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Hyporheic zones play a crucial role in ecological processes primarily orchestrated by hyporheic organisms, known as hyporheos. Our understanding of riverine biodiversity, encompassing hyporheic zones, remains limited. Therefore, the development of a method for the facile and accurate detection of hyporheic communities is imperative. Thus, we evaluated the applicability of environmental DNA (eDNA) metabarcoding surveys in the hyporheic zone in a small stream in Japan. We conducted simultaneous direct sampling and eDNA surveys at two different locations (head and tail of a rapid and a bar) and during two different seasons (less and more disturbed periods). Subsequently, we compared the outcomes of these sampling methods, locations, and seasons. Through eDNA metabarcoding targeting the cytochrome-c oxidase subunit I (COI) regions, we successfully identified a diverse array of hyporheic and benthic taxa in all samples. Remarkably, the performance of eDNA metabarcoding was comparable to the identification of directly sampled benthos and hyporheos. We observed a 62%–78% concordance between direct sampling and eDNA metabarcoding. Notably, eDNA metabarcoding revealed a higher number of hyporheic taxa compared to direct sampling. Moreover, the relative detectability of hyporheos by eDNA metabarcoding differed between the seasons, unlike direct sampling. Our findings underscore the importance of conducting both eDNA surveys and direct sampling to comprehensively assess the composition of the stream community while accounting for seasonal variations. This study demonstrates the utility of eDNA metabarcoding as a non-destructive approach for investigating the hyporheic zone, enabling a more effective assessment of riverine biodiversity.

Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short- and long-term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro-organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.

[Background] Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. [Methods] DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. [Results] No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.

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Hotspots of tropical marine biodiversity are areas that harbour disproportionately large numbers of species compared to surrounding regions. The richness and location of these hotspots have changed throughout the Cenozoic. Here, we review the global dynamics of Cenozoic tropical marine biodiversity hotspots, including the four major hotspots of the Indo-Australian Archipelago (IAA), western Tethys (present Mediterranean), Arabian Sea and Caribbean Sea. Our review supports the 'Hopping Hotspots' model, which proposes that the locations of peak biodiversity are related to Tethyan faunai elements and track broad-scale shallow-marine habitats and high coastal complexity created by the collision of tectonic plates. A null hypothesis is the 'Whack-A-Mole' model, which proposes that hotspots occur in habitats suitable for high diversity regardless of taxonomie identity or faunai elements. Earlier 'Centre-of theories (e.g. centres of origin with diversity decreasing with distance from supposed areas of exceptionally high rates of speciation, for which easy connection to adjacent regions to the east and west is important) were based on the analysis of recent biotas with no palaeontological foundation, and may better explain diversity dynamics within a hotspot rather than those between hotspots. More recently, however, human disturbance is massively disrupting these natural patterns.

Environmental DNA (eDNA) analysis has recently become a successful cost and time-efficient biomonitoring technique. Application of eDNA also has considerable potential for plants, for the successful detection of invasive, endangered and rare species, and community-level interpretations. Monitoring methods using eDNA were found to be equal to or more effective than traditional methods; however, species detection increased when the two methods were combined. Currently, elimination of potential obstacles and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some less-concern plant groups.Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than