Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues.

Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ13C and δ15N) analyses. We examined the degree of individual specialization in both species using the δ13C and δ15N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ15N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ13C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.

Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review.

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 traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) 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 plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.

Influence of DNA extraction kits on freshwater fungal DNA metabarcoding.

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.

Filtration extraction method using a microfluidic channel for measuring environmental DNA.

The environmental DNA (eDNA) method, which is widely applied in biomonitoring, is limited to laboratory analysis and processing. In this study, we developed a filtration/extraction component using a microfluidic channel, the Biryu-Chip (BC), and a filtration/extraction method, the BC method, to minimize the volume of the sample necessary for DNA extraction and subsequent PCR amplification. We tested the performance of the BC method and compared it with that of the Sterivex filtration/extraction method using aquarium and river water samples. We observed that using the BC method, the same concentration of extracted DNA was obtained with 1/20-1/40 of the filtration volume of the Sterivex method, suggesting that the BC method can be widely used for eDNA measurement. In addition, we performed on-site measurements of eDNA within 30 min using a mobile PCR device, demonstrating that filtration and extraction can be performed easily and quickly using the BC method. The PCR results obtained using the BC method were similar to those obtained using the Sterivex method. The BC method requires fewer steps; therefore, the risk of DNA contamination can be reduced. When combined with mobile PCR, the BC method can be applied to easily detect eDNA within 30 min from the collection of water sample, even on-site.

Long-term observation of the egg and chick size in the nests of Larus ichthyaetus in Lake Chany, Russia.

This data set describes the long-term observation and morphological study of the eggs of the great black-headed gull Larus ichthyaetus in the gull nesting colonies on the islands of Lake Chany. Lake Chany is located in the Baraba forest-steppe of the West Siberian Plain, Russia, between the Ob and Irtish rivers. Lake Chany is protected by the Ramsar Convention on the Wetlands of International Importance, indicating that the lake is an important site for migratory birds, including L. ichthyaetus. This dataset contains the size and fate of all eggs, as well as the size of hatched chicks in 1164 observed L. ichthyaetus nests from 1993 to 2003.

Assessing the potential repercussions of the COVID-19 pandemic on global SDG attainment.

The coronavirus disease (COVID-19) pandemic has led to a worldwide lockdown, and this restriction on human movements and activities has significantly affected society and the environment. Some effects might be quantitative, but some might be qualitative, and some effects could prolong immediately and/or persistently. This study examined the consequences of global lockdown for human movement and nitrogen dioxide (NO2) emissions using an air pollution index and dataset and satellite image analyses. We also evaluated the immediate (during lockdown) and persistent (after lockdown) effects of lockdown on achieving the SDGs. Our analysis revealed a drastic reduction in human movement and NO2 emissions and showed that many SDGs were influenced both immediately and persistently due to the global lockdown. We observed the immediate negative impacts on four goals and positive impacts on five goals, especially those concerning economic issues and ecosystem conservation, respectively. The persistent effects of lockdown were likely to be predominantly reversed from their immediate impacts due to economic recovery. The global lockdown has influenced the global community's ability to meet the SDGs, and our analysis provides powerful insights into the status of the internationally agreed-upon SDGs both during and after the COVID-19-induced global lockdown. Supplementary Information: The online version contains supplementary material available at 10.1007/s43621-021-00067-2.

Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA.

Environmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.

Correction: Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding.

[This corrects the article DOI: 10.1371/journal.pone.0250162.].

Estimation of deracinated trees area in temperate forest with satellite images employing machine learning methods.

Climate change can increase the number of uprooted trees. Although there have been an increasing number of machine learning applications for satellite image analysis, the estimation of deracinated tree area by satellite image is not well developed. Therefore, we estimated the deracinated tree area of forests via machine-learning classification using Landsat 8 satellite images. We employed support vector machines (SVMs), random forests (RF), and convolutional neural networks (CNNs) as potential machine learning methods, and tested their performance in estimating the deracinated tree area. We collected satellite images of upright trees, deracinated trees, soil, and others (e.g., waterbodies and cities), and trained them with the training data. We compared the accuracy represented by the correct classification rate of these methods, to determine the deracinated tree area. It was found that the SVM and RF performed better than the CNN for two-class classification (deracinated and upright trees), and the correct classification rates of all methods were up to 93%. We found that the CNN and RF performed significantly higher for the four- and two-class classification compared to the other methods, respectively. We conclude that the CNN is useful for estimating deracinated tree areas using Landsat 8 satellite images.

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding.

Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.

Causal analysis of the temperature impact on deep-sea biodiversity.

The deep sea comprises more than 90% of the ocean; therefore, understanding the controlling factors of biodiversity in the deep sea is of great importance for predicting future changes in the functioning of the ocean system. Consensus has recently been increasing on two plausible factors that have often been discussed as the drivers of deep-sea species richness in the contexts of the species-energy and physiological tolerance hypotheses: (i) seafloor particulate organic carbon (POC) derived from primary production in the euphotic zone and (ii) temperature. Nonetheless, factors that drive deep-sea biodiversity are still actively debated potentially owing to a mirage of correlations (sign and magnitude are generally time dependent), which are often found in nonlinear, complex ecological systems, making the characterization of causalities difficult. Here, we tested the causal influences of POC flux and temperature on species richness using long-term palaeoecological datasets derived from sediment core samples and convergent cross mapping, a numerical method for characterizing causal relationships in complex systems. The results showed that temperature, but not POC flux, influenced species richness over 103-104-year time scales. The temperature-richness relationship in the deep sea suggests that human-induced future climate change may, under some conditions, affect deep-sea ecosystems through deep-water circulation changes rather than surface productivity changes.

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding.

Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over 2 years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a 'trap' for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.

On-site environmental DNA detection of species using ultrarapid mobile PCR.

Molecular methods, including those for environmental DNA (eDNA), provide essential information for biological and conservation sciences. Molecular measurements are often performed in the laboratory, which limits their scope, especially for rapid on-site analysis. eDNA methods for species detection provide essential information for the management and conservation of species and communities in various environments. We have developed an innovative novel method for on-site eDNA measurements using an ultrarapid mobile PCR platform. We tested the ability of our method to detect the distribution of silver carp, Hypophthalmichthys molitrix, in rivers and lakes. Our method reduced the measurement time to 30 min and provided high detectability of aquatic organisms compared to national observation surveys that use multiple fishing nets and laboratory extraction/detection using a benchtop qPCR platform. Our on-site eDNA method can be immediately applied to various taxa and environments.

Future Land Use for Insect Meat Production Among Countries: A Global Classification.

A potentially suitable alternative to reduce land use by livestock production is insect meat production. However, land use predictions for insect meat production, which are important in the planning of food production strategies in each country, have not been well-performed. To consider the strategy of insect meat production with regard to land use, the categorical perspectives of countries would be highly useful. Here, using previous simulation results, we used random forest machine learning to classify the potential land use of 157 countries for insect meat production under future climate change. From the categorical maps, we showed the global distribution of five different country categories and found that the land area of the countries may be an important factor in considering the future increase in insect meat production. Our classification could be used to help formulate future food policies by considering the increase in insect meat production in each country, as well as regionally and/or globally.

Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020).

In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding.

Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.

Effects of sediment replenishment on riverbed environments and macroinvertebrate assemblages downstream of a dam.

Riverbeds downstream of dams are starved of sediment, impacting habitat structure and ecological function. Despite the implementation of sediment management techniques, there has been no evaluation of their conservational effectiveness; the impacts on high trophic level organisms remain unknown. This study examined the effects of sediment replenishment on riverbeds and macroinvertebrates in a dammed river before and after sediment replenishment. We evaluated the particle sizes of replenished sediments and the case material of a case-bearing caddisfly. We observed significant changes in macroinvertebrate assemblages before and after sediment replenishment, and between the upstream and tributary references and downstream of the dam. The percentages of Ephemeroptera, Plecoptera, and Trichoptera, and the number of inorganic case-bearing caddisflies downstream of the dam following sediment replenishment, were significantly higher than the upstream and tributary reference sites. The particle size of case materials used by case-bearing caddisfly corresponded to the size of the replenished sediment. Dissimilarity results after replenishment showed that assemblages downstream of the dam differed from upstream sites, although they were similar to the tributary sites. The dissimilarity between the tributary and downstream of the dam was the same as that between the upstream and tributary. Sediment replenishment was observed to reduce the harmful effects of the dam, and partly restore benefits such as increasing species diversity and altering community assemblages, similar to the effects of tributary inflows.