Modeling the current distribution suitability and future dynamics of Culicoides imicola under climate change scenarios
Background African horse sickness, a transboundary and non-contagious arboviral infectious disease of equids, has spread without any warning from sub-Saharan Africa towards the Southeast Asian countries in 2020. It is imperative to predict the global distribution of Culicoides imicola (C. imicola), which was the main vector of African horse sickness virus. Methods The occurrence records of C. imicola were mainly obtained from the published literature and the Global Biodiversity Information Facility database. The maximum entropy algorithm was used to model the current distribution suitability and future dynamics of C. imicola under climate change scenarios. Results The modeling results showed that the currently suitable habitats for C. imicola were distributed in most of the southern part areas of America, southwestern Europe, most of Africa, the coastal areas of the Middle East, almost all regions of South Asia, southern China, a few countries in Southeast Asia, and the whole Australia. Our model also revealed the important environmental variables on the distribution of C. imicola were temperature seasonality, precipitation of coldest quarter, and mean temperature of wettest quarter. Representative Concentration Pathways (RCPs) is an assumption of possible greenhouse gases emissions in the future. Under future climate change scenarios, the area of habitat suitability increased and decreased with time, and RCP 8.5 in the 2070s gave the worst prediction. Moreover, the habitat suitability of C. imicola will likely expand to higher latitudes. The prediction of this study is of strategic significance for vector surveillance and the prevention of vector-borne diseases.
Gao et al. (2021) Modeling the current distribution suitability and future dynamics of Culicoides imicola under climate change scenarios. PeerJ 9:e12308 https://doi.org/10.7717/peerj.12308
Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana)
Phylogenetic relationships of the subgenus Oxyphortica were reconstructed based on two mitochondrial genes (COI and ND2). The results revealed the paraphyly of Oxyphortica and supported high levels of cryptic diversity within this subgenus. By integrating morphological characteristics and molecular evidence, we identified 17 new species as members of Oxyphortica: S. (O.) amphigya sp. nov., S. (O.) armillata sp. nov., S. (O.) ashima sp. nov., S. (O.) bawo sp. nov., S. (O.) crypta sp. nov., S. (O.) gelea sp. nov., S. (O.) hengduanmontana sp. nov., S. (O.) jinmingi sp. nov., S. (O.) mengbalanaxi sp. nov., S. (O.) mouig sp. nov., S. (O.) setipes sp. nov., S. (O.) shangrila sp. nov., S. (O.) tsauri sp. nov., S. (O.) valleculata sp. nov., S. (O.) wanhei sp. nov., S. (O.) yangjin sp. nov. and S. (O.) hypophaia sp. nov. To test the early morphological identifications and confirm the species boundaries, different species delimitation methods, including Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BP&P), were used, together with traditional distance. All species boundaries were clearly defined. As Oxyphortica species are mainly distributed across Southwest China (e.g., 20 spp. from the Hengduan Mountains), the complex climate and topographic landforms of the area may be responsible for the high levels of species diversity and endemism.
Wang et al. (2021) Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana). PeerJ 9:e12347 https://doi.org/10.7717/peerj.12347
A new specimen of Sinopterus dongi (Pterosauria, Tapejaridae) from the Jiufotang Formation (Early Cretaceous, China)
The Tapejarinae are edentulous pterosaurs that are relatively common in Cretaceous continental deposits in South America, North Africa, Europe, and China (mostly Early Cretaceous). The Chinese Jiufotang Formation is particularly rich in tapejarine specimens, having yielded over 10 described specimens and dozens of undescribed ones. For the Jiufotang Formation, a total of seven nominal tapejarid species and two genera have been proposed. Some debate exists over how many of those are valid or, alternatively, sexual or ontogenetic morphs of fewer (or even a single) species. Despite the abundance of specimens and the relevant taxonomic problems involved, detailed revisions of the matter are still lacking. This is partly due to the relatively scarce knowledge on the comparative osteology of the Sinopterus complex, which is hampered by the fact that most specimens have been only preliminarily described. In this contribution, we present a new postcranial specimen, D3072, which we attribute to the type-species of the genus, Sinopterus dongi. This new specimen helps shed some new light in the osteology of Sinopterus dongi, hopefully serving as a basis for future comparative studies involving further specimens and other proposed species and, subsequently, taxonomic revisions.
Shen et al. (2021) A new specimen of Sinopterus dongi (Pterosauria, Tapejaridae) from the Jiufotang Formation (Early Cretaceous, China). PeerJ 9:e12360 https://doi.org/10.7717/peerj.12360
Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus
Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.
Zhang et al. (2021) Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus. PeerJ 9:e12390 https://doi.org/10.7717/peerj.12390
Improved isolation and detection of toxigenic Vibrio parahaemolyticus from coastal water in Saudi Arabia using immunomagnetic enrichment
Background Vibrio parahaemolyticus is recognized globally as a cause of foodborne gastroenteritis and its widely disseminated in marine and coastal environment throughout the world. The main aim of this study was conducted to investigate the presence of toxigenic V. parahaemolyticus in costal water in the Eastern Province of Saudi Arabia by using immunomagnetic separation (IMS) in combination with chromogenic Vibrio agar medium and PCR targeting toxR gene of species level and virulence genes. Methods A total of 192 seawater samples were collected from five locations and enriched in alkaline peptone water (APW) broth. One-milliliter portion from enriched samples in APW were mixed with an immunomagnetic beads (IMB) coated with specific antibodies against V. parahaemolyticus polyvalent K antisera and separated beads with captured bacteria streaked on thiosulfate citrate bile salts sucrose (TCBS) agar and CHROMagar Vibrio (CaV) medium. Results Of the 192 examined seawater samples, 38 (19.8%) and 44 (22.9%) were positive for V. parahaemolyticus, producing green and mauve colonies on TCBS agar and CaV medium, respectively. Among 120 isolates of V. parahaemolyticus isolated in this study, 3 (2.5%) and 26 (21.7%) isolates of V. parahaemolyticus isolated without and with IMB treatment tested positive for the toxin regulatory (toxR) gene, respectively. Screening of the confirmed toxR gene-positive isolates revealed that 21 (17.5%) and 3 (2.5%) were positive for the thermostable direct hemolysin (tdh) encoding gene in strains isolated with IMB and without IMB treatment, respectively. None of the V. parahaemolyticus strains tested positive for the thermostable related hemolysin (trh) gene. In this study, we found that the CaV medium has no advantage over TCBS agar if IMB concentration treatment is used during secondary enrichment steps of environmental samples. The enterobacterial repetitive intergenic consensus (ERIC)-PCR DNA fingerprinting analysis revealed high genomic diversity, and 18 strains of V. parahaemolyticus were grouped and identified into four identical ERIC clonal group patterns. Conclusions The presented study reports the first detection of tdh producing V. parahaemolyticus in coastal water in the Eastern Province of Saudi Arabia.
Almejhim et al. (2021) Improved isolation and detection of toxigenic Vibrio parahaemolyticus from coastal water in Saudi Arabia using immunomagnetic enrichment. PeerJ 9:e12402 https://doi.org/10.7717/peerj.12402
Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean
Pseudomonas savastanoi pv. glycinea (Psg) causes bacterial blight of soybean. To identify candidate virulence factors, transposon-mediated mutational analysis of Psg was carried out. We syringe-inoculated soybean leaves with Psg transposon mutants and identified 28 mutants which showed reduced virulence from 1,000 mutants screened. Next, we spray-inoculated soybean leaves with these mutants and demonstrated that the algU mutant showed significantly reduced virulence together with reduced bacterial populations in planta. Expression profiles comparison between the Psg wild-type (WT) and algU mutant in HSC broth revealed that expression of coronatine (COR)-related genes (including cmaA and corR) were down-regulated in the algU mutant compared with Psg WT. Moreover, we also showed that COR production were reduced in the algU mutant compared with WT. We also demonstrated that algD, which is related to alginate biosynthesis, showed reduced expression and biofilm formation was significantly suppressed in the algU mutant. Furthermore, hrpL also showed less expression in the algU mutant. These results indicate that AlgU plays a critical role in promoting Psg pathogenesis by regulating multiple virulence factors.
Nguyen et al. (2021) Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean. PeerJ 9:e12405 https://doi.org/10.7717/peerj.12405
Distribution and fractionation of rare earth elements in suspended particulate matter in a coastal river, Southeast China
Background In the river system, the geochemistry of rare earth elements (REEs, a series of elements from La to Lu) in suspended particulate matter (SPM) is generally controlled by rock weathering processes and hydrochemical characteristics, as well as being affected by anthropogenic activities. However, the variations of geochemical characteristics and behaviors of REEs in SPM with a salinity gradient from the inland river to the estuary have been short of a systematic understanding. Methods The REE concentrations, Post Archean Australia Shale (PAAS)-normalized REE, La/Yb, La/Sm, and Sm/Yb ratios of SPM were investigated in the Jiulongjiang River, which is a coastal river mainly flowing through granite rocks in Southeast China. The correlation relationships between physicochemical parameters (including water pH, total dissolved solids (TDS), HCO3– concentrations, and the concentrations of major elements of SPM) and PAAS-normalized REE ratios of SPM were analyzed to determine the factors that affect the REE concentration and fractionation of SPM in the different regions of Jiulongjiang River, including the main stream and tributary of Beixi River, Xixi River, Nanxi River, and estuary. Additionally, the Ce, Eu, and Gd anomalies of SPM were estimated. Results The average ∑REE concentration of SPM (352 mg/kg) in the granite rock basin was twice higher than the mean value (175 mg/kg) of the world’s rivers. The PAAS-normalized REE ratios of SPM in the main rivers including Beixi River (main stream), Xixi River, and Nanxi River were near due to the same lithologic distribution. In the tributary of Beixi River, the input of low-weathered carbonate minerals which contain very few REE caused the lower REE concentrations of SPM. The PAAS-normalized REE ratios of SPM in the estuary were significantly lower than those in the main rivers, which was mainly attributed to the significant REE removal with the increment of salinity. The enrichment of LREE relative to HREE in SPM increased with decreasing water pH in the main rivers. In the estuary, the preferential removal of dissolved LREE occurred compared to HREE with the increment of salinity. The negative Ce and Eu anomalies of SPM occurred in both the main rivers and estuary region and rare Gd pollution was present in the basin. Additionally, human activities caused the increment of REE concentrations and more negative Ce anomaly at some specific sites, such as dam effect and agricultural pollution. Conclusions The REE concentrations and fractionations of SPM in river water mainly depend on lithologic distribution and riverine pH, while they are affected by salinity in the estuary.
Environmental Contamination and Remediation
Liu et al. (2021) Distribution and fractionation of rare earth elements in suspended particulate matter in a coastal river, Southeast China. PeerJ 9:e12414 https://doi.org/10.7717/peerj.12414
Fusarium head blight in the Russian Far East: 140 years after description of the ‘drunken bread’ problem
The first appearance of Fusarium head blight (FHB)—and the beginning of scientific research of this disease—occurred the Far East region of Russia at the end of the 19th century. In the summer of 2019, in the Amur region, which comprises 60–70% of grain production in the Russian Far East, flooding caused a state of emergency. The quality of wheat and barley grains grown under natural conditions of FHB outbreaks, including grain infection, fungal species composition, DNA content of F. graminearum and chemotypes, and the presence of various mycotoxins, was studied. Fusarium infection rates reached extremely high percentages, 51–98%, the majority of which were F. graminearum infections. The amount of F. graminearum DNA in wheat grain samples was higher than in the barley grain samples and averaged 6.1 and 2.1 pg/ng, respectively. The content of deoxynivalenol (DON) in the wheat samples reached 13,343 ppb and in barley reached 7,755 ppb. A multilocus genotyping assay was conducted on the partially sequenced fragments of the translation elongation factor EF-1a, ammonium ligase gene, reductase gene, and 3-O-acetyltransferase gene in 29 Fusarium graminearum sensu lato strains from the grain harvested in the Amur region. All strains from the Far East region were characterized as F. graminearum sensu stricto; 70% were the 15-AcDON chemotype, while the other strains were the 3-AcDON chemotype. According to the results, after 140 years of study of FHB, we are still not very successful in controlling this disease if conditions are favorable for pathogen development. Even at present, some of the grain harvested must be destroyed, as high contamination of mycotoxins renders it unusable.
Gagkaeva et al. (2021) Fusarium head blight in the Russian Far East: 140 years after description of the ‘drunken bread’ problem. PeerJ 9:e12346 https://doi.org/10.7717/peerj.12346
The morphology and internal structure of dogwood (Cornus L.) endocarps in the taxonomy and phylogeny of the genus
The genus Cornus is known for its complicated taxonomy and extreme polymorphism. Currently, dogwoods are classified into four morphological groups reflected in four phylogenetic clades: blue- or white-fruited dogwoods (BW), cornelian cherries (CC), big-bracted dogwoods (BB), and dwarf dogwoods (DW). The present study is a continuation of a series of papers that started with the examination of the endocarp morphological diversity among BW species. The endocarps of 22 Cornus species were studied according to their morphology, internal structure, and sculpture; the aim was to evaluate the taxonomic importance of the examined characters and check whether endocarp differentiation supports the published phylogenies, according to which the relationships within the genus are indicated as (BW(CC(DW-BB))). Among the quantitative characters, the endocarp’s length, thickness, and width, its length/width ratio, and the number of vascular bundles on its surface were considered taxonomically important. Regarding the qualitative characters, the taxonomic significance of the stone shape, the endocarp apex and base outline, the position of vascular bundles on the endocarp surface, and the presence of the apical cavity and distinct furrow on the endocarp side walls was proved. Additionally, the uniform qualitative characters having a 100% share of a given character state were identified. Cornelian cherries and dwarf dogwoods were characterised by the presence of four uniform characters. In the big-bracted group, two uniform characters were found. Blue- or white-fruited species were the most heterogeneous, with no uniform characters. Regarding the endocarp’s internal structure, the presence of secretory cavities in the endocarp wall and in the septa, the presence of crystals in the outer endocarp, the number of cell layers in the transition sclereid zone, and the primary and secondary sculptures were found to be taxonomically significant. Additionally, the comparative analyses of dogwood endocarps found the following parameters to be useful: the germination valve thickness, the ratio of endocarp wall thickness to endocarp diameter, and the septum’s width and structure. Due to the great differentiation of the examined characters, it was difficult to verify the research hypothesis unambiguously. The calculated similarity coefficients of the endocarps’ qualitative and quantitative characters revealed the highest morphological similarity of endocarps between DW and BB groups, supporting the phylogenetic relationships based on molecular evidence. The number of vascular bundles on the endocarp surface was the character that supported this similarity the most. The similarity coefficients calculated separately for qualitative characters showed the closest similarity between groups CC-DW. However, these results do not directly reflect any of the published phylogenies.
Morozowska et al. (2021) The morphology and internal structure of dogwood (Cornus L.) endocarps in the taxonomy and phylogeny of the genus. PeerJ 9:e12170 https://doi.org/10.7717/peerj.12170
Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers
Background The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. Methods We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. Results A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.
Costantini et al. (2021) Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers. PeerJ 9:e12291 https://doi.org/10.7717/peerj.12291