Search Results (786)

The waters surrounding the Five West Sea Islands of South Korea are ecologically important but challenging to survey due to their location within a strategic military zone, strong tidal currents, and significant tidal variation. To assess the fish community in this region, we conducted Korea’s first parallel investigation combining traditional bottom trawl surveys with environmental DNA (eDNA) metabarcoding. Sampling was performed at 10 stations in March, May, and August 2023, and the relationship between fish species occurrence and environmental variables (water temperature, salinity, and depth) was examined. Dominant trawl-caught species included Engraulis japonicus, Johnius grypotus, Coilia nasus, and Okamejei kenojei, each showing seasonal migration and spawning patterns associated with temperature changes. eDNA analysis detected nine additional species absent from trawl catches, such as Ilisha elongata and Thamnaconus modestus, demonstrating its sensitivity in identifying both migratory and sedentary taxa. Our findings confirm that eDNA surveys can complement traditional sampling, improving biodiversity assessment in regions with limited accessibility and complex oceanographic conditions. Full article

The Indian Ocean is globally significant in terms of capture fisheries, and understanding the species composition of fish in the Indian Ocean is of great importance for the protection and development of its fishery resources. While coastal fish communities in the Indian Ocean are relatively well-documented, studies on pelagic zones remain sparse, especially for non-target species constituting fishery bycatch. Traditional biodiversity surveys rely on labor-intensive, inefficient trawling methods. To address these limitations, this study aims to apply environmental DNA (eDNA) metabarcoding for a species diversity survey in the Western Indian Ocean, offering a more reliable, efficient, and non-invasive alternative to traditional methods. The results will provide important insights into the region’s fish biodiversity, supporting sustainable management and conservation of fisheries resources in the area. Samples were collected from 130 stations in different water layers in the Western Indian Ocean, and species diversity was analyzed through 12S rRNA gene amplicon sequencing. The results showed that 98 fish species were detected from 176 seawater eDNA samples, belonging to two classes (Actinopteri and Chondrichthyes), 20 orders, 35 families, and 60 genera. Within a depth range of 300 m, there were no significant differences in species diversity parameters among samples from different depths. The orders with the highest relative abundance detected include Scombriformes, Aulopiformes, and Myctophiformes. The species with the highest relative abundance include Thunnus albacares, Alepisaurus ferox, Xiphias gladius, Diaphus fragilis, Decapterus macarellus, Thunnus maccoyii, and Platycephalus cultellatus. The species composition and relative abundance of economic species observed in this study showed, as expected, differences from fishery catch statistics. These results suggest that eDNA technology can not only monitor marine fish diversity more efficiently but also complement the lack of fisheries data. Integrating eDNA technology into routine monitoring in the Western Indian Ocean in the future could promote sustainable management of fisheries resources in the region. Full article

Invasive Phytophthora species are increasingly impacting UK landscapes. Most recently, cryptic outbreaks of P. pluvialis Reeser, Sutton & E. Hansen have occurred on western hemlock and Douglas fir at several forest sites across Britain. To better understand the ubiquity and life cycle of this pathogen in British forests and the assemblages of co-inhabiting Phytophthora species, metabarcoding and baiting methodologies were applied to soil, stream water, and rainwater samples collected over a full calendar year from seventeen sites across Britain. Thirty-five Phytophthora species were detected across all sites, substrates, and detection methods, with most detections occurring in stream water by metabarcoding. The three most frequently detected species were (1) P. pluvialis, (2) P. gonapodyides H.E. Petersen & Buisman and (3) P. ramorum Werres, De Cock & Man in ‘t’ veld. Other species detected included the regulated pathogens P. austrocedri Greslen & Hansen, P. kernoviae Brasier, Beales & S.A. Kirk and P. lateralis Tucker & Milbraith, as well as P. ornamentata Scanu, Linald & T. Jung, a new species record for the UK. Phytophthora pluvialis was most frequently detected in March, with rainfall trap metabarcoding data suggesting that aerial dissemination occurs predominantly in late winter/early spring. Consistent detections of P. pluvialis in soil by metabarcoding indicate the potential for soilborne transfer of this pathogen by animal or human vectors, including equipment or machinery in forest operations. The study’s findings are discussed in relation to understanding how P. pluvialis spreads and the approaches needed to address key knowledge gaps in relation to inoculum sources. The results provide a baseline for Phytophthora diversity in British commercial forests, facilitating a greater understanding of typical and unusual trends in species assemblages. This study also consolidates the value of metabarcoding as an effective surveillance tool for Phytophthora in commercial forests. Full article

River water enters human life in various ways, with many disease outbreaks closely linked to contaminated sources. This study collected water samples from the Perak River in Malaysia, extracted environmental DNA (eDNA), and analyzed biological communities using metabarcoding and sequencing techniques to assess the local environmental health of the river. Through 16S rRNA sequencing, 4045 bacterial OTUs were identified, while 18S rRNA sequencing revealed 3422 eukaryotic OTUs, highlighting the diverse microbial and eukaryotic communities in the Perak River. The results showed certain organisms such as Serratia marcescens and Strombidium with potentially abnormal abundance, based on comparisons with other studies, suggesting possible organic and heavy metal pollution. Additionally, 35 potential pathogens, including bacteria, fungi, and parasites, were detected in the samples, all of which pose potential threats to human and animal health. While most bacterial pathogens are opportunistic, their potential risks should not be overlooked. These findings provide valuable insights into the river’s ecological status and help guide targeted conservation, surveillance and pollution management strategies. Ultimately, this study highlights environmental health issues through biodiversity analysis and identifies pathogens, contributing to the protection of human and animal health and aligning with the principles of the One Health approach. Full article

Hybridization is common among minnows and shiners in the family Leuciscidae, and mitonuclear discordance can reveal evidence of historical hybridization and introgression events that have shaped extant species and populations. We have identified a notable case of serial mitogenome replacement in populations of two shiner species, Luxilus zonatus and L. chrysocephalus, which are syntopic in drainages throughout the northern and eastern Ozark Interior Highlands of North America. These mitogenome replacement events involved L. zonatus acquiring the mitogenome of L. chrysocephalus, and populations of L. chrysocephalus acquiring the mitogenome of an allopatric congeneric species, L. cornutus. The latter species has a more northern distribution that was likely shifted southward by glacial advances during the Pleistocene. The geographic extent of mitogenome replacements in both species spans multiple separate drainages encompassing most of the major river systems that comprise the northern and eastern Ozark Highlands. We attribute these patterns to shifting species distributions, which were impacted by multiple glacial advances and coincident geomorphological changes to Ozark Highland drainages throughout the Pleistocene. The serial nature of mitogenome replacements in L. zonatus and L. chrysocephalus may exclude a role for natural selection in these introgression events, but the dynamic shifts in species distributions and gene flow connections throughout the Pleistocene may have favored an invasion-with-hybridization model that predicts massive asymmetric introgression between invading and resident species. These results have applied significance for eDNA metabarcoding methods of biodiversity assessment in Ozark streams, as they are dependent on mitogenome detections. Full article

Assessing fish biodiversity is essential for freshwater ecosystem conservation. This study compares environmental DNA (eDNA) metabarcoding and traditional morphological surveys to investigate fish communities in the Gaya River, China. A total of 42 fish species were identified, with 13 detected only by eDNA, 7 exclusively by morphology, and 11 by both methods. A comparative analysis of species composition, functional diversity, and phylogenetic diversity revealed significant differences between the two approaches. Notably, eDNA data indicated higher phylogenetic diversity (PD), while morphological surveys captured greater functional evenness (FEve). Multivariate analyses indicated that total phosphorus (TP), total suspended solids (TSS), electrical conductivity (EC), temperature (T), and pH significantly influenced fish community composition, while dissolved oxygen (DO) was a key driver of species richness (SR), functional richness (FRic), and PD. These findings highlight the methodological differences and complementary strengths of eDNA and morphological approaches in biodiversity assessments. By providing comparative insights into fish diversity patterns, this study underscores the importance of using multi-method approaches to improve freshwater biodiversity monitoring and conservation strategies. Full article

Silvicultural practices significantly influence the diversity and composition of soil fungal communities, which play crucial roles in maintaining forest ecosystem functionality. This study evaluated the impact of three silvicultural treatments, consisting of liberation cutting, first thinning, and second thinning, on rhizospheric fungal and ectomycorrhizal (ECM) fungi communities in Pinus forests located in Puebla, Mexico. Using high-throughput metabarcoding of the internal transcribed spacer (ITS2) region, we identified 346 fungal genera across all treatments, with Ascomycota and Basidiomycota being the dominant phyla. Alpha diversity indices revealed a trend toward higher fungal richness for first thinning, followed by liberation cutting and lower values for second thinning. A beta diversity analysis demonstrated significant shifts in the fungal community composition across treatments, highlighting the influence of the thinning intensity. The proportions of different functional guilds were consistent across the treatments. However, compositional differences were observed, mainly in soil and wood saprotrophs and in pathogenic taxa. Liberation cutting showed enrichment in ECM taxa such as Russula and Cenococcum, whereas Tuber, Humaria, and Tricholoma were decreased for first thinning and Russula was decreased for second thinning. These findings underscore the need for sustainable forest management practices that balance productivity with the conservation of fungal biodiversity to ensure ecosystem stability and functionality. Full article

Fungicide treatment is one of the most common methods for controlling fungal plant diseases. However, many phytopathogenic fungi develop resistance to fungicides. Addressing this agriculturally important issue requires comprehensive investigations into fungicide resistance. Our study aims to assess the degree and prevalence of resistance to carbendazim—one of the most widely used fungicides—in populations of Microdochium nivale, the causal agent of the deleterious plant disease pink snow mold; to explore possible relationships between carbendazim resistance and physiological and genetic traits; and to gain insight into the molecular basis of carbendazim resistance in this species. We showed that carbendazim resistance is widespread in the analyzed M. nivale populations, and that the application of carbendazim increases the proportion of resistant strains. Nevertheless, carbendazim-resistant strains are present at high relative abundance in populations that have never been exposed to fungicides. Carbendazim resistance in M. nivale is strongly associated with sequence variations in the β-tubulin gene, resulting in amino acid sequence variability that leads to differential affinity for carbendazim. Additionally, we propose a metabarcoding-based approach employing a genetic marker linked to a specific phenotypic trait to assess the ratio of genotypes with contrasting properties within a particular fungal species in environmental communities. Full article

The genus Aspergillus, widely distributed across natural and urban environments, may cause allergies and opportunistic infections such as chronic or invasive pulmonary aspergillosis. Its high pathogenic potential for immunocompromised patients, together with the alarming increase of azole resistance reported in clinical and environmental isolates, claims urgent actions to assess and control the Aspergillus community in hospital environments. To contribute to that, here, we combine a large environmental survey covering numerous air and surface samples from different zones of three hospitals in Spain, with an integrated approach including general and selective culture- and eDNA-based analyses. Despite the high prevalence of Aspergillus observed, present in almost all indoor zones (mostly in air but also on surfaces) of the three hospitals, its relative abundance in the whole fungal community was limited and dependent on the used methods, with median values ranging from 1.4% (eDNA data) and 6.8% (cultivation at 28 °C) to 28.3% (cultivation at 37 °C). Remarkably, the most protected zones (intensive care units) showed the highest proportion of Aspergillus eDNA sequences. A total of 32 species belonging to 10 Aspergillus sections were molecularly identified, including well-known causal agents of invasive pulmonary infections such as A. fumigatus, A. flavus, A. terreus, A. niger, A. oryzae, A. sydowii, and A. tubingensis. This highlights the importance of such environmental assessments for monitoring and controlling the fungal burden in hospitals. Full article

Tree plantations can help reverse the negative impacts of deforestation and land degradation worldwide, and soil microbial communities play key roles in tree growth and productivity. We studied microbial communities in the bulk soil of five native species monoculture plantations in the Republic of Panamá to assess how bacteria and fungi were affected by soil chemistry and plant identity after seven years of tree growth. Relative to the other species, Terminalia amazonia accumulated over three times the aboveground biomass and had lower mortality. Soil nutrients, especially phosphorus, were low, and we found no differences in soil chemistry across the five plantation types. Similarly, there was no difference in alpha diversity of the soil microbial communities across plantation types, and the bacterial communities showed no compositional variation or enrichment of any individual taxa. However, soil fungal communities differed in T. amazonia plantations as compared to the others, exhibiting enrichment or absence of specific taxa of arbuscular mycorrhizal fungi and putative phytopathogens. Our results suggest that T. amazonia may associate with certain microbial taxa that help it overcome low nutrient availability in these habitats. Consideration of plant–soil–microbe interactions in restoration efforts may facilitate tree growth and help to promote climate resilient forested areas. Full article

Coral reef degradation has spurred the development of artificial structures to mitigate losses in coral cover. These structures serve as substrates for coral transplantation, with the expectation that growing corals will attract reef-associated taxa—while the substrate’s ability to directly support biodiversity is often neglected. We evaluated a novel 3D-printed modular tile made of porous terra cotta, designed with complex surface structures to enhance micro- and cryptic biodiversity, through a restoration project in Hong Kong. Over four years, we monitored 378 outplanted coral fragments using diver assessments and photography, while biodiversity changes were assessed through visual surveys and eDNA metabarcoding. Coral survivorship was high, with 88% survival after four years. Visual surveys recorded seven times more fish and almost 60% more invertebrates at the restoration site compared to a nearby unrestored area. eDNA analyses revealed a 23.5% higher eukaryote ASV richness at the restoration site than the unrestored site and 13.3% greater richness relative to a natural reference coral community. This study highlights the tiles’ dual functionality: (1) supporting coral growth and (2) enhancing cryptic biodiversity, an aspect often neglected in traditional reef restoration efforts. Our findings underscore the potential of 3D-printed ceramic structures to improve both coral restoration outcomes and broader reef ecosystem recovery. Full article

Assessing fishery resources is crucial for sustainable marine ecosystem management and the operation of fisheries. This study integrates trawl surveys, environmental DNA (eDNA) analysis, and scientific echo sounder techniques to analyze the fishery resource distribution of and seasonal variations in the East China Sea. Surveys were conducted in April, July, August, and November 2022, utilizing bottom trawl sampling, eDNA metabarcoding, and acoustic data collection. The results revealed temporal differences in species composition, with crustaceans dominating in terms of abundance and fish species in biomass. The integration of eDNA analysis provided broader species detection, including cryptic and pelagic species, while acoustic techniques enabled large-scale resource assessment. However, discrepancies between methods highlighted the need for methodological refinement. Dominant species exhibited seasonal variation, with Portunus trituberculatus prevailing in spring (April), Trachurus japonicus and Scomber japonicus in summer (July–August), and Pampus argenteus in late autumn (November). A comparative analysis revealed that eDNA is sensitive to pelagic and cryptic species, trawl surveys effectively detect demersal fish, and acoustics allow for broad-scale biomass estimation, highlighting the complementary value of method integration. Full article

Harmful algae are transported in various compartments of maritime vessels, making ports with heavy maritime traffic potential hotspots for their introduction and spread. In this study, we investigate the port of Papeete (Tahiti, French Polynesia), a key hub for numerous South Pacific shipping routes. Using metabarcoding on DNA extracted from water samples (environmental DNA, eDNA) we identified 21 species of harmful algae comprising to Bacillariophyceae (4), Dinophyceae (14), and Haptophyta (3 species). Three of those species are directly associated with fish mortality events without recognized toxigenic capacity. The remaining harmful algae species are known to produce a wide range of toxins, like the ciguatoxin produced by endemic Gambierdiscus sp., domoic acid, haemolysins, yessotoxins, and others. Health risks such as ciguatera and paralytic shellfish poisoning were identified. An increase in Gambierdiscus frequency in Papeete port waters was parallel to an increase in ciguatera fish poisoning events in Tahiti, which suggests the value of eDNA analysis for early warning of harmful algae presence. Management measures, including banning fishing near the ports, could prevent public health risks associated with harmful algae blooms. Full article

Although 5–20% of global crop production is lost to arthropod damage, current biomonitoring programs are extremely limited. This study evaluates the feasibility of using metabarcoding to assess overall insect diversity and detect pest species in agricultural settings. It introduces a curated DNA barcode reference library for Canadian insects that are agricultural pests and applies it to metabarcoding data from the analysis of Malaise trap samples from two experimental farms in Southern Ontario. A total of 7707 arthropod species were collected across the two farms, and projections indicate that another 4000 await detection. These taxa included 231 registered pest species. The composition of the overall arthropod community composition was more heavily influenced by site location than crop type, but pest species composition was influenced by the crop. This study confirms that metabarcoding enables the evaluation of the species composition of arthropod communities in agroecosystems, allowing pest species to be tracked. Full article

Microbial communities, as critical functional components of riverine ecosystems, play a pivotal role in biogeochemical cycles and water quality regulation. The South-to-North Water Diversion Middle Route Project (SNWD-MRP) is a major cross-basin water transfer initiative, and bacteria are essential for the stability of water quality in the project. This study employed environmental DNA (eDNA) metabarcoding targeting the 16S rRNA gene to investigate spatiotemporal variations in water quality and bacterial communities along the SNWD-MRP during summer and winter. Integrated analyses, including redundancy analysis (RDA), Mantel tests, and ecological network modeling, were applied to unravel the driving mechanisms of microbial succession. The water quality along the SNWD-MRP is generally classified as Grade I, with significant seasonal variations in water quality parameters and microbial community composition. In the summer, higher temperatures lead to an increased abundance of cyanobacteria. In contrast, during the winter, lower water temperatures and higher dissolved oxygen levels result in the dominance of Pseudomonas and Bacillota species. RDA identified the permanganate index as the primary driver of microbial composition across seasons, with total phosphorus and total nitrogen having a greater influence in winter. Mantel tests highlighted significant correlations between Cyanobacteria and total phosphorus during winter. Ecological network analysis revealed that the complexity and connectivity of the winter network increased, likely due to suitable nutrient levels rendering the microbial network more complex and stable. These findings underscore the synergistic effects of temperature and nutrient availability on microbial succession, providing actionable insights for optimizing water quality management and ecological stability in large-scale water diversion systems. Full article