specific-qPCR

Simple Summary: Many studies have shown that ground beetles feed on different agricultural pests, but little is known about their species communities from US cropping systems. We assessed the biological control potential of the most common carabid beetle species in Oregon annual ryegrass grown for seed by investigating spatial and temporal overlap of the most common species with those of the most damaging autumn-and winter-active pests (slugs, caterpillars and cranefly larvae) and determined the number of field-collected specimens that had fed on the respective pests using molecular gut content analysis. Only the non-native Nebria brevicollis was abundant during pest emergence and tested positive for all three pest groups. While the other common carabid beetle species-Agonum muelleri, Calosoma cancellatum and Poecilus laetulus-were also found to have consumed pests, they were active only during spring and summer, when crop damage by pests is less critical. We also show that disk til...

Simple Summary: Many studies have shown that ground beetles feed on different agricultural pests, but little is known about their species communities from US cropping systems. We assessed the biological control potential of the most common carabid beetle species in Oregon annual ryegrass grown for seed by investigating spatial and temporal overlap of the most common species with those of the most damaging autumn-and winter-active pests (slugs, caterpillars and cranefly larvae) and determined the number of field-collected specimens that had fed on the respective pests using molecular gut content analysis. Only the non-native Nebria brevicollis was abundant during pest emergence and tested positive for all three pest groups. While the other common carabid beetle species-Agonum muelleri, Calosoma cancellatum and Poecilus laetulus-were also found to have consumed pests, they were active only during spring and summer, when crop damage by pests is less critical. We also show that disk tilling did not affect any of the four common carabid beetle species and that only N. brevicollis was significantly associated with a vegetated field margin. This study contributes to expanding our knowledge on conservation biological control in a system where chemical pesticides are still the mainstay of control against invertebrate pests. Abstract: While carabid beetles have been shown to feed on a variety of crop pests, little is known about their species assemblages in US annual ryegrass crops, where invertebrate pests, particularly slugs, lepidopteran larvae and craneflies, incur major financial costs. This study assesses the biological control potential of carabid beetles for autumn-and winter-active pests in annual ryegrass grown for seed by: (a) investigating the spatial and temporal overlap of carabids with key pests; and (b) molecular gut content analysis using qPCR. Introduced Nebria brevicollis was the only common carabid that was active during pest emergence in autumn, with 18.6% and 8.3% of N. brevicollis collected between September and October testing positive for lepidopteran and cranefly DNA, respectively, but only 1.7% testing positive for slug DNA. While pest DNA was also detected in the guts of the other common carabid species-Agonum muelleri, Calosoma cancellatum and Poecilus laetulus-these were

Saad, O. S., Lin, X., Ng, T. Y., Li, L., Ang, P., & Lin, S. (2020). Genome Size, rDNA Copy, and qPCR Assays for Symbiodiniaceae. Frontiers in Microbiology, 11, 847.

Symbiodiniaceae community structure in corals is crucial for understanding the plasticity of different holobionts under environmental stress. While this relies on molecular analyses, accuracy of molecular quantification, as influenced by DNA extraction efficiency and rDNA copy number variations in particular, has rarely been systematically investigated. Here, we report the development of a set of genus-specific qPCR assays. First, a protocol for efficient DNA isolation and accurate measurements of genome size and rDNA copy number was established. Second, seven newly designed genus-specific ITS2 primer sets were validated using computational and empirical analyses and qPCR assays were developed. We find that while the genome size ranges between 1.75 ± 0.21 and 4.5 ± 0.96 Gbp, rDNA copy number shows over tenfold variation among Symbiodiniaceae species. Our protocol produced standard curves with high efficiencies (89.8 to 99.3%; R2 ≥ 0.999) and tight Cq values over different PCR conditions, illustrating high specificity and sensitivity of the qPCR assays. Tested on mock communities of mixed culture species, our qPCR results agreed well with microscopic counts and facilitated calibration of metabarcoding data. To test the applicability of our protocol for field samples, we analyzed three different Hong Kong coral samples. Six Symbiodiniaceae genera were detected in Acropora valida, Oulastrea crispata and Platygra acuta, with Breviolum, Effrenium, Fugacium and Gerakladium sp. being reported for the first time. Our results suggest that aggressively disrupting cells to ensure thorough cell lysis, estimating cell loss and DNA loss, and validating qPCR assays are critical for success. The number of species examined here is limited, but the primers are potentially applicable to most species in respective genera, and the protocol and the approach to develop it provide a base and template towards a standardized procedure for quantitatively characterizing Symbiodiniaceae communities in corals.