The role of the river in the functioning of marginal fen: a case study from the Biebrza Wetlands
Study region The area of interest is the Upper Biebrza Valley, located in NE Poland. Study focus We examined water exchange at the river-fen interface in a near-natural wetland system using the combined field research-modeling approach. The authors chose the Biebrza River as the research object: it is a specific case of fen marginal valley rivers, and it flows in the peat layer without direct connection to the mineral soil layer. Our case study introduces two new aspects not yet considered in the scientific literature: (1) the riparian aquifer is fen and (2) the river has no direct contact with the mineral layer. The following research questions were investigated: What is the role of the river in feeding and draining a fen? Which drainage paths are important for water exchange in a near-natural river-fen system? How important are the morphological settings for the river-fen relations? We applied a systematic hydrological research approach based on field measurements and observations of the river and surrounding fen hydrological characteristics, as well as on the modelling results. New hydrological insights for the region We demonstrated that morphological settings have a significant influence on river-fen relations. We also demonstrated that due to the undeniable need to introduce increased protection and restoration of marginal fens, we may focus on river status in narrow valleys; however, in the wide valleys, the limitation of the drainage layer by decreasing the intensity of evapotranspiration is more promising. We propose to distinguish zones in the fen river valley to include them when proposing protection or conservation plans.
Grodzka-Łukaszewska et al. (2022) The role of the river in the functioning of marginal fen: a case study from the Biebrza Wetlands. PeerJ 10:e13418 https://doi.org/10.7717/peerj.13418
Characterization of LC-MS based urine metabolomics in healthy children and adults
Previous studies reported that sex and age could influence urine metabolomics, which should be considered in biomarker discovery. As a consequence, for the baseline of urine metabolomics characteristics, it becomes critical to avoid confounding effects in clinical cohort studies. In this study, we provided a comprehensive lifespan characterization of urine metabolomics in a cohort of 348 healthy children and 315 adults, aged 1 to 78 years, using liquid chromatography coupled with high resolution mass spectrometry. Our results suggest that sex-dependent urine metabolites are much greater in adults than in children. The pantothenate and CoA biosynthesis and alanine metabolism pathways were enriched in early life. Androgen and estrogen metabolism showed high activity during adolescence and youth stages. Pyrimidine metabolism was enriched in the geriatric stage. Based on the above analysis, metabolomic characteristics of each age stage were provided. This work could help us understand the baseline of urine metabolism characteristics and contribute to further studies of clinical disease biomarker discovery.
Liu et al. (2022) Characterization of LC-MS based urine metabolomics in healthy children and adults. PeerJ 10:e13545 https://doi.org/10.7717/peerj.13545
Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in flowers of safflower (Carthamus tinctorius L.) during colour-transition
Background Safflower (Carthamus tinctorius L.), well known for its flower, is widely used as a dye and traditional Chinese medicine. Flavonoids, especially flavonoid glycosides, are the main pigments and active components. However, their biosynthesis is largely unknown. Interestingly, the colour of flowers in safflower changed from yellow to red during flower development, while much of the gene and chemical bases during colour transition are unclear. Methods In this research, widely targeted metabolomics and transcriptomics were used to elucidate the changes in flavonoid biosynthesis from the gene and chemical points of view in flowers of safflower during colour transition. The screening of differential metabolites depended on fold change and variable importance in project (VIP) value. Differential expressed genes (DEGs) were screened by DESeq2 method. RT-PCR was used to analyse relative expressions of DEGs. Results A total of 212 flavonoid metabolites, including hydroxysafflor yellow A, carthamin and anthocyanins, were detected and showed a large difference. The candidate genes of glycosyltransferases and flavonoid hydroxylase that might participate in flavonoid glycoside biosynthesis were screened. Ten candidate genes were screened. Through integrated metabolomics and transcriptome analysis, a uridine diphosphate glucose glycosyltransferase gene, CtUGT9 showed a significant correlation with flavonoid glycosides in safflower. In addition, expression analysis showed that CtUGT9 was mainly expressed in the middle development of flowers and was significantly upregulated under MeJA treatment. Our results indicated that CtUGT9 might play an important role in flavonoid glycoside biosynthesis during colour-transition in safflower.
Ren et al. (2022) Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in flowers of safflower (Carthamus tinctorius L.) during colour-transition. PeerJ 10:e13591 https://doi.org/10.7717/peerj.13591
Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda
We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla.
Rosenberg et al. (2022) Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda. PeerJ 10:e13139 https://doi.org/10.7717/peerj.13139
Effects of soft rock on soil properties and bacterial community in Mu Us Sandy Land, China
Soft rock is a new material that could be used for the improvement of Mu Us Sandy Land, China. It can be utilized for wind prevention and sand fixation, both of which are of great importance to ecological restoration aims and cultivated land replenishment in desert areas. Four treatments with different compound ratios of soft rock and sand—0:1 (CK), 1:5 (P1), 1:2 (P2), and 1:1 (P3)—were studied. Fluorescence quantitative PCR (qPCR) and high-throughput sequencing were used to analyze the structure and diversity of the bacterial community in the compound soil and its relationship with physical and chemical parameters in the soil. The results showed that in comparison to CK treatment, soil organic carbon (SOC), total nitrogen (TN), and NH4+-N increased significantly in the P1 treatment; available phosphorus (AP), available potassium (AK), and NO3−-N increased significantly in the P3 treatment. The bacterial gene copy number with P3 treatment was highest, showing a significant increase of 182.05% compared with the CK treatment. The three bacterial groups with the highest relative abundance at the phylum level were Actinobacteria, Proteobacteria, and Chloroflexi, accounting for more than 70% of the total population. The bacterial α diversity showed the same trend, the diversity and abundance indices of the P1 and P3 treatments were the highest, and the β diversity showed that the community structure of the two groups in these treatments were similar. norank_f__Roseiflexaceae and Gaiella (belonging to Actinobacteria) significantly differed with differing compound ratios in each treatment. NO3−-N, NH4+-N and SOC were the main factors affecting bacterial community structure, and had a significant positive correlation with Gaiella abundance. These species are known to play an important role in stabilizing the soil structure of sandy land. Overall, 1:5 and 1:1 compound soil mixtures were beneficial towards the microbial community of sandy land, which plays an important role in biological sand fixation. This study provides an important theoretical basis for the supplementation of arable land area and the improvement of sandy land productivity, and has a good promotion prospect.
Guo et al. (2022) Effects of soft rock on soil properties and bacterial community in Mu Us Sandy Land, China. PeerJ 10:e13561 https://doi.org/10.7717/peerj.13561
Targeted metabolomics suggests a probable role of the FTO gene in the kynurenine pathway in prediabetes
Background Genome-wide association studies have identified the alpha-ketoglutarate dependent dioxygenase gene (FTO) as the first susceptibility gene of obesity. In the present study, we utilized targeted metabolomics in an attempt to further elucidate mechanisms underlying the action of the FTO gene. Methods This study was part of a health survey of employees of the Electricity Generating Authority of Thailand (n = 79, 10 female and 69 male). Targeted metabolomics was performed by liquid chromatography–mass spectrometry using Biocrates AbsoluteIDQ-p180 kit. Genotyping of FTO rs9939609 was performed by real-time PCR (TaqMan™ MGB probes). Results Using OPLS-DA variable importance in projection (VIP), tryptophan was found to be among the metabolites with the 10 highest VIP scores. Pearson’s correlation analysis showed that kynurenine and tryptophan were positively correlated only in subjects with the rs9939609 A allele (n = 32, r = 0.56, p < 0.001) and the correlation coefficients were significantly higher in subjects having the A allele than in those without the A allele (p < 0.05). Moreover, the kynurenine/tryptophan ratio was significantly associated with the presence of the A allele, independently of body mass index and sex. Conclusions The FTO gene is likely to influences the conversion of tryptophan to kynurenine.
Chailurkit et al. (2022) Targeted metabolomics suggests a probable role of the FTO gene in the kynurenine pathway in prediabetes. PeerJ 10:e13612 https://doi.org/10.7717/peerj.13612
The influence of a manipulation of threat on experimentally-induced secondary hyperalgesia
Pain is thought to be influenced by the threat value of the particular context in which it occurs. However, the mechanisms by which a threat achieves this influence on pain are unclear. Here, we explore how threat influences experimentally-induced secondary hyperalgesia, which is thought to be a manifestation of central sensitization. We developed an experimental study to investigate the effect of a manipulation of threat on experimentally-induced secondary hyperalgesia in 26 healthy human adults (16 identifying as female; 10 as male). We induced secondary hyperalgesia at both forearms using high-frequency electrical stimulation. Prior to the induction, we used a previously successful method to manipulate threat of tissue damage at one forearm (threat site). The effect of the threat manipulation was determined by comparing participant-rated anxiety, perceived threat, and pain during the experimental induction of secondary hyperalgesia, between the threat and control sites. We hypothesized that the threat site would show greater secondary hyperalgesia (primary outcome) and greater surface area (secondary outcome) of induced secondary hyperalgesia than the control site. Despite a thorough piloting procedure to test the threat manipulation, our data showed no main effect of site on pain, anxiety, or threat ratings during high-frequency electrical stimulation. In the light of no difference in threat between sites, the primary and secondary hypotheses cannot be tested. We discuss reasons why we were unable to replicate the efficacy of this established threat manipulation in our sample, including: (1) competition between threats, (2) generalization of learned threat value, (3) safety cues, (4) trust, and requirements for participant safety, (5) sampling bias, (6) sample-specific habituation to threat, and (7) implausibility of (sham) skin examination and report. Better strategies to manipulate threat are required for further research on the mechanisms by which threat influences pain.
Bedwell et al. (2022) The influence of a manipulation of threat on experimentally-induced secondary hyperalgesia. PeerJ 10:e13512 https://doi.org/10.7717/peerj.13512
Remote sensing techniques for automated marine mammals detection: a review of methods and current challenges
Marine mammals are under pressure from multiple threats, such as global climate change, bycatch, and vessel collisions. In this context, more frequent and spatially extensive surveys for abundance and distribution studies are necessary to inform conservation efforts. Marine mammal surveys have been performed visually from land, ships, and aircraft. These methods can be costly, logistically challenging in remote locations, dangerous to researchers, and disturbing to the animals. The growing use of imagery from satellite and unoccupied aerial systems (UAS) can help address some of these challenges, complementing crewed surveys and allowing for more frequent and evenly distributed surveys, especially for remote locations. However, manual counts in satellite and UAS imagery remain time and labor intensive, but the automation of image analyses offers promising solutions. Here, we reviewed the literature for automated methods applied to detect marine mammals in satellite and UAS imagery. The performance of studies is quantitatively compared with metrics that evaluate false positives and false negatives from automated detection against manual counts of animals, which allows for a better assessment of the impact of miscounts in conservation contexts. In general, methods that relied solely on statistical differences in the spectral responses of animals and their surroundings performed worse than studies that used convolutional neural networks (CNN). Despite mixed results, CNN showed promise, and its use and evaluation should continue. Overall, while automation can reduce time and labor, more research is needed to improve the accuracy of automated counts. With the current state of knowledge, it is best to use semi-automated approaches that involve user revision of the output. These approaches currently enable the best tradeoff between time effort and detection accuracy. Based on our analysis, we identified thermal infrared UAS imagery as a future research avenue for marine mammal detection and also recommend the further exploration of object-based image analysis (OBIA). Our analysis also showed that past studies have focused on the automated detection of baleen whales and pinnipeds and that there is a gap in studies looking at toothed whales, polar bears, sirenians, and mustelids.
Spatial and Geographic Information Science
Rodofili et al. (2022) Remote sensing techniques for automated marine mammals detection: a review of methods and current challenges. PeerJ 10:e13540 https://doi.org/10.7717/peerj.13540
Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect
We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith’s Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.
Espinosa-Asuar et al. (2022) Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect. PeerJ 10:e13579 https://doi.org/10.7717/peerj.13579
Microplastics do not affect bleaching of Acropora cervicornis at ambient or elevated temperatures
Microplastic pollution can harm organisms and ecosystems such as coral reefs. Corals are important habitat-forming organisms that are sensitive to environmental conditions and have been declining due to stressors associated with climate change. Despite their ecological importance, it is unclear how corals may be affected by microplastics or if there are synergistic effects with rising ocean temperatures. To address this research gap, we experimentally examined the combined effects of environmentally relevant microplastic concentrations (i.e., the global average) and elevated temperatures on bleaching of the threatened Caribbean coral, Acropora cervicornis. In a controlled laboratory setting, we exposed coral fragments to orthogonally crossed treatment levels of low-density polyethylene microplastic beads (0 and 11.8 particles L−1) and water temperatures (ambient at 28 °C and elevated at 32 °C). Zooxanthellae densities were quantified after the 17-day experiment to measure the bleaching response. Regardless of microplastic treatment level, corals in the elevated temperature treatment were visibly bleached and necrotic (i.e., significant negative effect on zooxanthellae density) while those exposed to ambient temperature remained healthy. Thus, our study successfully elicited the expected bleaching response to a high-water temperature. However, we did not observe significant effects of microplastics at either individual (ambient temperature) or combined levels (elevated temperature). Although elevated temperatures remain a larger threat to corals, responses to microplastics are complex and may vary based on focal organisms or on plastic conditions (e.g., concentration, size, shape). Our findings add to a small but growing body of research on the effects of microplastics on corals, but further work is warranted in this emerging field to fully understand how sensitive ecosystems are affected by this pollutant.
Environmental Contamination and Remediation
Plafcan et al. (2022) Microplastics do not affect bleaching of Acropora cervicornis at ambient or elevated temperatures. PeerJ 10:e13578 https://doi.org/10.7717/peerj.13578