Monitoring bloom-forming Aphanizomenon using environmental DNA metabarcoding: Method development, validation, and field application.

Harmful algal blooms (HABs) have emerged as a critical global environmental and ecological concern. Timely and accurate monitoring of the prevalent bloom-forming genera is crucial for HAB management. Conventional microscope-based methods are time-consuming, labor-intensive, and specialized expertise-dependent, often making them impractical for large-scale surveillance. Molecular methods, such as metabarcoding, provide efficient technical solutions; however, the lack of competent PCR primers and further field validation present obstacles to their wide use. Here, we successfully developed Aphanizomenon-specific primers and validated the application of environmental DNA (eDNA) metabarcoding for field-based monitoring of Aphanizomenon in 37 sites across lentic and lotic freshwater ecosystems in Beijing. The sensitivity and specificity tests of newly developed primers demonstrated high performance - comprehensive recovery of biodiversity in Aphanizomenon communities and high ratios (>95%) of Aphanizomenon sequences in datasets. We observed significant correlations between the sequence abundance derived from eDNA metabarcoding and the total cell density determined through microscopic identification across all the sampling sites, both in the spring (r = 0.8086, p < 0.0001) and summer (r = 0.7902, p < 0.0001), thus validating the utility of eDNA metabarcoding based on the newly developed primers for monitoring in the field. Further, we identified key environmental variables that were primary drivers responsible for the spatiotemporal distribution of Aphanizomenon abundance. These variables included temperature, total nitrogen, and dissolved oxygen in lentic ecosystems, and total phosphorus in lotic ecosystems. The method developed and validated here offers an accurate, efficient, and high-throughput tool for the monitoring of Aphanizomenon blooms in freshwater ecosystems.

Smaller islands, bigger appetites: evolutionary strategies of insular endemic skinks.

Competitive dietary and morphological divergence among co-occurring species are fundamental aspects of ecological communities, particularly on islands. Cabo Verde (~570 km west of continental Africa) hosts several endemic reptiles descended from common ancestors, with sympatric species exhibiting wide morphological variation and competing for limited resources. To explore the mechanisms of resource partitioning between coexisting species, DNA metabarcoding was used to compare the diets of large and small skinks, Chioninia vaillantii and Chioninia delalandii, in sympatric and allopatric contexts on Fogo Island and in a more competitive context on the small and resource-poor Cima Islet. The morphological variation of all populations was also examined to test the character displacement hypothesis and to compare the effect of different competitive scenarios. Results showed significant differences in diet and linear measurements between species and populations. The two sympatric populations of C. delalandii on Fogo and Cima showed similar changes in head morphology compared to the allopatric population, supporting character displacement. The effect of higher competitive pressure on Cima was evidenced by the increased morphological and dietary variation observed. This study demonstrates how sister species develop dietary adaptations/morphologies to maintain stable coexistence, especially in highly competitive scenarios, providing useful insights for effective conservation strategies.

The impact of extraction method and pollen concentration on community composition for pollen metabarcoding.

Premise: Plants and pollinators closely interact with each other to form complex networks of species interactions. Metabarcoding of pollen collections has recently been proposed as an advantageous method for the construction of such networks, but the extent to which diversity and community analyses depend on the extraction method and pollen concentration used remains unclear. Methods: In this study, we used a dilution series of two pollen mixtures (a mock community and pooled natural pollen loads from bumblebees) to assess the effect of mechanical homogenization and two DNA extraction kits (spin column DNA extraction kit and magnetic bead DNA extraction kit) on the detected pollen richness and community composition. Results: All species were successfully detected using the three methods, even in the most dilute samples. However, the extraction method had a significant effect on the detected pollen richness and community composition, with simple mechanical homogenization introducing an extraction bias. Discussion: Our findings suggest that all three methods are effective for detecting plant species in the pollen loads on insects, even in cases of very low pollen loads. However, our results also indicate that extraction methods can have a profound impact on the ability to correctly assess the community composition of the pollen loads on insects. The choice of extraction methodology should therefore be carefully considered to ensure reliable and unbiased results in pollen diversity and community analyses.

Dietary plasticity in small Arctic copepods as revealed with prey metabarcoding.

Objectives: Small copepods (<2 mm) compose an important constituent of the Arctic marine food web, but their trophic interactions remain largely unexplored, partly due to methodological limitations. Methods: We here characterize the prey of the abundant cyclopoid Oithona similis, harpacticoid Microsetella norvegica and calanoid Microcalanus spp. from the Arctic Barents Sea and Nansen Basin during four seasons using brute force prey metabarcoding of the 18S rRNA gene. Key findings: Chaetognaths were unexpectedly the most consistently identified taxa and composed 47% of all prey reads. Some taxa were seasonally important, including diatoms in April-May (43%), dinoflagellates in December (15%) and March (17%), and urochordates in August (20%). Compositional differences among species were also discernible, and the M. norvegica diet was significantly different from both O. similis and Microcalanus spp. The diets varied nevertheless more with season than species despite the inherent trophic traits that distinguish the ambush-predator O. similis, chemosensoric particle-chaser M. norvegica and current-feeding Microcalanus spp. Conclusions: Our results thus indicate that dietary plasticity is common in small Arctic copepods, regardless of their behaviors or strategies for finding sustenance. We further hypothesize that such plasticity is an important adaptation in systems where prey availability is highly seasonal.

Stable Isotope Signatures Illuminate Diverse Nutritional Strategies in Rhizoctonias and Their Orchid Partners.

Understanding the nutritional ecology of orchids, particularly those in symbiosis with rhizoctonias, presents a complex challenge. This complexity arises partly from the absence of macroscopic fruit bodies in rhizoctonias, which impedes the acquisition of their stable isotope data. In this study, we investigated the fungal associations and isotopic signatures in the pelotons of Stigmatodactylus sikokianus (associated with non-ectomycorrhizal [non-ECM] rhizoctonias) and Chamaegastrodia shikokiana (associated with ECM rhizoctonias). Our research reveals elevated levels of 13C enrichment in S. sikokianus plants and their pelotons, similar to those found in fully mycoheterotrophic orchids and their mycobionts. Interestingly, C. shikokiana plants and their pelotons exhibited even higher levels of 13C and 15N enrichment than many other fully mycoheterotrophic species. Our findings imply that both ECM and saprotrophic mycobionts, including certain rhizoctonias, can fulfill the carbon needs of highly mycoheterotrophic orchids. This finding also indicates that 13C enrichment can be an indicator of mycoheterotrophy in at least some rhizoctonia-associated orchids, despite the typically low 13C enrichment in non-ECM rhizoctonias. Our demonstration of partial mycoheterotrophy in S. sikokianus suggests a broader prevalence of this nutritional strategy among orchids, given that almost all orchids are associated with non-ECM rhizoctonias.

Different coexistence patterns between apex carnivores and mesocarnivores based on temporal, spatial, and dietary niche partitioning analysis in Qilian Mountain National Park, China.

Carnivores play key roles in maintaining ecosystem structure and function as well as ecological processes. Understanding how sympatric species coexist in natural ecosystems is a central research topic in community ecology and biodiversity conservation. In this study, we explored intra- and interspecific niche partitioning along spatial, temporal, and dietary niche partitioning between apex carnivores (wolf Canis lupus, snow leopard Panthera uncia, Eurasian lynx Lynx lynx) and mesocarnivores (Pallas's cat Otocolobus manul, red fox Vulpes vulpes, Tibetan fox Vulpes ferrilata) in Qilian Mountain National Park, China, using camera trapping data and DNA metabarcoding sequencing data. Our study showed that apex carnivore species had more overlap temporally (coefficients of interspecific overlap ranging from 0.661 to 0.900) or trophically (Pianka's index ranging from 0.458 to 0.892), mesocarnivore species had high dietary overlap with each other (Pianka's index ranging from 0.945 to 0.997), and apex carnivore and mesocarnivore species had high temporal overlap (coefficients of interspecific overlap ranging from 0.497 to 0.855). Large dietary overlap was observed between wolf and snow leopard (Pianka's index = 0.892) and Pallas's cat and Tibetan fox (Pianka's index = 0.997), suggesting the potential for increased resource competition for these species pairs. We concluded that spatial niche partitioning is likely to key driver in facilitating the coexistence of apex carnivore species, while spatial and temporal niche partitioning likely facilitate the coexistence of mesocarnivore species, and spatial and dietary niche partitioning facilitate the coexistence between apex and mesocarnivore species. Our findings consider partitioning across temporal, spatial, and dietary dimensions while examining diverse coexistence patterns of carnivore species in Qilian Mountain National Park, China. These findings will contribute substantially to current understanding of carnivore guilds and effective conservation management in fragile alpine ecosystems.

Rapid expansion and ecosystem health risk of invasive biopollutants dispersed by maritime traffic in French Polynesia.

The introduction of biopollutant species challenge ecosystem health and economy in remote islands. Here we checked the advance of invasive fouling species in five French Polynesian islands. Expansion of invasive species (Acantophora spicifera, Bugula neritina, Chthamalus proteus, Dendostrea frons) was detected using individual barcoding (COI for animals, RBLC for algae), and metabarcoding on biofouling (COI and 18S sequences). They were especially abundant in Port Phaeton (Tahiti), Bora Bora and Rangiroa atoll. Chthamalus proteus is a vector of bacterial diseases and may harm native French Polynesian mollusks. Dendostrea frons is a vector of Perkinsus, a parasite to which black pearl oysters, the mainstay of the Polynesian economy, are susceptible. High ecological and epidemiological risks were estimated for C. proteus and D. frons, and ecological risks also for A. spicifera and especially for B. neritina. Strengthening marine biosecurity measures is highly recommended to conserve these unique ecosystems and their associated services.

Widespread occurrence of fecal indicator bacteria in oligotrophic tropical streams. Are common culture-based coliform tests appropriate?

Monitoring of stream water quality is a key element of water resource management worldwide, but methods that are commonly used in temperate habitats may not be appropriate in humid tropical systems. We assessed the influence of four land uses on microbial water quality in 21 streams in the Panama Canal Watershed over a one-year period, using a common culture-based fecal indicator test and 16S rDNA metabarcoding. Each stream was located within one of four land uses: mature forest, secondary forest, silvopasture, and traditional cattle pasture. Culturing detected total coliforms and Escherichia coli across all sites but found no significant differences in concentrations between land uses. However, 16S rDNA metabarcoding revealed variability in the abundance of coliforms across land uses and several genera that can cause false positives in culture-based tests. Our results indicate that culture-based fecal indicator bacteria tests targeting coliforms may be poor indicators of fecal contamination in Neotropical oligotrophic streams and suggest that tests targeting members of the Bacteroidales would provide a more reliable indication of fecal contamination.

Do red tide events promote an increase in zooplankton biodiversity?

Red tides occurring off the southern coast of Korea impact the marine ecosystem and aquaculture industries. Zooplankton are crucial in the food web, connecting primary producers to higher predators and interact diversely with red tide organisms. This study explores dynamics of the zooplankton community over seven years including three red tide and four non-red tide years in Tongyeong using metabarcoding. In non-red tide years, zooplankton diversity showed typical seasonal patterns, increasing from June to early October. However, during red tide years, diversity remained high, with a shift in species composition-decreased Copepoda and increased Branchiopoda, Echinodermata, Malacostraca, and Annelida. Diversity indices were significantly higher in red tide years across all periods except for the richness in "after" that showed an insignificant higher value. The differences in zooplankton assemblages across periods were influenced by surface temperatures and the density of the red tide-causing alga Margalefidinium polykrikoides. Eight species emerged as indicator species and showed direct correlations with M. polykrikoides and among them, seven species were indicator species for red tide occurrence years. The ecological characteristics of M. polykrikoides blooms and their recurrent occurrences over several decades suggest that zooplankton may adapt to the toxins and use these blooms as spawning cues. Overall, this study provides comprehensive understanding on changes in zooplankton communities during red tide events, offering novel insights into their ecology.

Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability.

Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing "green" season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a 2-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons.

Seasonal dynamics, Leishmania diversity, and nanopore-based metabarcoding of blood meal origins in Culicoides spp. in the newly emerging focus of leishmaniasis in Northern Thailand.

BACKGROUND: Clinical cases of leishmaniasis caused by Leishmania (Mundinia) parasites have been increasingly reported in Southeast Asia, particularly Thailand. Recent evidence has shown that Leishmania (Mundinia) parasites successfully developed into infective metacyclic promastigotes in Culicoides biting midges, strongly supporting their putative role in disease transmission. However, Culicoides diversity, host preference, and Leishmania prevalence in endemic areas remain largely unknown. METHODS: We investigated the seasonal dynamics, infection prevalence, and blood meal identification of Culicoides collected from the emerging focus of visceral leishmaniasis in Lampang Province, Northern Thailand, during 2021-2023. Midge samples were molecularly screened for Leishmania using SSU rRNA-qPCR and ITS1-PCR, followed by Sanger plasmid sequencing, and parasite haplotype diversity was analyzed. Host blood meal origins were comparatively identified using host-specific Cytb-PCRs and a nanopore-based metabarcoding approach. RESULTS: A total of 501 parous and gravid females and 46 blood-engorged ones belonging to at least 17 species of five subgenera (Remmia, Trithecoides, Avaritia, Hoffmania, and Meijerehelea) and two species groups (Shortti and Calvipalpis) were collected with temporal differences in abundance. Leishmania was detected by SSU rRNA-qPCR in 31 samples of at least 11 midge species, consisting of Culicoides oxystoma, C. guttifer, C. orientalis, C. mahasarakhamense, C (Trithecoides) spp., C. innoxius, C. shortti, C. arakawae, C. sumatrae, C. actoni, and C. fulvus, with the overall infection prevalence of 5.7%. The latter six species represent the new records as putative leishmaniasis vectors in Northern Thailand. The ITS1-PCR and plasmid sequencing revealed that Leishmania martiniquensis was predominantly identified in all qPCR-positive species, whereas L. orientalis was identified only in three C. oxystoma samples. The most dominant haplotype of L. martiniquensis in Thailand was genetically intermixed with those from other geographical regions, confirming its globalization. Neutrality test statistics were also significantly negative on regional and country-wide scales, suggesting rapid population expansion or selective sweeps. Nanopore-based blood meal analysis revealed that most Culicoides species are mammalophilic, with peridomestic and wild mammals (cow, pig, deer, and goat-like species) and humans as hosts, while C. guttifer and C. mahasarakhamense fed preferentially on chickens. CONCLUSIONS: This study revealed seasonal dynamics and sympatric circulation of L. martiniquensis and L. orientalis in different species of Culicoides. Evidence of human blood feeding was also demonstrated, implicating Culicoides as putative vectors of human leishmaniasis in endemic areas. Further research is therefore urgently needed to develop vector control strategies and assess the infection status of their reservoir hosts to effectively minimize disease transmission.

Evaluating the quantitative performance of environmental DNA metabarcoding for freshwater zooplankton community: a case study in Lake Biwa, Japan.

Zooplankton monitoring is important for understanding their population dynamics and life history, ecosystem health, and environmental changes. Compared with traditional morphological identification, environmental DNA (eDNA) analysis allows for more sensitive and efficient monitoring of zooplankton diversity. Previous eDNA studies have primarily used metabarcoding approaches to reveal their richness and composition, whereas its performance in predicting zooplankton abundance remains understudied. We conducted water and bulk sampling in Lake Biwa, Japan, showing that the number of sequence reads by metabarcoding moderately correlated with eDNA concentrations estimated by quantitative real-time PCR (qPCR). In addition, the eDNA read number was significantly related to cladoceran and copepod abundance estimated by microscopy sorting, although there remained too much uncertainty in the read-abundance relationship. Moreover, there was a significant difference in species composition between eDNA metabarcoding and sorting. Although our results indicated the potential applicability of eDNA metabarcoding for quantifying multiple zooplankton abundance, several methodological validations in eDNA metabarcoding would also be required to optimize its performance in the future.

Pollinator behaviour and prevalence of the anther smut Antherospora vindobonensis in its host, the Hungarian two-leaf squill (Scilla vindobonensis).

Anther smuts are fungal diseases that have detrimental effects on the biology of their host plants. We investigated the transmission of Anther smut Antherospora vindobonensis to its host, Scilla vindobonensis under natural and laboratory conditions. Plants flowering early in spring were less vulnerable to disease (∼ 20-30% of plants which appeared early in the season were diseased) than flowers that bloom at the end of the season (∼ 60% of plants which appeared late in the season were diseased) which contradicts the patterns observed for other anther smuts species. Diseased plants showed thicker stems, lower nectar production and smaller flower radius than healthy plants. The disease prevalence in S. vindobonensis was not influenced by plant density. The production of spores in diseased flowers was 125 times higher than the production of pollen in healthy flowers. The number of pollen grains attached to pollinator bodies from healthy plants under controlled conditions was similar to the number of spores attached from diseased plants. Experienced honeybees in the field showed almost identical preferences for healthy plants (65%) over diseased ones, as did naïve bumblebees under controlled laboratory conditions (69%). eDNA metabarcoding revealed that healthy flowers attracted a significantly higher number of arthropod species (M = 6.23, SE = 1.48) than diseased flowers (M = 2.32, SE = 0.31). Strong seasonal differences in the risk of infection suggest that S. vindobonensis solves the trade-off between low pollinator availability and low risk of infection at the beginning of the season and high risk of infection and high pollinator availability at the end of season. By reproducing early in the season, plants can reduce the risk of disease.

Plastisphere in an Antarctic environment: A microcosm approach.

Microplastics are present even in remote regions like the Southern Ocean. Once in the water, they are rapidly colonised by marine microorganisms, forming the plastisphere. To address this issue in Antarctic waters, we conducted a microcosm experiment by incubating polypropylene, polyethylene, polystyrene microplastic pellets, and quartz for 33 days on Livingston Island, South Shetland Islands, Antarctica. We analysed plastic colonisation and plastisphere dynamics using scanning electron microscopy, flow cytometry, bacterial cultivation, qPCR, and 16S rRNA gene metabarcoding. Our results show rapid and consistent colonisation, although biomass formation was slightly slower than in other oceans, indicating unique environmental constraints. Time was the main factor influencing biofilm communities, while plastic polymer types had little effect. We observed a transition in microbial communities from early- to late-biofilm stages between days 12 and 19. Additionally, we described the bacterial plastisphere composition in this Antarctic environment, including the presence of hydrocarbon-degrading bacteria.

Inferences based on diatom compositions improve estimates of nutrient concentrations in streams.

Nutrient concentrations in streams vary strongly with flow conditions, and routinely gathered field measurements of nutrients reflect this variability. Diatom assemblage composition has been used in previous studies to infer nutrient concentrations, and because diatoms integrate nutrient concentrations over longer periods of time, diatom inferences may be less susceptible to fluctuations in streamflow. We tested this hypothesis by leveraging differences in the flashiness of streams across a large continental data set. More specifically, we tested whether the variabilities of direct measurements and diatom inferences of dissolved phosphorus and nitrate were greater in flashy versus non-flashy streams. We further considered whether models linking landscape predictor variables to nutrient concentrations yielded consistent results across flashy and non-flashy streams. Our analysis indicated that measured nutrient concentrations were more variable in flashy compared to non-flashy streams and that landscape models identified different important predictors of nutrient concentrations when fit using data from flashy vs. non-flashy streams. In contrast, variabilities of diatom-inferred nutrient concentrations were similar among stream types, as were the important predictor variables (e.g., manure application rates for nitrate and number of wet days for dissolved phosphorus). These analyses indicate that use of diatom-inferred nutrient concentrations can potentially improve efforts to quantify stream nutrient concentrations.

Foraging of Honeybees from Different Ecological Areas Determined through Melissopalynological Analysis and DNA Metabarcoding.

The environment significantly impacts the lives of bees and their feeding. This study aimed to investigate bee foraging using melissopalynological analysis and DNA metabarcoding in intensive farming, reserved, and urbanized areas. The highest alpha diversity was observed in the reserved and intensive farming areas. The urbanized area had less diversity. In the intensive farming area, Sinapis, Helianthus, and Fagopyrum predominated; in the reserved area, Melilotus, Helianthus, and Brassica predominated. In the urbanized area, garden plants, namely radish (Raphanus sativus) and cucumber (Cucumis hystrix), and agricultural plants, namely soybean (Glycine max) and melon (Cucumis melo), were often found. The most significant agreement was between the rbcL and the melissopalynological analysis. The ITS2 revealed equal matches with both rbcL and melissopalynology, but this marker missed or underestimated some genera. Trifolium pretense and Brassica nigra were identified simultaneously by the melissopalinology method and two genetic markers in DNA metabarcoding. The species Convolvulus arvensis, Melilotus officinalis, Echium vulgare, Brassica rapa, Helianthus divaricatus, and Onobrychis viciifolia were found in all ecological areas. Imperfect databases impose some limits in the identification of some taxa using metabarcoding. The further research and expansion of plant databases is needed. Studying the food preferences of bees in different environmental conditions and landscapes is necessary to develop measures to preserve their populations.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity.

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

Fungal Diversity in an Undisturbed Andean Páramo Soil in Quimsacocha (Ecuador).

The Andean Páramo is an environment known for its high biodiversity; however, due to its remote location and difficult access, it is still relatively poorly studied. The aim of this work was to explore the fungal biodiversity of Ecuadorian Páramo soils in the undisturbed natural reserve of Quimsacocha through ITS metabarconding with an MiSeq platform. This analysis revealed the presence of 370 fungal Amplicon Sequence Variants (ASVs), mainly composed by Ascomycota, Mortierellomycota and Basidiomycota. The biodiversity had a great variability among the 19 samples, but the soil humidity proved to be a significant driver of diversity in the relatively dry environment of Páramo. Some of most abundant fungal genera have important relationships with plant roots. This work represents the first glimpse into the complex biodiversity of soil fungi in this understudied area, and further studies will be needed to better understand the fungal biodiversity in this region, together with the development of necessary measures of environmental protection.

Shifts in Fusarium Communities and Mycotoxins in Maize Residues, Soils, and Wheat Grains throughout the Wheat Cycle: Implications for Fusarium Head Blight Epidemiology.

Fusarium Head Blight (FHB), predominantly caused by Fusarium species, is a devastating cereal disease worldwide. While considerable research has focused on Fusarium communities in grains, less attention has been given to residues and soil, the primary inoculum sources. Knowledge of Fusarium spp. diversity, dynamics, and mycotoxin accumulation in these substrates is crucial for assessing their contribution to wheat head infection and the complex interactions among Fusarium communities throughout the wheat cycle. We monitored six minimum-tillage wheat fields, with maize as the preceding crop, over two years. Soils, maize residues, and wheat grains were sampled at four stages. Fusarium composition was analyzed using a culture-dependent method, species-specific qPCR, and EF1α region metabarcoding sequencing, enabling species-level resolution. The Fusarium communities were primarily influenced by substrate type, accounting for 35.8% of variance, followed by sampling location (8.1%) and sampling stage (3.2%). Among the 32 identified species, F. poae and F. graminearum dominated grains, with mean relative abundances of 47% and 29%, respectively. Conversely, residues were mainly contaminated by F. graminearum, with a low presence of F. poae, as confirmed by species-specific qPCR. Notably, during periods of high FHB pressure, such as in 2021, F. graminearum was the dominant species in grains. However, in the following year, F. poae outcompeted F. graminearum, resulting in reduced disease pressure, consistent with the lower pathogenicity of F. poae. Source Tracker analysis indicated that residues were a more significant source of Fusarium contamination on wheat in 2021 compared to 2022, suggesting that F. graminearum in 2021 primarily originated from residues, whereas F. poae's sources of infection need further investigation. Additionally, multiple mycotoxins were detected and quantified in maize residues during the wheat cycle, raising the question of their ecological role and impact on the soil microbiota.

Co-metabolic growth and microbial diversity: Keys for the depletion of the α, δ, ß and γ-HCH isomers.

The objective of this study was the isolation and enrichment of microbiomes capable of degrading the main hexachlorocyclohexane isomers quantified in environmental matrices, e.g.: the α, δ, ß and γ-HCH isomers. Four microbiomes were isolated and enriched from an HCH-contaminated dumpsite in Italy, both in the presence of HCH isomers (1:1:1:1) as the sole carbon sources and under co-metabolic growth conditions in presence of glucose (0.1 % v/v). The microbiomes were assessed for their relevant metabolic capabilities. A quantitative metabarcoding approach was employed to analyze the compositional evolution of the four microbiomes during the enrichment phase and the phase of testing of the HCH isomers degradation kinetics. The use of a co-metabolic substrate during enrichment process was essential for selecting microbiomes with higher biodiversity. All microbiomes efficiently degraded the α, δ, and γ-HCH isomers. The highest efficiency in the ß-HCH degradation capacity was positively correlated to the highest biodiversity of the microbiome, and the involvement of Chryseobacterium and Asinibacterium sps. have been proposed for a recorded increment in bacterial load during the HCH degradation process.