus sterilized FSI, and 3) AMF inoculant versus sterilized AMF inoculant.,

The data document the results of several microbe bioassays performed by the USGS on Phragmites australis plants, including those performed on mature leaves, seedlings, and dead leaf tissues exploration of the literature to find accounts of microbes associated with Phragmites worldwide. For the bioassays, we prepared 162 pure cultures isolated from Phragmites plants in North America along the east coast, Florida, the Gulf of Mexico, and the Great Lakes area, 125 of which were from a previous study, and 38 represent new collections. The DNA sequences used to identify the 37 new collections are included. Microbes were isolated from plants collected from 2015-2018. We performed assays using both North American plant lineages (Phragmites australis subsp. australis and Phragmites australis subsp. americanus) on mature leaves and seedlings. Data included here report each plant's reaction to microbial inoculation. Finally, to put our findings in context, we surveyed Phragmites-associated microbes assembled from multiple extensive literature sources representing a worldwide extent These data will be valuable to researchers interested in effects of leaf microbes on Phragmites health and invasiveness of the non-native lineage. Additionally, the data have implications for potential biocontrol of Phragmites.

"Three archaeal and 13 bacterial species were observed in fecal samples from four of the park's elk. The microbial species residing in elk digestive tracts showed seasonality. One of the three archaea was seen only in spring samples while a dominant species of archaea was seen at all times in all animals. All archaea found were related to the genus Methanobrevibacter, which produces methane and is commonly found in the rumen environment. Bacterial diversity patterns showed greater richness and yielded pronounced differences between individual elk and seasons. Bacteria were identified as belonging to species within the phylum Firmicutes (likely spore-forming strains that could survive the lower digestive tract). The researcher has also been visiting the Oconaluftee Visitor Center and Kephart Trail areas with his Methods of General Microbiology class since 2002 to collect samples for isolation and identification. New genera to this study continue to be observed each year as little or no overlap is observed in the species isolated by the students each year. Out of 345 DNA sequence isolates, very few have been identical. To date, they have detected 5 phyla (Firmicutes, Actinobacteria, Bacteroides, Thermus/Deinococcus, and Proteobacteria), 8 classes, 27 orders, 34 families, and 81 genera have been recorded in 13 years of effort, as well as several colonies that could not be classified down to the level of order. The phylum Bacteroides continued to dominate waters and Firmicutes prevailed in soils. Many taxa are consistantly unique to either soils or water. An offshoot of this project has been an attempt to culture Pseudomonas aeruginosa from the samples collected from this class. There has been no success in finding this important, opportunistic pathogen. Research also includes an ongoing examination of soil bacteria from the Purchase Knob, Cataloochee, and Albright Grove ATBI plots, using a variety of culture techniques. The results of the bacterial cloning revealed radically different pictures of diversity when compared to culturing. Cloned 16S rDNA was obtained for 178 bacterial species from the three ATBI plots, including six phyla previously undetected in GSMNP (Acidobacteria, OP10, Planctomyces, Verrucomicrobia, Termite Group 1, and Gemmatimonadetes), having no species overlap between molecular identification and clonal studies of the sites. Ammonia oxidation (amoA) gene diversity will also be compared for both bacteria and archaea using the T-RFLP method. This will give us some initial insight into functional ecology, with an important part of the nitrogen cycle examined. Cultivated strains (59) from hemlock roots in the Albright Grove include many that are only distantly related to known species (e.g., DNA similarities of 24-45%) and also groups that contain nitrogen-fixing species (Alphaproteobacteria such as the bradyrhizobia and the genus Janibacter within Actinobacteria). Across Albright (2008 and 2011), Purchase Knob, and Cataloochee plots, Acidobacteria, presumptive nitrogen-fixing species (e.g., Bradyrhizobium), and archaeal ammonia oxidizers appear to be important components of hemlock ecology. Understanding interactions between bacteria, archaea, and hemlock could aid in successfully reforesting areas and restoring benefits to numerous animals dependent on this tree. It was hypothesized that the exposed slopes and dark soils over Lake Chilhowee might support the growth of thermophilic spore-forming bacteria from the genus Geobacillus. Isolates were collected in 2007 that grew at 70 degrees C from surface samples as well as from depth to a few feet below the surface leaf litter. One other study that is ongoing has been examining bacterial and fungal diversity at the next sites of native ants (Aphaenogaster rudis). Preliminary work shows that bacterial diversity at sites in and near Albright Grove were too diverse to assess differences between control and experimental plots.

,Trapping of field-collected S. oryzae,To capture field-collected S. oryzae to evaluate how microbial vectoring over the course of a season in 2022, six commercial pitfall traps (Storgard, Trécé Inc., Adair, OK, USA) were baited with 5 g of wheat and the S. oryzae aggregation pheromone, (4S,5R)-5-hydroxy-4-methyl-3-heptanone (IL-703, Insects Limited, Westfield, IN, USA) and deployed 10 m apart. In 2023, 14 pitfall traps (Storgard, Trécé Inc.) were deployed, separated by 5–15 m and baited with the same stimuli. In addition, probe traps (WB Probe II, Storgard, Trécé Inc., Adair, OK, USA) were taken in identical locations in adjacent grain bins, but >90% of individuals came from the pitfall traps. Trapping took place at the Kansas State University Foundation Seed Farm (39°12'23"N, 96°35'42"W), and occurred on a weekly basis from 11 May 2022 to 28 Sep 2022 and 17 May 2023 to 1 Nov 2023. Live S. oryzae from each trap were placed in a sterile Ziplock bag and brought back to USDA-ARS Center for Grain and Animal Health in a cooler. Live weevils were stored at 23°C and 65% RH after brought back from the field. Within 24 h of being brought to the laboratory, S. oryzae were introduced to factitious, novel food patches as described below.,Linking with weather data,Weather data was obtained from the Kansas Mesonet system (https://mesonet.k-state.edu/) at a weather station located in the same location as the trapping on the Kansas State University Agronomy Farm (39°12'26"N, 96°35'42"W). Air temperature was measured at 1.98 m above ground level (HMP155 probe, Vaisala, Vantaa, Finland) inside of a non-aspirated radiation shield within an error range of ± 0.1°C. Data was acquired every hour with a microprocessor (CR3000 series, Campbell Scientific Inc., Logan, UT, USA), which accurately measures to the microvolt level and controls peripheral devices. Mean maximum and minimum temperature was compiled for each 7-day period preceding each date of collection for S. oryzae in 2022 and 2023, and it was linked to microbial growth measures detailed below from the same date.,Assessing microbial growth after dispersal to novel food patches,A total of n = 5 individual field-collected S. oryzae from each date were introduced individually onto petri dishes (100 ´ 20 mm) composed of potato dextrose agar as a factitious, novel food patch for 3 and 5 d to mimic dispersal (following the methods of Ponce et al. 2024). This was done within the confines of a permitted BSL2 (Permit# IBC-1693) space using a biosafety cabinet (75 × 73 × 95 cm L:H:W, #302381101, Labconco, Kansas City, MO, USA). After introduction of S. oryzae, the petri dishes were placed in an environmental chamber (Percival Scientific, Perry, IA, USA) set at constant conditions (30°C, 65% RH, and 14:10 L:D cycle). Petri dishes were photographed at 3 and 5 days of S. oryzae foraging in the novel food patch with a 3D-imaging system (Cognisys Inc., Traverse City, MI, USA) using a SLR camera (EOS 7D Mark II, Canon Inc., Tokyo, Japan) with a wide-angle lens (L series USM 17–40 mm, Canon Inc., Tokyo, Japan) and twin flash (MT-24X, Macro Twin Flash Lite, Canon Inc., Tokyo, Japan). Light was diffused using a partially cut frosted plastic jar (15.2 × 7.6 cm D:H). Images were processed using ImageJ v.1.53 (Wayne Rasband, National Institutes of Health, USA) individually by first subtracting the background, then finding edges, and converting the image to binary (white/black). As needed, erode and/or dilate was sparingly used to make sure the image reflected microbial growth in the original image. A circle encompassing only the Petri dish was created and the mean grayscale, standard deviation of the grayscale value, and count of pixels were measured as a surrogate for microbial growth on the dishes. This allowed a quantitative measure of microbial growth by creating an average in each image. The mean grayscale value could range from 0 (full white), indicating no microbial growth, to 255 (full black), indicating

These data include detailed sample description (sampling locations, sampling events, DNA concentrations in four separate spreadsheet in an Excel file) and DNA sequencing plate layout. This dataset is associated with the following publication: Li, L., D. Ning, Y. Jeon, H. Ryu, J. SantoDomingo, D. Kang, A. Kadudula, and Y. Seo. Ecological Insights into Assembly Processes and Network Structures of Bacterial Biofilms in Full-scale Biologically Active Carbon Filters under Ozone Implementation. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 751: 141409, (2021).

These data include detailed sample description (sampling locations, sampling events, DNA concentrations in four separate spreadsheet in an Excel file) and DNA sequencing plate layout. This dataset is associated with the following publication: Li, L., D. Ning, Y. Jeon, H. Ryu, J. SantoDomingo, D. Kang, A. Kadudula, and Y. Seo. Ecological Insights into Assembly Processes and Network Structures of Bacterial Biofilms in Full-scale Biologically Active Carbon Filters under Ozone Implementation. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 751: 141409, (2021).