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Microbial fuel cell based on nitrogen-fixing Rhizobium anhuiense bacteria /
No full textIn this study, the nitrogen-fixing, Gram-negative soil bacteria Rhizobium anhuiense was successfully utilized as the main biocatalyst in a bacteria-based microbial fuel cell (MFC) device. This research investigates the double-chambered, H-type R. anhuiense-based MFC that was operated in modified Norris medium (pH = 7) under ambient conditions using potassium ferricyanide as an electron acceptor in the cathodic compartment. The designed MFC exhibited an open-circuit voltage (OCV) of 635 mV and a power output of 1.07 mW m−2 with its maximum power registered at 245 mV. These values were further enhanced by re-feeding the anode bath with 25 mM glucose, which has been utilized herein as the main carbon source. This substrate addition led to better performance of the constructed MFC with a power output of 2.59 mW m−2 estimated at an operating voltage of 281 mV. The R. anhuiense-based MFC was further developed by improving the charge transfer through the bacterial cell membrane by applying 2-methyl-1,4-naphthoquinone (menadione, MD) as a soluble redox mediator. The MD-mediated MFC device showed better performance, resulting in a slightly higher OCV value of 683 mV and an almost five-fold increase in power density to 4.93 mW cm−2. The influence of different concentrations of MD on the viability of R. anhuiense bacteria was investigated by estimating the optical density at 600 nm (OD600) and comparing the obtained results with the control aliquot. The results show that lower concentrations of MD, ranging from 1 to 10 μM, can be successfully used in an anode compartment in which R. anhuiense bacteria cells remain viable and act as a main biocatalyst for MFC applications
The bacterial microbiota of edible insects Acheta domesticus and Gryllus assimilis revealed by high content analysis /
No full textIn the concept of novel food, insects reared under controlled conditions are considered mini livestock. Mass-reared edible insect production is an economically and ecologically beneficial alternative to conventional meat gain. Regarding food safety, insect origin ingredients must comply with food microbial requirements. House crickets (Acheta domesticus) and Jamaican field crickets (Gryllus assimilis) are preferred insect species that are used commercially as food. In this study, we examined cricket-associated bacterial communities using amplicon-based sequencing of the 16S ribosomal RNA gene region (V3–V4). The high taxonomic richness of the bacterial populations inhabiting both tested cricket species was revealed. According to the analysis of alpha and beta diversity, house crickets and Jamaican field crickets displayed significantly different bacterial communities. Investigation of bacterial amplicon sequence variants (ASVs) diversity revealed cricket species as well as surface and entire body-associated bacterial assemblages. The efficiency of crickets processing and microbial safety were evaluated based on viable bacterial counts and identified bacterial species. Among the microorganisms inhabiting both tested cricket species, the potentially pathogenic bacteria are documented. Some bacteria representing identified genera are inhabitants of the gastrointestinal tract of animals and humans, forming a normal intestinal microflora and performing beneficial probiotic functions. The novel information on the edible insect-associated microbiota will contribute to developing strategies for cricket processing to avoid bacteria-caused risks and reap the benefits
Global maps of soil temperature /
No full textResearch in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications
Two sides of one medal: Arable weed vegetation of Europe in phytosociological data compared to agronomical weed surveys /
No full textQuestions: Two scientific disciplines, vegetation science and weed science, study arable weed vegetation, which has seen a strong diversity decrease in Europe over the last decades. We compared two collections of plot-based vegetation records originating from these two disciplines. The aim was to check the suitability of the collections for joint analysis and for addressing research questions from the opposing domains. We asked: are these collections complementary? If so, how can they be used for joint analysis?. Location: Europe. Methods: We compared 13 311 phytosociological relevés and 13 328 records from weed science, concerning both data collection properties and the recorded species richness. To deal with bias in the data, we also analysed different subsets (i.e., crops, geographical regions, organic vs conventional fields, center vs edge plots). Results: Records from vegetation science have an average species number of 19.0 ± 10.4. Metadata on survey methodology or agronomic practices are rare in this collection. Records from weed science have an average species number of 8.5 ± 6.4. They are accompanied by extensive methodological information. Vegetation science records and the weed science records taken at field edges or from organic fields have similar species numbers. The collections cover different parts of Europe but the results are consistent in six geographical subsets and the overall data set. The difference in species numbers may be caused by differences in methodology between the disciplines, i.e., plot positioning within fields, plot sizes, or survey timing. Conclusion: This comparison of arable weed data that were originally sampled with a different purpose represents a new effort in connecting research between vegetation scientists and weed scientists. Both collections show different aspects of weed vegetation, which means the joint use of the data is valuable as it can contribute to a more complete picture of weed species diversity in European arable landscapes
Scalable open-source framework for machine learning-based image collection, annotation and classification: A case study for automatic fish species identification /
No full textCitizen science platforms, social media and smart phone applications enable the collection of large amounts of georeferenced images. This provides a huge opportunity in biodiversity and ecological research, but also creates challenges for efficient data handling and processing. Recreational and small-scale fisheries is one of the fields that could be revolutionised by efficient, widely accessible and machine learning-based processing of georeferenced images. Most non-commercial inland and coastal fisheries are considered data poor and are rarely assessed, yet they provide multiple societal benefits and can have substantial ecological impacts. Given that large quantities of georeferenced fish images are being collected by fishers every day, artificial intelligence (AI) and computer vision applications offer a great opportunity to automate their analyses by providing species identification, and potentially also fish size estimation. This would deliver data needed for fisheries management and fisher engagement. To date, however, many AI image analysis applications in fisheries are focused on the commercial sector, limited to specific species or settings, and are not publicly available. In addition, using AI and computer vision tools often requires a strong background in programming. In this study, we aim to facilitate broader use of computer vision tools in fisheries and ecological research by compiling an open-source user friendly and modular framework for large-scale image storage, handling, annotation and automatic classification, using cost- and labour-efficient methodologies. The tool is based on TensorFlow Lite Model Maker library, and includes data augmentation and transfer learning techniques applied to different convolutional neural network models. We demonstrate the potential application of this framework using a small example dataset of fish images taken through a recreational fishing smartphone application. The framework presented here can be used to develop region-specific species identification models, which could potentially be combined into a larger hierarchical model
Hexatoma crane flies (Diptera, Limoniidae) of Korea /
No full textHexatoma Latreille, 1809 is a large genus of short-palped crane flies with a worldwide distribution. Accounting for more than 60 percent of global species, 362 extant species occur in Asia. Prior to our study, Hexatoma crane flies on the Korean Peninsula (both the Democratic People’s Republic of Korea and the Republic of Korea) had been studied for 90 years starting in 1930, but only three species had been recorded, with one of them being a misidentification. This study adds six species to the fauna of the Korean Peninsula, all of which belong to the subgenus H. (Eriocera) Macquart, 1838. General information on genus and subgenus morphological characters is presented in this paper, with a redescription of each species based on Korean specimens, as well as illustrations of both sexes, the elevation range, the period of activity, habitat information, general distribution, and a distribution map for the Korean Peninsula. Three species H. (E.) ilwola Podenas, sp. nov., H. (E.) pianigra Podenas, sp. nov. and H. (E.) serenensis Podenas, sp. nov. are described as new to science. Hexatoma (E.) lygropis (Alexander, 1920) is deleted from the Korean species list as a misidentification. This publication is a continuation of our previous work on short-palped crane flies (Limoniidae) from Korea
A DNA barcode reference library for endemic Ponto-Caspian amphipods /
No full textThe Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species are severely threatened in their native range, while at the same time they are invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna is paramount for its conservation within the native region and monitoring outside of it. Here, we assemble a DNA barcode reference library for nearly 60% of all known Ponto-Caspian amphipod species. We use several methods to define molecular operational taxonomic units (MOTUs), based on two mitochondrial markers (COI and 16S), and assess their congruence with current species-level taxonomy based on morphology. Depending on the method, we find that 54–69% of species had congruent morpho-molecular boundaries. The cases of incongruence resulted from lumping distinct morphospecies into a single MOTU (7–27%), splitting a morphospecies into several MOTUs (4–28%), or both (4–11%). MOTUs defined by distance-based methods without a priori divergence thresholds showed the highest congruence with morphological taxonomy. These results indicate that DNA barcoding is valuable for clarifying the diversity of Ponto-Caspian amphipods, but reveals that extensive work is needed to resolve taxonomic uncertainties. Our study advances the DNA barcode reference library for the European aquatic biota, paving the way towards improved taxonomic knowledge needed to enhance monitoring and conservation efforts
Genomic characteristics and comparative genomics analysis of Parafenestella ontariensis sp. nov /
No full textA new ascomycetous species of Parafenestella was isolated from Acer negundo during the survey of diseased trees in Southern Ontario, Canada. The species is morphologically similar to other taxa of Cucurbitariacea (Pleosporales). The new species is different from the extant species in the morphology of ascospores, culture characteristics and molecular data. The novel species is described as Parafenestella ontariensis sp. nov. based on morphological and multi-gene phylogenetic analyses using a combined set of ITS, LSU, tef1 and tub2 loci. Additionally, the genome of P. ontariensis was sequenced and analyzed. The phylogenomic analysis confirmed the close relationship of the species to the fenestelloid clades of Cucurbitariaceae. The comparative genomics analysis revealed that the species lifestyle appears to be multitrophic (necrotrophic or hemi-biotrophic) with a capability to turn pathogenic on a corresponding plant host
Molecular identification of parasitic protozoa Sarcocystis in water samples /
No full textSarcocystis parasites are among the most common parasitic protozoa in farm animals. So far, the diversity of these parasites has been mainly studied in animal carcasses by morphological or molecular methods. Research on parasitic protozoa in environmental samples is scarce due to the lack of an appropriate methodology and low concentrations of parasites. For these reasons, there is a paucity of validated methods for Sarcocystis identification from environmental samples. Therefore, the present study aims to investigate various molecular methods for Sarcocystis parasite identification in water samples. In the present study, the sample volume, sporocysts isolation, and various conventional PCR were evaluated, and species-specific primers for the identification of different Sarcocystis species have been developed. Of the methods studied, based on data the most appropriate method for the identification of analyzed Sarcocystis spp. in water bodies is nested PCR, using species-specific primers targeting the cox1 gene. Sarcocystis DNA was detected in 111 out of 114 (97.4%) samples. This paper represents the first identification of S. bovifelis, S. cruzi, S. hirsuta, S. arieticanis, S. tenella, S. capracanis, S. bertrami, and S. miescheriana by PCR and sequencing in environmental water samples. Our pilot study is useful in developing techniques for the identification of Sarcocystis species from water samples
Stable isotope analysis supports omnivory in bank voles in apple orchards /
No full textWith only periodic and incomplete studies of its diet over time, all with differing methods and conclusions, the degree of omnivory in the bank vole (Clethrionomys glareolus) is not fully clear. We assessed the trophic niche of the species using isotopic (δ15N and δ13C) compositions from hair samples and analysed how C. glareolus shares trophic space with herbivores, granivores and insectivores living syntopically. According to the numbers trapped, C. glareolus was the fourth most numerous species in the apple orchards that we investigated, accounting for 14.4% of all trapped small mammals with a relative abundance of 1.12 individuals per 100 trap nights. The average values of both δ15N and δ13C in the hair of C. glareolus differed from the other trophic groups, with the average of δ15N in orchards and neighbouring habitats (6.55–6.95‰) being closest to that of insectivores. Intraspecific trophic niche differences (depending on age, gender and reproductive status) were not expressed, while correlations between body mass, body condition index and both δ15N and δ13C values were not consistent. In comparison to analysed basal resources, isotopic signatures in the hair were closest to the values in invertebrates and apple seeds. The degree of omnivory in C. glareolus was not the same in different habitats. This may be an indication of ecological plasticity within the species, allowing its inclusion/success in multi-species small mammal communities