From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion
Background Land gastropods of the Dry Chaco merit special attention because they comprise a highly diverse but barely studied group. Clessinia Doering, 1875 are typical inhabitants of this ecoregion. The inclusion of their distribution areas into Spixia range, their shell shape similarities, and a former molecular study raised doubts on the monophyly of this genus. The present study review the species of Clessinia, under a morphological, geometric morphometrics, and molecular combined approach. Methods Adults were collected, photographed, measured, and dissected for anatomical studies. Shell ultrastructure was studied with scanning electron microscope. Geometric morphometric analyses on shells were performed testing if they gave complementary information to anatomy. Two mitochondrial genes, and a nuclear region were studied. Phylogenetic reconstructions to explore the relationships of DNA sequences here obtained to those of Clessinia and Spixia species from GenBank were performed. Results Species description on shell, periostracal ornamentation and anatomy is provided. We raised former Clessinia cordovana striata to species rank, naming it as Clessinia tulumbensis sp. nov. The periostracum, consisting of hairs and lamellae, has taxonomic importance for species identification. Shell morphometric analyses, inner sculpture of penis and proportion of the epiphallus and penis, were useful tools to species identification. Nuclear markers do not exhibit enough genetic variation to determine species relationships. Based on the mitochondrial markers, genetic distances among Clessinia species were greater than 10%, and while C. cordovana, C. nattkemperi, and C. pagoda were recognized as distinct evolutionary genetic species, the distinction between C. stelzneri and C. tulumbensis sp. nov. was not evident. Clessinia and Spixia were paraphyletic in the molecular phylogenetic analyses. Species of Clessinia here treated have narrow distributional areas and are endemic to the Chaco Serrano subecoregion, restricted to small patches within the Dry Chaco. Clessinia and Spixia are synonymous, and the valid name of the taxon should be Clessinia Doering, 1875 which has priority over Spixia Pilsbry & Vanatta, 1894. Discussion Our results support the composition of C. cordovana complex by three species, C. cordovana, C. stelzneri, and C. tulumbensis sp. nov. The low genetic divergence between C. stelzneri and C. tulumbensis sp. nov. suggests that they have evolved relatively recently. The former Spixia and Clessinia are externally distinguished because Clessinia has a detached aperture from the body whorl forming a cornet, periostracal microsculpture extended over dorsal portion of the peristome, five inner teeth on the shell aperture instead of three–four found in Spixia. Morphological similarities exists between both genera in shell shape, type of periostracum microsculpture, reproductive anatomy, besides the overlap in geographic ranges.
Cuezzo et al. (2018) From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion. PeerJ 6:e5986 https://doi.org/10.7717/peerj.5986
Density-dependent changes in the distribution of Southern Right Whales (Eubalaena australis) in the breeding ground Peninsula Valdés
Background The Southern Right Whale (Eubalaena australis) population of the South–western Atlantic Ocean is recovering. In the breeding ground of Peninsula Valdés, as a consequence of the population growth, expansion to new areas by some types of groups and a change in the habitat use patterns at the coastal area were recorded. Methods We analysed information gathered from aerial surveys conducted along the coast of Peninsula Valdés in 15 years of effective sampling in a 19-year span. These surveys were divided into four periods (1999–2000; 2004–2007; 2008–2012 and 2013–2016) and estimated the density of whales in a 620 km of coast divided into segments of five km. Results The density of the whales increased to near three whales per km2 (averaged over each period) in the high-density areas. When this mean number was reached, the significant changes in density in the adjacent areas were detected in the following period. These changes were a decrease in density in the high-density areas and an increase of density in the low-density areas. Discussion We propose that a threshold in density elicits a response in habitat use, with the Mother-calf pairs remaining in the area, while the other groups are displaced to new areas.
Sueyro et al. (2018) Density-dependent changes in the distribution of Southern Right Whales (Eubalaena australis) in the breeding ground Peninsula Valdés. PeerJ 6:e5957 https://doi.org/10.7717/peerj.5957
Micro-remediation of chromium contaminated soils
Bacteria are tiny organisms which are ubiquitously found in the environment. These microscopic living bodies are responsible for the flow of nutrients in biogeochemical cycles and fertility imparted to the soil. Release of excessive chromium in agricultural soils due to rapid growth of industries may result in minimizing the fertility of soil in future, which will lead to reduction in crop production. Plant growth promoting bacteria (PGPB) are beneficial to the environment, some of which can tolerate chromium and protect plants against heavy metal stress. The current study aims to identify such chromium-tolerant auxin-producing rhizobacteria and to investigate their inoculation effects on the growth characteristics of Lens culinaris in chromium polluted soils by using two different chromium salts i.e., K2Cr2O7 and K2CrO4 in varying concentrations (0, 50, 100, 200, 400 and 500 µgml−1). The results revealed that Bacillus species are efficient in significantly reducing the deleterious effects of Cr. These effective bacterial strains were able to stimulate the growth of metal effected plants of Lens culinaris which were grown in chromium contaminated environment. Therefore, these plant growth promoting rhizobacteria PGPRs, having both auxin production potential and chromium-resistance ability, are considered as efficient micro-factories against chromium pollution.
Environmental Contamination and Remediation
Fatima et al. (2018) Micro-remediation of chromium contaminated soils. PeerJ 6:e6076 https://doi.org/10.7717/peerj.6076
Importance of biotic predictors in estimation of potential invasive areas: the example of the tortoise beetle Eurypedus nigrosignatus, in Hispaniola
Climatic variables have been the main predictors employed in ecological niche modeling and species distribution modeling, although biotic interactions are known to affect species’ spatial distributions via mechanisms such as predation, competition, and mutualism. Biotic interactions can affect species’ responses to abiotic environmental changes differently along environmental gradients, and abiotic environmental changes can likewise influence the nature of biotic interactions. Understanding whether and how to integrate variables at different scales in ecological niche models is essential to better estimate spatial distributions of species on macroecological scales and their responses to change. We report the leaf beetle Eurypedus nigrosignatus as an alien species in the Dominican Republic and investigate whether biotic factors played a meaningful role in the distributional expansion of the species into the Caribbean. We evaluate ecological niche models built with an additive gradient of unlinked biotic predictors—host plants, using likelihood-based model evaluation criteria (Akaike information criterion and Bayesian information criterion) within a range of regularization multiplier parameter values. Our results support the argument that ecological niche models should be more inclusive, as selected biotic predictors can improve the performance of models, despite the increased model complexity, and show that biotic interactions matter at macroecological scales. Moreover, we provide an alternative approach to select optimal combination of relevant variables, to improve estimation of potential invasive areas using global minimum model likelihood scores.
Spatial and Geographic Information Science
Simões et al. (2018) Importance of biotic predictors in estimation of potential invasive areas: the example of the tortoise beetle Eurypedus nigrosignatus, in Hispaniola. PeerJ 6:e6052 https://doi.org/10.7717/peerj.6052
Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices
Introduction Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species. Methods We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol. Results The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates. Discussion Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices.
Vivien et al. (2018) Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices. PeerJ 6:e6050 https://doi.org/10.7717/peerj.6050
Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China
Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.
Zhu et al. (2018) Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China. PeerJ 6:e6044 https://doi.org/10.7717/peerj.6044
Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China
The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.
Zhao et al. (2018) Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China. PeerJ 6:e6042 https://doi.org/10.7717/peerj.6042
Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli
Background DNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway. However, MutY does not discriminate between template and newly synthesized DNA strands. Therefore the ability to remove A from 8oxoG•A mispair, which is generated via misincorporation of an 8-oxo-2′-deoxyguanosine-5′-triphosphate precursor during DNA replication and in which A is the template base, can induce A•T→C•G transversions. Furthermore, it has been demonstrated that human MUTYH, homologous to the bacterial MutY, might be involved in the aberrant processing of ultraviolet (UV) induced DNA damage. Methods Here, we investigated the role of MutY in UV-induced mutagenesis in E. coli. MutY was probed on DNA duplexes containing cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproduct (6–4PP). UV irradiation of E. coli induces Save Our Souls (SOS) response characterized by increased production of DNA repair enzymes and mutagenesis. To study the role of MutY in vivo, the mutation frequencies to rifampicin-resistant (RifR) after UV irradiation of wild type and mutant E. coli strains were measured. Results We demonstrated that MutY does not excise Adenine when it is paired with CPD and 6–4PP adducts in duplex DNA. At the same time, MutY excises Adenine in A•G and A•8oxoG mispairs. Interestingly, E. coli mutY strains, which have elevated spontaneous mutation rate, exhibited low mutational induction after UV exposure as compared to MutY-proficient strains. However, sequence analysis of RifR mutants revealed that the frequencies of C→T transitions dramatically increased after UV irradiation in both MutY-proficient and -deficient E. coli strains. Discussion These findings indicate that the bacterial MutY is not involved in the aberrant DNA repair of UV-induced DNA damage.
Zutterling et al. (2018) Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli. PeerJ 6:e6029 https://doi.org/10.7717/peerj.6029
Association between dry eye disease and asthma: a nationwide population-based study
Background Dry eye disease (DED), a chronic ocular disease, is associated with numerous medical issues, including asthma. However, studies on these associations are limited. In this study, we investigated the incidence of DED among patients with asthma and its correlation with other allergic comorbidities. Methods We retrospectively analyzed data from the National Health Insurance Research Database of Taiwan. We compared the data of 41,229 patients with asthma with those of 164,916 sex- and age-matched non-asthma controls. We followed up the patient and control groups from 1998 to 2010, and compared the rate of DED in these two groups. We further analyzed the allergic comorbidities and asthma-related medication use among the patients with asthma to verify whether these factors were associated with DED. Results The patients in the asthma group were more likely to have DED than were the controls (6.35% vs. 4.92%, p < 0.0001). In the asthma group, female had a higher risk of DED (odds ratio (OR) = 1.70, 95% confidence interval (CI) [1.57–1.85]) than males did. After adjustment for sex, age, income, urbanization, and the other two allergic comorbidities, patients with allergic rhinitis (adjusted OR = 1.58, 95% CI [1.46–1.72]) and urticaria (adjusted OR = 1.25, 95% CI [1.12–1.38]) were more likely to have DED, but not patients with atopic dermatitis (adjusted OR = 1.17, 95% CI [0.98–1.40]). Patients with asthma who had prescriptions of leukotriene receptor antagonists (LTRAs) (adjusted OR = 1.29, 95% CI [1.01–1.64]), oral antihistamines (adjusted OR = 2.02, 95% CI [1.84–2.21]), and inhaled corticosteroids (adjusted OR = 1.19, 95% CI [1.04–1.36]) exhibited association with DED. Discussion Our findings reveal that patients with asthma—particularly females—were more likely to have DED, with comorbidities such as allergic rhinitis and urticaria, and prescriptions including LTRAs, antihistamines, and inhaled corticosteroids. The results suggest that in clinical practice, physicians should pay attention to DED, particularly in patients with a high risk of DED.
Huang et al. (2018) Association between dry eye disease and asthma: a nationwide population-based study. PeerJ 6:e5941 https://doi.org/10.7717/peerj.5941
An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA
Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness.
Cornman et al. (2018) An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA. PeerJ 6:e5871 https://doi.org/10.7717/peerj.5871