Terrence Gardner

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.

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.

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.

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.

Saprolite, weather 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 E. 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 tops 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 column and week 4 for the 45-cm column. 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.

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.

Biochar 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.

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.

Manganese oxides, which may be biogenically produced in both pristine and contaminated environments, have a large affinity for many trace metals.