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.

Global diversity of microbial communities in marine sediment.

Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ∼47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species-area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 103 to 6.10 × 105 and 3.28 × 104 to 2.46 × 106 amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth's global biosphere.

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.

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.

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.

The merits of entomophagy in the post COVID-19 world.

BACKGROUND: In 2020, human society underwent several drastic changes due to the coronavirus disease 2019 (COVID-19) pandemic, which generated an unprecedented global impact. Since the onset of the COVID-19 pandemic, various pressing concerns underlying food security, such as transport, production, and maintenance of the supply chain, have been raised. SCOPE AND APPROACH: The present study aimed to describe and review the merits of entomophagy in the post COVID-19 world, especially with regard to the low risk for zoonotic disease spread, high production rate, and future prospects for inducing entomophagy to enhance the diversity in the food system in comparison to conventional livestock. KEY FINDINGS AND CONCLUSIONS: The advantages of entomophagy in the post COVID-19 world have been elucidated herein, with particular emphasis on the minimal risk of zoonotic disease transmission and production efficiency, in addition to the future goal of establishment of entomophagy to expand redundancy and diversity in the food system as against the utility of conventional livestock. In the current scenario, as well as in the post COVID-19 situation, boosting entomophagy may play a pivotal role in global food security, as the aspects already touched upon have amply demonstrated.

A shady phytoplankton paradox: when phytoplankton increases under low light.

Light is a fundamental driver of ecosystem dynamics, affecting the rate of photosynthesis and primary production. In spite of its importance, less is known about its community-scale effects on aquatic ecosystems compared with those of nutrient loading. Understanding light limitation is also important for ecosystem management, as human activities have been rapidly altering light availability to aquatic ecosystems. Here we show that decreasing light can paradoxically increase phytoplankton abundance in shallow lakes. Our results, based on field manipulation experiments, field observations and models, suggest that, under competition for light and nutrients between phytoplankton and submersed macrophytes, alternative stable states are possible under high-light supply. In a macrophyte-dominated state, as light decreases phytoplankton density increases, because macrophytes (which effectively compete for nutrients released from the sediment) are more severely affected by light reduction. Our results demonstrate how species interactions with spatial heterogeneity can cause an unexpected outcome in complex ecosystems. An implication of our findings is that partial surface shading for controlling harmful algal bloom may, counterintuitively, increase phytoplankton abundance by decreasing macrophytes. Therefore, to predict how shallow lake ecosystems respond to environmental perturbations, it is essential to consider effects of light on the interactions between pelagic and benthic producers.

Droplet digital polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species.

Environmental DNA (eDNA) has been used to investigate species distributions in aquatic ecosystems. Most of these studies use real-time polymerase chain reaction (PCR) to detect eDNA in water; however, PCR amplification is often inhibited by the presence of organic and inorganic matter. In droplet digital PCR (ddPCR), the sample is partitioned into thousands of nanoliter droplets, and PCR inhibition may be reduced by the detection of the end-point of PCR amplification in each droplet, independent of the amplification efficiency. In addition, real-time PCR reagents can affect PCR amplification and consequently alter detection rates. We compared the effectiveness of ddPCR and real-time PCR using two different PCR reagents for the detection of the eDNA from invasive bluegill sunfish, Lepomis macrochirus, in ponds. We found that ddPCR had higher detection rates of bluegill eDNA in pond water than real-time PCR with either of the PCR reagents, especially at low DNA concentrations. Limits of DNA detection, which were tested by spiking the bluegill DNA to DNA extracts from the ponds containing natural inhibitors, found that ddPCR had higher detection rate than real-time PCR. Our results suggest that ddPCR is more resistant to the presence of PCR inhibitors in field samples than real-time PCR. Thus, ddPCR outperforms real-time PCR methods for detecting eDNA to document species distributions in natural habitats, especially in habitats with high concentrations of PCR inhibitors.

Different chemical cues originating from a shared predator induce common defense responses in two prey species.

In freshwater ecosystems, inducible defenses that involve behavioral or morphological changes in response to chemical cue detection are key phenomena in prey-predator interactions. Many species with different phylogenetic and ecological traits (e.g., general activity patterns and microhabitats) use chemical cues to avoid predators. We hypothesized that prey species with a shared predator, but having different ecological traits, would be adapted to detect different chemical cues from the predator. However, the proximate mechanisms by which prey use chemical cues to avoid predation remain little known. Here, we tested our hypothesis by using fractionated chemical components from predatory dragonfly nymphs (Lesser Emperor, Anax parthenope julius) to trigger anti-predator behavioral responses in two anuran tadpoles, the wrinkled frog Glandirana (Rana) rugosa and the Japanese tree frog Hyla japonica. Glandirana rugosa detected chemical cues that had either high or low hydrophobic properties, but H. japonica responded only to chemical cues with hydrophilic properties. During the normal behaviors of these tadpole species, G. rugosa remains immobile in benthic habitats, whereas H. japonica exhibits active swimming at the surface or in the middle of the water column. As we had hypothesized, these tadpole species, which have different general activity levels and microhabitats, detected different chemical cues that were exuded by their shared predator and responded by changing their activities to avoid predation. The specific chemical cues detected by each tadpole species are likely to have characteristics that optimize effective predator detection and encounter avoidance of the shared dragonfly predator.

A human thyroid cancer cell line, DH-14-3, newly established from poorly differentiated thyroid carcinoma.

Poorly differentiated thyroid carcinoma (PDTC) is a newly recognized histological type of malignant thyroid tumor, accounting for about 2 - 13% of all thyroid carcinomas. PDTC is considered as a morphologically and biologically intermediate stage between well-differentiated thyroid carcinoma and anaplastic thyroid carcinoma. PDTC preferentially manifests bone metastases. We here established a cell line from a resected tumor specimen from a 70-year-old male patient with PDTC who presented with multiple bone metastases. This new thyroid tumor cell line was designated as DH-14-3 and was subsequently grown in culture for several years. DH-14-3 cells express thyroglobulin in the cytoplasm and thyroid transcription factor-1 in the nuclei, both proteins of which are specific markers for the thyroid gland. Importantly, triiodothyronine (T3) was detected in the cultured medium of DH-14-3 cells, in which, however, thyroxine (T4) was undetectable. Moreover, DH-14-3 cells secreted interleukin-8, transforming growth factor-ß1, vascular endothelial growth factor, matrix metalloproteinase-1 and parathyroid hormone-related protein, all of which may be responsible for the aggressiveness or bone metastasis of PDTC. Thus, the production of these proteins may reflect the metastatic potential of this cell line. DH-14-3 cells also express CXC chemokine receptor-4 and epidermal growth factor receptor, and carry a missense mutation in the p53 tumor suppressor gene. In fact, transplantation of DH-14-3 cells into the back of nude mice resulted in the formation of tumors, thereby confirming the capability of tumorigenesis. DH-14-3 cells may be useful for investigating the biological features of PDTC and will contribute to the therapeutic study of thyroid cancer.

Global meta-analysis for controlling factors on carbon stable isotope ratios of lotic periphyton.

Carbon stable isotope ratios (δ(13)C) are widely used to trace resource transfer pathways, yet δ(13)C variation in freshwater autotrophs is not yet fully understood. We have analyzed data from 42 published studies, supplemented with some unpublished data, to show the determinants of lotic periphyton δ(13)C. At large spatial scales, we observed broad differences in periphyton δ(13)C among biomes and consistent longitudinal variation related to watershed area. Longitudinal increases in δ(13)C indicate the importance of in-stream processes on lotic carbon cycles and autotroph δ(13)C variation. At local spatial scales, periphyton δ(13)C was negatively related to canopy cover and water current velocity and positively related to chlorophyll a density. Autotroph δ(13)C varied among taxonomic groups. Cyanobacteria and red algae had significantly higher and lower δ(13)C than other taxa, respectively. A hierarchical model across spatial scales showed that local controls for periphyton δ(13)C were nested by regional controls, which suggested that productivity and CO(2) availability determine δ(13)C. Overall, our results reveal general patterns of periphyton δ(13)C and provide improved information for study design and the use of δ(13)C in isotopic mixing models in lotic food web studies.

Response of the Morus bombycis growing season to temperature and its latitudinal pattern in Japan.

Changes in leaf phenology lengthen the growing season length (GSL, the days between leaf budburst and leaf fall) under the global warming. GSL and the leaf phenology response to climate change is one of the most important predictors of climate change effect on plants. Empirical evidence of climatic effects on GSL remains scarce, especially at a regional scale and the latitudinal pattern. This study analyzed the datasets of leaf budburst and fall phenology in Morus bombycis (Urticales), which were observed by the agency of the Japan Meteorological Agency (JMA) from 1953 to 2005 over a wide range of latitudes in Japan (31 to 44° N). In the present study, single regression slopes of leaf phenological timing and air temperature across Japan were calculated and their spatial patterns using general linear models were tested. The results showed that the GSL extension was caused mainly by a delay in leaf fall phenology. Relationships between latitude and leaf phenological and GSL responses against air temperature were significantly negative. The response of leaf phenology and GSL to air temperature at lower latitudes was larger than that at higher latitudes. The findings indicate that GSL extension should be considered with regards to latitude and climate change.

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.

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.

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.

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.

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.

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.

Host-parasite interactions and global climate oscillations.

It is suspected that host-parasite interactions are influenced by climatic oscillations such as the North Atlantic Oscillation (NAO). However, the effects of climatic oscillations on host-parasite interactions have never been investigated. A long-term (1982-1999) dataset of the host snail Lymnaea stagnalis and trematode metacercariae infection has been collected for Lake Chany in Western Siberia. Using this dataset, we estimated the impact of the NAO on the population dynamics of hosts and parasites as well as their interactions. The results of general linear models showed that the abundance of dominant parasite species and the total parasite abundance significantly increased with NAO, with the exception of Moliniella anceps. Other climatic and biological factors were relatively weak to explain the abundance. There was no significant relationship between NAO and the population density of host snails. The prevalence of infection was related to the total abundance of parasites, but not to the NAO. Thus, the responses to the NAO differed between the host and parasites, indicating mismatching in host-parasite interactions. Therefore, climatic oscillations, such as the NAO, influence common parasitism.

Increased level of heme oxygenase-1 in rheumatoid arthritis synovial fluid.

We investigated the expression and localization of heme oxygenase-1 (HO-1) in synovial fluid and synovial tissue, and examined the stimulation of HO-1 production in rheumatoid synovial fibroblasts (RASFs). Synovial fluid samples were obtained from knee joints of 20 rheumatoid arthritis (RA) and 20 osteoarthritis (OA) patients, and concentration of HO-1 and matrix metalloproteinase-3 (MMP-3) were measured by enzyme-linked immunosorbent assay (ELISA). Synovial tissues obtained from RA or OA patients during total knee arthroplasty (TKA) were used for immunohistochemical analysis of HO-1. HO-1 production by RASFs in response to various cytokines was examined by ELISA. HO-1 levels in synovial fluid were higher in the RA group than in the OA group with significant difference (P < 0.001), and correlated with serum C-reactive protein (CRP) level (r = 0.80, P < 0.01) in the RA group. Higher levels of HO-1 were seen in the RA-L group (Larsen grade III-V) than in the RA-E (Larsen grade 0-II) group (P < 0.001). There was weak correlation between the levels of HO-1 protein and MMP-3 in synovial fluid in the RA group (r = 0.31, P < 0.01), while no positive correlation was observed in OA. Positive immunoreaction for HO-1 was observed in cells of synovial tissue including synovial fibroblasts and cells in synovial pannus. HO-1 protein levels in cultured media of RASFs were increased by stimulation by interleukin-1ß at 6 h and tumor necrosis factor-alpha at 12 h, but suppressed by interferon-gamma at 12 and 24 h. These results indicated that HO-1 expression in synovial tissue might be stimulated by inflammatory cytokines. The correlation of HO-1 concentration in synovial fluid with serum CRP and MMP-3 in joint fluid indicated that HO-1 might be useful as a marker of joint inflammation in RA patients.