TY - JOUR TI - Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis AU - Whitham, Jason M. AU - Grunden, Amy M. T2 - CURRENT BIOINFORMATICS AB - Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. Objective: This study was designed to evaluate the impacts JGI trimming and decontamination procedures have on assembly and binning metrics, placement of MAGs into species trees, and functional profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive trimming impacts these binning metrics. Methods: Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk. Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to evaluate the effects of trimming and decontamination on downstream analyses. Results: We found that JGI trimmed and decontaminated reads had significant impacts on assembly and binning metrics compared to raw reads, including significantly higher total contig counts, more contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies, and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also found that differences in the placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly reduce MAG counts. Conclusion: Trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing?” However, mild trimming and decontamination of metagenomic reads with high-quality scores are recommended for removing sample processing and sequencing artifacts. DA - 2023/// PY - 2023/// DO - 10.2174/1574893618666230227145952 VL - 18 IS - 5 SP - 428-439 SN - 2212-392X KW - Trimming KW - decontamination KW - binning KW - assembly KW - metagenomics KW - MAG KW - QC KW - accessibility ER - TY - JOUR TI - Biochemical characterization of a psychrophilic and halotolerant a-carbonic anhydrase from a deep-sea bacterium, Photobacterium profundum AU - Somalinga, Vijayakumar AU - Foss, Emily AU - Grunden, Amy M. T2 - AIMS MICROBIOLOGY AB - <abstract> <p>Prokaryotic α–carbonic anhydrases (α-CA) are metalloenzymes that catalyze the reversible hydration of CO<sub>2</sub> to bicarbonate and proton. We had reported the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, <italic>Photobacterium profundum</italic> SS9. In this manuscript, we report the first biochemical characterization of <italic>P. profundum</italic> α–CA (PprCA) which revealed several catalytic properties that are atypical for this class of CA's. Purified PprCA exhibited maximal catalytic activity at psychrophilic temperatures with substantial decrease in activity at mesophilic and thermophilic range. Similar to other α–CA's, Ppr9A showed peak activity at alkaline pH (pH 11), although, PprCA retained 88% of its activity even at acidic pH (pH 5). Exposing PprCA to varying concentrations of oxidizing and reducing agents revealed that N-terminal cysteine residues in PprCA may play a role in the structural stability of the enzyme. Although inefficient in CO<sub>2</sub> hydration activity under mesophilic and thermophilic temperatures, PprCA exhibited salt-dependent thermotolerance and catalytic activity under extreme halophilic conditions. Similar to other well-characterized α–CA's, PprCA is also inhibited by monovalent anions even at low concentrations. Finally, we demonstrate that PprCA accelerates CO<sub>2</sub> biomineralization to calcium carbonate under alkaline conditions.</p> </abstract> DA - 2023/// PY - 2023/// DO - 10.3934/microbiol.2023028 VL - 9 IS - 3 SP - 540-553 SN - 2471-1888 KW - Photobacterium profundum KW - a-carbonic anhydrase KW - halotolerance KW - biomineralization KW - carbon capture ER - TY - JOUR TI - Evaluation of electrical and mechanical Palmer amaranth (Amaranthus palmeri) management in cucumber, peanut, and sweetpotato AU - Moore, Levi D. D. AU - Jennings, Katherine M. M. AU - Monks, David W. W. AU - Boyette, Michael D. D. AU - Leon, Ramon G. G. AU - Jordan, David L. L. AU - Ippolito, Stephen J. J. AU - Blankenship, Colton D. D. AU - Chang, Patrick T2 - WEED TECHNOLOGY AB - Abstract Field studies were conducted to assess the efficacy of physical weed management of Palmer amaranth management in cucumber, peanut, and sweetpotato. Treatments were arranged in a 3 × 4 factorial in which the first factor included a treatment method of electrical, mechanical, or hand-roguing Palmer amaranth control and the second factor consisted of treatments applied when Palmer amaranth was approximately 0.3, 0.6, 0.9, or 1.2 m above the crop canopy. Four wk after treatment (WAT), the electrical applications controlled Palmer amaranth at least 27 percentage points more than the mechanical applications when applied at the 0.3- and 0.6-m timings. At the 0.9- and 1.2-m application timings 4 WAT, electrical and mechanical applications controlled Palmer amaranth by at most 87%. Though hand removal generally resulted in the greatest peanut pod count and total sweetpotato yield, mechanical and electrical control resulted in similar yield to the hand-rogued plots, depending on the treatment timing. With additional research to provide insight into the optimal applications, there is potential for electrical control and mechanical control to be used as alternatives to hand removal. Additional studies were conducted to determine the effects of electrical treatments on Palmer amaranth seed production and viability. Treatments consisted of electricity applied to Palmer amaranth at first visible inflorescence, 2 wk after first visible inflorescence (WAI) or 4 WAI. Treatments at varying reproductive maturities did not reduce the seed production immediately after treatment. However, after treatment, plants primarily died and ceased maturation, reducing seed production assessed at 4 WAI by 93% and 70% when treated at 0 and 2 WAI, respectively. Treatments did not have a negative effect on germination or seedling length. DA - 2023/1/22/ PY - 2023/1/22/ DO - 10.1017/wet.2023.1 SP - SN - 1550-2740 KW - Palmer amaranth KW - Amaranthus palmeri S KW - Watson KW - cucumber KW - Cucumis sativus L KW - 'Maxi pick' KW - peanut KW - Arachis hypogaea L KW - 'Walton' KW - sweetpotato KW - Ipomoea batatas (L KW - ) Lam KW - 'Covington' KW - Electric weed control KW - mechanical weed control KW - weed control KW - alternative weed management KW - organic weed control ER - TY - JOUR TI - Survivability of Salmonella Typhimurium (ATCC 14208) and Listeria innocua (ATCC 51742) on lignocellulosic materials for paper packaging AU - Zwilling, Jacob D. AU - Whitham, Jason AU - Zambrano, Franklin AU - Pifano, Alonzo AU - Grunden, Amy AU - Jameel, Hasan AU - Venditti, Richard AU - Gonzalez, Ronalds T2 - HELIYON AB - Lignocellulosic materials are widely used for food packaging due to their renewable and biodegradable nature. However, their porous and absorptive properties can lead to the uptake and retention of bacteria during food processing, transportation, and storage, which pose a potential risk for outbreaks of foodborne disease. Thus, it is of great importance to understand how bacteria proliferate and survive on lignocellulosic surfaces. The aim of this research was to compare the growth and survivability of Salmonella Typhimurium and Listeria innocua on bleached and unbleached paper packaging materials. Two different paper materials were fabricated to simulate linerboard from fully bleached and unbleached market pulps and inoculated with each bacterium at high bacterial loads (107 CFU). The bacteria propagated during the first 48 h of incubation and persisted at very high levels (>107 CFU/cm2) for 40 days for all paper and bacterium types. However, the unbleached paper allowed for a greater degree of bacterial growth to occur compared to bleached paper, suspected to be due to the more hydrophobic nature of the unbleached, lignin-containing fibers. Several other considerations may also alter the behavior of bacteria on lignocellulosic materials, such as storage conditions, nutrient availability, and chemical composition of the fibers. DA - 2023/3// PY - 2023/3// DO - 10.1016/j.heliyon.2023.e14122 VL - 9 IS - 3 SP - SN - 2405-8440 KW - Lignocellulosic KW - Food safety KW - Paper KW - Survivability KW - Bacteria KW - Packaging ER - TY - JOUR TI - Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste AU - Cuebas-Irizarry, Mara F. AU - Grunden, Amy M. T2 - MICROBIAL BIOTECHNOLOGY AB - Abstract Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial‐catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces‐ based technologies for use in the textile and pulp‐milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment. DA - 2023/4/5/ PY - 2023/4/5/ DO - 10.1111/1751-7915.14258 VL - 4 SP - SN - 1751-7915 ER - TY - JOUR TI - Tolerance of muscadine grape to 2,4-D choline postemergence-directed AU - Sims, Kira C. AU - Mitchem, Wayne E. AU - Jennings, Katherine M. AU - Monks, David W. AU - Jordan, David L. AU - Hoffmann, Mark T2 - WEED TECHNOLOGY AB - Abstract Field studies were conducted in commercial muscadine vineyards in western North Carolina in 2018 and eastern North Carolina in 2019, 2020, and 2021 to determine tolerance of younger (< 9 yr) and older (≥ 9 yr) bearing muscadine grapevines to 2,4-D directed beneath the crop postemergence (POST). Treatments included 2,4-D choline at 0, 0.53, 1.06, 1.60, and 2.13 kg ae ha −1 applied as a single treatment in May or June (spring) at immediate pre-bloom, and sequential treatments at 0.53 followed by (fb) 0.53, 1.06 fb 1.06, 1.6 fb 1.6, or 2.13 fb 2.13 kg ha −1 . The first sequential treatment was applied in spring fb another application of the same amount in July (summer) at pre-veraison. No differences in injury on muscadine grapevines were observed from 2,4-D treatments. Differences among treatments were not observed for yield of younger vines. However, for older vines, a difference due to 2,4-D rate was observed in 2018, when yield was higher when 2,4-D was applied at 1.6 kg ha −1 compared with nontreated grapevines, and when 2,4-D was applied at 0.53 and 2.13 kg ha −1 . A rate-by-timing interaction was observed in 2019 when yield was lower from 0.53 kg ha −1 2,4-D summer application compared with all other summer treatments but similar to the nontreated. However, no biological pattern was observed from either of these differences. No differences among treatments were observed for fruit pH, titratable acidity, or soluble solid content of either younger or older vines. DA - 2023/2/27/ PY - 2023/2/27/ DO - 10.1017/wet.2023.8 SP - SN - 1550-2740 KW - 2 KW - 4-D choline KW - muscadine grape KW - Vitis rotundifolia Michx KW - 'Carlos' 'Nesbitt' KW - herbicide tolerance KW - small fruit KW - perennial fruit ER - TY - JOUR TI - Nitrogen Fixation and Ammonium Assimilation Pathway Expression of Geobacter sulfurreducens Changes in Response to the Anode Potential in Microbial Electrochemical Cells AU - Ortiz-Medina, Juan F. AU - Poole, Mark R. AU - Grunden, Amy M. AU - Call, Douglas F. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Biological nitrogen fixation coupled with ammonium recovery provides a sustainable alternative to the carbon-, water-, and energy-intensive Haber-Bosch process. Aerobic biological nitrogen fixation technologies are hindered by oxygen gas inhibition of the nitrogenase enzyme. DA - 2023/3/28/ PY - 2023/3/28/ DO - 10.1128/aem.02073-22 VL - 3 SP - SN - 1098-5336 KW - electromicrobiology KW - Geobacter KW - nitrogen fixation ER - TY - JOUR TI - Flue-cured tobacco and Cl rates: Implications on yield, quality, and nutrient concentration AU - Tiecher, Tales AU - Pace, Cara Ruth AU - Gatiboni, Luke AU - Vann, Matthew AU - Hardy, David AU - Fisher, Loren T2 - AGRONOMY JOURNAL AB - Abstract The increase in flue‐cured tobacco ( Nicotiana tabacum L.) yields in recent decades due to genetic improvements of new cultivars and management technologies may increase the plant demand for Cl, and the increased dry mass may dilute Cl concentration, thereby reducing negative effects. This study evaluated the effect of increasing doses of Cl on tobacco production, quality, and chemical composition of leaves, in four growing environments located at research stations where flue‐cured tobacco is produced in North Carolina. The treatments consisted of 11 rates of Cl (0, 11, 22, 34, 45, 56, 67, 78, 90, 101, and 112 kg ha −1 ) in each growing environment, with four replications in a randomized complete block design. The yield and visual quality, total alkaloids, and reducing sugars concentrations of cured leaf were determined. In addition, the concentration of selected nutrients (N, P, K, Ca, Mg, S, and Cl) and nitrate (NO 3 − ) in tobacco leaves was measured in five different periods. Rates of Cl up to 112 kg ha −1 did not reduce the productivity or quality of flue‐cured tobacco in any environment. The Cl rate required to reach the threshold of 1.0% Cl content in cured leaf was site‐specific, being surpassed even in the control treatment at one location, or with Cl rates higher than 34 and 90 kg ha −1 in two environments. In one environment, the Cl rates increased tobacco yield, probably due the direct effect of Cl as a nutrient. Although the increasing Cl rates increased the reducing sugars concentration, visual quality was not attenuated. DA - 2023/2/13/ PY - 2023/2/13/ DO - 10.1002/agj2.21272 SP - SN - 1435-0645 ER -