The conservation value of freshwater habitats for frog communities of lowland fynbos
Amphibians are more threatened than any other vertebrate class, yet evidence for many threats is missing. The Cape lowland fynbos (endemic scrub biome) is threatened by habitat loss, and natural temporary freshwater habitats are removed in favour of permanent impoundments. In this study, we determine amphibian assemblages across different freshwater habitat types with special attention to the presence of invasive fish. We find that anuran communities differ primarily by habitat type, with permanent water habitats having more widespread taxa, while temporary water bodies have more range restricted taxa. Invasive fish are found to have a significant impact on frogs with toads most tolerant of their presence. Temporary freshwater habitats are a conservation priority in the area, and their amphibian assemblages represent endemic taxa that are intolerant of invasive fish. Conservation of a biodiverse amphibian assemblage in lowland fynbos areas will rely on the creation of temporary freshwater habitats, rather than a northern hemisphere pond based solution.
Terblanche et al. (2023) The conservation value of freshwater habitats for frog communities of lowland fynbos. PeerJ 11:e15516 https://doi.org/10.7717/peerj.15516
Association between free thyroxine levels and clinical phenotype in first-episode psychosis: a prospective observational study
Aim To determine whether thyroid hormone levels are associated with a specific clinical phenotype in patients with first-episode psychosis (FEP). Methods Ninety-eight inpatients experiencing FEP and with less than 6 weeks of antipsychotic treatment were included in the study and were followed up for one year. Baseline psychiatric evaluation included assessment of prodromal symptoms, positive and negative symptoms, depressive symptoms, stressful life events and cycloid psychosis criteria. Thyroid function (thyroid-stimulating hormone (TSH) and free thyroxin (FT4)) was determined at admission. Partial correlation analysis was conducted to analyse the correlation between levels of TSH/FT4 and symptoms. Logistic regression was performed to explore the association between psychopathological symptoms, 12-month diagnoses and thyroid hormones while adjusting for covariates. Results Patients with prodromal symptomatology showed lower baseline FT4 levels (OR = 0.06; p = 0.018). The duration of untreated psychosis (DUP) was inversely associated with FT4 concentrations (r = − 0.243; p = 0.039). FEP patients with sudden onset of psychotic symptoms (criteria B, cycloid psychosis) showed higher FT4 levels at admission (OR = 10.49; p = 0.040). Patients diagnosed with affective psychotic disorders (BD or MDD) at the 12-month follow-up showed higher FT4 levels at admission than patients diagnosed with nonaffective psychosis (schizophrenia, schizoaffective) (OR = 8.57; p = 0.042). Conclusions Our study suggests that higher free-thyroxine levels are associated with a specific clinical phenotype of FEP patients (fewer prodromal symptoms, shorter DUP duration and sudden onset of psychosis) and with affective psychosis diagnoses at the 12-month follow-up.
Gine-Serven et al. (2023) Association between free thyroxine levels and clinical phenotype in first-episode psychosis: a prospective observational study. PeerJ 11:e15347 https://doi.org/10.7717/peerj.15347
Influence of SPIO labelling on the function of BMSCs in chemokine receptors expression and chemotaxis
Bone marrow-derived mesenchymal stem cells (BMSCs) are increasingly being used in bone marrow transplantation (BMT) to enable homing of the allogeneic hematopoietic stem cells and suppress acute graft versus host disease (aGVHD). The aim of this study was to optimize the labelling of BMSCs with superparamagnetic iron oxide particles (SPIOs), and evaluate the impact of the SPIOs on the biological characteristics, gene expression profile and chemotaxis function of the BMSCs. The viability and proliferation rates of the SPIO-labeled BMSCs were analyzed by trypan blue staining and CCK-8 assay respectively, and the chemotaxis function was evaluated by the transwell assay. The expression levels of chemokine receptors were measured by RT-PCR and flow cytometry. The SPIOs had no effect on the viability of the BMSCs regardless of the labelling concentration and culture duration. The labelling rate of the cells was higher when cultured for 48 h with the SPIOs. Furthermore, cells labeled with 25 µg/ml SPIOs for 48 h had the highest proliferation rates, along with increased expression of chemokine receptor genes and proteins. However, there was no significant difference between the chemotaxis function of the labeled and unlabeled BMSCs. To summarize, labelling BMSCs with 25 µg/ml SPIOs for 48h did not affect their biological characteristics and chemotaxis function, which can be of significance for in vivo applications.
Liu et al. (2023) Influence of SPIO labelling on the function of BMSCs in chemokine receptors expression and chemotaxis. PeerJ 11:e15388 https://doi.org/10.7717/peerj.15388
Functional responses of male and female European green crabs suggest potential sex-specific impacts of invasion
Predicting the impacts of predatory invasive species is important for prioritising conservation interventions. Functional response experiments, which examine consumption by predators in relation to prey density, are a useful way to assess the potential strength of novel predator-prey relationships. However, such experiments are often conducted without consideration of sex or only with males to reduce invasion risk. Here, we compared the functional responses of male and female European green crabs (Carcinus maenas), a global invader, feeding on varnish clams (Nuttallia obscurata) to test whether the two sexes have similar potential for impact. We also examined potential correlates of predation behaviour by measuring sex-specific movement and prey choice. Both sexes displayed a Type II hyperbolic functional response, which can destabilise prey populations at low prey densities. However, males and females exhibited some differences in foraging behaviour. Female green crabs had slightly lower attack rates, which were not linked to sex differences in movement, and slightly longer handling times, which were not linked to sex differences in prey choice. These small, non-significant differences nevertheless translated into significantly greater functional response ratios, which are used to predict the ecological impact of invasive species, for males than females. There was no difference in the proportion of clams consumed between males and females with similar crusher claw heights, but females have smaller crusher claws on average, hence they consumed a smaller proportion of clams. Repeated surveys of four populations of European green crabs established in British Columbia, Canada, showed that sex ratio is highly variable. Taken together, these results and population-level modelling suggest that trying to evaluate the potential impact of European green crabs on clam populations by sampling only males could result in overestimation, even in populations that have male-biased sex-ratios. Consumer sex might generally be an important feature to consider when using functional response experiments to forecast the impact of new invasive species, especially those with marked sexual dimorphism that affect foraging.
Kattler et al. (2023) Functional responses of male and female European green crabs suggest potential sex-specific impacts of invasion. PeerJ 11:e15424 https://doi.org/10.7717/peerj.15424
Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection
Background Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer. Objectives This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq. Patients and Methods Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum β-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI). Results The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3rd generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed. Conclusion Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.
Abubaker et al. (2023) Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection. PeerJ 11:e15429 https://doi.org/10.7717/peerj.15429
Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum
The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.
Adedayo et al. (2023) Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum. PeerJ 11:e15432 https://doi.org/10.7717/peerj.15432
Uncertainty in projections of future lake thermal dynamics is differentially driven by lake and global climate models
Freshwater ecosystems provide vital services, yet are facing increasing risks from global change. In particular, lake thermal dynamics have been altered around the world as a result of climate change, necessitating a predictive understanding of how climate will continue to alter lakes in the future as well as the associated uncertainty in these predictions. Numerous sources of uncertainty affect projections of future lake conditions but few are quantified, limiting the use of lake modeling projections as management tools. To quantify and evaluate the effects of two potentially important sources of uncertainty, lake model selection uncertainty and climate model selection uncertainty, we developed ensemble projections of lake thermal dynamics for a dimictic lake in New Hampshire, USA (Lake Sunapee). Our ensemble projections used four different climate models as inputs to five vertical one-dimensional (1-D) hydrodynamic lake models under three different climate change scenarios to simulate thermal metrics from 2006 to 2099. We found that almost all the lake thermal metrics modeled (surface water temperature, bottom water temperature, Schmidt stability, stratification duration, and ice cover, but not thermocline depth) are projected to change over the next century. Importantly, we found that the dominant source of uncertainty varied among the thermal metrics, as thermal metrics associated with the surface waters (surface water temperature, total ice duration) were driven primarily by climate model selection uncertainty, while metrics associated with deeper depths (bottom water temperature, stratification duration) were dominated by lake model selection uncertainty. Consequently, our results indicate that researchers generating projections of lake bottom water metrics should prioritize including multiple lake models for best capturing projection uncertainty, while those focusing on lake surface metrics should prioritize including multiple climate models. Overall, our ensemble modeling study reveals important information on how climate change will affect lake thermal properties, and also provides some of the first analyses on how climate model selection uncertainty and lake model selection uncertainty interact to affect projections of future lake dynamics.
Wynne et al. (2023) Uncertainty in projections of future lake thermal dynamics is differentially driven by lake and global climate models. PeerJ 11:e15445 https://doi.org/10.7717/peerj.15445
The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae
It is common to use whole mitochondrial genomes to analyze phylogenetic relationships among insects. In this study, seven mitogenomes of Tenebrionidae are newly sequenced and annotated. Among them, four species (Cerogira janthinipennis (Fairmaire, 1886), Luprops yunnanus (Fairmaire, 1887), Anaedus unidentasus Wang & Ren, 2007, and Spinolyprops cribricollis Schawaller, 2012) represent the subfamily Lagriinae. In this subfamily, the mitogenomes of the tribes Goniaderini (A. unidentasus) and Lupropini (L. yunnanus and S. cribricollis) were first reported; they were found to be 15,328–16,437 bp in length and encode 37 typical mitochondrial genes (13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region). Most protein-coding genes in these mitogenomes have typical ATN start codons and TAR or an incomplete stop codon T–. In these four lagriine species, F, L2, I, and N are the most frequently used amino acids. In the 13 PCGs, the gene atp8 (Pi = 0.978) was the most diverse nucleotide, while cox1 was the most conserved gene with the lowest value (Pi = 0.211). The phylogenetic results suggest that Pimelinae, Lagriinae, Blaptinae, Stenochiinae, and Alleculinae are monophyletic, Diaperinae is paraphyletic, and Tenebrioninae appears polyphyletic. In Lagriinae, the tribe Lupropini appears paraphyletic because Spinolyprops is clustered with Anaedus in Goniaderini. These mitogenomic data provide important molecular data for the phylogeny of Tenebrionidae.
Wei et al. (2023) The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae. PeerJ 11:e15483 https://doi.org/10.7717/peerj.15483
Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis
Macrophytes are one of the important indicators used in assessing the anthropic impact on aquatic ecosystems. The structure of macrophyte communities of two rivers were compared by species composition, dominant species and projective cover using statistical methods. It is shown that the influence of storm runoff on these rivers is manifested in the form of a change in the dominant species composition. Based on the statistical analysis carried out, it can be argued that, despite the peculiarities of the flora composition of each of the rivers, the influence of storm runoffs largely neutralizes this specificity, determining the situation in local areas immediately below the runoff. In the area of the effluent discharge the dominance of individual species and an increase in the area overgrown with macrophytes was observed. In the area of stormwater discharge on the Psel River, species were usually present: Nuphar lutea, Ceratophyllum demersum, Myriophyllum spicatum and on the Bystrica River—Glyceria maxima, Sagitaria sagittiformis, Stuckenia pectinata and Potamogeton crispus. The use of the NMDS method has been found to provide good insight into the structural rearrangements in macrophyte communities affected by runoff from stormwater systems.
Environmental Contamination and Remediation
Babko et al. (2023) Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis. PeerJ 11:e15248 https://doi.org/10.7717/peerj.15248
New seed coating containing Trichoderma viride with anti-pathogenic properties
Background To ensure food security in the face of climate change and the growing world population, multi-pronged measures should be taken. One promising approach uses plant growth-promoting fungi (PGPF), such as Trichoderma, to reduce the usage of agrochemicals and increase plant yield, stress tolerance, and nutritional value. However, large-scale applications of PGPF have been hampered by several constraints, and, consequently, usage on a large scale is still limited. Seed coating, a process that consists of covering seeds with low quantities of exogenous materials, is gaining attention as an efficient and feasible delivery system for PGPF. Methods We have designed a new seed coating composed of chitin, methylcellulose, and Trichoderma viride spores and assessed its effect on canola (Brassica napus L.) growth and development. For this purpose, we analyzed the antifungal activity of T. viride against common canola pathogenic fungi (Botrytis cinerea, Fusarium culmorum, and Colletotrichum sp.). Moreover, the effect of seed coating on germination ratio and seedling growth was evaluated. To verify the effect of seed coating on plant metabolism, we determined superoxide dismutase (SOD) activity and expression of the stress-related RSH (RelA/SpoT homologs). Results Our results showed that the T. viride strains used for seed coating significantly restricted the growth of all three pathogens, especially F. culmorum, for which the growth was inhibited by over 40%. Additionally, the new seed coating did not negatively affect the ability of the seeds to complete germination, increased seedling growth, and did not induce the plant stress response. To summarize, we have successfully developed a cost-effective and environmentally responsible seed coating, which will also be easy to exploit on an industrial scale.
Turkan et al. (2023) New seed coating containing Trichoderma viride with anti-pathogenic properties. PeerJ 11:e15392 https://doi.org/10.7717/peerj.15392