Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation

Innovative multiplex qPCR method for rapid and reliable detection of microcystin-producing genes during harmful algal blooms: Insights from Utah Reservoirs

Cyanobacterial harmful algal blooms (cyanoHABs) have the potential to produce cyanotoxins, which pose significant health risks to both humans and animals. The gold standard methods for monitoring cyanoHABs involve enzyme-linked immunosorbent assay (ELISA), liquid chromatography combined with triple quadrupole mass spectrometry (LC-MS/MS) and manual cell counting under microscopy. However, these techniques, while effective, are costly and time-consuming, which may not be optimal for timely decision-making to safeguard public health. Quantitative polymerase chain reaction (qPCR) offers a complementary approach that serves as an indicator of the potential for toxin production. It provides accurate results with a rapid turnaround time and high throughput capacity, and greater affordability. To assess the reliability of qPCR in predicting toxin production and determining when toxin levels exceed recreational advisory thresholds, we conducted experiments utilizing two DNA extraction methods for qPCR testing: RapidDNA and ClassicDNA. Sampling was conducted across nine water bodies in Utah throughout the recreational season from June 1 to October 31, 2023. We targeted cyanotoxin-encoding genes mainly associated with microcystins, the dominant cyanotoxin reported for these water bodies, for qPCR analysis. Toxin levels were measured using both ELISA and LC-MS/MS with cyanobacteria cell counting conducted as a reference. Out of nine water bodies studied, cyanoHABs were detected in five (i.e., Utah Lake, and Deer Creek, Echo, Schofield, and Pineview Reservoirs). Analysis of the data revealed a significant linear relationship between both the qPCR results of mcyE (associated with microcystin production) obtained from RapidDNA and ClassicDNA methods, and the levels of microcystins measured by ELISA and LC-MS/MS. RapidDNA qPCR methods offer a potential warning tool for indicating toxin production during blooming events, though this method is not suitable for determining risk during the pre-blooming period. Conversely, ClassicDNA methods can be utilized during the pre-blooming period to prepare for potential blooms. These results provide insight into the genetic potential of blooms around the state to produce microcystins. Findings can be implemented in both Recreational Water Quality and Drinking Water programs nationally.

Microbial communities and their role in enhancing hemp fiber quality through field retting

The current development of industrial hemp "Cannabis Sativa L." fibers for technical textiles and industrial applications requires high-quality fibers with homogeneous properties. However, several factors have been reported to influence the fibers' intrinsic properties, including a post-harvest process known as retting. This process plays a crucial role in facilitating the mechanical extraction of fibers from hemp stems. Retting involves the degradation of the amorphous components surrounding the fiber bundles enabling their decohesion from stems. Microorganisms play a central role in mediating this bioprocess. During retting, they colonize the stems' surface. Therefore, the biochemical components of plant cell wall, acting as natural binding between fibers, undergo a breakdown through the production of microbial enzymes. Although its critical role, farmers often rely on empirical retting practices, and considering various biotic and abiotic factors, resulting in fibers with heterogenous properties. These factors limit the industrial applications of hemp fibers due to their inconsistent properties. Thus, the purpose of this review is to enhance our comprehension of how retting influences the dynamics of microbial communities and, consequently, the evolution of the biochemical properties of hemp stems throughout this process. Better understanding of retting is crucial for effective process management, leading to high-value fibers. KEY POINTS: • Retting enables degradation of cell wall components, controlling fiber properties. • Microbial enzymatic activity is crucial for successful decohesion of fiber bundles. • Understanding retting mechanisms is essential for consistent fiber production.

Water retting process with hemp pre-treatment: effect on the enzymatic activities and microbial populations dynamic

Proper retting process of hemp stems, in which efficient separation of cellulose fiber from the rest of the stem is promoted by indigenous microorganisms able to degrade pectin, is essential for fiber production and quality. This research aimed to investigate the effect of a pre-treatment dew retting in field of hemp stalks on the pectinolytic enzymatic activity and microbiota dynamic during lab-scale water retting process. A strong increase in the pectinase activity as well as in the aerobic and anaerobic pectinolytic concentration was observed from 14 to 21 days, especially using hemp stalks that were not subjected to a pre-retting treatment on field (WRF0 0.690 ± 0.05 U/mL). Results revealed that the microbial diversity significantly varied over time during the water retting and the development of microbiota characterizing the water retting of hemp stalks of different biosystems used in this study was affected by pre-treatment conditions in the field and water retting process and by an interaction between the two methods. Although at the beginning of the experiment a high biodiversity was recorded in all biosystems, the water retting led to a selection of microbial populations in function of the time of pre-treatment in field, especially in bacterial populations. The use of hemp stems did not subject to a field pre-treatment seems to help the development of a homogeneous and specific pectinolytic microbiota with a higher enzymatic activity in respect to samples exposed to uncontrolled environmental conditions for 10, 20, or 30 days before the water retting process. KEY POINTS: • Microbial diversity significantly varied over time during water retting. • Water retting microbiota was affected by dew pre-treatment in the field. • Retting of no pretreated hemp allows the development of specific microbiota with high enzymatic activity.

Study on the microbial diversity of ear canal secretions from patients with otomycosis

Otomycosis is caused by fungi, which usually cause discharge and additional discomfort. The highest incidence of otomycosis occurs in summer. To better treat this disease, it is necessary to study the microbial diversity of otomycosis secretions. In this regard, this study used high-throughput sequencing technology to determine the microbial diversity of the ear canal secretions of six typical patients with otomycosis in Wuhan via internal transcribed spacer (ITS) and 16S rRNA analyses and proposed a reasonable clinical treatment plan. Six patients with otomycosis in the Department of Otorhinolaryngology, Hubei Third People's Hospital Affiliated with Jianghan University, were selected from June 2022 to August 2022. The results showed that Staphylococcus spp. (average abundance 29.05%) was the dominant bacteria and Aspergillus spp. (average abundance 90.68%) was the dominant fungus involved in otomycosis secretion. Aspergillus spp. can cause inflammation of the external auditory canal combined with bacterial infections such as Staphylococcus spp., which can cause discharge in the ear canal. High-throughput sequencing provides comprehensive information on the microbial community involved in otomycosis discharge and will aid in evaluating the efficacy of clinical treatment and medication.