@article{frene_lawson_sue_crawford_gardner_2024, title={Effects of tree species identity on soil microbial communities in <i>Juglans nigra</i> and <i>Quercus rubra</i> plantations}, volume={15}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2024.1442026}, abstractNote={Understanding how different tree species affect soil microbial communities is crucial for sustainable forestry and ecosystem management practices. Despite Black walnut (}, journal={FRONTIERS IN MICROBIOLOGY}, author={Frene, Juan P. and Lawson, Shaneka S. and Sue, Niall D. Lue and Crawford, Ralph H. and Gardner, Terrence G.}, year={2024}, month={Oct} }
 @article{alarcon_hernandez_garcia_ziarelli_gutierrez-rivera_musule_vazquez-marrufo_gardner_2022, title={Changes in chemical and structural composition of sugarcane bagasse caused by alkaline pretreatments [Ca(OH)(2) and NaOH] modify the amount of endoglucanase and beta-glucosidase produced by Aspergillus niger in solid-state fermentation}, volume={209}, ISSN={["1563-5201"]}, DOI={10.1080/00986445.2021.1881777}, abstractNote={Abstract The aim of this study was to evaluate the treatment effects of Ca(OH)2 solutions applied at different concentrations (2.5%, 5%, and 7.5%) on the structural and chemical composition of sugarcane bagasse (SCB). The feasibility of using the SCB as a substrate for endoglucanase and β-glucosidase production by Aspergillus niger through solid-state fermentation was also assessed. Sodium hydroxide (NaOH) 5% was used as a positive control/benchmark. Changes in SCB cell wall compositions was determined using 13C solid-state nuclear magnetic resonance. While cellulosic fiber content and the production of endoglucanase (345.01 ± 139 U.gDM−1) increased using Ca(OH)2 as pretreatment for sugarcane bagasse, hemicellulose, lignin, alkyl C and carboxyl C content decreased. Comparisons between pretreated and non-pretreated SCB revealed that the highest values of β-glucosidase (58.18 ± 9.86 U.gDM−1) occurred in non-pretreated samples. The SCB pretreated with NaOH resulted in the highest delignification values (-49.88%) and the greatest hemicellulose remotion (-53.47%). However, this treatment also increased crystallinity index (CI; + 23.61%) in cellulose and showed the lowest endoglucanase (22.79 ± 11 U.gDM−1) and β-glucosidase (4.71 ± 1.44 U.gDM−1) activities. This study claims that cellulose CI, hemicellulose, and other nutrients (e.g., amino acids) are important variables that should be considered along with delignification, in the substrates selection for cellulase production using filamentous fungi.}, number={5}, journal={CHEMICAL ENGINEERING COMMUNICATIONS}, author={Alarcon, Enrique and Hernandez, Christian and Garcia, Gabriela and Ziarelli, Fabio and Gutierrez-Rivera, Beatriz and Musule, Ricardo and Vazquez-Marrufo, Gerardo and Gardner, Terrence G.}, year={2022}, month={May}, pages={594–606} }
 @article{frene_frazier_liu_clark_parker_gardner_2021, title={Early Effect of Pine Biochar on Peach-Tree Planting on Microbial Community Composition and Enzymatic Activity}, volume={11}, ISSN={["2076-3417"]}, url={https://doi.org/10.3390/app11041473}, DOI={10.3390/app11041473}, abstractNote={Biochar offers several benefits as a soil amendment, including increased soil fertility, carbon sequestration, and water-holding capacity in nutrient-poor soils. In this study, soil samples with and without biochar additives were collected for two consecutive years from an experimental field plot to examine its effect on the microbial community structure and functions in sandy soils under peach-trees (Prunus persica). The four treatments evaluated consisted of two different rates of biochar incorporated into the soil (5%, and 10%, v/v), one “dynamic” surface application of biochar, and a 0% biochar control. Fatty acid methyl ester (FAME) analysis was used to assess the microbial community structure, and enzyme activities involved in C, N, P, and S nutrient cycling were used as a means of assessing soil functionality. Total FAME and bacterial indicators increased by 18% and 12%, respectively, in the 10% incorporated and 5% surface applied treatments. Biochar applications increased β-glucosaminidase and arylsulfatase activities, 5–30% and 12–46%, respectively. β-glucosidase and acid phosphatase activities decreased by approximately 18–35% and 5–22% in the 0–15 cm soils. The overall results suggest that biochar’s addition to the sandy soils stimulated microbial activity, contributing to the increased mean weight diameter (MWD), C sequestration, and consequential soil health. The changes in microbial community structure and functions may be useful predictors of modifications in soil organic matter (SOM) dynamics due to the long-term application of pine biochar in these systems.}, number={4}, journal={APPLIED SCIENCES-BASEL}, author={Frene, Juan Pablo and Frazier, Mattie and Liu, Shuang and Clark, Bernadette and Parker, Michael and Gardner, Terrence}, year={2021}, month={Feb} }
 @article{vepraskas_amoozegar_gardner_2021, title={Estimation of Saprolite Thickness Needed to Remove E. coli from Wastewater}, volume={11}, ISSN={["2076-3417"]}, url={https://doi.org/10.3390/app11052066}, DOI={10.3390/app11052066}, abstractNote={Saprolite, weathered bedrock, is being used to dispose of domestic sewage through septic system drainfields, but the thickness of saprolite needed to remove biological contaminants is unknown for most saprolites. This study developed and tested a simple method for estimating the thickness of saprolite needed below septic drainlines to filter E. coli from wastewater using estimates of the volume of pores that are smaller than the length of the coliform (≤10 μm). Particle size distribution (texture) and water retention data were obtained for 12 different saprolites from the Piedmont and Mountain regions of North Carolina (N.C.). Saprolite textures ranged from clay loam to coarse sand. The volume of pores with diameters ≤10 μm were determined by water retention measurements for each saprolite. The data were used in an equation to estimate the saprolite thickness needed to filter E. coli. The estimated saprolite thicknesses ranged from 36 cm in the clay loam to 113 cm for the coarse sand. The average thickness across all samples was 58 cm. Saprolite thickness estimates increased as silt percentage decreased and as sand percentage and in situ saturated hydraulic conductivity increased. Silt percentage may be most useful for estimating appropriate saprolite thicknesses in the field.}, number={5}, journal={APPLIED SCIENCES-BASEL}, publisher={MDPI AG}, author={Vepraskas, Michael J. and Amoozegar, Aziz and Gardner, Terrence}, year={2021}, month={Mar} }
 @article{dick_gardner_frene_heitman_sucre_leggett_2022, title={Forest floor manipulation effects on the relationship between aggregate stability and ectomycorrhizal fungi}, volume={505}, ISSN={["1872-7042"]}, DOI={10.1016/j.foreco.2021.119873}, abstractNote={Forest floor and mineral soil manipulations influence the soil biogeochemical properties important for loblolly pine (Pinus taeda L.) tree growth. The impacts of forest floor manipulations on soil aggregate stability and the presence of ectomycorrhizal fungi (EMF), was assessed to elucidate the relationship between EMF abundance and aggregate stability. The study site consists of a 14-year-old loblolly pine plantation managed by Weyerhaeuser Company in the Lower Coastal Plain, approximately 8 miles east of New Bern, North Carolina, USA. The soil samples were collected from the top 7.62 cm of each soil treatment which includes three levels of forest floor retention: removed, control, and doubled and two levels of forest floor mixing with the mineral soil: mixed and unmixed. Ectomycorrhizal fungi abundance was evaluated by ester-linked fatty acid methyl ester analysis and microbial community functionality was assessed by acid-phosphatase activity measurement. Aggregate stability was assessed using the aggregate mean weight diameter approach. Results indicate that the forest floor manipulations had no significant impact on aggregate stability and EMF abundance. However, a positive relationship between EMF abundance and aggregate stability was identified. Removing the forest floor resulted in a soil bulk density increase of 0.18 g cm−3 compared to doubling the forest floor. Our results demonstrate that some mineral soil properties recover relatively quickly from forest floor manipulations. The study informs forest managers interested in how soil responds to forest floor manipulation and the interaction between EMF and aggregate stability.}, journal={FOREST ECOLOGY AND MANAGEMENT}, author={Dick, David L. and Gardner, Terrence G. and Frene, Juan P. and Heitman, Joshua L. and Sucre, Eric B. and Leggett, Zakiya H.}, year={2022}, month={Feb} }
 @article{alarcon gutierrez_hernandez_gardner_garcia perez_caballero_perroni_silva_gaime perraud_barois_2021, title={Soil bioindicators associated to different management regimes of Cedrela odorata plantations}, volume={27}, ISSN={["2448-7597"]}, url={https://doi.org/10.21829/myb.2021.2711912}, DOI={10.21829/myb.2021.2711912}, abstractNote={A good bioindicator of soil health is one that perceives minor changes due to changes in soil management and leads to changes in the processes of the soil ecosystem. The aim was to evaluate the use of soil bioindicators in the determination of the utility of two different Cedrela odorata forestry management systems. The litter and soil samples were collected from the rhizosphere of a monoculture (with no fertilization nor irrigation), and a co-culture (with fertilization and irrigation) stand with Citrus latifolia. The soil and litter bioindicators measured were the activity of acetylesterase (FDA), acid phosphatase (AcPh), alkaline phosphatase (AlkPh), laccase, and the estimation of the potential net rate of carbon mineralization (PNRCM). The results indicated that soil enzyme activities (FDA and phosphatases) in the litter were sensitive to the different management system treatments. Enzymatic activity, per unit dry weight, was higher in litter of co-culture (FDA = 1.05 nkat g-1 AcPh = 1.33 nkat g-1; AlkPh = 03.0 nkat g-1) than in litter of monoculture (FDA = 0.617nkat g-1; AcPh = 0.40 nkat g-1; AlkPh = 0. 983 nkat g-1). Differences in soil total nitrogen content, organic matter (OM) content, and micronutrients were found. In general, the co-culture stand (with fertilization and irrigation) with C. latifolia showed the best results.}, number={1}, journal={MADERA Y BOSQUES}, publisher={Instituto de Ecologia, A.C.}, author={Alarcon Gutierrez, Enrique and Hernandez, Christian and Gardner, Terrence and Garcia Perez, Jose Antonio and Caballero, Mayra and Perroni, Yareni and Silva, Anne Marie A. and Gaime Perraud, Isabelle and Barois, Isabelle}, year={2021} }
 @article{park_liu_gardner_johnson_keeler_ortiz_rabah_ford_2020, title={Biohybrid nanofibers containing manganese oxide-forming fungi for heavy metal removal from water}, volume={15}, ISSN={["1558-9250"]}, DOI={10.1177/1558925019898954}, abstractNote={ Manganese-oxidizing fungi support bioremediation through the conversion of manganese ions into manganese oxide deposits that in turn adsorb manganese and other heavy metal ions from the environment. Manganese-oxidizing fungi were immobilized onto nanofiber surfaces to assist remediation of heavy metal–contaminated water. Two fungal isolates, Coniothyrium sp. and Coprinellus sp., from a Superfund site (Lot 86, Farm Unit #1) water treatment system were incubated in the presence of nanofibers. Fungal hyphae had strong association with nanofiber surfaces. Upon fungal attachment to manganese chloride–seeded nanofibers, Coniothyrium sp. catalyzed the conformal deposition of manganese oxide along hyphae and nanofibers, but Coprinellus sp. catalyzed manganese oxide only along its hyphae. Fungi–nanofiber hybrids removed various heavy metals from the water. Heavy metal ions were adsorbed into manganese oxide crystalline structure, possibly by ion exchange with manganese within the manganese oxide. Hybrid materials of fungal hyphae and manganese oxides confined to nanofiber-adsorbed heavy metal ions from water. }, journal={JOURNAL OF ENGINEERED FIBERS AND FABRICS}, author={Park, Yaewon and Liu, Shuang and Gardner, Terrence and Johnson, Drake and Keeler, Aaron and Ortiz, Nathalia and Rabah, Ghada and Ford, Ericka}, year={2020}, month={Jan} }
 @article{frene_frazier_rutto_jones_liu_clark_parker_gardner_2020, title={Early response of organic matter dynamics to pine‐biochar in sandy soil under peach trees}, url={https://doi.org/10.1002/agg2.20094}, DOI={10.1002/agg2.20094}, abstractNote={AbstractBiochar may enhance soil health in sandy soils under peach [Prunus persica (L.) Batsch] tree production. A study was initiated in the Sandhills of North Carolina by applying pine‐biochar at two different rates (5 and 10%, v/v) and types of application (incorporation to 30 cm [‐Inc] and surface [‐Sur]) in 2017. Soil organic matter (SOM) dynamics was assessed via soil organic carbon (SOC), total nitrogen (TN), permanganate‐oxidizable carbon (POXC), aggregate fractions (macro‐, micro‐aggregates, and clay + silt particles), and enzyme activities (CNPS activity) at 0–15 and 15–30 cm in 2018 and 2019. After the first year of pine‐biochar application, POXC decreased in all biochar treatments, SOC was higher in the 10%‐Inc treatment, whereas CNPS activities and macroaggregates were highest in the 5%‐Sur compared with the non‐treated control. These results suggest early changes in SOM dynamics and biogeochemical cycling and have the potential to guide producers with the long‐term application of pine‐biochar to sandy soils.}, journal={Agrosystems, Geosciences & Environment}, author={Frene, Juan Pablo and Frazier, Mattie and Rutto, Edwin and Jones, McGwire and Liu, Shuang and Clark, Bernadette and Parker, Michael and Gardner, Terrence G.}, year={2020}, month={Jan} }
 @article{gardner_vepraskas_amoozegar_2020, title={Efficiency of saprolite for removing E. coli from simulated wastewater}, volume={10}, url={http://dx.doi.org/10.2166/wst.2020.514}, DOI={10.2166/wst.2020.514}, abstractNote={AbstractSaprolite, weathered bedrock, is being used to dispose of domestic sewage through septic system drainfields, but its ability to remove coliforms is unknown. This study determined if Escherichia coli could be removed by a sandy loam saprolite material. Triplicate columns containing saprolite were prepared with lengths of 30, 45, and 60 cm. A 215-mL solution containing 1 × 105 CFU/100 mL of non-toxic E. coli was applied to the top of each column for 5 days/week for 13 weeks, and selected outflow samples were analyzed for E. coli. Control columns had only tap water applied to them at the same time. Significantly higher (p ≤ 0.10 compared to controls) E. coli concentrations were only detected in samples collected at the end of week 3 for the 30-cm columns and week 4 for the 45-cm columns. E. coli concentrations were small and ranged from approximately 2 to 3 MPN/100 mL. No E. coli were detected in any outflow from the 60-cm columns. From weeks 5 to 13, E. coli concentrations from all columns were either undetectable or not significantly different from the control. The results showed that 60 cm of sandy loam saprolite was sufficient for the removal of E. coli from simulated wastewater.}, journal={Water Science and Technology}, publisher={IWA Publishing}, author={Gardner, T. and Vepraskas, M. J. and Amoozegar, A.}, year={2020}, month={Oct} }
 @article{enzymatic hydrolysis of an organic sulfur compound_2019, url={http://dx.doi.org/10.4236/aer.2019.71001}, DOI={10.4236/aer.2019.71001}, abstractNote={Sulfatases which cleave sulfate esters in biological systems are key enzymes that deserve special attention due to their significant roles in organic sulfur (OS) mineralization and inorganic sulfur () release. In this study, in-vitro experiments were conducted to evaluate S bonded substrate hydrolysis by a commercially available arylsulfatase (EC 3.1.6.1) from Aerobacter aerogenes. The enzyme-substrate interactions were assessed to determine: 1) rate of hydrolysis, 2) catalytic efficiency, 3) thermal stability, and 4) optimal pH of this enzyme. Arylsulfatase exhibited substrate hydrolysis with a high affinity for p-nitrophenyl sulfate (potassium 4-nitrophenyl sulfate (pNPS)). The optimum activity for the enzyme was observed to occur at a pH of 7.1. The optimal temperature was 37°C but ranged from 35°C - 45°C. The apparent Km and Kcat of the enzyme for pNPS hydrolysis at the optimal pH, and temperature were determined to be 1.03 mM and 75.73 μM/min, respectively. This work defines the catalytic and kinetic properties of arylsulfatase (EC 3.1.6.1) and confirms the optimal conditions for sulfatase activity testing. The resulting information is useful in elucidating the contributions that individual enzymes have for specific reactions rather than relying on traditional total enzyme activity measurements.}, year={2019} }
 @inproceedings{relationships between nutrient content, microbial communities, and presence of siderophores in north carolina soils._2019, url={https://scisoc.confex.com/scisoc/2019sssa/meetingapp.cgi/Paper/115671}, year={2019}, month={Jan} }
 @article{rivers_weber_gardner_liu_armstrong_2018, title={ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis [version 1; referees: awaiting peer review]}, volume={7}, url={https://f1000research.com/articles/7-1418/v1}, DOI={10.12688/f1000research.15704.1}, abstractNote={The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.}, number={1418}, journal={F1000Research}, publisher={F1000 Research, Ltd.}, author={Rivers, Adam R. and Weber, Kyle C. and Gardner, Terrence G. and Liu, Shuang and Armstrong, Shalamar D.}, year={2018}, month={Sep}, pages={1418} }
 @article{ntoko_gardner_2018, title={Microbial Compositions and Enzymes of a Forest Ecosystem in Alabama: Initial Response to Thinning and Burning Management Selections}, url={https://www.scirp.org/journal/PaperInformation.aspx?PaperID=86043}, journal={Journal of Forestry}, author={Ntoko, F.A. and Gardner}, year={2018}, month={Jul} }
 @inbook{duckworth_franzluebbers_gardner_2016, place={SSSA, Madison, WI}, title={Biogeochemical Processes Underpin Ecosystem Services}, DOI={10.2136/2015.soilecosystemsservices.2015.0024.}, booktitle={Soil Ecosystems Services}, author={Duckworth, O.W. and Franzluebbers, A.J. and Gardner, T.G.}, editor={Stromberger, M. and Comerford, N. and Lindbo, D.Editors}, year={2016} }
 @article{duckworth_rivera_gardner_andrews_santelli_polizzotto_2016, title={Morphology, Structure, and Metal Binding Mechanisms of Biogenic Manganese Oxides in a Superfund Site Treatment System}, volume={19}, journal={Duckworth, O. W., Rivera, N.A., Gardner, T.G., Andrews, M.Y., Santelli, C.M., and Polizzotto, M.L. 2016. Morphology, Structure, and Metal Binding Mechanisms of Biogenic Manganese Oxides in a Superfund Site Treatment System. Environmental Science: Process & Impacts 19:50-58}, author={Duckworth, O.W. and Rivera, N.A. and Gardner, T.G. and Andrews, M.Y. and Santelli, C.M. and Polizzotto, M.L.}, year={2016}, pages={50–58} }
 @article{duckworth_rivera_gardner_andrews_santelli_polizzotto_2017, title={Morphology, structure, and metal binding mechanisms of biogenic manganese oxides in a superfund site treatment system}, volume={19}, ISSN={["2050-7895"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85010739340&partnerID=MN8TOARS}, DOI={10.1039/c6em00525j}, abstractNote={Manganese oxides, which may be biogenically produced in both pristine and contaminated environments, have a large affinity for many trace metals.}, number={1}, journal={ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS}, author={Duckworth, O. W. and Rivera, N. A. and Gardner, T. G. and Andrews, M. Y. and Santelli, C. M. and Polizzotto, M. L.}, year={2017}, month={Jan}, pages={50–58} }
 @article{padilla_calderon_acosta-martinez_van pelt_gardner_baddock_zobeck_noveron_2014, title={Diffuse-reflectance mid-infrared spectroscopy reveals chemical differences in soil organic matter carried in different size wind eroded sediments}, volume={15}, ISSN={["2212-1684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84908288231&partnerID=MN8TOARS}, DOI={10.1016/j.aeolia.2014.06.003}, abstractNote={Soil organic matter (SOM) is essential for soil water holding capacity, aggregation, and biodiversity. Little information is available regarding the carbon (C) functional groups carried away in wind eroded sediments away from the source soil. Mid-infrared (MidIR) spectroscopy was used on wind tunnel-blown sediments eroded from a loam soil during the fallow period of different cropping systems and tillage managements in Akron, Colorado. The soil was managed as fallow-winter wheat (Triticum aestivum L.) under conventional tillage (F–Wct) or no tillage (F–Wnt) and fallow–wheat–corn under no tillage (F–W–Cnt). Two wind eroded sediments were evaluated: fine dust (<35 μm mean dia.) and saltation-size material (<175 μm mean dia.). Our study showed that there is a partition of C groups within wind eroded sediments of different sizes and that they can reflect the tillage management history of soil. The fine dust had higher levels of aliphatic CH (2930 cm−1), and clays (3690–3620 cm−1). The saltation-sized material showed higher absorbance for quartz from 2000–1800 cm−1 and reduced absorbance from 1250–1050 cm−1. Both wind eroded sediments showed higher absorbance for –OH/NH groups and aliphatic CH from no-till soil. Finer dust sediments, which travel greater distances from the source soil than saltation size material, can carry away higher levels of aliphatic-carbon compounds and clays with potential negative impacts on SOM quantity and quality, and consequently the sustainability of these agroecosystems.}, journal={AEOLIAN RESEARCH}, author={Padilla, Julio E. and Calderon, Francisco J. and Acosta-Martinez, Veronica and Van Pelt, Scott and Gardner, Terrence and Baddock, Matthew and Zobeck, Ted M. and Noveron, Juan C.}, year={2014}, month={Dec}, pages={193–201} }
 @article{acosta-martinez_cotton_gardner_moore-kucera_zak_wester_cox_2014, title={Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling}, volume={84}, ISSN={["1873-0272"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84904319460&partnerID=MN8TOARS}, DOI={10.1016/j.apsoil.2014.06.005}, abstractNote={Identification of microbial assemblages predominant under natural extreme climatic events will aid in our understanding of the resilience and resistance of microbial communities to climate change. From November 2010 to August 2011, the Southern High Plains (SHP) of Texas, USA, received only 39.6 mm of precipitation (vs. the historical average of 373 mm) and experienced the three hottest months (June–August 2011) since record keeping began in 1911. The objective of this study was to characterize soil bacterial (16 S rRNA gene) and fungal (internal transcribed spacer 1–4, ITS1-ITS4) species distribution and diversity via pyrosequencing during the peak of the drought/heat wave in July 2011 and when the Drought Index and temperatures were lower in March 2012. Samples were collected from two different soil types (loam and sandy loam) under two different dryland cropping histories (monoculture vs. rotation). Fungal Diversity Indexes were significantly higher after the drought/heat wave while Bacterial Indexes were similar. Bacterial phyla distribution in July 2011 was characterized by lower relative abundance of Acidobacteriaand Verrucomicrobia, and greater relative abundance of Proteobacteria, Chloroflexi, Actinobacteria and Nitrospirae than March 2012 samples. Further grouping of pyrosequencing data revealed approximately equal relative proportions of Gram positive (G+) and Gram negative (G−) bacteria in July 2011, while G− bacteria predominated in March 2012. Fungal class Dothideomycetes was approximately two times greater in July 2011 than in March 2012, while the class Sordariomycetes and a group of unidentified OTUs from Ascomycota increased from July 2011 to March 2012. Microbial community composition was less influenced by management history than by the difference in climatic conditions between the sampling times. Correspondence analysis identified assemblages of fungal and bacterial taxa associated with greater enzyme activities (EAs) of C, N, or P cycling found during the drought/heat wave. Microbial assemblages associated with arylsulfatase activity (key to S cycling), which increased after the drought/heat wave, were identified (Streptomyces parvisporogenes, Terrimonas ferruginea and Syntrophobacter sp.) regardless of the soil and management history. The distinct microbial composition found in July 2011 may represent assemblages essential to maintaining ecosystem function during extreme drought and intense heat waves in semiarid agroecosystems.}, journal={APPLIED SOIL ECOLOGY}, author={Acosta-Martinez, V. and Cotton, J. and Gardner, T. and Moore-Kucera, J. and Zak, J. and Wester, D. and Cox, S.}, year={2014}, month={Dec}, pages={69–82} }
 @article{a workshop for developing learning modules for science classes based on biogeochemical research_2013, journal={Natural Sciences Education}, year={2013}, month={May} }
 @article{acosta-martinez_moore-kucera_cotton_gardner_wester_2014, title={Soil enzyme activities during the 2011 Texas record drought/heat wave and implications to biogeochemical cycling and organic matter dynamics}, volume={75}, ISSN={["1873-0272"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84888420330&partnerID=MN8TOARS}, DOI={10.1016/j.apsoil.2013.10.008}, abstractNote={Extreme droughts and heat waves due to climate change may have permanent consequences on soil quality and functioning in agroecosystems. During November 2010 to August 2011, the Southern High Plains (SHP) region of Texas, U.S., a large cotton producing area, received only 39.6 mm of precipitation (vs. the historical avg. of 373 mm) and experienced the hottest summer since record keeping began in 1911. Several enzyme activities (EAs) important in biogeochemical cycling were evaluated in two soils (a loam and a sandy loam at 0–10 cm) with a management history of monoculture (continuous cotton) or rotation (cotton and sorghum or millet). Samplings occurred under the most extreme drought and heat conditions (July 2011), after precipitation resulted in a reduction in a drought severity index (March 2012), and 12 months after the initial sampling (July 2012; loam only). Eight out of ten EAs, were significantly higher in July 2011 compared to March 2012 for some combinations of soil type and management history. Among these eight EAs, enzymes key to C (β-glucosidase, β-glucosaminidase) and P cycling (phosphodiesterase, acid and alkaline phosphatases) were significantly higher (19–79%) in July 2011 than in March 2012 for both management histories regardless of the soil type (P > 0.05). When comparing all sampling times, the activities of alkaline phosphatase, aspartase and urease (rotation only) showed this trend: July 2011 > March 2012 > July 2012. Activities of phosphodiesterase, acid phosphatase, α-galactosidase, β-glucosidase and β-glucosaminidase were higher in July 2011 than July 2012 in at least one of the two management histories. Total C was reduced significantly from July 2011 to March 2012 in the rotation for both soils. Only the activities of arylsulfatase (avg. 36%) and asparaginase showed an increase from July 2011 to March 2012 for both soil types, which may indicate they have a different origin/location than the other enzymes. EAs continued to be a fingerprint of the soil management history (i.e., higher EAs in the rotation than in monoculture) during the drought/heat wave. This study provided some of the first evidence of the adverse effects of a natural, extreme drought and heat wave on soil quality in agroecosystems as indicated by EAs involved in biogeochemical cycling.}, journal={APPLIED SOIL ECOLOGY}, author={Acosta-Martinez, V. and Moore-Kucera, J. and Cotton, J. and Gardner, T. and Wester, D.}, year={2014}, month={Mar}, pages={43–51} }
 @article{gardner_acosta-martinez_calderón_zobeck_baddock_van pelt_senwo_dowd_cox_2012, title={Pyrosequencing reveals bacteria carried in different wind-eroded sediments}, volume={41}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84862266252&partnerID=MN8TOARS}, DOI={10.2134/jeq2011.0347}, abstractNote={Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. The novel technique of pyrosequencing promises to expand our understanding of the microbial diversity of soils and eroded sediments because it can sequence 10 to 100 times more DNA fragments than previous techniques, providing enhanced exploration into what microbes are being lost from soil due to wind erosion. Our study evaluated the bacterial diversity of two types of wind-eroded sediments collected from three different organic-rich soils in Michigan using a portable field wind tunnel. The wind-eroded sediments evaluated were a coarse sized fraction with 66% of particles >106 μm (coarse eroded sediment) and a finer eroded sediment with 72% of particles <106 μm. Our findings suggested that (i) bacteria carried in the coarser sediment and fine dust were effective fingerprints of the source soil, although their distribution may vary depending on the soil characteristics because certain bacteria may be more protected in soil surfaces than others; (ii) coarser wind-eroded sediment showed higher bacterial diversity than fine dust in two of the three soils evaluated; and (iii) certain bacteria were more predominant in fine dust (, , and ) than coarse sediment ( and ), revealing different locations and niches of bacteria in soil, which, depending on wind erosion processes, can have important implications on the soil sustainability and functioning. Infrared spectroscopy showed that wind erosion preferentially removes particular kinds of C from the soil that are lost via fine dust. Our study shows that eroded sediments remove the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functioning of the source soil.}, number={3}, journal={Journal of Environmental Quality}, author={Gardner, T. and Acosta-Martinez, V. and Calderón, F.J. and Zobeck, T.M. and Baddock, M. and Van Pelt, R.S. and Senwo, Z. and Dowd, S. and Cox, S.}, year={2012}, pages={744–753} }
 @inproceedings{gardner_acosta-martinez_zobeck_baddock_pelt_senwo, title={Characterization of Microbes Carried in Dust}, DOI={10.13031/2013.39191}, abstractNote={There is still a lack of understanding of how soil microbial community distribution is controlled by wind erosion. This information is of international concern as eroded sediments can potentially carry away the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functional potential of the soil. Pyrosequencing techniques promises to expand our understanding of the vast microbial diversity with respect to soils that experience high rates of wind erosion; because it is able to sequence 10-100 times more DNA fragments than previous techniques (traditional cloning). Our study evaluated the bacterial diversity on coarse and fine dust collected from three different silty soils in Michigan by using a portable field wind tunnel instrument. Our results indicated that Acidobacter was the predominant bacteria in these soils as well as the predominant bacteria carried via wind dispersion in coarse and fine dust from these soil sources. Soil 1, which had higher P levels than the other 2 soils, pH was basically 6 and it had higher organic matter (OM) content (47.3-55%), while showing this order of bacterial predominance: Acidobacter, Streptomyces, Levilinea, Patulibacter and Gemmatimonas. Although Streptomyces was the second most abundant bacteria in soil source 1, fine dust did not carry this species, and Levilinea was the second most predominant bacteria in this dust. Soil 2, which had lower P levels than soil 1 (within a range of 122-136 mg P kg-1), pH of about 5.5, and an intermediate OM content (42.9%) also showed the species predominance of Acidobacter followed by Patulibacter, Conexibacter, Rhizobium and Levilinea. Three of the 5 predominant bacteria in the soil source were also predominant in the fine dust except for Conexibacter and Rhizobium. Soil 3 had the lowest OM content (16.3-20.8%) of the 3 soils evaluated, and it had an average pH of 5.7, and P levels within a range of 123-153 P mg kg-1. This soil also showed a predominance of Acidobacter followed by Patulibacter, Rhizobium, Gemmatimonas, and Conexibacter. In addition to Acidobacter in fine dust, Conexibacter and Patulibacter were also carried. The coarse dust samples collected from these 3 soils demonstrated some differences in bacterial distribution compared to the fine dust, which may indicate that fine dust dispersion caused by wind erosion is the major carrier of soil predominant bacteria. The highest abundance of Acidobacter is explained by the acidic pH of these soils, and thus, it appears that they play an important ecological role in these soils functioning. Our findings suggested that bacteria carried in coarse or fine dust represent fingerprints of the soil source, but certain specific group of bacteria was more abundant in fine dust than coarse dust, revealing different niches in these soils. We are in the process of identifying the ecological role of the bacterial groups carried in these dust samples as they can have important implications on the soil sustainability and functioning. This research is focused on coupling the diversity of the soil microbial communities carried by wind erosion with biogeochemical functionality using enzymatic activities involved in nutrient cycling. This will allow us to identify keystone microbial species-assemblages associated with biogeochemical processes of the soil source.}, booktitle={International Symposium on Erosion and Landscape Evolution (ISELE), 18-21 September 2011, Anchorage, Alaska}, publisher={American Society of Agricultural and Biological Engineers}, author={Gardner, Terrence G and Acosta-Martinez, Veronica and Zobeck, Ted and Baddock, Matthew C and Pelt, Robert Scott Van and Senwo, Zachary} }
 @article{gardner_acosta-martinez_senwo_dowd_2011, title={Soil rhizosphere microbial communities and enzyme activities under organic farming in Alabama}, volume={3}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84859391710&partnerID=MN8TOARS}, DOI={10.3390/d3030308}, abstractNote={Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME) and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa), potato (Solanum tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall fescue pasture grass (Festuca arundinacea). Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c) varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the bacterial species level) at 0–10 cm (581.7–770.0) compared to 10–20 cm (563.3–727.7) soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7); whereas the lowest OTUs found at 10–20 cm were under potato (563.3). The predominant phyla (85%) in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria), and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more abundant under pasture compared to the cultivated soils under broccoli, potato, onion and lettuce. This study found significant differences in microbial community structure and diversity, and enzyme activities of nutrient cycling in this organic farming system under different rhizospheres, which can have implications in soil health and metabolic functioning, and the yield and nutritional value of each crop.}, number={3}, journal={Diversity}, author={Gardner, T. and Acosta-Martinez, V. and Senwo, Z. and Dowd, S.E.}, year={2011}, pages={308–328} }
 @article{bhatnagar_gülland_bascand_palmer_gardner_kearse_bäckström_2003, title={Mutational analysis of conserved amino acids in the T cell receptor α-chain transmembrane region: A critical role of leucine 112 and phenylalanine 127 for assembly and surface expression}, volume={39}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0345701216&partnerID=MN8TOARS}, DOI={10.1016/S0161-5890(03)00027-0}, abstractNote={Correct assembly of all TCR complex polypeptides is essential for its cell surface expression and function. The transmembrane region of the TCRalpha chain is highly conserved and to gain insight into the structural and functional role of these residues, single amino acid substitutions were introduced and surface expression and signaling ability studied in T hybridoma cells. Introduction of acid residues within the TCRalpha chain transmembrane region were mostly tolerated, indicating that the net charge within this region of the TCR complex is not crucial to either assembly or signaling. However, mutations of leucine 112 or phenylalanine 127 to aspartic acids (L112D or F127D, respectively) resulted in dramatic loss of surface expression and, therefore, their signaling ability. Intracellular flow cytometry showed that the mutant TCRalpha polypeptides were present at levels comparable to wild-type, indicating that the reduced surface expression was not a consequence of impaired protein survival. The defect was characterized by immunoprecipitation and showed that residues L112 and F127 were involved in early interactions with the CD3 complex. A large proportion of the TCRalpha chain mutants L112D and F127D consisted of immature protein, indicative of a problem during early assembly of the TCR. Our findings provide evidence for the involvement of the conserved L112 and F127 residues of the TCRalpha chain transmembrane region in the assembly process of the TCR complex.}, number={15}, journal={Molecular Immunology}, author={Bhatnagar, A. and Gülland, S. and Bascand, M. and Palmer, E. and Gardner, T.G. and Kearse, K.P. and Bäckström, B.T.}, year={2003}, pages={953–963} }
 @article{gardner_kearse_1999, title={Purification of Immature CD4<sup>+</sup>CD8</sup>+</sup> Thymocytes by Panning with Anti-CD8 Antibody}, volume={12}, DOI={10.1385/1-59259-682-7:47}, abstractNote={Most T lymphocytes of the immune system differentiate within the thymus along the CD4/CD8 developmental pathway by a highly ordered process termed thymic selection (,). The maturation status of thymocytes is commonly assessed by their expression of the coreceptor proteins CD4 and CD8 and their surface density of aβ T cell receptors (αβ TCR), (). Three major subpopulations of T cells exist within the thymus that exemplify the progression of thymocytes along the CD4/CD8 developmental pathway: 1. CD4−CD8− (double-negative) thymocytes which express no αβ TCR; 2. CD4+CD8+ (double-positive) thymocytes, which express no/low αβ TCR; and 3. CD4+CD8− and CD4−CD8+ (single positive) thymocytes, both of which express high surface density of αβ TCR (, , , ), (Fig. 1). Open image in new window Fig. 1. Intrathymic development of thymocytes along the CD4/CD8 developmental pathway. Immature CD4−CD8− thymocytes develop into progeny CD4+CD8+ thymocytes which maintain low expression of αβTCR. Immature CD4+CD8+ thymocytes expressing αβTCR of appropriate specificities are selected for further differentiation into mature T cells that express either CD4 (CD4+CD8−) or CD8 (CD4−CD8+) coreceptor molecules, but not both. Mature CD4+CD8− and CD4−CD8+ thymocytes emigrate from the thymus to the periphery where they may localize in lymphoid organs (for example, lymph node or spleen).}, journal={T Cell Protocols}, publisher={Humana Press}, author={Gardner, Terrence G. and Kearse, Kelly P.}, year={1999}, pages={47–53} }
 @article{gardner_kearse_2000, title={Purification of immature CD4+CD8+ thymocytes by panning with anti-CD8 antibody.}, volume={134}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033643752&partnerID=MN8TOARS}, journal={Methods in molecular biology (Clifton, N.J.)}, author={Gardner, T.G. and Kearse, K.P.}, year={2000}, pages={47–53} }
 @article{gardner_franklin_robinson_pederson_howe_kearse_2000, title={T cell receptor assembly and expression in the absence of calnexin}, volume={378}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034214002&partnerID=MN8TOARS}, DOI={10.1006/abbi.2000.1804}, abstractNote={Most subunits of the alphabeta deltaepsilon gammaepsilon zetazeta T cell antigen receptor (TCR) complex associate with the molecular chaperone calnexin shortly after their synthesis in the endoplasmic reticulum, including clonotypic TCRalpha,beta molecules and invariant CD3gamma,delta,epsilon chains. While calnexin interaction is suggested to be important for the stability of newly synthesized TCRalpha subunits, the role of calnexin in the survival and assembly of remaining TCR components is unknown. Here we evaluated the expression of TCR proteins in CEM T cells and the calnexin-deficient CEM variant CEM.NK(R). We found that CEM and CEM.NK(R) cells constitutively synthesized all TCR subunits except for TCRalpha and that CD3gamma,delta,epsilon components and CD3-beta complexes were effectively assembled together in both cell types. The stability and folding of core CD3epsilon chains were similar in CEM and CEM.NK(R) cells. Interestingly, TCRalpha synthesis was differentially induced by phorbol myristate acetate treatment in CEM and CEM.NK(R) cells and TCRalpha proteins synthesized in CEM.NK(R) cells showed reduced survival compared to those made in CEM cells. Importantly, these data show that TCR complexes were inducibly expressed on CEM.NK(R) cells in the absence of calnexin synthesis. These results demonstrate that TCR complexes can be expressed in the absence of calnexin and suggest that the role of calnexin in the quality control of TCR assembly is primarily restricted to the stabilization of newly synthesized TCRalpha proteins.}, number={1}, journal={Archives of Biochemistry and Biophysics}, author={Gardner, T.G. and Franklin, R.A. and Robinson, P.J. and Pederson, N.E. and Howe, C. and Kearse, K.P.}, year={2000}, pages={182–189} }
 @article{gardner_kearse_1999, title={Modification of the T cell antigen receptor (TCR) complex by UDP- glucose:glycoprotein glucosyltransferase: TCR folding is finalized convergent with formation of αβδεγε complexes}, volume={274}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033553467&partnerID=MN8TOARS}, DOI={10.1074/jbc.274.20.14094}, abstractNote={Most T lymphocytes express on their surfaces a multisubunit receptor complex, the T cell antigen receptor (TCR) containing α, β, γ, δ, ε, and ζ molecules, that has been widely studied as a model system for protein quality control. Although the parameters of TCR assembly are relatively well established, little information exists regarding the stage(s) of TCR oligomerization where folding of TCR proteins is completed. Here we evaluated the modification of TCR glycoproteins by the endoplasmic reticulum folding sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (GT) as a unique and sensitive indicator of how TCR subunits assembled into multisubunit complexes are perceived by the endoplasmic reticulum quality control system. These results demonstrate that all TCR subunits containing N-glycans were modified by GT and that TCR proteins were differentially reglucosylated during their assembly with partner TCR chains. Importantly, these data show that GT modification of most TCR subunits persisted until assembly of CD3αβ chains and formation of CD3-associated, disulfide-linked αβ heterodimers. These studies provide a novel evaluation of the folding status of TCR glycoproteins during their assembly into multisubunit complexes and are consistent with the concept that TCR folding is finalized convergent with formation of αβδεγε complexes.}, number={20}, journal={Journal of Biological Chemistry}, author={Gardner, T.G. and Kearse, K.P.}, year={1999}, pages={14094–14099} }